U.S. patent application number 14/079864 was filed with the patent office on 2014-06-19 for tissue-specific micrornas and compositions and uses thereof.
This patent application is currently assigned to THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK. The applicant listed for this patent is THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK. Invention is credited to Andrea CALIFANO, Riccardo DALLA-FAVERA.
Application Number | 20140171484 14/079864 |
Document ID | / |
Family ID | 40260339 |
Filed Date | 2014-06-19 |
United States Patent
Application |
20140171484 |
Kind Code |
A1 |
CALIFANO; Andrea ; et
al. |
June 19, 2014 |
TISSUE-SPECIFIC MICRORNAS AND COMPOSITIONS AND USES THEREOF
Abstract
The invention provides for isolated nucleic acid sequences of
newly discovered micro RNAs that have been identified to exist in
normal Human B cells and/or in tumor-related Human B cells, using
an integrated bioinformatics method and pipeline described
herein.
Inventors: |
CALIFANO; Andrea; (New York,
NY) ; DALLA-FAVERA; Riccardo; (New York, NY) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW
YORK |
New York |
NY |
US |
|
|
Assignee: |
THE TRUSTEES OF COLUMBIA UNIVERSITY
IN THE CITY OF NEW YORK
New York
NY
|
Family ID: |
40260339 |
Appl. No.: |
14/079864 |
Filed: |
November 14, 2013 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12688680 |
Jan 15, 2010 |
8586726 |
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14079864 |
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PCT/US08/70082 |
Jul 15, 2008 |
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12688680 |
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60950474 |
Jul 18, 2007 |
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61020625 |
Jan 11, 2008 |
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Current U.S.
Class: |
514/44A ;
435/375; 536/24.5 |
Current CPC
Class: |
C12N 2310/141 20130101;
C12N 15/113 20130101; A61P 43/00 20180101 |
Class at
Publication: |
514/44.A ;
536/24.5; 435/375 |
International
Class: |
C12N 15/113 20060101
C12N015/113 |
Goverment Interests
GOVERNMENT INTERESTS
[0004] The work described herein was supported in whole, or in
part, by National Cancer Institute Grant No. R01-CA109755 "Genetic
Network Interference with Combinatorial Phenotypes", and National
Institute of Allergy and Infectious Diseases Grant No. R01 AI066116
"Regulatory Modules in Normal and Transformed b-Cell". The
Government has certain rights to the invention.
Claims
1. An isolated nucleotide sequence consisting of from about 14 to
about 31 nucleotides in length; and consisting essentially of a
nucleotide sequence selected from the group consisting of SEQ ID
NOS: 1-130 and 1094, wherein the nucleotide sequence is about 97%,
about 98%, or about 99% identical to a nucleic acid sequence
comprising any one of SEQ ID NOS: 1-130 and 1094.
2. An isolated nucleotide sequence consisting of from about 14 to
about 31 nucleotides in length; and consisting essentially of a
nucleotide sequence selected from the group consisting of SEQ ID
NOS: 131-401, wherein the nucleotide sequence is about 97%, about
98%, or about 99% identical to a nucleic acid sequence having a SEQ
ID NO: 131-401, and wherein the nucleotide sequence is not SEQ ID
NO: 236.
3. An isolated nucleotide sequence that is complementary to a
nucleotide sequence of claim 1 or 2.
4. An isolated nucleotide sequence that is complementary to all but
1, 2, 3, 4, or 5 nucleotides of the nucleotide sequence of claim 1
or 2.
5. The nucleotide sequence of claim 3, wherein the nucleotide
sequence is complementary to at least 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 contiguous
nucleotides of the nucleotide sequence of claim 1.
6. The nucleotide sequence of claim 3, wherein the nucleotide
sequence is complementary to at least 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 contiguous
nucleotides of the nucleotide sequence of claim 2.
7. The nucleotide sequence of claim 1 or 2, wherein the nucleotide
sequence is single stranded.
8. The nucleotide sequence of claim 3, wherein the nucleotide
sequence is single stranded.
9. The nucleotide sequence of claim 4, wherein the nucleotide
sequence is single stranded.
10. The nucleotide sequence of claim 1 or 2, wherein the nucleotide
sequence is double stranded.
11. The nucleotide sequence of claim 3, wherein the nucleotide
sequence is double stranded.
12. The nucleotide sequence of claim 4, wherein the nucleotide
sequence is double stranded.
13. The acid nucleotide sequence of claim 1 or 2, wherein the
nucleotide sequence is expressed in a lymphocyte.
14. The nucleotide sequence of claim 1 or 2, wherein the nucleotide
sequence is expressed in a B cell.
15. The nucleotide sequence of claim 14, wherein the B cell
comprises a Naive B cell, a centroblast, a memory B cell, or a
Ramos Burkitt Lymphoma cell.
16. A composition comprising one or more nucleotide sequences of
claim 1, 2, 3, or 4, in any combination or permutation thereof.
17. A composition comprising one or more nucleotide sequences,
wherein the one or more nucleotide sequences consist essentially of
a nucleotide sequence of any one of SEQ ID NOS: 1-401 and 1094, and
wherein the nucleotide sequence is not SEQ ID NO: 236.
18. The composition of claim 16, further comprising one or more
carriers, excipients, solvents, bases, or a combination
thereof.
19. The composition of claim 17, further comprising one or more
carriers, excipients, solvents, bases, or a combination
thereof.
20. A method for modulating the activity of a target nucleic acid
in a cell, the method comprising contacting a cell with a
nucleotide sequence of claim 1, 2, 3, or 4.
21. The method of claim 20, wherein the target nucleic acid is a
mRNA, a mature miRNA, or a precursor to a mature miRNA.
22. The method of claim 20, wherein the cell is a hematopoetic
cell.
23. The method of claim 20, wherein the cell is a B cell.
24. The method of claim 20, wherein the cell is in vitro or in
vivo.
Description
[0001] This application is a Divisional of U.S. patent application
Ser. No. 12/688,680, filed Jan. 15, 2010, which is a
Continuation-In-Part of International Patent Application No.
PCT/US2008/070082, filed Jul. 15, 2008, which claims priority of
U.S. Provisional Patent Application No. 60/950,474, filed Jul. 18,
2007, and of U.S. Provisional Patent Application No. 61/020,625,
filed Jan. 11, 2008 each of which is incorporated herewith in its
entirety.
[0002] All patents, patent applications and publications cited
herein are hereby incorporated by reference in their entirety. The
disclosures of these publications in their entireties are hereby
incorporated by reference into this application in order to more
fully describe the state of the art as known to those skilled
therein as of the date of the invention described and claimed
herein.
[0003] This patent disclosure contains material that is subject to
copyright protection. The copyright owner has no objection to the
facsimile reproduction by anyone of the patent document or the
patent disclosure as it appears in the U.S. Patent and Trademark
Office patent file or records, but otherwise reserves any and all
copyright rights.
SEQUENCE LISTING
[0005] The instant application contains a Sequence Listing which
has been submitted electronically in ASCII format and is hereby
incorporated by reference in its entirety. Said ASCII copy, created
on Jan. 27, 2014, is named 19240.740US5_SL.txt and is 1,135,002
bytes in size.
Lengthy Table
[0006] A lengthy table (for example, Table 11) is referenced in
this application and has been filed as an Appendix to this
invention. The specification of the application contains reference
to the single table, Table 11, which consists of more than 51
pages, and is hereby incorporated by reference in its entirety.
Table 11 contains information encompassing gene sequences
pertaining to the analysis of cross-species conservation for
miRNAs. The Table displays results for conservation of full-length
mature miRNA sequences, and seed of the mature sequence.
BACKGROUND OF THE INVENTION
[0007] Various nucleic acid species are capable of modifying gene
expression. These species include antisense RNA, siRNA, microRNA,
RNA and DNA aptamers, antagomirs, and decoy RNAs. Each of these
nucleic acid species can inhibit target nucleic acid activity,
including gene expression.
[0008] MicroRNAs (miRNAs, miRs) are 20-23 nucleotides (nt) RNA
molecules that are produced by the processing of a larger enclosing
stem-loop structure (>50 bp), called precursors, by cellular
enzymes. miRNAs are processed from hairpin precursors of 70 nt
(pre-miRNA) which are derived from primary transcripts (pri-miRNA)
through sequential cleavage by the RNAse III enzymes drosha and
dicer. miRNAs target the messenger RNA of other genes by binding to
their 3' UTR and interfering with their translation or causing
degradation by enzyme targeting double-stranded RNA. miRNAs are
non-coding RNAs (ncRNAs) that exist in a variety of organisms,
including mammals, and are conserved in evolution. Many miRNAs tend
to be clustered and transcribed as polycistrons and often have
similar spatial temporal expression patterns. miRNAs have been
implicated in various biological processes including developmental
timing, differentiation, apoptosis, cell proliferation, organ
development, and metabolism
SUMMARY OF THE INVENTION
[0009] The invention is based, at least in part, on the discovery
of newly-identified microRNAs from normal and tumor-related Human B
cells. Accordingly, in one aspect, the invention features an
isolated nucleic acid, wherein the nucleic acid: (a) consists of
from about 14 to about 31 nucleotides in length; (b) exhibits
expression in a human tissue; (c) has a nucleotide sequence not
present in an exon; and (d) consists essentially of a nucleotide
sequence selected from the group consisting of SEQ ID NOS: 1-130
and 1094, and a nucleotide sequence which is about 97%, about 98%,
or about 99% identical to a nucleic acid sequence comprising any
one of SEQ ID NOS: 1-130 and 1094. In one embodiment, the nucleic
acid is single stranded. In another embodiment, the nucleic acid is
double-stranded. In a further embodiment, the human tissue
comprises a lymphocyte. In some embodiments, the human tissue is a
B cell. In other embodiments, the B cell comprises a Naive B cell,
a centroblast, a memory B cell, or a Ramos Burkitt Lymphoma
cell.
[0010] An aspect of the invention provides for an isolated nucleic
acid, wherein the nucleic acid: (a) consists of from about 14 to
about 31 nucleotides in length; (b) exhibits expression in a human
tissue; (c) has a nucleotide sequence not present in an exon; and
(d) consists essentially of a nucleotide sequence selected from the
group consisting of SEQ ID NOS: 131-401, and a nucleotide sequence
which is about 97%, about 98%, or about 99% identical to a nucleic
acid sequence having a SEQ ID NO: 131-401. In one embodiment, the
nucleic acid is single stranded. In another embodiment, the nucleic
acid is double-stranded. In a further embodiment, the human tissue
comprises a lymphocyte. In some embodiments, the human tissue is a
B cell. In other embodiments, the B cell comprises a Naive B cell,
a centroblast, a memory B cell, or a Ramos Burkitt Lymphoma
cell.
[0011] The invention provides for an isolated nucleic acid that is
complementary to a nucleic acid described in the aspects herein. In
one embodiment, the nucleic acid is single stranded. In another
embodiment, the nucleic acid is double-stranded.
[0012] The invention provides for an isolated nucleic acid that is
complementary to all but 1, 2, 3, 4, or 5 nucleotides of the
nucleic acids described in the aspects herein. In one embodiment,
the nucleic acid is complementary to at least 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 contiguous
nucleotides of a nucleic acid described in the aspects herein
consisting from about 14 to about 31 nucleotides in length. In one
embodiment, the nucleic acid is single stranded. In another
embodiment, the nucleic acid is double-stranded.
[0013] The invention provides for a composition comprising one or
more nucleic acids of described in the aspects herein, in any
combination or permutation thereof. In one embodiment, the
composition further comprises one or more carriers, excipients,
solvents, bases, or a combination thereof.
[0014] The invention provides for a composition comprising one or
more nucleic acids, wherein the one or more nucleic acids consist
essentially of a nucleotide sequence of any one of SEQ ID NOS:
1-401 and 1094. In one embodiment, the composition further
comprises one or more carriers, excipients, solvents, bases, or a
combination thereof.
[0015] The invention provides for a method for modulating the
activity of a target nucleic acid in a cell, wherein the method
comprises contacting a cell with a nucleic acid described in the
aspects herein. In one embodiment, the target nucleic acid is a
mRNA, a mature miRNA, or a precursor to a mature miRNA. In another
embodiment, the cell is a hematopoetic cell. In a further
embodiment, the cell is a B cell. In some embodiments, the cell is
in vitro or in vivo.
BRIEF DESCRIPTION OF THE FIGURES
[0016] The patent or application file contains at least one drawing
executed in color. Copies of this patent or patent application
publication with color drawing(s) will be provided by the Office
upon request and payment of the necessary fee.
[0017] FIG. 1 is a flow diagram of a computational pipeline.
[0018] FIG. 2 is a flow diagram of a computational pipeline.
[0019] FIG. 3 is a flow diagram of a computational pipeline.
[0020] FIG. 4 is a graph depicting frequency distributions.
[0021] FIG. 5 is a diagram for new miRNAs identified in CB, Memory,
and Naive cells.
[0022] FIG. 6 is a diagram for known miRNAs identified in CB,
Memory, and Naive cells.
[0023] FIG. 7 is a diagram for new miRNAs identified in CB and RA
cells.
[0024] FIG. 8 is a diagram for known miRNAs identified in CB and RA
cells
[0025] FIG. 9 is a bar graph depicting computational predictions of
precursors from cloned mature miRNA.
[0026] FIG. 10 is a schematic depicting the experimental procedure.
The experimental approach includes two main steps: cloning and
sequencing of short-RNA and computational analysis of sequences in
order to identify potential miRNAs.
[0027] FIG. 11 is a diagram representing the Computational analysis
of short-RNA libraries. Short-RNA sequences were grouped in three
main categories: miRNAs, short-RNAs of unknown function and
short-RNAs not matching the human genome. Short-RNA sequences were
aligned to the human genome (hg18 assembly) and if a favorable
match was identified the sequences were subject to computational
identification of candidate miRNAs. Short-RNAs which aligned in the
same genomic location were clustered and considered as supporting
sequences for the same miRNA. Annotations were used to eliminate
RNA aligning with mRNA, tRNA, rRNA and other non-coding RNA
species. Overall, 401 unique candidate mature miRNA were identified
and compared to the miRBase database to detect previously reported
miRNA. Among the short-RNAs lacking miRNA features 30% were
annotated and the remaining might represent a part of the
transcriptome whose functions are still unknown. Short-RNAs which
could be matched to the human genome only with 2 or more mismatches
were considered as potential short-RNA or miRNA with unknown
genomic locations.
[0028] FIG. 12 is a bar graph depicting a computational prediction
of precursors and mature miRNA. The number of predicted precursor
miRNAs (pre-miR) and mature miRNAs (mature-miR) are plotted
independently for each library and overall. The sequences matching
miRNAs deposited in the miRBase database (v.11.0) are defined as
"known" and conversely the sequences not previously reported are
named "new".
[0029] FIG. 13A is a line graph depicting the analysis of miRNA
identified in B cells short-RNA libraries. It shows the previously
reported (known) miRNA and newly identified (new) miRNAs as
occurring in naive, centroblasts, memory and Ramos cells.
[0030] FIG. 13B are schematics depicting number of miRNAs
specifically or commonly identified in naive, centroblasts and
memory B cell short-RNA libraries. A larger overlap is observed for
known compared to new miRNA (42% versus 15%).
[0031] FIG. 13C is a bar graph depicting the conservation analysis
for orthologous miRNAs was performed in 5 mammal species for all
miRNA reported in the miRBase database (miRBase-all) and for known
and new mature miRNA identified in B cell libraries. Frequency of
conserved miRNAs in each species is displayed.
[0032] FIG. 14 are photographs depicting the detection of miRNA by
Northern Blot. FIG. 14A shows the detection of newly identified
mature-miRNA species by Northern Blot in Ramos cell line,
centroblasts (CB), and naive B cells isolated from human tonsils.
The naming of miRNA is provisional. FIG. 14B shows images
displaying both the mature (20-25 nt) and the precursor (60-80 nt)
miRNA species. miRNA expression can be regulated at transcriptional
level (top panel) or at the processing level (bottom panel) when
intermediate forms (pre-miRNA) are generated but are not fully
processed to mature miRNA.
[0033] FIG. 15 is an image of a microarray-based miRNA expression
profiling that distinguishes developmental stages of normal as well
as malignant B cells. FIG. 15A represents unsupervised clustering
performed using miRNA frequencies values (>=0.16) calculated as
the fraction of the total pool of cloned miRNAs represented by a
given miRNA in a library FIG. 15B Unsupervised clustering of
microarray-based miRNA expression profiles distinguishes
centroblasts, naive and memory B cells purified from tonsil tissue
of six patients/each.
[0034] FIG. 16 is an image of a microarray-based miRNA expression
profiling of GC-derived lymphomas. Unsupervised clustering of miRNA
expression profiles of Burkitt lymphomas (BL), follicular lymphomas
(FL) and diffuse large B cell lymphomas (DLBCL).
[0035] FIG. 17 are graphs demonstrating the complexity of
libraries. The curves represent the estimation of the numbers of
mature miRNA expressed in each library. Discarding outliers
(extreme 5%), the lowest and highest miRNA counts observed per
library sample are plotted. The current set of predicted mature
miRNAs represents more than 80% of the estimated miRNA set
expressed in the libraries.
[0036] FIG. 18 is flow chart depicting an overview of computational
analysis for the short RNA libraries.
[0037] FIG. 19 is a graph of the predicted precursor and mature
miRNAs. The number of predicted precursor miRNAs (pre-miR) and
mature miRNAs (mature-miR) are plotted independently for each
library and overall. Throughout the figures, the sequences matching
miRNAs deposited in the miRBase database (v.11.0) are defined as
"known," and the sequences that to our knowledge have not been
previously reported are named "new."
[0038] FIGS. 20A-20C show graphs and charts pertaining to the
abundance and evolutionary conservation of the B-cell miRNome. FIG.
20A is a graph of the frequencies of previously reported (known)
and to our knowledge newly identified (new) miRNAs as occurring in
naive, centroblasts, memory and Ramos cells. Single occurrences
miRNAs are not included. FIG. 20B are Venn diagrams showing the
number of miRNAs cloned multiple times and identified in naive,
centroblasts and memory B cells. A larger overlap is observed for
known compared to new miRNA (48% versus 38%). FIG. 20C are bar
graphs that show the conservation analysis for orthologous miRNAs
that was performed in 5 mammal species for all miRNA reported in
the miRBase database (miRBase-all) and for known and new mature
miRNA expressed in the B-cell libraries. The percentages of miRNAs
having either perfect conservation for the entire mature miRNA (top
panel) or for its seeds (bottom panel) are displayed.
[0039] FIGS. 21A-21C are photographs showing the detection of
previously unreported miRNAs by RT-PCR and RNA blot. FIG. 21A shows
representative results of RT-PCR detection of miRNA in Ramos cell
line and tonsil cells. miR-30c was used as loading control. FIG.
21B shows the detection of mature-miRNA species by RNA blot in
Ramos cell line, centroblasts (CB) and naive B cells isolated from
human tonsils. RNU44 was used as loading control. FIG. 21C are RNA
blot images displaying both the mature (20-25 nt) and the precursor
(60-80 nt) miRNA species. miRNA expression can be regulated at
transcriptional level (top panel) or at the processing level
(bottom panel) when intermediate forms (pre-miRNA) are generated
but are not fully processed to mature miRNA. The naming of miRNAs
is provisional.
[0040] FIGS. 22A-B are a schematic that shows miRNA expression
profiling distinguishes developmental stages of normal as well as
malignant B cells. FIG. 22A depicts unsupervised clustering
performed using miRNA frequencies values (A.08) calculated as the
fraction of the total pool of cloned miRNAs represented by a given
miRNA in a library. FIG. 22B shows unsupervised clustering of
microarray-based miRNA expression profiles distinguishes
centroblasts, naive and memory B cells purified from tonsil tissue
of six patients/each.
[0041] FIG. 23 are graphs that show the complexity of the
libraries. The curves represent the estimation of the numbers of
mature miRNA (including single occurrence candidate miRNA)
expressed in each library. Discarding outliers (extreme 5%), the
lowest and highest miRNA counts observed per library sample are
plotted. The current set of predicted mature miRNAs represents more
than 85% of the estimated miRNA set expressed in the libraries.
[0042] FIG. 24 is a schematic that shows the computational analysis
of short-RNA libraries. Short-RNA sequences were grouped in three
main categories: miRNAs, short-RNAs of unknown function and
short-RNAs not matching the human genome.
[0043] FIG. 25 is a bar graph that shows new miRNAs are found in
association with Ago2 protein complex. New miRNAs as well as known
(miR-16) are enriched in Ago2 compared to control IgG
immunoprecipitates (IP). The binding is specific since other RNA
species (5s rRNA) are not enriched in the Ago2 immunoprecipitates.
Bars represent the internally normalized average of two independent
qPCR assays, each from two sets of three pooled
immunoprecipitations. Error bars are the standard deviation of the
measurements. The 4 new miRNAs found to be associated with the Ago2
complex are representative of miRNA cloned at higher level in
non-GC B cells (CU-1254), in GC B cells (CU-1403; CU-1276) or
aberrantly over-expressed in Ramos Burkitt lymphoma cells
(CU-1137).
[0044] FIG. 26 is a bar graph that shows enrichment for predicted
miRNA targets in genes down-regulated in GC compared to Naive B
cells. Target prediction was performed for 15 new miRNAs expressed
at higher level in GC compared to naive B cells (>3 fold) by
miRanda v1.0 and RNA22. Targets predicted by both algorithms were
tested for enrichment in the down-regulated genes of the GC
transcriptome. Eleven out of 15 GC-over-expressed miRNAs showed an
increase in their candidate target enrichment p-value in GC vs.
naive down-regulated genes compared to control populations (memory
vs. naive), two showed a decrease and two showed no differences.
Enrichment p-values are reported in Table 13.
[0045] FIG. 27 is a plot showing the correlation measurement
between cloning and miRNA expression array data. miRNA normalized
clone counts and average expressions measured by miRNA expression
arrays are represented in a scatter plot format. The plot includes
data for miRNAs which have been cloned more than once and were
represented on the Agilent Human miRNA Microarray. Overall, this
analysis include 89 miRNA sequences distributed as following in the
three libraries: 54 in naive, 80 in centroblasts (CB) and 48 in
memory. The Spearman correlation is 0.7 corresponding to a p-value
<3.9e-28.
[0046] FIG. 28 is a bar graph showing the analysis of single
nucleotide mismatches identified in cloned known miRNA. The plot
represents the percentage of short-RNA corresponding to known miRNA
and displaying mismatches to the human genome. Nucleotide in
position 1 to 3 starting from both 5'- and 3'-end as well as all
remaining middle nucleotides (nt middle) of each sRNA were analyzed
for single substitutions.
DETAILED DESCRIPTION OF THE INVENTION
[0047] This invention provides for the discovery of a large number
of new micro RNAs that have been identified to exist in normal
Human B cells and/or in tumor-related Human B cells, using an
integrated bioinformatics method and pipeline described herein.
[0048] Micro RNAs (miRNAs) are naturally-occurring 19 to 25
nucleotide transcripts found in over one hundred distinct organisms
(such as nematodes, fruit flies, and humans). miRNAs can be
processed from 60- to 70-nucleotide foldback RNA precursor
structures, which are transcribed from the miRNA gene. The miRNA
precursor processing reaction requires Dicer RNase III and
Argonaute family members (Sasaki et al., 2003 Genomics 82,
323-330). The miRNA precursor or processed miRNA products are
easily detected, and an alteration in the levels of these molecules
within a cell can indicate a perturbation in the chromosomal region
containing the miRNA gene.
[0049] At least 222 separate miRNA genes have been identified in
the human genome. For example, 2 miRNA genes (miR15a and miR16a)
have been localized to a homozygously deleted region on chromosome
13 that is correlated with chronic lymphocytic leukemia (Calin et
al. (2002), Proc. Natl. Acad. Sci. USA 99:15524-29). However, the
distribution of miRNA genes throughout the genome, and the
relationship of the miRNA genes to diverse chromosomal features,
has not been systematically studied. A further review of miRNAs is
provided in U.S. Pat. No. 7,232,806, U.S. Patent Application
Publication No. 2006/0105360, and in the references: Landgraf et
al., 2007, Cell 129: 1401-1414; Mendell, J T, 2005 Cell Cycle
4(9):1179-84; Shivdasani R A, 2006 Blood 108(12):3646-53; Hwang and
Mendell, 2006 Br J Cancer 94(6):776-80; Hammond S M, 2006; Curr
Opin Genet Dev. 16(1):4-9; Osada and Takahashi, 2007 Carcinogenesis
28(1):2-12; and Zhang et al., 2007 Dev Biol. 302(1):1-12, all of
which are hereby incorporated by reference in their entirety.
[0050] All nucleic acid sequences herein are given in the 5' to 3'
direction, for example the mature miRNA sequences listed in Table 1
(SEQ ID NOS: 1-401).
[0051] The unprocessed miRNA gene transcript is called a miRNA
precursor (pre-miRNA) and comprises an RNA transcript of about 70
nucleotides in length. The pre-miRNA can be processed by digestion
with an RNAse (such as, Dicer, Argonaut, or RNAse III, e.g., E.
coli RNAse III)) into an active 19-25 nucleotide RNA molecule. This
active 19-25 nucleotide RNA molecule is also called the processed
miRNA gene transcript.
[0052] The active 19-25 nucleotide RNA molecule can be obtained
from the miRNA precursor through natural processing routes (for
example, using intact cells or cell lysates) or by synthetic
processing routes (for example, using isolated processing enzymes,
such as isolated Dicer, Argonaut, or RNAase III). The active 19-25
nucleotide RNA molecule can also be produced directly by biological
or chemical syntheses, without having been processed from the miRNA
precursor.
[0053] The invention provides for an isolated nucleic acid that:
(a) consists of from about 14 to about 31 nucleotides in length;
(b) exhibits expression in a human tissue; and (c) has a nucleotide
sequence not present in an exon. In one embodiment, the isolated
nucleic acid consists essentially of a nucleotide sequence selected
from the group consisting of SEQ ID NOS: 1-401 and 1094, and a
nucleotide sequence which is about 97%, about 98%, or about 99%
identical to a nucleic acid sequence comprising any one of SEQ ID
NOS: 1-401 and 1094. In some embodiments, the human tissue
comprises a lymphocyte (for example, a human B cell). In other
embodiments, the B cell comprises a Naive B cell, a centroblast, or
a memory B cell.
[0054] For example, an isolated nucleic acid, such as a miRNA of
the invention, can be synthesized, or altered, or removed from the
natural state through human intervention. A synthetic miRNA, or a
miRNA partially or completely separated from the coexisting
materials of its natural state, is considered isolated. An isolated
miRNA can exist in substantially purified form, or can exist in a
cell into which the miRNA has been delivered.
[0055] An isolated nucleic acid, such as a miRNA of the invention,
can be obtained using a number of standard techniques utilized in
the art. For example, the miRNA gene products can be chemically
synthesized or recombinantly produced using methods known in the
art. For example, a miRNA can be chemically synthesized using
appropriately protected ribonucleoside phosphoramidites and a
conventional DNA/RNA synthesizer. Commercial suppliers of synthetic
RNA molecules or synthesis reagents include, e.g., Proligo
(Hamburg, Germany), Dharmacon Research (Lafayette, Colo., USA),
Rosetta Genomics (North Brunswick, N.J.), Pierce Chemical (part of
Perbio Science, Rockford, Ill., USA), Glen Research (Sterling, Va.,
USA), ChemGenes (Ashland, Mass., USA), Ambion (Foster City, Calif.,
USA), and Cruachem (Glasgow, UK).
[0056] miRNA can also be expressed from recombinant circular or
linear DNA plasmids using any suitable promoter. Suitable promoters
for expressing RNA from a plasmid include, e.g., the U6 or H1 RNA
pol III promoter sequences, or the cytomegalovirus promoters.
Selection of other suitable promoters is within the skill in the
art. Recombinant plasmids can comprise inducible or regulatable
promoters for expression of the miRNA in cancer cells (such as
hematopoietic cells, i.e., B cells). For example, a miRNA or a
precursor miRNA of the invention (such as a miRNA molecule
comprising any one of SEQ ID NOS: 1-401 and 1094) can be placed
under the control of the CMV intermediate-early promoter, whereby
the nucleic acid sequences encoding the miRNA molecule are located
3' of the promoter, so that the promoter can initiate transcription
of the miRNA gene product coding sequences.
[0057] miRNAs expressed from recombinant plasmids can be isolated
from cultured cell expression systems by standard techniques.
miRNAs which are expressed from recombinant plasmids can also be
delivered to, and expressed directly in, the cancer cells. A miRNA
can be expressed as an RNA precursor molecule from a single
plasmid, and the precursor molecules are subsequently processed
into functional miRNAs by a suitable processing system, including
the processing systems naturally existing within a cell. Other
suitable processing systems include, e.g., the in vitro Drosophila
cell lysate system as described in U.S. Application Publication No.
2002/0086356 to Tuschl et al. and the E. coli RNAse III system
described in U.S. Application Publication No. 2004/0014113 to Yang
et al., which are herein incorporated by reference in their
entireties.
[0058] Plasmids suitable for expressing a miRNA of the invention,
methods for inserting nucleic acid sequences into the plasmid to
express the miRNA of interest, and methods of delivering the
recombinant plasmid to cells of interest are well-established and
practiced in the art. See, for example, Zeng et al. (2002),
Molecular Cell 9:1327-1333; Tuschl (2002), Nat. Biotechnol,
20:446-448; Brummelkamp et al. (2002), Science 296:550-553;
Miyagishi et al. (2002), Nat. Biotechnol. 20:497-500; Paddison et
al. (2002), Genes Dev. 16:948-958; Lee et al. (2002), Nat.
Biotechnol. 20:500-505; and Paul et al. (2002), Nat. Biotechnol.
20:505-508, the entire disclosures of which are herein incorporated
by reference.
[0059] miRNA molecules of the invention can also be expressed from
recombinant viral vectors. The RNA expressed from the recombinant
viral vectors can either be isolated from cultured cell expression
systems by standard techniques, or can be expressed directly in
cancer cells (such as hematopoietic cells, i.e., B cells). For
example, the recombinant viral vectors can comprise sequences that
encode the miRNA molecule of interest and any suitable promoter for
expressing the RNA sequences. Vectors can also comprise inducible
or regulatable promoters for expression of the miRNA molecule in
cells, such as cancer cell. As discussed previously, non-limiting
examples of suitable promoters include the U6 or H1 RNA pol III
promoter sequences, or the cytomegalovirus promoters. Selection of
other suitable promoters is practiced by those of ordinary skill in
the art.
[0060] Any viral vector that can harbor the nucleotide sequences
for the miRNA molecules of the invention can be used. Non-limiting
examples of such vectors include: vectors derived from adenovirus
(AV); adeno-associated virus (AAV); retroviruses (e.g.,
lentiviruses (LV), Rhabdoviruses, murine leukemia virus); herpes
virus, and the like. The tropism of the viral vectors can be
modified by pseudotyping the vectors with envelope proteins or
other surface antigens from other viruses, or by substituting
different viral capsid proteins, as appropriate. For example,
lentiviral vectors can be pseudotyped with surface proteins from
vesicular stomatitis virus (VSV), rabies, Ebola, Mokola, and the
like. For example, AAV vectors can be made to target different
cells by engineering the vectors to express different capsid
protein serotypes. An AAV vector expressing a serotype 2 capsid on
a serotype 2 genome is called AAV 2/2. This serotype 2 capsid gene
in the AAV 2/2 vector can be replaced by a serotype 5 capsid gene
to produce an AAV 2/5 vector. Techniques for constructing AAV
vectors which express different capsid protein serotypes are within
the skill in the art; see, e.g., Rabinowitz J. E. et al. (2002), J
Virol 76:791-801, the entire disclosure of which is herein
incorporated by reference.
[0061] Recombinant viral vectors suitable for expressing miRNA
molecules of the invention, methods for inserting nucleic acid
sequences for expressing RNA in the vector, methods of delivering
the viral vector to cells of interest, and recovery of the
expressed RNA molecules are within the skill in the art. See, for
example, Dornburg (1995), Gene Therap. 2:301-310; Eglitis (1988),
Biotechniques 6:608-614; Miller (1990), Hum. Gene Therap. 1:5-14;
and Anderson (1998), Nature 392:25-30, the entire disclosures of
which are herein incorporated by reference. Useful viral vectors
can be those derived from AV and AAV. A suitable AV vector for
expressing an mRNA molecule of the invention, a method for
constructing the recombinant AV vector, and a method for delivering
the vector into target cells, are described in Xia et al. (2002),
Nat. Biotech. 20:1006-1010, the entire disclosure of which is
herein incorporated by reference. Suitable AAV vectors for
expressing a miRNA molecule having a sequence shown in Table 1
(i.e., any one of SEQ ID NOS: 1-401), methods for constructing the
recombinant AAV vector, and methods for delivering the vectors into
target cells are described in Samulski et al. (1987), J. Virol.
61:3096-3101; Fisher et al. (1996), J Virol., 70:520-532; Samulski
et al. (1989), J. Virol. 63:3822-3826; U.S. Pat. No. 5,252,479;
U.S. Pat. No. 5,139,941; International Patent Application No. WO
94/13788; and International Patent Application No. WO 93/24641, the
entire disclosures of which are herein incorporated by
reference.
[0062] Inhibition of RNA can effectively inhibit expression of a
gene from which the RNA is transcribed. Inhibitors are selected
from the group comprising: siRNA; interfering RNA or RNAi; dsRNA;
RNA Polymerase III transcribed DNAs; ribozymes; and antisense
nucleic acid, which can be RNA, DNA, or artificial nucleic acid.
Also within the scope of the present invention are oligonucleotide
sequences that include antisense oligonucleotides, antagomirs (also
referred to as miRNA inhibitory nucleic acids), aptamers, and
ribozymes that function to inhibit miRNA expression via purportedly
binding to or degrading a miRNA molecule comprising any one of SEQ
ID NOS: 1-401 and 1094.
[0063] The invention provides for a nucleic acid molecule that is
substantially complementary to an isolated nucleic acid of the
invenion described above. "Substantially complementary" means that
two sequences are substantially complementary that a duplex can be
formed between them. The duplex can have one or more mismatches but
the region of duplex formation is sufficient to down-regulate
expression of the target nucleic acid. The region of substantial
complementarity can be perfectly paired. In one embodiment, there
can be nucleotide mismatches in the region of substantial
complementarity. In one embodiment, the region of substantial
complementarity will have no more than 1, 2, 3, 4, or 5
mismatches.
[0064] For example, an antagomir, an antisense RNA, a small
interfering RNA (siRNA), a short hairpin RNA (snRNA), and the like)
can be complementary to the guide strand of a miRNA having a
nucleotide sequence shown in Table 1, positioned in the RNA
silencing complex. This nucleic acid molecule can be single
stranded or can be double stranded, and can inhibit the expression
or activity of a miRNA molecule of the invention. In one
embodiment, the nucleic acid molecule that inhibits a miRNA
molecule of the invention (such as those described above) can
complement at least 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, or 31 contiguous nucleotides of a miRNA having
a nucleic acid sequence selected from the group consisting of SEQ
ID NOS: 1-401 and 1094, and a nucleotide sequence which is about
97%, about 98%, or about 99% identical to a nucleic acid sequence
comprising any one of SEQ ID NOS: 1-401 and 1094.
[0065] The invention also provides a method for modulating a target
nucleic acid in a cell (for example, a miRNA molecule having a
nucleotide sequence comprising any one of SEQ ID NOS: 1-401 and
1094) via contacting the cell with a nucleic acid of the invention
(for example, those described above). For example, the nucleic acid
can be substantially complementary to at least 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 contiguous
nucleotides of a nucleic acid sequence selected from the group
consisting of SEQ ID NOS: 1-401 and 1094, and a nucleotide sequence
which is about 97%, about 98%, or about 99% identical to a nucleic
acid sequence comprising any one of SEQ ID NOS: 1-401 and 1094.
[0066] Expression of a miRNA molecule of the invention can be
inhibited by an antisense oligonucleotide. Antisense
oligonucleotides can comprise antisense DNA, RNA, and DNA/RNA
molecule and act via altering the activity of the target RNA by
binding to a target nucleic acid (such as a miRNA of interest) by
means of RNA-RNA, RNA-DNA or RNA-PNA (protein nucleic acid)
interactions (for a review, see Stein and Cheng, 1993 Science 261,
1004 and Woolf et al., U.S. Pat. No. 5,849,902). Antisense
oligonucleotides suitable for use in the present methods are
single-stranded nucleic acids (e.g., RNA, DNA, RNA-DNA chimeras,
PNA) that generally comprise a nucleic acid sequence complementary
to a contiguous nucleic acid sequence in a miRNA molecule. For
example, the antisense oligonucleotide comprises a nucleic acid
sequence that is 50-100% complementary, 75-100% complementary, or
95-100% complementary to a contiguous nucleic acid sequence in a
miRNA molecule of the invention having a nucleic acid sequence of
SEQ ID NO: 1-401, shown in Table 1. However, in some instances, an
antisense molecule can form a loop and binds to a substrate nucleic
acid which forms a loop. Thus, an antisense molecule can be
complementary to two (or more) non-contiguous substrate sequences,
or two (or more) non-contiguous sequence portions of an antisense
molecule can be complementary to a target sequence, or both. For a
review of current antisense strategies, see Schmajuk et al., 1999,
J. Biol. Chem., 274, 21783-21789; Delihas et al., 1997, Nature, 15,
751-753; Stein et al., 1997, Antisense N A. Drug Dev., 7, 151;
Crooke, 2000, Methods Enzymol., 313, 3-45; Crooke, 1998, Biotech.
Genet. Eng. Rev., 15, 121-157; Crooke, 1997, Ad. Pharmacol., 40,
1-49.
[0067] Antisense DNA can also be used to target nucleic acid by
means of DNA-RNA interactions, thereby activating RNase H, which
digests the target nucleic acid in the duplex. The antisense
oligonucleotides can comprise one or more RNAse H activating
region, which is capable of activating RNAse H to cleave a target
nucleic acid. Antisense DNA can be synthesized chemically or
expressed via the use of a single stranded DNA expression vector or
equivalent thereof. An RNase H activating region refers to a region
(generally greater than or equal to 4-25 nucleotides in length, for
example, from 5-11 nucleotides in length) of a nucleic acid
compound capable of binding to a target nucleic acid to form a
non-covalent complex that is recognized by cellular RNase H enzyme
(see for example Arrow et al., U.S. Pat. No. 5,849,902; Arrow et
al., U.S. Pat. No. 5,989,912). The RNase H enzyme binds to a
nucleic acid compound-target nucleic acid complex and cleaves the
target nucleic acid sequence.
[0068] Antisense nucleic acids can be produced chemically or
biologically, or can be expressed from a recombinant plasmid or
viral vector, as described above for the isolated miRNA molecules.
For example, antisense oligonucleotides of at least about 15 bases
and complementary to unique regions of the miRNA molecules of the
invention can be synthesized, e.g., by conventional phosphodiester
techniques (Dallas et al., (2006) Med. Sci. Monit. 12(4):RA67-74;
Kalota et al., (2006) Handb. Exp. Pharmacol. 173:173-96;
Lutzelburger et al., (2006) Handb. Exp. Pharmacol. 173:243-59).
Exemplary methods for producing and testing are within the skill in
the art; see, e.g., Stein and Cheng (1993), Science 261:1004 and
U.S. Pat. No. 5,849,902 to Woolf et al., the entire disclosures of
which are herein incorporated by reference.
[0069] Antisense polynucleotides include, but are not limited to:
morpholinos, 2'-O-methyl polynucleotides, DNA, RNA and the like.
RNA polymerase III transcribed DNAs contain promoters, such as the
U6 promoter. These DNAs can be transcribed to produce small hairpin
RNAs in the cell that can function as siRNA or linear RNAs that can
function as antisense RNA. The inhibitor can be polymerized in
vitro, recombinant RNA, contain chimeric sequences, or derivatives
of these groups. The inhibitor can contain ribonucleotides,
deoxyribonucleotides, synthetic nucleotides, or any suitable
combination such that the target RNA and/or gene is inhibited. In
addition, these forms of nucleic acid can be single, double,
triple, or quadruple stranded. (see for example Bass (2001) Nature,
411, 428 429; Elbashir et al., (2001) Nature, 411, 494 498; and PCT
Publication Nos. WO 00/44895, WO 01/36646, WO 99/32619, WO
00/01846, WO 01/29058, WO 99/07409, WO 00/44914).
[0070] siRNA comprises a double stranded structure that can contain
15 to 50 base pairs, or 21 to 25 base pairs, and having a
nucleotide sequence identical or nearly identical to an expressed
target gene or RNA within the cell. The siRNA comprise a sense RNA
strand and a complementary antisense RNA strand annealed together
by standard Watson-Crick base-pairing interactions. The sense
strand comprises a nucleic acid sequence which is substantially
identical to a nucleic acid sequence contained within the target
miRNA molecule. "Substantially identical" to a target sequence
contained within the target mRNA refers to a nucleic acid sequence
that is identical to the target sequence, or that differs from the
target sequence by one or two nucleotides. The sense and antisense
strands of the siRNA can comprise two complementary,
single-stranded RNA molecules, or can comprise a single molecule in
which two complementary portions are base-paired and are covalently
linked by a single-stranded "hairpin" area.
[0071] The siRNA can also be altered RNA that differs from
naturally-occurring RNA by the addition, deletion, substitution
and/or alteration of one or more nucleotides. Such alterations can
include addition of non-nucleotide material, such as to the end(s)
of the siRNA or to one or more internal nucleotides of the siRNA,
or modifications that make the siRNA resistant to nuclease
digestion, or the substitution of one or more nucleotides in the
siRNA with deoxyribonucleotides. One or both strands of the siRNA
can also comprise a 3' overhang. As used herein, a 3' overhang
refers to at least one unpaired nucleotide extending from the
3'-end of a duplexed RNA strand. For example, the siRNA can
comprise at least one 3' overhang of from 1 to about 6 nucleotides
(which includes ribonucleotides or deoxyribonucleotides) in length,
or from 1 to about 5 nucleotides in length, or from 1 to about 4
nucleotides in length, or from about 2 to about 4 nucleotides in
length. For example, each strand of the siRNA can comprise 3'
overhangs of dithymidylic acid ("TT") or diuridylic acid
("uu").
[0072] siRNA can be produced chemically or biologically, or can be
expressed from a recombinant plasmid or viral vector, as described
above for the miRNA molecules of the invention having a sequence
shown in Table 1. Exemplary methods for producing and testing dsRNA
or siRNA molecules are described in U.S. Patent Application
Publication No. 2002/0173478 to Gewirtz, U.S. Patent Application
Publication No. 2007/0072204 to Hannon et al., and in U.S. Patent
Application Publication No. 2004/0018176 to Reich et al., the
entire disclosures of which are herein incorporated by
reference.
[0073] Expression of a miRNA molecule of the invention can also be
inhibited by a short hairpin RNA (shRNA). The hairpin RNAs can be
synthesized exogenously or can be formed by transcribing from RNA
polymerase III promoters in vivo. Examples of making and using such
hairpin RNAs for gene silencing in mammalian cells are described
in, for example, Paddison et al., 2002, Genes Dev, 16:948-58;
McCaffrey et al., 2002, Nature, 418:38-9; McManus et al., 2002,
RNA, 8:842-50; Yu et al., 2002, Proc Natl Acad Sci USA,
99:6047-52). Such hairpin RNAs are engineered in cells or in an
animal to ensure continuous and stable suppression of a desired
gene. It is known in the art that siRNAs can be produced by
processing a hairpin RNA in the cell.
[0074] Expression of a miRNA molecule of the invention can also be
inhibited by a ribozyme. Ribozymes are enzymatic RNA molecules
capable of catalyzing the specific cleavage of RNA. The mechanism
of ribozyme action involves sequence specific hybridization of the
ribozyme molecule to complementary target RNA sequences (for
example those shown in Table 1), followed by endonucleolytic
cleavage. Engineered hammerhead motif ribozyme molecules that
specifically and efficiently catalyze endonucleolytic cleavage of a
miRNA sequence shown in Table 1, are also within the scope of the
present invention. Scanning the target molecule for ribozyme
cleavage sites that include the following sequences, GUA, GUU, and
GUC initially identifies specific ribozyme cleavage sites within
any potential RNA target. Once identified, short RNA sequences of
between about 15 and 20 ribonucleotides corresponding to the region
of the target gene containing the cleavage site can be evaluated
for predicted structural features such as secondary structure that
can render the oligonucleotide sequence unsuitable.
[0075] The suitability of candidate targets can also be evaluated
by testing their accessibility to hybridization with complementary
oligonucleotides using, e.g., ribonuclease protection assays (see
Romkes et al., 2005, Methods Mol Biol.; 291:387-98; Dvorak et al.,
2003, Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub
147(2):131-5). The construction and production of hammerhead
ribozymes is well known in the art and is described more fully in
Haseloff and Gerlach, 1988, Nature, 334:585-591. Ribozymes can also
include RNA endoribonucleases such as the one which occurs
naturally in Tetrahymena thermophila (known as the IVS or L-19 IVS
RNA) and which has been described (see, e.g., Zaug, et al., 1984,
Science, 224:574-578; Zaug and Cech, 1986, Science, 231:470-475;
Zaug, et al., 1986, Nature, 324:429-433; published International
patent application No. WO88/04300 by University Patents Inc.; Been
and Cech, 1986, Cell, 47:207-216).
[0076] Both the antisense oligonucleotides and ribozymes of the
present invention can be prepared by known methods. These include
techniques for chemical synthesis such as, e.g., by solid phase
phosphoamite chemical synthesis. Alternatively, antisense RNA
molecules can be generated by in vitro or in vivo transcription of
DNA sequences encoding the RNA molecule. Such DNA sequences can be
incorporated into a wide variety of vectors that incorporate
suitable RNA polymerase promoters such as the T7 or SP6 polymerase
promoters.
[0077] Alternatively, expression of a miRNA molecule of the
invention can be inhibited by an antagomir. An antagomir is a
single-stranded, double stranded, partially double stranded or
hairpin structured chemically modified oligonucleotide agent that
comprises at least 12 or more contiguous nucleotides substantially
complementary to an endogenous miRNA or agents that include 12 or
more contiguous nucleotides substantially complementary to a target
sequence of an miRNA or pre-miRNA nucleotide sequence. The
antagomir can be RNA, DNA, or a combination of RNA and DNA, and is
antisense with respect to its target nucleotide sequence. An
antagomir can target RNA, e.g., an endogenous pre-miRNA or miRNA of
the subject. For example, the antagomir can target a miRNA having a
nucleic acid sequence shown in Table 1. Exemplary methods for
producing and testing antagomirs are discussed in U.S. Patent
Application Publication No. 2007/0123482 and U.S. Patent
Application Publication No. 005/0182005, in addition to Mattes et
al., 2007 Am J Resp Cell Mol Biol 36: 8-12; Krutzfeldt et al., 2007
Nuc Acid Res 35(9): 2885-2892, which are all incorporated by
reference in their entireties.
[0078] Various modifications to the nucleic acid molecules of the
present invention can be introduced as a means of increasing
intracellular stability and half-life. Some modifications include
but are not limited to the addition of flanking sequences of
ribonucleotides or deoxyribonucleotides to the 5' and/or 3' ends of
the molecule, or the use of phosphorothioate or 2'-O-methyl rather
than phosphodiesterase linkages within the oligonucleotide
backbone.
[0079] Expression of a miRNA molecule of the invention can be
inhibited by an aptamer. Aptamer nucleic acid sequences are readily
made that bind to a wide variety of target molecules. The aptamer
nucleic acid sequences of the invention can be comprised entirely
of RNA or partially of RNA, or entirely or partially of DNA and/or
other nucleotide analogs. A nucleic acid aptamer is a nucleic acid
or a nucleic acid-like molecule that is capable of binding to a
specific molecule of interest with high affinity and specificity. A
nucleic acid aptamer also can be a nucleic acid molecule that
mimics the three dimensional structure of active portions of
miRNAs. A nucleic acid-aptamer can be between about 9 and about 300
nucleotides or the like in length. More commonly, an aptamer is
between about 30 and about 100 nucleotides or the like in
length.
[0080] Aptamers are developed to bind specific ligands by employing
known in vivo or in vitro selection techniques known as SELEX
(Systematic Evolution of Ligands by Exponential Enrichment).
Nucleic acid-aptamers can be prepared by any known method,
including synthetic, recombinant, and purification methods. Such
methods are described in, for example, Ellington and Szostak (1990)
Nature 346:818, Tuerk and Gold (1990) Science 249:505, James W.,
(2001) Current Opinion in Pharmacology, 1:540-546, Colas et al.,
(1996) Nature 380:548-550, U.S. Pat. No. 5,582,981; PCT Publication
No. WO 00/20040; U.S. Pat. No. 5,270,163; Lorsch and Szostak (1994)
Biochem. 33:973; Mannironi et al., (1997) Biochem. 36:9726; Blind
(1999) Proc. Nat'l. Acad. Sci. USA 96:3606-3610; Huizenga and
Szostak (1995) Biochem. 34:656-665; PCT Publication Nos. WO
99/54506, WO 99/27133, and WO 97/42317; and U.S. Pat. No.
5,756,291, all of which are incorporated by reference in their
entireties.
[0081] Expression of a given miRNA molecule can be inhibited or
decreased by inducing RNA interference of the miRNA molecule with
an isolated double-stranded or single-stranded RNA molecule. For
example, the miRNA inhibitor molecule can be those molecules
discussed above, such as an antagomir, an antisense RNA, a small
interfering RNA (siRNA), a short hairpin RNA (snRNA), and the like)
which has at least about 75%, 80%, 90%, 95%, 98%, 99% or 100%,
sequence homology to a portion of a miRNA molecule having a
sequence shown in Table 1. For further discussion of modulation of
miRNA expression, see: Lu et al., (2005) Adv Genet. 54:117-42;
Leung and Whittaker (2005) Pharmacol Ther. 107(2):222-39; Takeshita
and Ochiva (2006) Cancer Sci. 97(8):689-96; and Alexander et al.,
(2007) Arch Immunol Ther Exp (Warsz). 2007 May-June;
55(3):139-49.
[0082] A subject in need thereof, according to the invention, can
refer to any animal classified as a mammal, including humans,
domestic and farm animals, and zoo, sports, or pet animals. In some
embodiments, the subject can be a mouse, a rat, a bird, a dog, a
cat, a cow, a horse, a sheep, or a pig. In exemplary embodiments, a
mammal is a human.
[0083] Methods for determining RNA expression levels in cells from
a biological sample are within the level of skill in the art. For
example, tissue sample can be removed from a subject suspected of
having cancer associated with a cancer-associated chromosomal
feature by conventional biopsy techniques. In another example, a
blood sample can be removed from the subject, and white blood cells
isolated for DNA extraction by standard techniques. The blood or
tissue sample should be obtained from the subject prior to
initiation of radiotherapy, chemotherapy or other therapeutic
treatment. A corresponding control tissue or blood sample can be
obtained from unaffected tissues of the subject, from a normal
human individual or population of normal individuals, or from
cultured cells corresponding to the majority of cells in the
subject's sample. The control tissue or blood sample is then
processed along with the sample from the subject, so that the
levels of miRNA molecules in cells from the subject's sample can be
compared to the corresponding miRNA molecule levels from cells of
the control sample. For example, the relative miRNA expression in
the control and normal samples can be conveniently determined with
respect to one or more RNA expression standards. The standards can
comprise, for example, a zero miRNA expression level, the miRNA
expression level in a standard cell line, or the average level of
miRNA expression previously obtained for a population of normal
human controls.
[0084] Suitable techniques for determining the level of RNA
transcripts of a gene of interest in cells are within the skill in
the art. According to one such method, total cellular RNA can be
purified from cells by homogenization in the presence of nucleic
acid extraction buffer, followed by centrifugation. Nucleic acids
are precipitated, and DNA is removed by treatment with DNase and
precipitation. The RNA molecules are then separated by gel
electrophoresis on agarose gels according to standard techniques,
and transferred to nitrocellulose filters by, e.g., the so-called
"Northern" blotting technique. The RNA is then immobilized on the
filters by heating. Detection and quantification of specific RNA is
accomplished using appropriately labeled DNA or RNA probes
complementary to the RNA in question. See, for example, Molecular
Cloning: A Laboratory Manual, J. Sambrook et al., eds., 2nd
edition, Cold Spring Harbor Laboratory Press, 1989, Chapter 7, the
entire disclosure of which is incorporated by reference.
[0085] Suitable probes for Northern blot hybridization of a given
miRNA molecule can be produced from the nucleic acid sequences
provided in Table 1. Methods for preparation of labeled DNA and RNA
probes, and the conditions for hybridization thereof to target
nucleotide sequences, are described in Molecular Cloning: A
Laboratory Manual, J. Sambrook et al., eds., 2nd edition, Cold
Spring Harbor Laboratory Press, 1989, Chapters 10 and 11, the
disclosures of which are herein incorporated by reference. For
example, the nucleic acid probe can be labeled with, e.g., a
radionuclide such as .sup.3H, .sup.32P, .sup.33P, .sup.14C, or
.sup.35S; a heavy metal; or a ligand capable of functioning as a
specific binding pair member for a labeled ligand (e.g., biotin,
avidin or an antibody), a fluorescent molecule, a chemiluminescent
molecule, an enzyme or the like.
[0086] Probes can be labeled to high specific activity by either
the nick translation method of Rigby et al. (1977), J. Mol. Biol.
113:237-251 or by the random priming method of Fienberg et al.
(1983), Anal. Biochem. 132:6-13, the entire disclosures of which
are herein incorporated by reference. Fienberg et al. provides a
useful method for synthesizing .sup.32P-labeled probes of high
specific activity from single-stranded DNA or from RNA templates.
For example, by replacing preexisting nucleotides with highly
radioactive nucleotides according to the nick translation method,
.sup.32P-labeled nucleic acid probes can be prepared with a
specific activity well in excess of 10.sup.8 cpm/microgram.
Autoradiographic detection of hybridization can then be performed
by exposing hybridized filters to photographic film. Densitometric
scanning of the photographic films exposed by the hybridized
filters provides an accurate measurement of miRNA molecule levels.
Using another approach, miRNA molecule levels can be quantified by
computerized imaging systems, such the Molecular Dynamics 400-B 2D
Phosphorimager available from Amersham Biosciences, Piscataway,
N.J.
[0087] Where radionuclide labeling of DNA or RNA probes is not
practical, the random-primer method can be used to incorporate an
analogue, for example, the dTTP analogue
5-(N--(N-biotinyl-epsilon-aminocaproyl)-3-aminoallyl)deoxyuridine
triphosphate, into the probe molecule. The biotinylated probe
oligonucleotide can be detected by reaction with biotin-binding
proteins, such as avidin, streptavidin, and antibodies (e.g.,
anti-biotin antibodies) coupled to fluorescent dyes or enzymes that
produce color reactions.
[0088] In addition to Northern and other RNA blotting hybridization
techniques, determining the levels of RNA transcripts can be
accomplished using the technique of in situ hybridization. This
technique requires fewer cells than the Northern blotting
technique, and involves depositing whole cells onto a microscope
cover slip and probing the nucleic acid content of the cell with a
solution containing radioactive or otherwise labeled nucleic acid
(e.g., cDNA or RNA) probes. This technique is well-suited for
analyzing tissue biopsy samples from subjects. The practice of the
in situ hybridization technique is described in more detail in U.S.
Pat. No. 5,427,916, the entire disclosure of which is incorporated
herein by reference. Suitable probes for in situ hybridization of a
given miRNA molecule can be produced from the nucleic acid
sequences provided in Table 1, as described above.
[0089] The relative number of miRNA transcripts in cells can also
be determined by reverse transcription of miRNA transcripts,
followed by amplification of the reverse-transcribed transcripts by
polymerase chain reaction (RT-PCR). The levels of miRNA gene
transcripts can be quantified in comparison with an internal
standard, for example, the level of mRNA from a housekeeping gene
present in the same sample, such as myosin or
glyceraldehyde-3-phosphate dehydrogenase (G3PDH). The methods for
quantitative RT-PCR and variations thereof are within the skill in
the art.
[0090] It is desirable to simultaneously determine the expression
level of a plurality of different of miRNA molecules in a sample,
for example determine the expression level of the transcripts of
known miRNAs correlated with cancer or other cell division
disorders (for example, a hematopoietic cell division disorder,
such as a B cell lymphoma). Since examining cancer-specific
expression levels for hundreds of miRNA molecules is time
consuming, requires a large amount of total RNA (at least 20 .mu.g
for each Northern blot) and utilizes autoradiographic techniques
that require radioactive isotopes, an oligolibrary in microchip
format can be constructed containing a set of probe
oligonucleotides specific for a set of miRNA molecules (for
example, miRNA molecules having any one nucleic acid sequence of
SEQ ID NOS: 1-401, shown in Table 1, or any one miRNA molecule of
Table 7, Table 9, or Table 10).
[0091] A nucleic acid microchip array is a plurality of probe
elements, each probe element comprising one or more nucleic acid
molecules immobilized on one or more solid surfaces to which sample
nucleic acids can be hybridized. Microarrays are known in the art
and comprise a surface to which probes that correspond in sequence
to gene products (e.g., cDNAs, mRNAs, cRNAs, polypeptides, and
fragments thereof), can be specifically hybridized or bound at a
known position. The microarray can be an array (i.e., a matrix) in
which each position represents a discrete binding site for an RNA,
and in which binding sites are present for products of most of the
genes in the organism's genome, or a specific tissue or cellular
subset of the organism. Here, the binding site can be a nucleic
acid or nucleic acid analogue to which a cognate cDNA or RNA, such
as miRNA molecule of the invention, can specifically hybridize. The
nucleic acid or analogue of the binding site can be, e.g., a
synthetic miRNA oligomer.
[0092] The nucleic acid or analogue is attached to a solid support,
which can be made from glass, plastic (e.g., polypropylene, nylon),
polyacrylamide, nitrocellulose, or other materials. A useful method
for attaching the nucleic acids to a surface is by printing on
glass plates, as is described generally by Schena et al., 1995. See
also DeRisi et al., 1996; Shalon et al., 1996; Schena et al., 1996.
Each of these articles is incorporated by reference in its
entirety.
[0093] The microchip is prepared from gene-specific oligonucleotide
probes generated from known miRNAs. A nucleic acid array can
contain two different oligonucleotide probes for each miRNA, one
containing the active sequence and the other being specific for the
precursor of the miRNA (for example, see Table 1). The array can
also contain controls such as one or more mouse sequences differing
from human orthologs by only a few bases, which can serve as
controls for hybridization stringency conditions. tRNAs from both
species can also be printed on the microchip, providing an
internal, relatively stable positive control for specific
hybridization. One or more appropriate controls for non-specific
hybridization can also be included on the microchip. For this
purpose, sequences are selected based upon the absence of any
homology with any known miRNAs. For example, the array can also
contain miRNA sequences found to be specific for human B cells.
Non-limiting examples of such miRNA's include: mir-15, mir-17,
mir-14, mir-124a-3, mir-99b, mir-167a, mir-167b, mir-129-1,
mir-30c-2, mir-143, mir-27b, mir-125b-1, mir-128a, mir-140,
mir-142, mir-191, mir-125b-2, mir-127, mir-129-2, mir-146a,
mir-154, mir-185, mir-186, mir-322, mir-124a-1, mir-124a-2,
mir-30c-1, mir-302a, and mir-99b.
[0094] The microchip can be fabricated by techniques known in the
art. For example, probe oligonucleotides of an appropriate length,
e.g., 40 nucleotides, are 5'-amine modified at position C6 and
printed using commercially available microarray systems, e.g., the
GeneMachine OmniGrid.TM. 100 Microarrayer and Amersham CodeLink.TM.
activated slides. Labeled cDNA oligomer corresponding to the target
RNAs is prepared by reverse transcribing the target RNA with
labeled primer. Following first strand synthesis, the RNA/DNA
hybrids are denatured to degrade the RNA templates. The labeled
target cDNAs thus prepared are then hybridized to the microarray
chip under hybridizing conditions, e.g. 6.times.SSPE/30% formamide
at 25.degree. C. for 18 hours, followed by washing in
0.75.times.TNT at 37.degree. C. for 40 minutes. At positions on the
array where the immobilized probe DNA recognizes a complementary
target cDNA in the sample, hybridization occurs. The labeled target
cDNA marks the exact position on the array where binding occurs,
allowing automatic detection and quantification. The output
consists of a list of hybridization events, indicating the relative
abundance of specific cDNA sequences, and therefore the relative
abundance of the corresponding complementary miRs, in the patient
sample. According to one embodiment, the labeled cDNA oligomer is a
biotin-labeled cDNA, prepared from a biotin-labeled primer. The
microarray is then processed by direct detection of the
biotin-containing transcripts using, e.g., Streptavidin-Alexa647
conjugate, and scanned utilizing conventional scanning methods.
Images intensities of each spot on the array are proportional to
the abundance of the corresponding miR in the patient sample.
[0095] Other methods for making microarrays (see U.S. Patent
Application Publication No. 2006/0051771, which is incorporate by
reference in its entirety), e.g., by masking (Fodor et al., 1991;
Maskos and Southern, 1992), can also be used. In principal, any
type of array, for example, dot blots on a nylon hybridization
membrane (see Sambrook et al., 1989, which is incorporated in its
entirety for all purposes), can be used, although, as will be
recognized by those of skill in the art, very small arrays are
useful because hybridization volumes will be smaller.
[0096] Labeled cDNA can be prepared from mRNA by oligo dT-primed or
random-primed reverse transcription, both of which are well known
in the art. Reverse transcription can be carried out in the
presence of a dNTP conjugated to a detectable label, for example, a
fluorescently labeled dNTP. Alternatively, isolated mRNA can be
converted to labeled antisense RNA synthesized by in vitro
transcription of double-stranded cDNA in the presence of labeled
dNTPs (Lockhart et al., 1996, which is incorporated by reference in
its entirety for all purposes). In alternative embodiments, the
cDNA or aRNA probe can be synthesized in the absence of detectable
label and can be labeled subsequently, e.g., by incorporating
biotinylated dNTPs or rNTP, or some similar means (e.g.,
photo-cross-linking a psoralen derivative of biotin to RNAs),
followed by addition of labeled streptavidin (e.g.,
phycoerythrin-conjugated streptavidin) or the equivalent.
Alternatively, cDNA or aRNA can be labeled indirectly by
incorporation of 5-(3-aminoallyl) dNTPs or rNTPs to provide a amine
reactive group for subsequent addition of label with any moiety
bearing an N-Hydroxysuccinimide (NHS) ester.
[0097] Fluorescently labeled probes can be used, including suitable
fluorophores such as fluorescein, lissamine, phycoerythrin,
rhodamine (Perkin Elmer Cetus), Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7,
FluorX (Amersham) and others (see, e.g., Kricka, 1992, Nonisotopic
DNA Probe Techniques, Academic Press San Diego, Calif.). It will be
appreciated that pairs of fluorophores are chosen that have
distinct emission spectra so that they can be easily distinguished.
In another embodiment, a label other than a fluorescent label is
used. For example, a radioactive label, or a pair of radioactive
labels with distinct emission spectra, can be used (see Zhao et
al., 1995; Pietu et al., 1996).
[0098] The analysis of microarray data can be accomplished using
methods of statistical analysis known to those skilled in the art.
For example, clustering analysis is commonly used for
interpretation of microarray data. It provides both a visual
representation of complex data and a method for measuring
similarity between experiments. Some widely used methods for
clustering microarray data include: hierarchical, K-means, and
self-organizing map.
[0099] Southern blot hybridization techniques are also within the
skill in the art. For example, genomic DNA isolated from a
subject's sample can be digested with restriction endonucleases.
This digestion generates restriction fragments of the genomic DNA
that can be separated by electrophoresis, for example, on an
agarose gel. The restriction fragments are then blotted onto a
hybridization membrane (e.g., nitrocellulose or nylon), and
hybridized with labeled probes specific for a given miRNA
molecule(s). A deletion or mutation of these genes is indicated by
an alteration of the restriction fragment patterns on the
hybridization membrane, as compared to DNA from a control sample
that has been treated identically to the DNA from the subject's
sample. Probe labeling and hybridization conditions suitable for
detecting alterations in gene structure or sequence can be readily
determined by one of ordinary skill in the art. The miRNA nucleic
acid probes for Southern blot hybridization can be designed based
upon the nucleic acid sequences having SEQ ID NOS: 1-401, provided
in Table 1, or any one miRNA molecule of Table 7, Table 9, or Table
10. Nucleic acid probe hybridization can then be detected by
exposing hybridized filters to photographic film, or by employing
computerized imaging systems, such the Molecular Dynamics 400-B 2D
Phosphorimager available from Amersham Biosciences, Piscataway,
N.J.
[0100] Human miRNAs are associated with different classes of
chromosomal features that are subsequently associated with cancer
(Xu and Li (2007) Chin Med J (Engl). 120(11):996-9; Bandres et al.,
(2007) DNA Cell Biol. 26(5):273-82). These cancers are purportedly
partly caused by perturbing the chromosome or genomic DNA caused by
the cancer-associated chromosomal feature, which can affect
expression of oncogenes or tumor-suppressor genes located near the
site of perturbation. A given cancer can be treated by restoring
the level of miRNA expression associated with that cancer to
normal. For example, if the level of miRNA expression is
down-regulated in cancer cells of a subject, then the cancer can be
treated by increasing the miRNA expression level. Alternatively, if
the miRNA expression level is up-regulated in cancer cells of a
subject, then the cancer can be treated by decreasing the miRNA
expression level.
[0101] For example, the level of a miRNA in a cancerous or
neoplastic cell of a subject (for example a hematopoietic
malignancy or a hematopoietic neoplasm) is first determined
relative to control cells. Techniques suitable for determining the
relative level of a miRNA molecule in cells have been described
above. If miRNA expression is down-regulated in the cancer or
neoplastic cell relative to control cells, then the cancer or
neoplastic cells are treated with an effective amount of a
composition comprising an isolated miRNA molecule which is
down-regulated (for example, a miRNA of the invention comprising
any one of SEQ ID NOS: 1-401, as shown in Table 1, or any one miRNA
molecule of Table 7, Table 9, or Table 10). If miRNA expression is
up-regulated in cancer or neoplastic cells relative to control
cells, then the cancer or neoplastic cells are treated with an
effective amount of a composition that inhibits miRNA expression
(for example, a miRNA of the invention comprising any one of SEQ ID
NOS: 1-401, as shown in Table 1, or any one miRNA molecule of Table
7, Table 9, or Table 10).
[0102] One skilled in the art can also readily determine an
appropriate dosage for the administration of an isolated miRNA
molecule to a given subject. For example, a miRNA molecule can be
administered to the subject once (e.g., as a single injection or
deposition). Alternatively, a miRNA molecule of the invention can
be administered once or twice daily to a subject for a period of
from about two to about twenty-eight days, for example, from about
seven to about ten days. Furthermore, the miRNA molecule of the
invention can be co-administrated with another therapeutic, such as
a chemotherapy drug. Where a dosage regimen comprises multiple
administrations, the effective amount of the miRNA molecule
administered to the subject can comprise the total amount of gene
product administered over the entire dosage regimen.
[0103] The miRNA molecules of the invention comprising any one of
SEQ ID NOS: 1-401, as shown in Table 1, or any one miRNA molecule
of Table 7, Table 9, or Table 10, can be administered to a subject
by any means suitable for delivering the miRNA molecules to cells
of the subject, such as hematopoietic cells (either cancerous or
neoplastic). For example, miRNA molecules can be administered by
methods suitable to transfect cells (such as of the subject with
the miRNA molecules of the invention. Transfection methods for
eukaryotic cells (such as hematopoietic malignant cells or a
hematopoietic neoplastic cells) are well known in the art, and
include direct injection of the nucleic acid into the nucleus or
pronucleus of a cell; electroporation; liposome transfer or
transfer mediated by lipophilic materials; receptor mediated
nucleic acid delivery, bioballistic or particle acceleration;
calcium phosphate precipitation, and transfection mediated by viral
vectors.
[0104] The compositions of this invention can be formulated and
administered to inhibit a variety of disease states by any means
that produces contact of the active ingredient with the agent's
site of action in the body of a mammal They can be administered by
any conventional means available for use in conjunction with
pharmaceuticals, either as individual therapeutic active
ingredients or in a combination of therapeutic active ingredients.
They can be administered alone, but are generally administered with
a pharmaceutical carrier selected on the basis of the chosen route
of administration and standard pharmaceutical practice.
[0105] Pharmaceutical compositions for use in accordance with the
invention can be formulated in conventional manner using one or
more physiologically acceptable carriers or excipients. The
therapeutic compositions of the invention can be formulated for a
variety of routes of administration, including systemic and topical
or localized administration. Techniques and formulations generally
can be found in Remmington's Pharmaceutical Sciences, Meade
Publishing Co., Easton, Pa. (1985), the entire disclosure of which
is herein incorporated by reference. For systemic administration,
injection is useful, including intramuscular, intravenous,
intraperitoneal, and subcutaneous. For injection, the therapeutic
compositions of the invention can be formulated in liquid
solutions, for example, in physiologically compatible buffers such
as Hank's solution or Ringer's solution. In addition, the
therapeutic compositions can be formulated in solid form and
redissolved or suspended immediately prior to use. Lyophilized
forms are also included. Pharmaceutical compositions of the present
invention are characterized as being at least sterile and
pyrogen-free. These pharmaceutical formulations include
formulations for human and veterinary use.
[0106] The present pharmaceutical formulations comprise the miRNA
molecules of the invention comprising any one of SEQ ID NOS: 1-401,
as shown in Table 1, or any one miRNA molecule of Table 7, Table 9,
or Table 10 (e.g., 0.1 to 90% by weight), or a physiologically
acceptable salt thereof, mixed with a pharmaceutically-acceptable
carrier. The pharmaceutical formulations of the invention can also
comprise the miRNA molecules of the invention comprising any one of
SEQ ID NOS: 1-401, as shown in Table 1, or any one miRNA molecule
of Table 7, Table 9, or Table 10, which are encapsulated by
liposomes and a pharmaceutically-acceptable carrier. Useful
pharmaceutically-acceptable carriers are water, buffered water,
normal saline, 0.4% saline, 0.3% glycine, hyaluronic acid, and the
like.
[0107] Pharmaceutical compositions of the invention can also
comprise conventional pharmaceutical excipients and/or additives.
Suitable pharmaceutical excipients include stabilizers,
antioxidants, osmolality adjusting agents, buffers, and pH
adjusting agents. Suitable additives include physiologically
biocompatible buffers (e.g., tromethamine hydrochloride), additions
of chelants (such as, for example, DTPA or DTPA-bisamide) or
calcium chelate complexes (as for example calcium DTPA,
CaNaDTPA-bisamide), or, optionally, additions of calcium or sodium
salts (for example, calcium chloride, calcium ascorbate, calcium
gluconate or calcium lactate). Pharmaceutical compositions of the
invention can be packaged for use in liquid form, or can be
lyophilized.
[0108] For solid pharmaceutical compositions of the invention,
conventional nontoxic solid pharmaceutically-acceptable carriers
can be used; for example, pharmaceutical grades of mannitol,
lactose, starch, magnesium stearate, sodium saccharin, talcum,
cellulose, glucose, sucrose, magnesium carbonate, and the like.
[0109] For oral administration, the therapeutic compositions can
take the form of, for example, tablets or capsules prepared by
conventional means with pharmaceutically acceptable excipients such
as binding agents (e.g., pregelatinised maize starch,
polyvinylpyrrolidone or hydroxypropyl methylcellulose); fillers
(e.g., lactose, microcrystalline cellulose or calcium hydrogen
phosphate); lubricants (e.g., magnesium stearate, talc or silica);
disintegrants (e.g., potato starch or sodium starch glycolate); or
wetting agents (e.g., sodium lauryl sulphate). The tablets can be
coated by methods well known in the art. Liquid preparations for
oral administration can take the form of, for example, solutions,
syrups or suspensions, or they can be presented as a dry product
for constitution with water or other suitable vehicle before use.
Such liquid preparations can be prepared by conventional means with
pharmaceutically acceptable additives such as suspending agents
(e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible
fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous
vehicles (e.g., ationd oil, oily esters, ethyl alcohol or
fractionated vegetable oils); and preservatives (e.g., methyl or
propyl-p-hydroxybenzoates or sorbic acid). The preparations can
also contain buffer salts, flavoring, coloring and sweetening
agents as appropriate.
[0110] Preparations for oral administration can be suitably
formulated to give controlled release of the active agent. For
buccal administration the therapeutic compositions can take the
form of tablets or lozenges formulated in a conventional manner.
For administration by inhalation, the compositions for use
according to the present invention are conveniently delivered in
the form of an aerosol spray presentation from pressurized packs or
a nebuliser, with the use of a suitable propellant, e.g.,
dichlorodifluoromethane, trichlorofluoromethane,
dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In
the case of a pressurized aerosol the dosage unit can be determined
by providing a valve to deliver a metered amount. Capsules and
cartridges of e.g., gelatin for use in an inhaler or insufflate or
can be formulated containing a powder mix of the therapeutic agents
and a suitable powder base such as lactose or starch.
[0111] The therapeutic compositions can be formulated for
parenteral administration by injection, e.g., by bolus injection or
continuous infusion. Formulations for injection can be presented in
unit dosage form, e.g., in ampoules or in multi-dose containers,
with an added preservative. The compositions can take such forms as
suspensions, solutions or emulsions in oily or aqueous vehicles,
and can contain formulatory agents such as suspending, stabilizing
and/or dispersing agents. Alternatively, the active ingredient can
be in powder form for constitution with a suitable vehicle, e.g.,
sterile pyrogen-free water, before use.
[0112] Suitable enteral administration routes for the present
methods include oral, rectal, or intranasal delivery. Suitable
parenteral administration routes include intravascular
administration (e.g. intravenous bolus injection, intravenous
infusion, intra-arterial bolus injection, intra-arterial infusion
and catheter instillation into the vasculature); peri- and
intra-tissue injection (e.g., peri-tumoral and intra-tumoral
injection, intra-retinal injection, or subretinal injection);
subcutaneous injection or deposition including subcutaneous
infusion (such as by osmotic pumps); direct application to the
tissue of interest, for example by a catheter or other placement
device (e.g., a retinal pellet or a suppository or an implant
comprising a porous, non-porous, or gelatinous material); and
inhalation. The miRNA molecules of the invention are administered
by injection or infusion.
[0113] In addition to the formulations described previously, the
therapeutic compositions can also be formulated as a depot
preparation. Such long acting formulations can be administered by
implantation (for example subcutaneously or intramuscularly) or by
intramuscular injection. Thus, for example, the therapeutic
compositions can be formulated with suitable polymeric or
hydrophobic materials (for example as an emulsion in an acceptable
oil) or ion exchange resins, or as sparingly soluble derivatives,
for example, as a sparingly soluble salt.
[0114] Systemic administration can also be by transmucosal or
transdermal means. For transmucosal or transdermal administration,
penetrants appropriate to the barrier to be permeated are used in
the formulation. Such penetrants are generally known in the art,
and include, for example, for transmucosal administration bile
salts and fusidic acid derivatives. In addition, detergents can be
used to facilitate permeation. Transmucosal administration can be
through nasal sprays or using suppositories. For topical
administration, the compositions of the invention are formulated
into ointments, salves, gels, or creams as generally known in the
art. A wash solution can be used locally to treat an injury or
inflammation to accelerate healing. For oral administration, the
therapeutic compositions are formulated into conventional oral
administration forms such as capsules, tablets, and tonics.
[0115] A composition of the present invention can also be
formulated as a sustained and/or timed release formulation. Such
sustained and/or timed release formulations can be made by
sustained release means or delivery devices that are well known to
those of ordinary skill in the art, such as those described in U.S.
Pat. Nos. 3,845,770; 3,916,899; 3,536,809; 3,598,123; 4,008,719;
4,710,384; 5,674,533; 5,059,595; 5,591,767; 5,120,548; 5,073,543;
5,639,476; 5,354,556; and 5,733,566, the disclosures of which are
each incorporated herein by reference. The pharmaceutical
compositions of the present invention can be used to provide slow
or sustained release of one or more of the active ingredients
using, for example, hydropropylmethyl cellulose, other polymer
matrices, gels, permeable membranes, osmotic systems, multilayer
coatings, microparticles, liposomes, microspheres, or the like, or
a combination thereof to provide the desired release profile in
varying proportions. Suitable sustained release formulations known
to those of ordinary skill in the art, including those described
herein, can be readily selected for use with the pharmaceutical
compositions of the invention. Thus, single unit dosage forms
suitable for oral administration, such as, but not limited to,
tablets, capsules, gel caps, caplets, powders, and the like, that
are adapted for sustained release are encompassed by the present
invention.
[0116] In the present methods, the miRNA molecules of the current
invention comprising any one of SEQ ID NOS: 1-401, as shown in
Table 1, or any one miRNA molecule of Table 7, Table 9, or Table
10, can be administered to the subject either as naked RNA, in
conjunction with a delivery reagent, or as a nucleic acid (e.g., a
recombinant plasmid or viral vector) comprising sequences which
expresses the gene product. Suitable delivery reagents for
administration of the miRNA molecules include the Mirus Transit TKO
lipophilic reagent; lipofectin; lipofectamine; cellfectin; or
polycations (e.g., polylysine), or liposomes.
[0117] The dosage administered will be a therapeutically effective
amount of the composition sufficient to result in amelioration of
symptoms of B cell lymphoma disease and can vary depending upon
known factors such as the pharmacodynamic characteristics of the
particular active ingredient and its mode and route of
administration; age, sex, health and weight of the recipient;
nature and extent of symptoms; kind of concurrent treatment,
frequency of treatment and the effect desired.
[0118] Toxicity and therapeutic efficacy of therapeutic
compositions of the present invention can be determined by standard
pharmaceutical procedures in cell cultures or experimental animals,
e.g., for determining the LD50 (The Dose Lethal To 50% Of The
Population) and the ED50 (the dose therapeutically effective in 50%
of the population). The dose ratio between toxic and therapeutic
effects is the therapeutic index and it can be expressed as the
ratio LD50/ED50. Therapeutic agents which exhibit large therapeutic
indices are useful. Therapeutic compositions that exhibit some
toxic side effects can be used.
[0119] Appropriate doses of small molecule agents depends upon a
number of factors known to those or ordinary skill in the art,
e.g., a physician. The dose(s) of the small molecule will vary, for
example, depending upon the identity, size, and condition of the
subject or sample being treated, further depending upon the route
by which the composition is to be administered, if applicable, and
the effect which the practitioner desires the small molecule to
have upon the nucleic acid or polypeptide of the invention.
Exemplary doses include milligram or microgram amounts of the small
molecule per kilogram of subject or sample weight (e.g., about 1
microgram per kilogram to about 500 milligrams per kilogram, about
TOO micrograms per kilogram to about 5 milligrams per kilogram, or
about 1 microgram per kilogram to about 50 micrograms per
kilogram.
[0120] These methods described herein are by no means
all-inclusive, and further methods to suit the specific application
will be apparent to the ordinary skilled artisan. Moreover, the
effective amount of the compositions can be further approximated
through analogy to compounds known to exert the desired effect.
[0121] The practice of aspects of the present invention can employ,
unless otherwise indicated, conventional techniques of cell
biology, cell culture, molecular biology, transgenic biology,
microbiology, recombinant DNA, and immunology, which are within the
skill of the art. Such techniques are explained fully in the
literature. See, for example, Molecular Cloning A Laboratory
Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring
Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D.
N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed.,
1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid
Hybridization (B. D. Hames & S. J. Higgins eds. 1984);
Transcription And Translation (B. D. Hames & S. J. Higgins eds.
1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc.,
1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal,
A Practical Guide To Molecular Cloning (1984); the treatise,
Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer
Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds.,
1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols.
154 and 155 (Wu et al. eds), Immunochemical Methods In Cell And
Molecular Biology (Mayer and Walker, eds., Academic Press, London,
1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M.
Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse
Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor,
N.Y., 1986). All patents, patent applications and references cited
herein are incorporated in their entirety by reference.
EXAMPLES
[0122] A number of Examples are provided below to facilitate a more
complete understanding of the present invention. The following
examples illustrate the exemplary modes of making and practicing
the present invention. However, the scope of the invention is not
limited to specific embodiments disclosed in these Examples, which
are for purposes of illustration only, since alternative methods
can be utilized to obtain similar results.
Example 1
Experimental Analysis
[0123] We have used an established process for the identification
of miRNAs candidates by sequencing size-fractionated cDNA libraries
from three normal B cell populations, including Naive B cells,
Centroblasts and Memory B cells and from a Burkitt Lymphoma cell
line (Ramos). Briefly, short RNAs (sRNA) extracted from the cells
were linked to adaptor oligonucleotides, reverse transcribed, PCR
amplified, cloned into an expression vector, and sequenced.
Individual sequences, corresponding to short RNAs, were then
analyzed bioinformatically to determine whether they would
constitute appropriate miRNA candidates.
[0124] Bioinformatics Analysis:
[0125] The computational analysis starts with the identification of
short RNA (sRNA) sequences from cloned cDNA sequences using the
adaptor oligonucleotides as oriented markers. Then, each sRNA was
matched to the human genome (ncbi36, October 2006) by using
Megablast (NCBI).
[0126] A Bayesian evidence integration scheme was used to identify
candidate sRNAs from partial matches to the human genome. Single
and multiple base mismatches can occur for several reasons,
including polymorphisms, sequencing errors, PCR errors that are
more frequent in the 3' and 5' region of the miRNA cDNA, and RNA
editing enzymes.
[0127] To identify sequences that correspond to real sRNAs, we used
the following Bayesian approach to compute the posterior
probability that a sequence is a candidate miRNA genomic match
given specific base pair substitutions under the assumption that
individual mutations are uncorrelated (Naive Bayes). The individual
p(m.sub.i| match) and p(m.sub.i) can be measured using matches to
the miRNAs deposited in the miRNABase database. Sequences with p
(match|m.sub.1, m.sub.2, . . . , m.sub.n)>0.5 were considered
bona-fide matches to the human genome sequences and further
processed together with the exact matching ones. m.sub.1, m.sub.2,
. . . , m.sub.n:
p ( match m 1 , m 2 , , m n ) = p ( m 1 , m 2 , , m n match ) p (
match ) p ( m 1 , m 2 , , m n ) = p ( match ) p ( m i match ) p ( m
i ) ##EQU00001##
[0128] Resulting sRNA genome locations, both for exact and partial
matches, were analyzed and merged, if necessary, to remove
overlapping sequences. For each sRNA hit a sequence from -80 bp
upstream to +80 b.p. downstream of the sRNA match was selected
leading to a set of candidate microRNA genes, including the full
length precursors.
[0129] These longer sequences were then analyzed to determine if
they can lead to the formation of precursor miRNA structures,
including favorable energetics to for the established stem-loop
secondary RNA structure required for further miRNA processing.
Using a set of established mammalian miRNA's and data from the
scientific literature the following criteria were established:
[0130] 1. Mature sequence, which is defined by matching sRNA's,
should occupy only one arm of hairpin (not the loop). [0131] 2.
Loop structure cannot be shorter that 3 b.p. or longer than 20 b.p.
[0132] 3. Hairpin stem should not host additional secondary RNA
structures with more than 10 b.p. [0133] 4. The ratio between the
number of complementary base pairs and the total number of base
pairs comprising hairpin arms should be bigger than 0.55. [0134] 5.
Free energy should not be bigger than -20 kcal/mole.
[0135] We do not apply highly popular conservation criteria because
of: [0136] significant incompleteness of many genome assemblies
especially in intergenic regions [0137] Risk to lose unique or
diverged miRNA's (this invention is directed to obtaining an
exhaustive search and outcome) [0138] Possibility of further
experimental verification of candidates.
[0139] Since the exact sites of transcription initiation and
termination for miRNA genes is not known and since concentration
and temperature can vary, it is important to consider not just the
optimal folding variant but an entire distribution of variants near
the optimal one. We used the Vienna RNA package to perform this
type of analysis, with appropriate modifications to allow the
analysis of suboptimal folding variants.
[0140] Candidate miRNA genes were filtered against non-coding RNA
database and repeats database (repbase). Database of human
non-coding RNA's is manually compiled and contains genes like
ribosomal RNA's, snRNA, tRNA's, Y-RNA and others. Comparison
performed using MEGABLAST program (NCBI).
[0141] Finally, candidate miRNAs emerging from this analysis were
compared to miRNABase database to identify previously known miRNAs.
Candidate miRNAs that were not identified in the miRNABase were
considered. Diagrams illustrating these steps are included as FIGS.
1-3.
[0142] Validation:
[0143] Some of the newly identified miRNAs were tested by Northern
in the corresponding population in which the sRNA was isolated.
[0144] Newly Identified miRNAs
[0145] The following have been identified as newly identified
miRNAs (miRNAs) in one or more of the four B cell populations from
which the size-fractionated cDNA libraries were isolated.
Example 2
Protocol for microRNA Cloning
[0146] Preparation and Labeling of Decade Marker (Ambion #7778)
[0147] Decade marker is radio labeled using [.gamma.-.sup.32P]ATP
according to the manufacturer instructions.
[0148] Labeling of the RNA Carrier
[0149] 20 pmol of #909 carrier RNA oligo is radio labeled using
[.gamma.-.sup.32P]ATP and T4 Polynucleotide kinase (NEB).
[0150] Purification of 18-26Mers from Total RNA
[0151] A 15% denaturing polyacrylamide gel was prepared using the
Sequagel System (National Diagnostics) following the manufacturer
instructions. A metal plate was placed on the front of the gel and
was pre-run at 50 W for 30 minutes using a running buffer of
0.5.times.TBE. Each RNA sample [10 .mu.g of total RNA] was
subsequently spiked 1 pmol (2.5 .mu.l) of [.gamma.-.sup.32P]
labeled-#909 carrier and an equal volume of 2.times.RNA loading
buffer (Ambion) was added. For total RNA, extraction procedures
like Trizol Reagent (Invitrogen) that purify all sizes RNA are
recommended. Samples were then boiled for 5 minutes and were loaded
with decade marker. After samples were loaded onto the gel, it was
run for 3-4 hours at 50 W. After the gel was run, the apparatus was
disassemble and one of the glass pieces was removed. The hot area
of the gel was cut out and placed on the side of the lane for
alignment with the markers. The gel was subsequently covered with a
plastic wrap and was exposed to a phosphoimage screen for about 30
minutes to an 1 hour. The gel image was printed at 100%
magnification and placed under the glass. It was then aligned with
the hot spot that had been previously cut. The RNA band was cut
approximately from 18mers up to 26mers using the marker and the 1
nt ladder below the carrier as reference. RNA was eluted from the
gel using 2 ml of 0.3M NaCl in DEPC H.sub.2O, and the eluted sample
was subsequently rotated overnight at 4.degree. C. The supernatant
was then recovered and 450 .mu.l (max) was distributed into
separate tubes. A 2.times. volume of 100% EtOH and 10 .mu.g
glycogen were added to each tube, which were then incubated at
-20.degree. C. for at least 2 hours. Samples were then spun for 30
minutes at 14,000 rpm, and were subsequently washed with 75% EtOH.
The pellets were then air dried and dissolved in 10 .mu.l DEPC
H.sub.2O.
[0152] 3'-Adaptor Ligation and Purification
[0153] The following were first mixed in a tube and were then
incubated at 25.degree. C. for 6 hours:
TABLE-US-00001 1.5 .mu.l 10X 3'Ligation Buffer* 7.5 .mu.l purified
small RNA 2 .mu.l App.17.91 [100 pmol/.mu.l] (adenylated) 1.5 .mu.l
T4 RNA Ligase [30 U/.mu.l] (Amersham) 2.5 .mu.l H.sub.2O *500 mM
Tris-HCl (pH 7.5), 100 mM MgCl.sub.2, 100 mM DTT, 600 .mu.g/ml BSA.
Store at -20.degree. C.
[0154] 15 .mu.l of 2.times. Loading Buffer (Ambion) was added to
the samples and boiled for 5 minutes, which were then loaded onto a
12% denaturing polyacrylamide gel that was prepared using the
Sequagel System (National Diagnostics) following the manufacturer
instructions. A metal plate was placed on the front of the gel and
was pre-run at 50 W for 30 minutes using a running buffer of
0.5.times.TBE. The decade RNA marker and 1 .mu.l of
[.gamma.-.sup.32P] labeled-#909 carrier was then loaded into
separated lanes and run for 3-4 hours at 50 W. After the gel was
run, the apparatus was disassemble and the gel was exposed to a
phosphoimage screen for 2-4 hours. The gel image was printed at
100% magnification and placed under the glass. The ligation product
ranging approximately from 35 up to 42-45 nt was cut and RNA was
eluted from the gel using 2 ml of 0.3M NaCl in DEPC H.sub.2O. The
eluted sample was subsequently rotated overnight at 4.degree. C.
The supernatant was then recovered and 450.sub.111 (max) was
distributed into separate tubes. A 2.times. volume of 100% EtOH and
10 mg glycogen were added to each tube, which were then incubated
at -20.degree. C. for at least 2 hours. Samples were then spun for
30 minutes at 14,000 rpm, and were subsequently washed with 75%
EtOH. The pellets were then air dried and dissolved in 12 .mu.l
DEPC H.sub.2O.
[0155] 5'-Adaptor Ligation and Purification
[0156] The following were first mixed in a tube and were then
incubated at 25.degree. C. for 6 hours:
TABLE-US-00002 1 .mu.l 10X Ligation Buffer (Amersham) 6 .mu.l
purified small RNA 2 .mu.l 17.93 oligo [100 pmol/.mu.l] 1 .mu.l T4
RNA Ligase [30 U/.mu.l] (Amersham)
[0157] Samples can be stored at 4.degree. C. after the 6 hour
incubation until further processed. 10 .mu.l of 2.times. Loading
Buffer (Ambion) was added to the samples and boiled for 5 minutes,
which were then loaded onto a 10% denaturing polyacrylamide gel
that was prepared using the Sequagel System (National Diagnostics)
following the manufacturer instructions. A metal plate was placed
on the front of the gel and was pre-run at 50 W for 30 minutes
using a running buffer of 0.5.times.TBE. The decade RNA marker and
1 .mu.l of [.gamma.-.sup.32P] labeled-#909 carrier was then loaded
into separated lanes and run for 3 hours at 50 W. After the gel was
run, the apparatus was disassemble and the gel was exposed to a
phosphoimage screen for 12-18 hours. The gel image was printed at
100% magnification and placed under the glass. The ligation product
ranging approximately from 35 up to 48-62 nt was cut and RNA was
eluted from the gel using 2 ml of 0.3M NaCl in DEPC H.sub.2O. The
eluted sample was subsequently rotated overnight at 4.degree. C.
The supernatant was then recovered and 450 .mu.l (max) was
distributed into separate tubes. A 2.times. volume of 100% EtOH and
10 ng glycogen were added to each tube, which were then incubated
at -20.degree. C. for at least 2 hours. Samples were then spun for
30 minutes at 14,000 rpm, and were subsequently washed with 75%
EtOH. The pellets were then air dried and dissolved in 20 .mu.l
DEPC H.sub.2O.
[0158] Reverse Transcription
[0159] The following were first mixed in a PCR tube and were then
incubated at 80.degree. C. for 2 minutes:
TABLE-US-00003 10 .mu.l ligated RNA 3 .mu.l #918 primer [100
.mu.M]
[0160] The sample was subsequently spun down to cool. Using the
First Strand Synthesis System kit (Invitrogen), the following was
added to the sample which was then incubated at 48.degree. C. for 2
minutes:
TABLE-US-00004 5 .mu.l 5X First Strand Buffer 7 .mu.l dNTPs 3 .mu.l
0.1M DTT
[0161] 3 .mu.l of SuperScriptII (Invitrogen) was then added to the
sample, which was further incubated at 48.degree. C. for 1 hour.
Samples can then be stored at -20.degree. C. until further
processing.
[0162] PCR Amplification
[0163] The PCR reaction was prepared as follows:
[0164] 5% Reverse Transcription product
[0165] 1.times.PCR buffer
[0166] 1.5 mM MgCl.sub.2
[0167] 0.8 mM dNTP
[0168] 2 .mu.M #913 primer
[0169] 2 .mu.M #914 primer
[0170] 2 U Taq polymerase
[0171] The sample was then amplified according to the following
protocol:
TABLE-US-00005 2' 94.degree. C. 30'' 94.degree. C. 30'' 52.degree.
C. {close oversize brace} X30 cycles 30'' 72.degree. C. 10'
72.degree. C.
[0172] The sample was then extracted using Phenol/CIA and was
precipitated with sodium acetate. The sample was then spun for 30
minutes at 14,000 rpm, and was subsequently washed with 75% EtOH.
The pellet was then air dried and dissolved in 45 .mu.l DEPC
H.sub.2O.
[0173] PACI Digestion
[0174] The digestion was prepared as follows and was subsequently
incubate at 37.degree. C. for 90 minutes:
[0175] 1.times.NEB Buffer 1
[0176] 1.times.BSA
[0177] 1,000 U/.mu.l PACI
[0178] 42.5 .mu.l DNA
[0179] The sample was then extracted using Phenol/CIA and was
precipitated with sodium acetate. The sample was then spun for 30
minutes at 14,000 rpm, and was subsequently washed with 75% EtOH.
The pellet was then air dried and dissolved in 15 .mu.l DEPC
H.sub.2O. Non-denaturing Loading Buffer was added to the sample and
the sample was subsequently loaded onto a 12% non-denaturing
acrylimide gel using pUC19/Sau3AI as a marker (Ambion #7760), which
was run at 13 W for approximately 1 hr. The gel was then stained
with 1:10,000 SybrGold (Molecular Probes #S-11494) in 0.5.times.TBE
for 30 to 60 minutes. The smear of digested samples was then cut
between 46 and 75 nt according to the marker size. Cut out samples
were then eluted with 500 .mu.l of 0.3M NaCl in 1.5 ml screw top
tubes, rotating overnight at 4.degree. C. Samples were spun
briefly, and about 450 .mu.l of eluted volume was recovered for
each sample. The samples were then extracted using Phenol/CIA and
were precipitated with sodium acetate. The samples were then spun
for 30 minutes at 14,000 rpm, and were subsequently washed with 75%
EtOH. The pellet was then air dried and dissolved in 10 .mu.l DEPC
H.sub.2O. If the amount of digested product on the gel appeared to
be low, a second PCR amplification was required.
[0180] Second PCR Amplification
[0181] The PCR reaction was prepared as follows:
[0182] 2% Reverse Transcription product
[0183] 1.times.PCR buffer
[0184] 1.5 mM MgCl.sub.2
[0185] 0.8 mM dNTP
[0186] 2 .mu.M #913 primer
[0187] 2 .mu.M #914 primer
[0188] 2 U Taq polymerase
[0189] The sample was then amplified according to the following
protocol:
TABLE-US-00006 2' 94.degree. C. 30'' 94.degree. C. 30'' 52.degree.
C. {close oversize brace} X20 cycles 30'' 72.degree. C. 10'
72.degree. C.
[0190] The amount of product generated was examined via adding
non-denaturing Loading Buffer to 5 .mu.l of sample, which was then
loaded onto a 12% non-denaturing acrylimide gel, and was
subsequently run at 13 W for approximately 1 hr. Samples were cut
out and eluted with 500 .mu.l of 0.3M NaCl in 1.5 ml screw top
tubes, rotating overnight at 4.degree. C. Samples were spun
briefly, and about 450 .mu.l of eluted volume was recovered for
each sample. The samples were then extracted using Phenol/CIA and
were precipitated with sodium acetate. The samples were then spun
for 30 minutes at 14,000 rpm, and were subsequently washed with 75%
EtOH. The pellet was then air dried and dissolved in 45 DEPC
H.sub.2O. Samples were further quantified, wherein amount of
sampled needed to be within the range of 200-500 ng/.mu.l.
[0191] BanI Digestion
[0192] The following digestion was prepared for each sample as
follows, and were subsequently incubated at 37.degree. C. for 2.5
hours:
[0193] 1.times.NEB Buffer 4
[0194] 1.times.BSA
[0195] 1000 U/.mu.l BanI
[0196] Samples were then extracted using Phenol/CIA and were
precipitated with sodium acetate. The samples were spun for 30
minutes at 14,000 rpm, and were subsequently washed with 75% EtOH.
The pellet was then air dried and dissolved in 26 .mu.l DEPC
H.sub.2O.
[0197] Concatemerization
[0198] The following sample was mixed in a 0.5 or 0.2 ml tube as
follows, and was incubated at 25.degree. C. for 2 hours:
TABLE-US-00007 26 .mu.l Digested DNA 3 .mu.l 10X Ligation Buffer
(Roche) 1 .mu.l T4 DNA Ligase [5 U/.mu.l] (Roche) 1 .mu.l of dNTP
as well as 1 .mu.l of DNA Polymerase I was subsequently added,
and the sample was then incubated at 16.degree. C. for 1 hour. The
sample was run on a 2% LM agarose-EtBr gel in 0.5.times.TBE with
100 bp Ladder loaded in the first lane. The concatamers were then
cut starting from about 500 bp and above. Samples were then gel
purified with QlAquick gel extraction kit (Qiagen cat.#28706),
using the manufacturer's instructions.
[0199] Vector Digestion
[0200] The pCR2.1-TOPO (Invitrogen, 3.9 Kb) vector was digested
according to the manufacturer's instructions for the EcoRV enzyme
(NEB). The samples was then subjected to gel electrophoresis using
a 1% agarose gel. The sample was then gel purified with QlAquick
gel extraction kit (Qiagen cat.#28706), using the manufacturer's
instructions.
[0201] Ligation
[0202] The ligation reaction was set up using the Rapid Ligation
Kit (Roche cat.#11635379001) according to the procedure recommended
by the manufacturer. 10 .mu.l of the ligation product was used for
transformation in high efficiency bacteria (One Shot
OminMAX--Invitrogen cat.# C8540-03). X-gal/IPTG Ampicillin agarose
plates were prepared fresh and a specified volume of the
transformation reaction was spread onto the plates. Plated samples
were then incubated overnight at 37.degree. C. Colonies were then
obtained the next day and grown in 30 .mu.l of LB medium at
37.degree. C. for 1 hour. Once DNA was obtained from the amplified
bacteria, 2.5 .mu.l was used as template for the colony PCR
reaction.
[0203] Colony PCR
[0204] The PCR reaction was prepared as follows:
[0205] 2.5 .mu.l template
[0206] 1.times.PCR buffer
[0207] 1.5 mM MgCl.sub.2
[0208] 0.8 mM dNTP
[0209] 0.2 .mu.M #913 primer
[0210] 0.2 .mu.M #914 primer
[0211] 1 U Taq polymerase
[0212] The sample was then amplified according to the following
protocol:
TABLE-US-00008 5' 94.degree. C. 30'' 94.degree. C. 30'' 52.degree.
C. {close oversize brace} X30 cycles 30'' 72.degree. C. 10'
72.degree. C.
[0213] 1 .mu.l of PCR product was examined on a 1.5% agarose gel
and clones were selected carrying an insert longer than 350 bp.
Samples were then confirmed by sequencing.
[0214] Oligonucleotides
TABLE-US-00009 909 carrier RNA oligo: [SEQ ID NO: 517]
5'-(P)-UGUCAGUUUGUUAAUUAACCCAA-3'
5' phosphate; 3' none; includes PACI restriction site
TABLE-US-00010 App. 17.91 (3' end Donor oligo): [SEQ ID NO: 518]
5'-rAppCTGTAGGCACCATCAAT/3ddC-3'
5' adenylated containing a pyrophosphate; 3' modified terminal
dideoxy-C(ddC) (available from IDT Inc. as the "miRNA cloning
linker"); includes BanI restriction site.
TABLE-US-00011 17.93 (5' end Acceptor oligo): [SEQ ID NO: 519]
5'-ATCGTAGGCACCTGAAA-3'
It includes BanI restriction site.
TABLE-US-00012 #918 RT primer oligo: [SEQ ID NO: 520]
5'-ATTGATGGTGCCTAC-3'
It includes BanI restriction site.
TABLE-US-00013 #913 (5' PCR primer oligo): [SEQ ID NO: 521]
5'-ATCGTAGGCACCTGAAA-3'
It includes BanI restriction site.
TABLE-US-00014 #914 (3' PCR primer oligo): [SEQ ID NO: 522]
5'-ATTGATGGTGCCTACAG-3'
It includes BanI restriction site.
[0215] Screening/Sequencing Primers:
TABLE-US-00015 M13F [SEQ ID NO: 523] 5'-GTAAAACGACGGCCAG-3' M13R
[SEQ ID NO: 524] 5'-CAGGAAACAGCTATGAC-3'
REFERENCES
[0216] Lau et al., Science (2001) 294:858-62; Chen et al., Science
(2004) 303: 83-6
Example 3
Identification of the Human Mature B Cells miRNome
[0217] The discovery of microRNAs (miRNAs) has added a new
dimension to the mechanisms that regulate gene expression in normal
cell development. Initial evidence also shows that structural or
functional alterations of miRNAs are associated with tumorigenesis.
The full set of microRNAs (miRNAs) in the human genome is not
known. Since presently known miRNAs have been identified by virtue
of their abundant expression in a few cell types, tissue-specific
miRNAs may remain unrevealed. To understand the role of miRNAs in
B-cell function and lymphomagenesis, short-RNA libraries were
generated from normal human B cells at different stages of
development (naive, germinal-center, memory) and from a Burkitt
lymphoma cell-line. The combination of cloning and computational
analysis identified 401 miRNA (miRNome) expressed during normal
B-cell development and/or in transformed B-cells. Most notably,
this analysis identified 272 new miRNAs that were not previously
reported. Numerous miRNAs are expressed in a stage-specific as well
as transformation-specific fashion, suggesting specific functional
roles. These results significantly increase the number of presently
known miRNAs and provide a resource for the study of their role in
B-cell development, immune function, and lymphomagenesis.
[0218] A new level of post-transcriptional regulation has been
revealed with the discovery of microRNAs (miRNAs) a class of
short-RNAs that impair translation or induce mRNA degradation by
binding to the 3' untranslated region of target mRNA.sup.1,2. The
most recent release of the miRBase database (v.11.0).sup.3,4
reports 839 human miRNAs, but the discovery of miRNAs is still an
on-going process with variable predictions about the total number
of miRNAs expressed in mammalian cells ranging from one thousand to
several thousands.sup.5,6. The reported miRNAs have been identified
from a limited number of cell types or from tissues whose cellular
heterogeneity may favor the identification of ubiquitous and
abundant miRNA. In fact, a recent report aiming to the
identification of the miRNA expression profiles from 26 different
mammalian tissues and cell types led to the discovery of only 12
new human miRNA.sup.7. These findings led to the conclusion that
most miRNAs are known and that most of them are ubiquitously
expressed.sup.7. Nonetheless, additional analyses of purified cell
populations may lead to the identification of tissue- and stage of
differentiation-specific miRNAs, as has been the case for messenger
RNAs.
[0219] The role of specific miRNAs in B-cell immunity and
malignancy has only just begun to be elucidated. Using mouse
models, miR-155 has been demonstrated to affect regulation of
germinal center response through modulation of cytokine
production.sup.8,9. Recently, miR-150 has been shown to target
c-Myb, a critical transcription factor involved in the control of B
cell differentiation.sup.10. In B cell lymphomas, 13q31
amplification has been associated with the over-expression of the
miR-17-92 cluster and its enforced expression in a murine B cell
lymphoma model showed a role in accelerating tumor
development.sup.11. Furthermore, miR-15a and miR-16 have been
implicated in the pathogenesis of B cell chronic lymphocytic
leukemia (CLL).sup.12,13.
[0220] To further explore the role of miRNAs in B cell function and
lymphomagenesis, this study was aimed at identifying the miRNAs
expressed (miRNome) in the human mature B-cell compartment,
including naive, germinal centers (GCs), and memory B cells. These
B cell subpopulations are relevant for the development of
antibody-mediated immunity as well as for tumorigenesis, since
common human B-cell malignancies originate from the malignant
transformation of GC B cells (most B-cell non-Hodgkin lymphomas,
B-NHL), or naive and memory B cells (mantle cell lymphoma and
chronic lymphocytic leukemia).sup.14,15. Using a combination of
cloning and computational analysis, we report the identification of
401 miRNA representing the mature B cell miRNome, including 272 new
miRNAs, and illustrate their pattern of expression during B cell
differentiation and transformation.
[0221] Construction of Short-RNA Libraries from Human B Cell
Sub-Populations
[0222] Short-RNA libraries were generated by cloning RNA fractions
of 18-30 nt from human centroblasts, naive and memory B cells
purified from tonsils as well as from the Burkitt lymphoma cell
line Ramos, which is representative of malignant transformation of
GC B cells (FIG. 10). Approximately 3,500 sequences were analyzed
from each library, corresponding to 13,991 total short-RNAs (2,661
non-redundant sequences). Using a bootstrap approach.sup.16,17, we
estimated the expected number of miRNAs that could be predicted
using our computational pipeline from various size of short-RNA
libraries. The results suggested that at the current sequencing
depth, 80% of the possible predictions have been identified FIG.
17).
[0223] The cloned sequences were matched to the human genome
assembly from March 2006 (hgl 8) to retrieve the genomic regions
from which the short-RNAs originated. One or more genomic locations
were identified for approximately 80% of the cloned sequences
considering both perfect matches and single mismatches. Consistent
with previous observations, 3'-end mismatches were the most common
and showed a clear preference for A in the last position (.sup.18.
Approximately 546 short-RNA sequences did not align to the human
genome according to the above criteria and are likely due to PCR
errors introduced during the cloning procedure (FIG. 11).
Nevertheless, a small subset of these short-RNAs lacking a
corresponding genomic region in Homo sapiens have been cloned with
high frequencies in multiple libraries and showed differential
expression during B cell differentiation, suggesting they may
represent bona fide short-RNA species. However, given the
difficulty of assigning genomic coordinates to these sequences they
were omitted from further analyses.
[0224] Computational Prediction of miRNA Precursors
[0225] In order to identify candidate miRNAs among the cloned
sequences, we developed a computational pipeline aiming at the
identification of potential miRNA precursors based on the
investigation of their genomic location and folding characteristics
(FIG. 18 and Supplementary Methods). Briefly, short RNA sequences
were mapped to the human genome and candidate genomic precursors
(+/-90 nt) were then retrieved and analyzed for secondary
structure, size and energy of the loop, and number of complimentary
base pairs in the stem of the loop (Supplementary Methods). The
prediction was performed on the full set of non-redundant
short-RNAs (2,115 sequences) for which one or more genomic
locations could be identified (FIG. 11). The analysis led to the
identification of candidate precursors for 1,667 short-RNA
sequences, which were then clustered to account for the variability
observed at the miRNA 3'-ends (and less dramatically at the
5'-ends) including nucleotide substitutions and deletions.
Moreover, editing of miRNA has been previously reported.sup.19,20
and a few cases compatible with an editing process have been
observed in the libraries described here. Since most clusters of
short-RNA are affected by these modifications, we applied the
following criteria in order to define mature miRNA sequences: i)
each nucleotide must occur in more than 50% of the cloned
sequences; sequences supported by a short-RNA set that is fully
contained in a larger set were eliminated while matching clusters
with partial containment were merged (Supplementary Methods). After
annotating each candidate mature miRNA, those which had evidences
of originating from mRNA, rRNA, tRNA and other ncRNA (yRNA,
sn/snoRNA) and occurred once were eliminated. Overall, the
computational analysis identified 401 mature miRNA (Table 1).
[0226] The human miRNAs deposited in the miRBase database (v.11.0)
were identified only at the end of the analysis and any lack of
prediction was checked by matching the starting set with the final
predictions. Overall, previously reported miRNA represented 32% of
cloned and computationally validated mature miRNA. In addition, our
analysis identified 146 previously reported precursors as well as
761 genomic locations containing precursors potentially coding for
272 new mature miRNA and 19 new precursors for 8 mature miRNAs
deposited in the miRBase database (FIG. 12 and Table 1).
TABLE-US-00016 TABLE 1A List of known and newly identified mature
miRNAs. ID SEQ ID NO. Mature miRNA sequence Annotations CU-1026 1
TGTAGTGTTTCCTACTTTATGGA Mature:hsa-miR-142-3p:MIMAT0000434 CU-1064
2 TAGCTTATCAGACTGATGTTGA Mature:hsa-miR-21:MIMAT0000076 CU-1061 3
TAAAGTGCTTATAGTGCAGGTAG Mature:hsa-miR-20a:MIMAT0000075 CU-1035 4
TAGCAGCACATCATGGTTTACA Mature:hsa-miR-15b:MIMAT0000417 CU-1037 5
TAGCAGCACGTAAATATTGGCG Mature:hsa-miR-16:MIMAT0000069 CU-1001 6
TGAGGTAGTAGGTTGTATAGTT Mature:hsa-let-7a:MIMAT0000062 CU-1116 7
TATTGCACTTGTCCCGGCCTGT Mature:hsa-miR-92a:MIMAT0000092 CU-1018 8
TCCCACCGCTGCCACCA Mature:hsa-miR-1280:MIMAT0005946 CU-1006 9
TGAGGTAGTAGATTGTATAGTT Mature:hsa-let-7f:MIMAT0000067 CU-1079 10
TAGCACCATCTGAAATCGGTTA Mature:hsa-miR-29a:MIMAT0000086 CU-1033 11
TAGCAGCACATAATGGTTTGT Mature:hsa-miR-15a:MIMAT0000068 CU-1124 12
CCCATAAAGTAGAAAGCACTA Mature:hsa-miR-142-5p:MIMAT0000433 CU-1007 13
TGAGGTAGTAGTTTGTACAGTT Mature:hsa-let-7g:MIMAT0000414 CU-1008 14
TGAGGTAGTAGTTTGTGCTGTT Mature:hsa-let-7i:MIMAT0000415 CU-1082 15
TAGCACCATTTGAAATCGGTTA Mature:hsa-miR-29c:MIMAT0000681 CU-1085 16
TGTAAACATCCTACACTCTCAGC Mature:hsa-miR-30c:MIMAT0000244 CU-1039 17
CAAAGTGCTTACAGTGCAGGTAG Mature:hsa-miR-17:MIMAT0000070 CU-1071 18
CATTGCACTTGTCTCGGTCTGA Mature:hsa-miR-25:MIMAT0000081 CU-1046 19
CAACGGAATCCCAAAAGCAGCTG Mature:hsa-miR-191:MIMAT0000440 CU-1057 20
TGTGCAAATCCATGCAAAACTGA Mature:hsa-miR-19b:MIMAT0000074 CU-1024 21
TACCACAGGGTAGAACCACGGA Mature:hsa-miR-140-3p:MIMAT0004597 CU-1084
22 TGTAAACATCCTACACTCAGCT Mature:hsa-miR-30b:MIMAT0000420 CU-1003
23 TGAGGTAGTAGGTTGTGTGGTT Mature:hsa-let-7b:MIMAT0000063 CU-1080 24
TAGCACCATTTGAAATCAGTGTT Mature:hsa-miR-29b:MIMAT0000100 CU-1012 25
TAAAGTGCTGACAGTGCAGAT Mature:hsa-miR-106b:MIMAT0000680 CU-1092 26
TCCCTGTCCTCCAGGAGCTC Mature:hsa-miR-339-5p:MIMAT0000764 CU-1072 27
TTCAAGTAATCCAGGATAGGCT Mature:hsa-miR-26a:MIMAT0000082 CU-1118 28
CAAAGTGCTGTTCGTGCAGGTAG Mature:hsa-miR-93:MIMAT0000093 CU-1067 29
TGTCAGTTTGTCAAATACCCCA Mature:hsa-miR-223:MIMAT0000280 CU-1027 30
TGAGAACTGAATTCCATGGGTT Mature:hsa-miR-146a:MIMAT0000449 CU-1029 31
TCTCCCAACCCTTGTACCAGT Mature:hsa-miR-150:MIMAT0000451 CU-1015 32
TCCCTGAGACCCTAACTTGTGA Mature:hsa-miR-125b:MIMAT0000423 CU-1093 33
TCTCACACAGAAATCGCACCCGTC Mature:hsa-miR-342-3p:MIMAT0000753 CU-1016
34 GTCCCTGTTCGGGCGCCA Mature:hsa-miR-1274b:MIMAT0005938 CU-1056 35
TGTGCAAATCTATGCAAAACTGA Mature:hsa-miR-19a:MIMAT0000073 CU-1086 36
TGTAAACATCCCCGACTGGAAG Mature:hsa-miR-30d:MIMAT0000245 CU-1065 37
AGCTACATTGTCTGCTGGGTT Mature:hsa-miR-221:MIMAT0000278 CU-1004 38
AGAGGTAGTAGGTTGCATAGTT Mature:hsa-let-7d:MIMAT0000065 CU-1011 39
CCGCACTGTGGGTACTTGCT Star:hsa-miR-106b*:MIMAT0004672 CU-1010 40
AGCAGCATTGTACAGGGCTATGA Mature:hsa-miR-103:MIMAT0000101 CU-1050 41
AACTGGCCCTCAAAGTCCCGCT Mature:hsa-miR-193b:MIMAT0002819 CU-1091 42
GCCCCTGGGCCTATCCTAGAA Mature:hsa-miR-331-3p:MIMAT0000760 CU-1023 43
AGCTGGTGTTGTGAATCAGGCCGT Mature:hsa-miR-138:MIMAT0000430 CU-1101 44
TGAGGGGCAGAGAGCGAGACTT Mature:hsa-miR-423-5p:MIMAT0004748 CU-1066
45 AGCTACATCTGGCTACTGGGTCT Mature:hsa-miR-222:MIMAT0000279 CU-1017
46 GTGGGGGAGAGGCTGTA Mature:hsa-miR-1275:MIMAT0005929 CU-5001 47
CTATACGACCTGCTGCCTTTC Star:hsa-let-7d*:MIMAT0004484 CU-1032 48
TTAATGCTAATCGTGATAGGGGT Mature:hsa-miR-155:MIMAT0000646 CU-1108 49
AGGGGGAAAGTTCTATAGTC Mature:hsa-miR-625:MIMAT0003294 CU-1055 50
ACAGTAGTCTGCACATTGGTT Mature:hsa-miR-199b-3p:MIMAT0004563 CU-1042
51 AACATTCAACGCTGTCGGTGAGTT Mature:hsa-miR-181a:MIMAT0000256
CU-1113 52 TGGAAGACTAGTGATTTTGTTGT Mature:hsa-miR-7:MIMAT0000252
CU-1098 53 TAATGCCCCTAAAAATCCTTAT Mature:hsa-miR-365:MIMAT0000710
CU-1052 54 TAGCAGCACAGAAATATTGGCA Mature:hsa-miR-195:MIMAT0000461
CU-1568 55 TGAGGTAGTAGGTTGTAT Mature:hsa-let-7c:MIMAT0000064
CU-1103 56 TCCTGTACTGAGCTGCCCCGAG
Mature:hsa-miR-486-5p:MIMAT0002177 CU-1014 57
TCCCTGAGACCCTTTAACCTGTGA Mature:hsa-miR-125a-5p:MIMAT0000443
CU-1068 58 ATCACATTGCCAGGGATTTCCA Mature:hsa-miR-23a:MIMAT0000078
CU-1019 59 TCACAGTGAACCGGTCTCTTT Mature:hsa-miR-128:MIMAT0000424
CU-1076 60 CACTAGATTGTGAGCTCCTGGA Mature:hsa-miR-28-3p:MIMAT0004502
CU-1111 61 CAACAAATCACAGTCTGCCAT Star:hsa-miR-7-1*:MIMAT0004553
CU-1062 62 CAAAGTGCTTATAGTGCAGGTAG
Mature:hsa-miR-20b-mm:MIMAT0001413 CU-1115 63
AGGTTGGGATCGGTTGCAATGCT Star:hsa-miR-92a-1*:MIMAT0004507 CU-1126 64
ACATTCATTGCTGTCGGTGGGTT Mature:hsa-mir-181b-1:MI0000270 CU-1096 65
TCCCCCAGGTGTGATTCTGATT Mature:hsa-miR-361-3p:MIMAT0004682 CU-1054
66 CCCAGTGTTCAGACTACCTGTTC Mature:hsa-miR-199a-5p:MIMAT0000231
CU-1125 67 ACCAATATTACTGTGCTGCTT Star:hsa-miR-16-2*:MIMAT0004518
CU-1087 68 TGTAAACATCCTTGACTGGAAGCT Mature:hsa-miR-30e:MIMAT0000692
CU-1045 69 TAAGGTGCATCTAGTGCAGATA Mature:hsa-miR-18a:MIMAT0000072
CU-1069 70 ATCACATTGCCAGGGATTACCA Mature:hsa-miR-23b:MIMAT0000418
CU-1044 71 ACTGCCCTAAGTGCTCCTTCTG Star:hsa-miR-18a*:MIMAT0002891
CU-1083 72 TGTAAACATCCTCGACTGGA Mature:hsa-miR-30a:MIMAT0000087
CU-1009 73 TACAGTACTGTGATAACTGAAG Mature:hsa-miR-101:MIMAT0000099
CU-1030 74 CTAGACTGAAGCTCCTTGAGG Mature:hsa-miR-151-3p:MIMAT0000757
CU-1095 75 TGGCAGTGTCTTAGCTGGTTGTT Mature:hsa-miR-34a:MIMAT0000255
CU-1119 76 TGAGGTAGTAAGTTGTATTGTT Mature:hsa-miR-98:MIMAT0000096
CU-1028 77 TGAGAACTGAATTCCATAGGCTGT
Mature:hsa-miR-146b-5p:MIMAT0002809 CU-1031 78
TCGAGGAGCTCACAGTCTAGTA Mature:hsa-miR-151-5p:MIMAT0004697 CU-1100
79 AGCTCGGTCTGAGGCCCCTCAG Mature:hsa-miR-423-3p:MIMAT0001340
CU-1038 80 ACTGCAGTGAAGGCACTTGTAG Star:hsa-miR-17*:MIMAT0000071
CU-1040 81 ACCATCGACCGTTGATTGTA Star:hsa-miR-181a*:MIMAT0000270
CU-1053 82 TTCACCACCTTCTCCACCCAG Mature:hsa-miR-197:MIMAT0000227
CU-1075 83 TTCACAGTGGCTAAGTTCTG Mature:hsa-miR-27b:MIMAT0000419
CU-1073 84 TTCAAGTAATTCAGGATAGGTT Mature:hsa-miR-26b:MIMAT0000083
CU-1110 85 TGGGTTTACGTTGGGAGAACT Mature:hsa-miR-629:MIMAT0004810
CU-1088 86 TGGGTTGAGAGGGCGA Mature:hsa-miR-320a:MIMAT0000510
CU-1005 87 TGAGGTAGGAGGTTGTATAGTT Mature:hsa-let-7e:MIMAT0000066
CU-1081 88 TGACCGATTTCTCCTGGTGTT Star:hsa-miR-29c*:MIMAT0004673
CU-1117 89 TATTGCACTCGTCCCGGCC Mature:hsa-miR-92b:MIMAT0003218
CU-1094 90 GGGGTGCTATCTGTGATTGA Mature:hsa-miR-342-5p:MIMAT0004694
CU-1021 91 GCATGGGTGGTTCAGTGGTAGAA Mature:hsa-miR-1308:MIMAT0005947
CU-1089 92 CTGGCCCTCTCTGCCCTT Mature:hsa-miR-328:MIMAT0000752
CU-1047 93 CTGACCTATGAATTGACAGC Mature:hsa-miR-192:MIMAT0000222
CU-1099 94 CTCCTGACTCCAGGTCCTGTG Star:hsa-miR-378*:MIMAT0000731
CU-1105 95 CGTCAACACTTGCTGGTT Mature:hsa-miR-505:MIMAT0002876
CU-1034 96 CGAATCATTATTTGCTGCTCT Star:hsa-miR-15b*:MIMAT0004586
CU-5002 97 CATCGGGAATGTCGTGTCCGCC Star:hsa-miR-425*:MI0001448
CU-1025 98 CAGTGGTTTTACCCTATGGTA Mature:hsa-miR-140-5p:MIMAT0000431
CU-1022 99 CAGTGCAATGATGAAAGGGCAT Mature:hsa-miR-130b:MIMAT0000691
CU-1104 100 CAGCAGCACACTGTGGTTTGT Mature:hsa-miR-497:MIMAT0002820
CU-1106 101 CACGCTCATGCACACACCCAC
Mature:hsa-miR-574-3p:MIMAT0003239 CU-1077 102
AAGGAGCTCACAGTCTATTGAG Mature:hsa-miR-28-5p:MIMAT0000085 CU-1123
103 TTGGTCCCCTTCAACCAGCTGT Mature:hsa-miR-133a:MIMAT0000427 CU-1074
104 TTCACAGTGGCTAAGTTCCGA Mature:hsa-miR-27a:MIMAT0000084 CU-1097
105 TTATCAGAATCTCCAGGGGTAA Mature:hsa-miR-361-5p:MIMAT0000703
CU-1043 106 TGGAGAGAAAGGCAGTTCCTGAT Mature:hsa-miR-185:MIMAT0000455
CU-1112 107 TGAGACCTCTGGGTTCTGAGCT
Mature:hsa-miR-769-5p:MIMAT0003886 CU-1122 108
TCTTTGGTTATCTAGCTGTATGA Mature:hsa-miR-9:MIMAT0000441 CU-1109 109
TCTAGTAAGAGTGGCAGTCGA Mature:hsa-miR-628-3p:MIMAT0003297 CU-1090
110 TATTGCACATTACTAAGTTGA Mature:hsa-miR-32:MIMAT0000090 CU-1013
111 TAAGGCACGCGGTGAATGCCA Mature:hsa-miR-124:MIMAT0000422 CU-1058
112 TAACACTGTCTGGTAACGATGTT Mature:hsa-miR-200a:MIMAT0000682
CU-1059 113 GTGAAATGTTTAGGACCACTAG Mature:hsa-miR-203:MIMAT0000264
CU-1102 114 GCAGTCCATGGGCATATACACA
Mature:hsa-miR-455-3p:MIMAT0004784 CU-1107 115
GAGCTTATTCATAAAAGTGCAG Mature:hsa-miR-590-5p:MIMAT0003258 CU-1114
116 CTGCCCTGGCCCGAGGGACCGA Mature:hsa-miR-874:MIMAT0004911 CU-1002
117 CTATACAACCTACTGCCTTC Star:hsa-let-7b*:MIMAT0004482 CU-1049 118
CGGGGTTTTGAGGGCGAGATGA Star:hsa-miR-193b*:MIMAT0004767 CU-1051 119
CCAGTGGGGCTGCTGTTATCTG Star:hsa-miR-194*:MIMAT0004671 CU-1036 120
CCAGTATTAACTGTGCTGCTGA Star:hsa-miR-16-1*:MIMAT0004489 CU-1121 121
CACCCGTAGAACCGACCTTGCG Mature:hsa-miR-99b:MIMAT0000689 CU-1120 122
CAAGCTCGTGTCTGTGGGTCCG Star:hsa-miR-99b*:MIMAT0004678 CU-1063 123
CAACACCAGTCGATGGGCTGTA Star:hsa-miR-21*:MIMAT0004494
CU-1070 124 AGGCGGAGACTTGGGCAATT Star:hsa-miR-25*:MIMAT0004498
CU-1060 125 ACTGCATTATGAGCACTTAAAGT Star:hsa-miR-20a*:MIMAT0004493
CU-1078 126 ACTGATTTCTTTTGGTGTTCA Star:hsa-miR-29a*:MIMAT0004503
CU-1020 127 ACTCGGCGTGGCGTCGGTCGTGG
Mature:hsa-miR-1307:MIMAT0005951 CU-1041 128 ACCACTGACCGTTGACTGTAC
Star:hsa-miR-181a-2*:MIMAT0004558 CU-1048 129
AACTGGCCTACAAAGTCCCAGT Mature:hsa-miR-193a-3p:MIMAT0000459 CU-1127
130 TGTCTGAGCGTCGCT preCursor:hsa-mir-1826:MI0008194 CU-1132 131
GCCGGGTACTTTCGTATTTT NEW CU-1137 132 GCTAAGGAAGTCCTGTGCTCAGTTTT NEW
CU-1130 133 CCCGGGTTTCGGCACCA NEW CU-1136 134 TCGGGCGGGAGTGGTGGCTTT
NEW CU-1383 135 TAGAGGCACCGCCTGCCCA NEW CU-1131 136
CGGGGCGCGGCCTCGCTG NEW CU-1135 137 CCCACGGGGGTCTCCGGGCGAG NEW
CU-1392 138 CCCACGGGAAACAGCA NEW CU-1133 139 CAGCCCGGCCTGGCTCCTCCAT
NEW CU-1134 140 CACGGAAGGTGGCCCGG NEW CU-1170 141 CTGTAGGCACCTGAAA
NEW CU-1153 142 CCCCCCACTGCTAAATTTGACTGGCTT NEW CU-1191 143
GCCCGCATCCTCCACCA NEW CU-1140 144 CCCGGCCAACGCACCA NEW CU-1173 145
ATCCCACTCCTGACACCA NEW CU-1149 146 CCGGGCGGAAACACCA NEW CU-1159 147
TGTCAGTTTGTTAATTA NEW CU-1178 148 AGGGTGTGCGTGTTTTT NEW CU-1142 149
TCGATTCCCGGCCCATGCACCA NEW CU-1164 150 GAGAGCGCTCGGTTTTT NEW
CU-1148 151 TGGTGTGGTCTGTTGTTTT NEW CU-1221 152
TGTGCTCCGGAGTTACCTCGTTT NEW CU-1186 153 TCCCCGACACCTCCACCA NEW
CU-1224 154 CTGTAGGCATCATCAAT NEW CU-1180 155
AACCGAGCGTCCAAGCTCTTTCCATTTT NEW CU-1155 156 TCCCCGCACCTCCACCA NEW
CU-1212 157 TCCCCGGCACTTCCACCA NEW CU-1213 158 TCACCCCATAAACACCA
NEW CU-1193 159 CTGTAGGCACCATCATAA NEW CU-1202 160 CCCACCAGAGTCGCCA
NEW CU-1220 161 TTCCCCGACGGGGAGCCA NEW CU-1175 162
GGCGTGATTCATACCTTTT NEW CU-1194 163 GCGGGCGGACCTTTT NEW CU-1205 164
CGGCTCGAAGGACCA NEW CU-1187 165 CCCCGGCCCCGCGTA NEW CU-1206 166
CCCACCTCTGACACCA NEW CU-1210 167 CCACGAGGTCGGCCGG NEW CU-1156 168
CAGGATCGGCCCACT NEW CU-1197 169 ATGTGGTGGCTTACTTTT NEW CU-1183 170
ATCCCGGACGAGCCCA NEW CU-1570 171 ATCCCCAGCATCTCCACCA NEW CU-1146
172 AGAAAGGCCGAATTTTA NEW CU-1165 173 TGTCAGTTTTTACCCAA NEW CU-1160
174 TGTCAGTTTGAACCCAA NEW CU-1189 175 TGTAGTGTTTCTTACTTTA NEW
CU-1219 176 TGGCGAAGGTCGGCCGCG NEW CU-1203 177 TGCAGGGCCGGCGGGGAGG
NEW CU-1211 178 TCGGGCGGCGGGCGT NEW CU-1190 179
TCGGCTTTCCCTGCTAACTGGGCTTTTT NEW CU-1144 180 TCAGAGCGCGGGCCGACCCC
NEW CU-1376 181 TCAACACCCACTCCCTC NEW CU-1138 182
TATCAATGATGCTTCTGAGA NEW CU-1384 183 TAACCCCAGGGTTGGTCA NEW CU-1154
184 GGGGTCCCCGGTAGA NEW CU-1171 185 GGGCGTGGGTGTGATGATTC NEW
CU-1199 186 GGGAGGTGAGTAGGTCTG NEW CU-1226 187 GGAGACGTGGCCGAGAG
NEW CU-1572 188 GCGGAATACCACGGGGA NEW CU-1151 189
GCAGGCGGGGGATTAGCTA NEW CU-1227 190 GCAGCGGAACGTCGGCGCGC NEW
CU-1200 191 GACGTCACCCTCCTCA NEW CU-1152 192 CTTGGACTAACCTGGTGTA
NEW CU-1158 193 CTGTAGGCCACCATCCA NEW CU-1216 194 CTGTAGGCACCACCA
NEW CU-1188 195 CTGGTAGGCACCTGAAA NEW CU-1157 196
CTGATGTTGATGCATATGATGACA NEW CU-1207 197 CGGTGGAACCTGCATTGGTTT NEW
CU-1181 198 CGGGGCCGGGGCTAGGGT NEW CU-1185 199 CGGGCCGCCCCCGCCCACCG
NEW CU-1163 200 CGGGCCCCGGGGCTCG NEW CU-1366 201
CGGCCTATCCGGAATGCCCC NEW CU-1225 202 CGGACCTCCCTGGCCC NEW CU-1145
203 CGCGGCCAGTGTCCCCTTGTA NEW CU-1201 204 CGACACACGGCCCGTGGCGC NEW
CU-1141 205 CCTCATAAATACCGG NEW CU-1172 206 CCTCACTGGGGGCTCCA NEW
CU-1209 207 CCTCACCTGGAGCACCA NEW CU-1147 208 CCGTACTGGCCACCA NEW
CU-1223 209 CCGCCGCCCCCCCCT NEW CU-1217 210 CCGCCCCGACCTTAGCTA NEW
CU-1176 211 CCCGTCCGCTGCGCCA NEW CU-1139 212 CCCGTCCACTCCGCCA NEW
CU-1166 213 CCCCGGCCCATGCACCA NEW CU-1177 214 CCCCGGCATCTCCATCA NEW
CU-1214 215 CCCCAGTACCTCCACCA NEW CU-1184 216 CCCAGCGGTGCCTCCA NEW
CU-1574 217 CCACGCTCTGCTACCA NEW CU-1360 218 CCACCCTGGAGCCTCCGT NEW
CU-1150 219 ATGGTAGGCACCTGAAA NEW CU-1162 220 ATGGGCGGTCCTCGTT NEW
CU-1179 221 ATGGCCTGGACCCCACTCCT NEW CU-1161 222 ATGGCCGCATATATTTT
NEW CU-1218 223 ATCCTGTTCGTGACGCCA NEW CU-1204 224
ATCCTGCTCACAGCCCCA NEW CU-1168 225 AGCGAGGGTTCCGCCGGCC NEW CU-1195
226 ACTGGGGAGGGGGAGGAGCCTCGAGG NEW CU-1215 227 ACCCCGAGGGGACGGGCG
NEW CU-1208 228 ACAGCGCTGTGTTCCCGT NEW CU-1192 229
ACAAAAAAAAAAGCCCAACCCT NEW CU-1373 230 AACTAAAACCCCTACGCA NEW
CU-1196 231 AAAGGAGCCGAATCTTT NEW CU-1251 232 CCCACCCAGGGACGCCA
refseqGeneIntron-annotate CU-1254 233 TCCCCGGCACCTCCACCA
refseqGeneIntron-annotate CU-1298 234 ATCCCGGACGAGCCCCCA
refseqGeneIntron-annotate CU-1229 235 CCCACGTTGGGCGCCA
refseqGeneIntron-annotate CU-1276 236 TCGATTCCCGGCCAATGCACCA
refseqGeneIntron-annotate CU-1303 237 ATCCCACTTCTGACACCA
refseqGeneIntron-annotate CU-1270 238 TCGTAGGCACCTGAAA
refseqGeneIntron-annotate CU-1242 239 TCCCCGTACGGGCCACCA
refseqGeneIntron-annotate CU-1273 240 TTGACCGCTCTGACCA
refseqGeneIntron-annotate CU-1328 241 CCCAGCGGGGCCTCCA
refseqGeneIntron-annotate CU-1257 242 CAGGAACGGTGCACCA
mRNAall-annotate; refseqGeneIntron-annotate CU-1241 243
AGTCCCATCTGGGTCGCCA refseqGeneIntron-annotate CU-1575 244
CCCCCCACTGCTAAATTTGACTGGA refseqGeneIntron-annotate;
rnaGene-annotate CU-1274 245 GTTTGTTAATTAACCCAA
refseqGeneIntron-annotate CU-1243 246 GTCCCTTCGTGGTCGCCA
refseqGeneIntron-annotate CU-1284 247 CTGTAGCACCTGAAA
mRNAall-annotate; refseqGeneIntron-annotate; rnaGene-annotate
CU-1300 248 TCCTCACACGGGGCACCA refseqGeneIntron-annotate CU-1278
249 TAACGGCCGCGGTACCC refseqGeneIntron-annotate CU-1264 250
GAGGGGGACCAAAAAAAA refseqGeneIntron-annotate CU-1275 251
CCCGCATTCTCCACCA refseqGeneIntron-annotate CU-1246 252
AGGGGGGTAAAAAAAAA refseqGeneIntron-annotate CU-1315 253
TCCACCGCTGCCACCA refseqGeneIntron-annotate CU-1277 254
GAGCCATGATGATACCACTGAGC refseqGeneIntron-annotate CU-1288 255
CGTCCATGATGTTCCGCAA mRNAall-annotate; snoRNA-annotate;
piRNA-annotate; wgRNA-annotate; refseqGeneIntron-annotate CU-1234
256 CATCCTCTGCTACCA mRNAall-annotate; refseqGeneIntron-annotate;
exEID- annotate CU-1345 257 AGAACACTACGAGCCACA mRNA-annotate;
refseqGeneIntron-annotate CU-1352 258 ACCCCACTTCTGGTACCA
refseqGeneIntron-annotate CU-1323 259 TGTATTGTGAGACATTC
mRNAall-annotate; refseqGeneIntron-annotate; wgRNA-annotate;
rnaGene-annotate CU-1324 260 TCTCGGTGGAACCTCCA
refseqGeneIntron-annotate CU-1302 261 TCCCCGGCACCTCCAA
refseqGeneIntron-annotate CU-1269 262 TACCGAGCCTGGTGATAGC
refseqGeneIntron-annotate CU-1281 263 GCAGCGCCAGCCTCCCGCCCTAC
refseqGeneIntron-annotate CU-1292 264 CCGCCTGGGGAGTAC
refseqGeneIntron-annotate CU-1339 265 ATCCCCAGCACCTCCACCA
refseqGeneIntron-annotate CU-1293 266 AGCAGTGATGTCCTGAAAATTCTGAAG
refseqGeneIntron-annotate CU-1307 267 ACCCCACTATGCTTAGCCCT
mRNA-annotate; refseqGeneIntron-annotate CU-1294 268
AAAGGACCTGGCGGTGCTTC mRNA-annotate; refseqGeneIntron-annotate
CU-1325 269 TTTGCCACACTGCAACACCTT refseqGeneIntron-annotate CU-1333
270 TTCCTTGGATGTCTGAGTGAC refseqGeneIntron-annotate CU-1310 271
TTAAACCACCAAGATCGCTGATGCAC refseqGeneIntron-annotate CU-1299 272
TGTTCGCCGACCGTTGA refseqGeneIntron-annotate CU-1265 273
TGGGGTCTGGGAGGGA refseqGeneIntron-annotate CU-1322 274
TGGGAGAGCAGGGTATTGT refseqGeneIntron-annotate CU-1279 275
TGCAGATGATGTAAAAGA snoRNA-annotate; refseqGeneIntron-annotate;
wgRNA-annotate; rnaGene-annotate CU-1267 276
TCGCTATGATGATGGATTCCAAAA mRNAall-annotate; refseqGeneIntron-
annotate; rnaGene-annotate CU-1308 277 TCCGAAAGGCCTCCCGCACCG
refseqGeneIntron-annotate CU-1331 278 TCCCGCACCTCCACCA
refseqGeneIntron-annotate CU-1297 279 TAGATGAATAGGTAAAGAG
refseqGeneIntron-annotate CU-1235 280 GTGTATGATGACCTCATGTAGCCTGAAC
refseqGeneIntron-annotate CU-1253 281 GTGAAGCGTTCCATATTTTT
mRNAall-annotate; refseqGeneIntron-annotate; rnaGene-annotate
CU-1348 282 GGGGGGGGGTTTGGAA refseqGeneIntron-annotate CU-1337 283
GGGGGGAGGGAAGGCAA refseqGeneIntron-annotate CU-1316 284
GGGGGCTGGGCTGGGTA refseqGeneIntron-annotate CU-1343 285
GGGGCCGCCGCCTGTGT refseqGeneIntron-annotate CU-1326 286
GGGAGTCCGCGGCGAGC refseqGeneIntron-annotate CU-1329 287
GGGACCTGGGGACCA refseqGeneIntron-annotate CU-1286 288
GGCTTGGTCTAGGGGTA refseqGeneIntron-annotate CU-1332 289
GGCTGGGACCCTGGACAC refseqGeneIntron-annotate CU-1262 290
GGCGACCTGCGACTCCTT refseqGeneIntron-annotate CU-1236 291
GGAGGGGGGAAACAAA refseqGeneIntron-annotate CU-1317 292
GGAGGGGGGAAAAAAAAAA computGene-annotate; refseqGeneIntron-annotate
CU-1327 293 GGAAGACCTGCACCACTGTC mRNAall-annotate;
computGene-annotate; refseqGeneIntron-annotate; exEID-annotate
CU-1239 294 GCGGGTGTCAGGCCT refseqGeneIntron-annotate CU-1266 295
GCCGGGCGTGGTGGTCTG refseqGeneIntron-annotate CU-1261 296
GCCGCCGAGACCCCAGGACCC refseqGeneIntron-annotate CU-1260 297
GCAGCCGTGCTTTTA refseqGeneIntron-annotate CU-1259 298
GCAAATGATGCCCTCTGATC refseqGeneIntron-annotate CU-1349 299
GAGGGGGGTCAAAAAAA refseqGeneIntron-annotate CU-1272 300
CTTGATGATGAGCAGGATCTGAGT refseqGeneIntron-annotate CU-1341 301
CTGTAGGCACTGAAA refseqGeneIntron-annotate CU-1231 302
CTGTAGGCACCATTAA refseqGeneIntron-annotate CU-1313 303
CTGCTTAAGTCCTGACCAG refseqGeneIntron-annotate CU-1296 304
CTGAGCACCTTTCCCTTCC refseqGeneIntron-annotate CU-1291 305
CTAGCCCCAAACCCA piRNA-annotate; refseqGeneIntron-annotate CU-1245
306 CGGTCACACGATTAACCCA mRNA-annotate; refseqGeneIntron-annotate
CU-1338 307 CGGGGGGAGGAAAAAA refseqGeneIntron-annotate CU-1268 308
CGGGGGGAAAAAAAAA refseqGeneIntron-annotate CU-1290 309
CGGGGCCGCACGCGC refseqGeneIntron-annotate CU-1319 310
CGGGAGTGGGGTGGCGCCCAG refseqGeneIntron-annotate CU-1318 311
CGGGAGCCCCGGGTT refseqGeneIntron-annotate CU-1569 312
CGGACCTGATAAATTCCCAC refseqGeneIntron-annotate CU-1320 313
CGCGGCTCTTGCGGT refseqGeneIntron-annotate CU-1249 314
CGCCTGAGTCAGAAC refseqGeneIntron-annotate CU-1240 315
CGCCGCCGCCCCCCCC mRNAall-annotate; refseqGeneIntron-annotate;
exEID-annotate CU-1351 316 CCTTCCTTGGATGTCTGAGTGAG
mRNAall-annotate; refseqGeneIntron-annotate; wgRNA-annotate;
rnaGene-annotate CU-1354 317 CCTCGCTGGGGCCTCCA
refseqGeneIntron-annotate CU-1233 318 CCTCACAGGGACGCCA
refseqGeneIntron-annotate CU-1289 319 CCTAGGAGTGCGACAATT
mRNAall-annotate; refseqGeneIntron-annotate; wgRNA-annotate;
rnaGene-annotate CU-1283 320 CCGCTCTGAGACCTA
refseqGeneIntron-annotate CU-1228 321 CCGCCCGTCACCCTCCTCAAGTA
mRNA-annotate; refseqGeneIntron-annotate CU-1344 322
CCCGGGCGGCACACCA refseqGeneIntron-annotate CU-1271 323
CCCGCGGGCTTGCTGGGCGTCCC refseqGeneIntron-annotate CU-1321 324
CCCCTGCGATTTCCCCA refseqGeneIntron-annotate; rnaGene-annotate
CU-1285 325 CCCCGGCATCTCCACTA refseqGeneIntron-annotate CU-1571 326
CCCCAGTGAGTGCCCTCTTCC refseqGeneIntron-annotate CU-1353 327
CCCAGAGACGCCGTCCTCGA refseqGeneIntron-annotate CU-1355 328
CCCACCGAGGATGCCA refseqGeneIntron-annotate CU-1238 329
CCATCACTACCCACCA refseqGeneIntron-annotate CU-1347 330
CCACTCCAGCCTAGCCCC refseqGeneIntron-annotate CU-1295 331
CAGTACAGGCACACCTC refseqGeneIntron-annotate CU-1256 332
CACGTCGGGGTCCCCA refseqGeneIntron-annotate CU-1250 333
CACGATTAACCCAAGTC mRNA-annotate; refseqGeneIntron-annotate CU-1305
334 CACCACACCCGGGCCA refseqGeneIntron-annotate CU-1287 335
CAACACAGGCATGCT refseqGeneIntron-annotate CU-1314 336
ATAGGGTTTACGACCTCGATGTTGGATCA refseqGeneIntron-annotate CU-1311 337
ATACCATGATGAACAATAGCTGAGA refseqGeneIntron-annotate CU-1282 338
AGGGTTCAGCTGTCTC refseqGeneIntron-annotate CU-1350 339
AGGCTGTGATGGACCTGGCTGAGCCTG refseqGeneIntron-annotate CU-1252 340
AGAGAGTAGGGGGAGGT refseqGeneIntron-annotate CU-1334 341
ACTGTCCCTGTCTACTA refseqGeneIntron-annotate CU-1340 342
ACCGCATCTGGCCTATTTTT refseqGeneIntron-annotate CU-1342 343
ACCAGACCTCCTGTGCGAAG refseqGeneIntron-annotate CU-1304 344
ACAGCCCGGATCCCAGCCCACTTA refseqGeneIntron-annotate CU-1230 345
ACACTGAGCCACAACCCA refseqGeneIntron-annotate CU-1312 346
AAGGGCTTGGCTTAATTA refseqGeneIntron-annotate CU-1255 347
AACCCGGAAGGCGGAGGTTGCGG computGene-annotate;
refseqGeneIntron-annotate CU-1336 348 AACCCCACACCAACC
refseqGeneIntron-annotate CU-1346 349 AACAAGCTTCTTTGACGTCCCATCCAC
refseqGeneIntron-annotate CU-1369 350 TCCCCGGCATCTCCACCA
computGene-annotate CU-1370 351 CTGATTGCTCCTGTCTGATT
mRNAall-annotate; exEID-annotate; rnaGene-annotate CU-1371 352
TCTAGAGGAGCCTGTTCTGTA mRNA-annotate CU-1381 353
TCGATTCCCGGTCAGGGAACCA repeats-annotate CU-1380 354
ATAGGTTTGGTCCTAGCCTTTCT piRNA-annotate CU-1363 355
CGTTCGCGCTTTCCCCTG rnaGene-annotate CU-1396 356 TAAGTGTTTGTGGGTTA
rnaGene-annotate CU-1361 357 GGCGGCGGGAGACCCA computGene-annotate
CU-1359 358 CCCCGGCAGGTTTGA rnaGene-annotate CU-1573 359
TGCCGTGATCGTATAGTGGTTA piRNA-annotate CU-1169 360
TCAGACTACTCTCCTCCGCCCATT mRNAall-annotate CU-1167 361
GGACACAGAGGCTTCG mRNAall-annotate CU-1395 362 CTGACAGCCGGGGTTTTGGA
computGene-annotate
CU-1365 363 CGGCGGGGCCTGGAGTCTG mRNAall-annotate;
computGene-annotate; exEID-annotate CU-1375 364 CCTGGCTCGCTGCGCCA
computGene-annotate CU-1182 365 CCGCCCCACCCCGCGCGC
mRNAall-annotate; exEID-annotate CU-1174 366 CCCGAACGCTGCCAACCC
exEID-annotate CU-1385 367 AGACCCGCGGGCGCTCTCCAGTC rnaGene-annotate
CU-1524 368 CCCCCACAACCGCGCTTGACTAGC mRNAall-annotate;
yRNA-eliminate; rnaGene-annotate CU-1453 369 CCCTGCTCGCTGCGCCA
refseqGeneExon-eliminate CU-1477 370 CTCCCACTGCTTCACTTGACTAGC
yRNA-eliminate; refseqGeneIntron-annotate; rnaGene-annotate CU-1466
371 CCCATCCTCGTCGCCA refseqGeneExon-eliminate CU-1222 372
TCACGTCGGGGTCACCA Morozov-eliminate CU-1388 373
TCCCTGGTGGTCTAGTGGTTAGGATTCG tRNAcomputational-annotate;
rnaGene-annotate; HStRNA-eliminate; piRNA-annotate CU-1428 374
GGTAGCGTGGCCGAG tRNAcomputational-annotate; tRNA-eliminate;
HStRNA-eliminate; rnaGene-annotate CU-1488 375 TCCTGCCGCGGTCGCCA
refseqGeneExon-eliminate CU-1557 376 GGAGAGAACGCGGTCTGAGTGGT
snoRNA-eliminate; wgRNA-annotate; rnaGene-annotate CU-1379 377
TCGGGTGCGAGAGGTCCCGGGT tRNAcomputational-annotate; HStRNA-
eliminate; rnaGene-annotate CU-1542 378 GGCTGGTCCGATGGTAGTGGGTT
mRNAall-annotate; yRNA-eliminate; refseqGeneIntron-annotate;
rnaGene-annotate CU-1550 379 CGGAAGCGTGCTGGGCCC
tRNAcomputational-annotate; tRNA-eliminate; rnaGene-annotate;
HStRNA-eliminate; piRNA-annotate CU-1232 380 CCCGGGCGGCGCACCA
Morozov-eliminate; refseqGeneIntron-annotate CU-1513 381
GCGGGTGATGCGAACTGGAGTCTGAGC computGene-annotate; snoRNA-annotate;
snoRNA-eliminate; wgRNA-annotate; rnaGene-annotate CU-1368 382
GACGAGGTGGCCGAGTGG tRNAcomputational-annotate; rnaGene-annotate;
HStRNA-eliminate; piRNA-annotate CU-1474 383 GGGGGTGTAGCTCAG
tRNAcomputational-annotate; tRNA-eliminate; rnaGene-annotate;
HStRNA-eliminate; piRNA- annotate CU-1470 384 CTCCTGGCTGGCTCGCCA
mRNAall-annotate; computGene-annotate; refseqGeneExon-eliminate;
exEID-annotate CU-1471 385 CGGGAGGCCCGGGTT rnaGene-annotate;
tRNAcomputational- annotate; piRNA-annotate; tRNA-eliminate;
refseqGeneIntron-annotate; mRNA-annotate; HStRNA-eliminate CU-1538
386 GGCTGGTCCGAGTGCAGTGGTGTTTA yRNA-eliminate;
refseqGeneIntron-annotate; rnaGene-annotate CU-1486 387
CTGCTGTGATGACATTC computGene-annotate; snoRNA-annotate;
snoRNA-eliminate; wgRNA-annotate; rnaGene- annotate CU-1386 388
TGTCACGCGGGAGACC tRNAcomputational-annotate; mRNAall-annotate;
rnaGene-annotate; HStRNA-eliminate; piRNA- annotate CU-1382 389
TCCTCGTTAGTATAGTGGTGAGTATCCC tRNAcomputational-annotate;
rnaGene-annotate; HStRNA-eliminate; piRNA- annotate CU-1433 390
GGCCGGTTAGCTCAG mRNAall-annotate; exEID-annotate; rnaGene-annotate;
tRNAcomputational-annotate; piRNA-annotate;
refseqGeneIntron-annotate; refseqGeneExon- eliminate;
HStRNA-eliminate CU-1403 391 GCATTGGTGGTTCAGTGGTAGA
rnaGene-annotate; tRNAcomputational- annotate; piRNA-annotate;
tRNA-eliminate; refseqGeneIntron-annotate; HStRNA-eliminate CU-1362
392 CTGTCACGCGGGAGA tRNAcomputational-annotate; mRNAall-annotate;
rnaGene-annotate; HStRNA-eliminate; piRNA-annotate CU-1490 393
CTACGGGGATGATTTT mRNAall-annotate; snoRNA-annotate;
snoRNA-eliminate; wgRNA-annotate; rnaGene-annotate CU-1469 394
CCAGGGGCTGAGGGCA snoRNA-eliminate; refseqGeneIntron-annotate;
wgRNA- annotate CU-1457 395 TTCTCACTACTGCACTTGACTA
mRNAall-annotate; yRNA-eliminate; refseqGeneIntron-annotate;
exEID-annotate; rnaGene-annotate CU-1440 396 TGGTTATCACGTTCGCC
tRNAcomputational-annotate; tRNA-eliminate; rnaGene-annotate;
HStRNA-eliminate; piRNA-annotate CU-1528 397 TAGGGGTATGATTCTCGCT
tRNAcomputational-annotate; tRNA-eliminate; HStRNA-eliminate;
rnaGene-annotate CU-1545 398 CCACGAGGAAGAGAGGTAGC snoRNA-eliminate;
wgRNA-annotate; snoRNA-annotate CU-1244 399 GTCAGGATGGCCGAGCGGTCT
tRNAcomputational-annotate; rnaGene-annotate; HStRNA-eliminate;
refseqGeneIntron- annotate CU-1390 400 GGGGATGTAGCTCAG
tRNAcomputational-annotate; rnaGene-annotate; HStRNA-eliminate;
piRNA-annotate CU-1377 401 GCAGCGATGGCCGAG
tRNAcomputational-annotate; HStRNA-eliminate; rnaGene-annotate
TABLE-US-00017 TABLE 1B List of known and newly identified mature
miRNAs including information on frequencies. Corrected Counts
Frequencies SEQ Memory Centroblasts Ramos Memory Centroblasts Ramos
Mature miRNA sequence ID NO. Naive (N) (M) (CB) (RA) Naive (N) (M)
(CB) (RA) TGTAGTGTTTCCTACTTTATGGA 1 1329 592 635 391 38.5 19.83
24.93 16.02 TAGCTTATCAGACTGATGTTGA 2 196 353 144 13 5.68 11.83 5.65
0.53 TAAAGTGCTTATAGTGCAGGTAG 3 54 19 49.82 257.89 1.56 0.64 1.96
10.57 TAGCAGCACATCATGGTTTACA 4 38 61 176.84 105 1.1 2.04 6.94 4.3
TAGCAGCACGTAAATATTGGCG 5 131 97 53 35 3.79 3.25 2.08 1.43
TGAGGTAGTAGGTTGTATAGTT 6 62.84 78.99 92.19 63.25 1.82 2.65 3.62
2.59 TATTGCACTTGTCCCGGCCTGT 7 17 21 46 207 0.49 0.7 1.81 8.48
TCCCACCGCTGCCACCA 8 68 97 25 28 1.97 3.25 0.98 1.15
TGAGGTAGTAGATTGTATAGTT 9 41.28 44 64 51.38 1.2 1.47 2.51 2.11
TAGCACCATCTGAAATCGGTTA 10 78 60 42 22 2.26 2.01 1.65 0.9
TAGCAGCACATAATGGTTTGT 11 90 39 32.16 8 2.61 1.31 1.26 0.33
CCCATAAAGTAGAAAGCACTA 12 88 53 7 10 2.55 1.78 0.27 0.41
TGAGGTAGTAGTTTGTACAGTT 13 41.28 47 30.77 21.16 1.2 1.57 1.21 0.87
TGAGGTAGTAGTTTGTGCTGTT 14 23 24 32 42 0.67 0.8 1.26 1.72
TAGCACCATTTGAAATCGGTTA 15 44 41 16 1 1.27 1.37 0.63 0.04
TGTAAACATCCTACACTCTCAGC 16 27 25 26 20 0.78 0.84 1.02 0.82
CAAAGTGCTTACAGTGCAGGTAG 17 9 6 10.18 65.04 0.26 0.2 0.4 2.67
CATTGCACTTGTCTCGGTCTGA 18 11 9 34 39 0.32 0.3 1.33 1.6
CAACGGAATCCCAAAAGCAGCTG 19 17 21 36 18 0.49 0.7 1.41 0.74
TGTGCAAATCCATGCAAAACTGA 20 0 1 25 65 0 0.03 0.98 2.66
TACCACAGGGTAGAACCACGGA 21 31 22 17 21 0.9 0.74 0.67 0.86
TGTAAACATCCTACACTCAGCT 22 31 11 27 16 0.9 0.37 1.06 0.66
TGAGGTAGTAGGTTGTGTGGTT 23 19.48 19 29 5.08 0.56 0.64 1.14 0.21
TAGCACCATTTGAAATCAGTGTT 24 22 14 12 4 0.64 0.47 0.47 0.16
TAAAGTGCTGACAGTGCAGAT 25 7 6 13 26 0.2 0.2 0.51 1.07
TCCCTGTCCTCCAGGAGCTC 26 6 3 3 32 0.17 0.1 0.12 1.31
TTCAAGTAATCCAGGATAGGCT 27 2 8 13 16 0.06 0.27 0.51 0.66
CAAAGTGCTGTTCGTGCAGGTAG 28 9 2 13 14 0.26 0.07 0.51 0.57
TGTCAGTTTGTCAAATACCCCA 29 25 10 1 0 0.72 0.34 0.04 0
TGAGAACTGAATTCCATGGGTT 30 4 7 21 4 0.12 0.23 0.82 0.16
TCTCCCAACCCTTGTACCAGT 31 12 18 2 0 0.35 0.6 0.08 0
TCCCTGAGACCCTAACTTGTGA 32 0 1 28 2 0 0.03 1.1 0.08
TCTCACACAGAAATCGCACCCG 33 10 8 8 3 0.29 0.27 0.31 0.12 TC
GTCCCTGTTCGGGCGCCA 34 12 10 6 1 0.35 0.34 0.24 0.04
TGTGCAAATCTATGCAAAACTGA 35 0 0 9 19 0 0 0.35 0.78
TGTAAACATCCCCGACTGGAAG 36 7 3 14 3 0.2 0.1 0.55 0.12
AGCTACATTGTCTGCTGGGTT 37 17 6 4 0 0.49 0.2 0.16 0
AGAGGTAGTAGGTTGCATAGTT 38 2 4 10 10 0.06 0.13 0.39 0.41
CCGCACTGTGGGTACTTGCT 39 8 6 2 8 0.23 0.2 0.08 0.33
AGCAGCATTGTACAGGGCTATGA 40 1 1 10 11 0.03 0.03 0.39 0.45
AACTGGCCCTCAAAGTCCCGCT 41 0 0 2 21 0 0 0.08 0.86
GCCCCTGGGCCTATCCTAGAA 42 1 0 10 10 0.03 0 0.39 0.41
AGCTGGTGTTGTGAATCAGGCC 43 0 0 15 5 0 0 0.59 0.2 GT
TGAGGGGCAGAGAGCGAGACTT 44 5 1 7 4 0.14 0.03 0.27 0.16
AGCTACATCTGGCTACTGGGTCT 45 6 6 5 0 0.17 0.2 0.2 0 GTGGGGGAGAGGCTGTA
46 2 6 3 5 0.06 0.2 0.12 0.2 CTATACGACCTGCTGCCTTTC 47 6 3 4 1 0.17
0.1 0.16 0.04 TTAATGCTAATCGTGATAGGGGT 48 3 4 5 1 0.09 0.13 0.2 0.04
AGGGGGAAAGTTCTATAGTC 49 0 2 0 11 0 0.07 0 0.45
ACAGTAGTCTGCACATTGGTT 50 0 0 13 0 0 0 0.51 0 AACATTCAACGCTGTCGGTGAG
51 0 0 7 6 0 0 0.27 0.25 TT TGGAAGACTAGTGATTTTGTTGT 52 1 1 1 8 0.03
0.03 0.04 0.33 TAATGCCCCTAAAAATCCTTAT 53 0 0 6 4 0 0 0.24 0.16
TAGCAGCACAGAAATATTGGCA 54 4 0 5 0 0.12 0 0.2 0 TGAGGTAGTAGGTTGTAT
55 0.11 0.01 0.01 0.13 0 0 0 0.01 TCCTGTACTGAGCTGCCCCGAG 56 0 0 7 1
0 0 0.27 0.04 TCCCTGAGACCCTTTAACCTGTGA 57 0 0 8 0 0 0 0.31 0
ATCACATTGCCAGGGATTTCCA 58 0 0.5 7 0 0 0.02 0.27 0
TCACAGTGAACCGGTCTCTTT 59 1 0 0 6 0.03 0 0 0.25
CACTAGATTGTGAGCTCCTGGA 60 2 0 4 1 0.06 0 0.16 0.04
CAACAAATCACAGTCTGCCAT 61 3 0 1 3 0.09 0 0.04 0.12
CAAAGTGCTTATAGTGCAGGTAG 62 0 1 1 0.08 0 0.03 0.04 0
AGGTTGGGATCGGTTGCAATGCT 63 0 0 0 7 0 0 0 0.29
ACATTCATTGCTGTCGGTGGGTT 64 0 0 1 6 0 0 0.04 0.25
TCCCCCAGGTGTGATTCTGATT 65 4 1 0 1 0.12 0.03 0 0.04
CCCAGTGTTCAGACTACCTGTTC 66 0 0 6 0 0 0 0.24 0 ACCAATATTACTGTGCTGCTT
67 1 1 2 2 0.03 0.03 0.08 0.08 TGTAAACATCCTTGACTGGAAGCT 68 2 0 3 0
0.06 0 0.12 0 TAAGGTGCATCTAGTGCAGATA 69 0 0 1 4 0 0 0.04 0.16
ATCACATTGCCAGGGATTACCA 70 0 0.5 3 1 0 0.02 0.12 0.04
ACTGCCCTAAGTGCTCCTTCTG 71 0 0 0 5 0 0 0 0.2 TGTAAACATCCTCGACTGGA 72
1 0 3 0 0.03 0 0.12 0 TACAGTACTGTGATAACTGAAG 73 1 0 0 3 0.03 0 0
0.12 CTAGACTGAAGCTCCTTGAGG 74 2 1 1 0 0.06 0.03 0.04 0
TGGCAGTGTCTTAGCTGGTTGTT 75 0 1 2 0 0 0.03 0.08 0
TGAGGTAGTAAGTTGTATTGTT 76 0 1 1 1 0 0.03 0.04 0.04
TGAGAACTGAATTCCATAGGCT 77 1 0 2 0 0.03 0 0.08 0 GT
TCGAGGAGCTCACAGTCTAGTA 78 1 0 1 1 0.03 0 0.04 0.04
AGCTCGGTCTGAGGCCCCTCAG 79 0 0 2 1 0 0 0.08 0.04
ACTGCAGTGAAGGCACTTGTAG 80 0 0 0 3 0 0 0 0.12 ACCATCGACCGTTGATTGTA
81 0 1 0 2 0 0.03 0 0.08 TTCACCACCTTCTCCACCCAG 82 0 0 0 2 0 0 0
0.08 TTCACAGTGGCTAAGTTCTG 83 0 0 2 0 0 0 0.08 0
TTCAAGTAATTCAGGATAGGTT 84 0 0 1 1 0 0 0.04 0.04
TGGGTTTACGTTGGGAGAACT 85 0 0 0 2 0 0 0 0.08 TGGGTTGAGAGGGCGA 86 1 0
1 0 0.03 0 0.04 0 TGAGGTAGGAGGTTGTATAGTT 87 0 0 1.02 0 0 0 0.04 0
TGACCGATTTCTCCTGGTGTT 88 2 0 0 0 0.06 0 0 0 TATTGCACTCGTCCCGGCC 89
0 0 1 1 0 0 0.04 0.04 GGGGTGCTATCTGTGATTGA 90 2 0 0 0 0.06 0 0 0
GCATGGGTGGTTCAGTGGTAGAA 91 0 0 2 0 0 0 0.08 0 CTGGCCCTCTCTGCCCTT 92
0 0 1 1 0 0 0.04 0.04 CTGACCTATGAATTGACAGC 93 0 0 0 2 0 0 0 0.08
CTCCTGACTCCAGGTCCTGTG 94 0 0 0 2 0 0 0 0.08 CGTCAACACTTGCTGGTT 95 0
0 1 1 0 0 0.04 0.04 CGAATCATTATTTGCTGCTCT 96 0 0 1 1 0 0 0.04 0.04
CATCGGGAATGTCGTGTCCGCC 97 0 2 0 0 0 0.07 0 0 CAGTGGTTTTACCCTATGGTA
98 0 0 1 1 0 0 0.04 0.04 CAGTGCAATGATGAAAGGGCAT 99 0 0 2 0 0 0 0.08
0 CAGCAGCACACTGTGGTTTGT 100 0 0 2 0 0 0 0.08 0
CACGCTCATGCACACACCCAC 101 0 0 2 0 0 0 0.08 0 AAGGAGCTCACAGTCTATTGAG
102 0 0 2 0 0 0 0.08 0 TTGGTCCCCTTCAACCAGCTGT 103 0 0 1 0 0 0 0.04
0 TTCACAGTGGCTAAGTTCCGA 104 0 1 0 0 0 0.03 0 0
TTATCAGAATCTCCAGGGGTAA 105 1 0 0 0 0.03 0 0 0
TGGAGAGAAAGGCAGTTCCTGAT 106 0 0 1 0 0 0 0.04 0
TGAGACCTCTGGGTTCTGAGCT 107 0 0 0 1 0 0 0 0.04
TCTTTGGTTATCTAGCTGTATGA 108 0 0 0 1 0 0 0 0.04
TCTAGTAAGAGTGGCAGTCGA 109 0 0 0 1 0 0 0 0.04 TATTGCACATTACTAAGTTGA
110 1 0 0 0 0.03 0 0 0 TAAGGCACGCGGTGAATGCCA 111 1 0 0 0 0.03 0 0 0
TAACACTGTCTGGTAACGATGTT 112 0 0 0 1 0 0 0 0.04
GTGAAATGTTTAGGACCACTAG 113 0 0 1 0 0 0 0.04 0
GCAGTCCATGGGCATATACACA 114 0 0 1 0 0 0 0.04 0
GAGCTTATTCATAAAAGTGCAG 115 0 0 1 0 0 0 0.04 0
CTGCCCTGGCCCGAGGGACCGA 116 0 0 0 1 0 0 0 0.04 CTATACAACCTACTGCCTTC
117 0 0 1 0 0 0 0.04 0 CGGGGTTTTGAGGGCGAGATGA 118 0 0 0 1 0 0 0
0.04 CCAGTGGGGCTGCTGTTATCTG 119 0 0 1 0 0 0 0.04 0
CCAGTATTAACTGTGCTGCTGA 120 0 0 0 1 0 0 0 0.04
CACCCGTAGAACCGACCTTGCG 121 0 0 1 0 0 0 0.04 0
CAAGCTCGTGTCTGTGGGTCCG 122 0 0 1 0 0 0 0.04 0
CAACACCAGTCGATGGGCTGTA 123 0 0 0 1 0 0 0 0.04 AGGCGGAGACTTGGGCAATT
124 0 0 0 1 0 0 0 0.04 ACTGCATTATGAGCACTTAAAGT 125 0 0 0 1 0 0 0
0.04 ACTGATTTCTTTTGGTGTTCA 126 0 0 0 1 0 0 0 0.04
ACTCGGCGTGGCGTCGGTCGTGG 127 0 0 0 1 0 0 0 0.04
ACCACTGACCGTTGACTGTAC 128 0 1 0 0 0 0.03 0 0 AACTGGCCTACAAAGTCCCAGT
129 0 0 1 0 0 0 0.04 0 TGTCTGAGCGTCGCT 130 0 0 4 0 0 0 0.16 0
GCCGGGTACTTTCGTATTTT 131 3 3 0 34 0.09 0.1 0 1.39
GCTAAGGAAGTCCTGTGCTCAG 132 0 0 1 19 0 0 0.04 0.78 TTTT
CCCGGGTTTCGGCACCA 133 0 3 0 1 0 0.1 0 0.04 TCGGGCGGGAGTGGTGGCTTT
134 0 0 0 1 0 0 0 0.04 TAGAGGCACCGCCTGCCCA 135 0 1 0 0 0 0.03 0 0
CGGGGCGCGGCCTCGCTG 136 1 0 0 0 0.03 0 0 0 CCCACGGGGGTCTCCGGGCGAG
137 1 0 0 0 0.03 0 0 0 CCCACGGGAAACAGCA 138 0 1 0 0 0 0.03 0 0
CAGCCCGGCCTGGCTCCTCCAT 139 0 1 0 0 0 0.03 0 0 CACGGAAGGTGGCCCGG 140
0 1 0 0 0 0.03 0 0 CTGTAGGCACCTGAAA 141 1 0 0 148.06 0.03 0 0 6.07
CCCCCCACTGCTAAATTTGACTG 142 18 8 61 22 0.52 0.27 2.39 0.9 GCTT
GCCCGCATCCTCCACCA 143 38 61 2 4 1.1 2.04 0.08 0.16 CCCGGCCAACGCACCA
144 28.76 36.71 4.12 4 0.83 1.23 0.16 0.16 ATCCCACTCCTGACACCA 145 7
13 11.31 3 0.2 0.44 0.44 0.12 CCGGGCGGAAACACCA 146 9 9 6 0 0.26 0.3
0.24 0 TGTCAGTTTGTTAATTA 147 1 1 3 16 0.03 0.03 0.12 0.66
AGGGTGTGCGTGTTTTT 148 0 0 0 20 0 0 0 0.82 TCGATTCCCGGCCCATGCACCA
149 1 2 10 4 0.03 0.07 0.39 0.16 GAGAGCGCTCGGTTTTT 150 0 0 1 9 0 0
0.04 0.37 TGGTGTGGTCTGTTGTTTT 151 0 0 0 9 0 0 0 0.37
TGTGCTCCGGAGTTACCTCGTTT 152 0 0 0 8 0 0 0 0.33 TCCCCGACACCTCCACCA
153 2 2 2 1 0.06 0.07 0.08 0.04 CTGTAGGCATCATCAAT 154 0 0 1 3.57 0
0 0.04 0.15 AACCGAGCGTCCAAGCTCTTTC 155 0 0 0 5 0 0 0 0.2 CATTTT
TCCCCGCACCTCCACCA 156 0 2 1 1 0 0.07 0.04 0.04 TCCCCGGCACTTCCACCA
157 0 3 0 0 0 0.1 0 0 TCACCCCATAAACACCA 158 2 1 0 0 0.06 0.03 0 0
CTGTAGGCACCATCATAA 159 0 0 0 2.43 0 0 0 0.1 CCCACCAGAGTCGCCA 160 1
2 0 0 0.03 0.07 0 0 TTCCCCGACGGGGAGCCA 161 1 0 0 1 0.03 0 0 0.04
GGCGTGATTCATACCTTTT 162 0 0 0 2 0 0 0 0.08 GCGGGCGGACCTTTT 163 1 1
0 0 0.03 0.03 0 0 CGGCTCGAAGGACCA 164 0 2 0 0 0 0.07 0 0
CCCCGGCCCCGCGTA 165 0 2 0 0 0 0.07 0 0 CCCACCTCTGACACCA 166 0 1 1 0
0 0.03 0.04 0 CCACGAGGTCGGCCGG 167 0 2 0 0 0 0.07 0 0
CAGGATCGGCCCACT 168 2 0 0 0 0.06 0 0 0 ATGTGGTGGCTTACTTTT 169 0 0 0
2 0 0 0 0.08 ATCCCGGACGAGCCCA 170 0 2 0 0 0 0.07 0 0
ATCCCCAGCATCTCCACCA 171 0 0 2 0 0 0 0.08 0 AGAAAGGCCGAATTTTA 172 0
0 1 1 0 0 0.04 0.04 TGTCAGTTTTTACCCAA 173 0 0 0 1 0 0 0 0.04
TGTCAGTTTGAACCCAA 174 0 0 0 1 0 0 0 0.04 TGTAGTGTTTCTTACTTTA 175 1
0 0 0 0.03 0 0 0 TGGCGAAGGTCGGCCGCG 176 0 1 0 0 0 0.03 0 0
TGCAGGGCCGGCGGGGAGG 177 0 1 0 0 0 0.03 0 0 TCGGGCGGCGGGCGT 178 1 0
0 0 0.03 0 0 0 TCGGCTTTCCCTGCTAACTGGG 179 0 0 0 1 0 0 0 0.04 CTTTTT
TCAGAGCGCGGGCCGACCCC 180 1 0 0 0 0.03 0 0 0 TCAACACCCACTCCCTC 181 0
1 0 0 0 0.03 0 0 TATCAATGATGCTTCTGAGA 182 0 0 0 1 0 0 0 0.04
TAACCCCAGGGTTGGTCA 183 0 1 0 0 0 0.03 0 0 GGGGTCCCCGGTAGA 184 0 1 0
0 0 0.03 0 0 GGGCGTGGGTGTGATGATTC 185 0 0 0 1 0 0 0 0.04
GGGAGGTGAGTAGGTCTG 186 0 1 0 0 0 0.03 0 0 GGAGACGTGGCCGAGAG 187 0 1
0 0 0 0.03 0 0 GCGGAATACCACGGGGA 188 0 1 0 0 0 0.03 0 0
GCAGGCGGGGGATTAGCTA 189 1 0 0 0 0.03 0 0 0 GCAGCGGAACGTCGGCGCGC 190
0 1 0 0 0 0.03 0 0 GACGTCACCCTCCTCA 191 0 1 0 0 0 0.03 0 0
CTTGGACTAACCTGGTGTA 192 0 0 1 0 0 0 0.04 0 CTGTAGGCCACCATCCA 193 0
0 0 1 0 0 0 0.04 CTGTAGGCACCACCA 194 1 0 0 0 0.03 0 0 0
CTGGTAGGCACCTGAAA 195 0 0 0 1 0 0 0 0.04 CTGATGTTGATGCATATGATGACA
196 0 0 0 1 0 0 0 0.04 CGGTGGAACCTGCATTGGTTT 197 0 0 1 0 0 0 0.04 0
CGGGGCCGGGGCTAGGGT 198 0 1 0 0 0 0.03 0 0 CGGGCCGCCCCCGCCCACCG 199
0 1 0 0 0 0.03 0 0 CGGGCCCCGGGGCTCG 200 0 1 0 0 0 0.03 0 0
CGGCCTATCCGGAATGCCCC 201 0 1 0 0 0 0.03 0 0 CGGACCTCCCTGGCCC 202 1
0 0 0 0.03 0 0 0 CGCGGCCAGTGTCCCCTTGTA 203 1 0 0 0 0.03 0 0 0
CGACACACGGCCCGTGGCGC 204 1 0 0 0 0.03 0 0 0 CCTCATAAATACCGG 205 0 1
0 0 0 0.03 0 0 CCTCACTGGGGGCTCCA 206 1 0 0 0 0.03 0 0 0
CCTCACCTGGAGCACCA 207 0 0 1 0 0 0 0.04 0 CCGTACTGGCCACCA 208 0 1 0
0 0 0.03 0 0 CCGCCGCCCCCCCCT 209 0 1 0 0 0 0.03 0 0
CCGCCCCGACCTTAGCTA 210 0 1 0 0 0 0.03 0 0 CCCGTCCGCTGCGCCA 211 0 1
0 0 0 0.03 0 0 CCCGTCCACTCCGCCA 212 0 1 0 0 0 0.03 0 0
CCCCGGCCCATGCACCA 213 0 1 0 0 0 0.03 0 0 CCCCGGCATCTCCATCA 214 1 0
0 0 0.03 0 0 0 CCCCAGTACCTCCACCA 215 0 1 0 0 0 0.03 0 0
CCCAGCGGTGCCTCCA 216 0 1 0 0 0 0.03 0 0 CCACGCTCTGCTACCA 217 1 0 0
0 0.03 0 0 0 CCACCCTGGAGCCTCCGT 218 0 1 0 0 0 0.03 0 0
ATGGTAGGCACCTGAAA 219 0 0 0 1 0 0 0 0.04 ATGGGCGGTCCTCGTT 220 0 1 0
0 0 0.03 0 0 ATGGCCTGGACCCCACTCCT 221 0 0 0 1 0 0 0 0.04
ATGGCCGCATATATTTT 222 0 0 0 1 0 0 0 0.04 ATCCTGTTCGTGACGCCA 223 0 0
1 0 0 0 0.04 0 ATCCTGCTCACAGCCCCA 224 0 1 0 0 0 0.03 0 0
AGCGAGGGTTCCGCCGGCC 225 0 0 0 1 0 0 0 0.04 ACTGGGGAGGGGGAGGAGCCT
226 0 0 0 1 0 0 0 0.04 CGAGG ACCCCGAGGGGACGGGCG 227 0 1 0 0 0 0.03
0 0 ACAGCGCTGTGTTCCCGT 228 0 0 1 0 0 0 0.04 0
ACAAAAAAAAAAGCCCAACCCT 229 0 0 0 1 0 0 0 0.04 AACTAAAACCCCTACGCA
230 0 0 1 0 0 0 0.04 0 AAAGGAGCCGAATCTTT 231 0 0 1 0 0 0 0.04 0
CCCACCCAGGGACGCCA 232 223 218 6 2 6.46 7.3 0.24 0.08
TCCCCGGCACCTCCACCA 233 60.47 101.82 40.28 34 1.75 3.41 1.58 1.39
ATCCCGGACGAGCCCCCA 234 48 60 80 45 1.39 2.01 3.14 1.84
CCCACGTTGGGCGCCA 235 37 50 1 0 1.07 1.68 0.04 0
TCGATTCCCGGCCAATGCACCA 236 2.24 15.29 35.88 4 0.06 0.51 1.41 0.16
ATCCCACTTCTGACACCA 237 11 9 26.69 14 0.32 0.3 1.05 0.57
TCGTAGGCACCTGAAA 238 0 0 0 7.94 0 0 0 0.33 TCCCCGTACGGGCCACCA 239
11 6 3 2 0.32 0.2 0.12 0.08 TTGACCGCTCTGACCA 240 4 9 2 5 0.12 0.3
0.08 0.2 CCCAGCGGGGCCTCCA 241 11 8 1 0 0.32 0.27 0.04 0
CAGGAACGGTGCACCA 242 6 10 2 0 0.17 0.34 0.08 0
AGTCCCATCTGGGTCGCCA 243 4 2 3 6 0.12 0.07 0.12 0.25
CCCCCCACTGCTAAATTTGACTG 244 1 1 6 2 0.03 0.03 0.24 0.08 GA
GTTTGTTAATTAACCCAA 245 0 0 1 5 0 0 0.04 0.2 GTCCCTTCGTGGTCGCCA 246
1 2 1 2 0.03 0.07 0.04 0.08 CTGTAGCACCTGAAA 247 0 0 0 6 0 0 0 0.25
TCCTCACACGGGGCACCA 248 2 1 2 0 0.06 0.03 0.08 0 TAACGGCCGCGGTACCC
249 0 3 1 0 0 0.1 0.04 0 GAGGGGGACCAAAAAAAA 250 0 0 0 4 0 0 0 0.16
CCCGCATTCTCCACCA 251 3 0 1 0 0.09 0 0.04 0 AGGGGGGTAAAAAAAAA 252 0
0 0 4 0 0 0 0.16 TCCACCGCTGCCACCA 253 0 3 0 0 0 0.1 0 0
GAGCCATGATGATACCACTGAGC 254 0 1 0 2 0 0.03 0 0.08
CGTCCATGATGTTCCGCAA 255 1 0 2 0 0.03 0 0.08 0 CATCCTCTGCTACCA 256 3
0 0 0 0.09 0 0 0 AGAACACTACGAGCCACA 257 3 0 0 0 0.09 0 0 0
ACCCCACTTCTGGTACCA 258 0 0 1 2 0 0 0.04 0.08 TGTATTGTGAGACATTC 259
0 1 1 0 0 0.03 0.04 0 TCTCGGTGGAACCTCCA 260 0 0 1 1 0 0 0.04 0.04
TCCCCGGCACCTCCAA 261 0 1.01 0 0 0 0.03 0 0 TACCGAGCCTGGTGATAGC 262
0 1 1 0 0 0.03 0.04 0 GCAGCGCCAGCCTCCCGCCCTAC 263 2 0 0 0 0.06 0 0
0 CCGCCTGGGGAGTAC 264 0 2 0 0 0 0.07 0 0 ATCCCCAGCACCTCCACCA 265 0
0 0 2 0 0 0 0.08 AGCAGTGATGTCCTGAAAATTCT 266 0 0 0 2 0 0 0 0.08
GAAG ACCCCACTATGCTTAGCCCT 267 0 0 2 0 0 0 0.08 0
AAAGGACCTGGCGGTGCTTC 268 1 0 1 0 0.03 0 0.04 0
TTTGCCACACTGCAACACCTT 269 0 0 1 0 0 0 0.04 0 TTCCTTGGATGTCTGAGTGAC
270 0 0 1 0 0 0 0.04 0 TTAAACCACCAAGATCGCTGATG 271 0 0 1 0 0 0 0.04
0 CAC TGTTCGCCGACCGTTGA 272 0 0 1 0 0 0 0.04 0 TGGGGTCTGGGAGGGA 273
0 1 0 0 0 0.03 0 0 TGGGAGAGCAGGGTATTGT 274 1 0 0 0 0.03 0 0 0
TGCAGATGATGTAAAAGA 275 0 0 1 0 0 0 0.04 0 TCGCTATGATGATGGATTCCAAAA
276 0 0 1 0 0 0 0.04 0 TCCGAAAGGCCTCCCGCACCG 277 0 0 1 0 0 0 0.04 0
TCCCGCACCTCCACCA 278 0 0 1 0 0 0 0.04 0 TAGATGAATAGGTAAAGAG 279 0 0
1 0 0 0 0.04 0 GTGTATGATGACCTCATGTAGC 280 0 0 0 1 0 0 0 0.04 CTGAAC
GTGAAGCGTTCCATATTTTT 281 0 0 1 0 0 0 0.04 0 GGGGGGGGGTTTGGAA 282 0
0 0 1 0 0 0 0.04 GGGGGGAGGGAAGGCAA 283 0 0 1 0 0 0 0.04 0
GGGGGCTGGGCTGGGTA 284 0 1 0 0 0 0.03 0 0 GGGGCCGCCGCCTGTGT 285 1 0
0 0 0.03 0 0 0 GGGAGTCCGCGGCGAGC 286 0 0 0 1 0 0 0 0.04
GGGACCTGGGGACCA 287 1 0 0 0 0.03 0 0 0 GGCTTGGTCTAGGGGTA 288 0 0 0
1 0 0 0 0.04 GGCTGGGACCCTGGACAC 289 0 0 0 1 0 0 0 0.04
GGCGACCTGCGACTCCTT 290 0 1 0 0 0 0.03 0 0 GGAGGGGGGAAACAAA 291 0 0
0 1 0 0 0 0.04 GGAGGGGGGAAAAAAAAAA 292 0 0 0 1 0 0 0 0.04
GGAAGACCTGCACCACTGTC 293 0 1 0 0 0 0.03 0 0 GCGGGTGTCAGGCCT 294 1 0
0 0 0.03 0 0 0 GCCGGGCGTGGTGGTCTG 295 0 1 0 0 0 0.03 0 0
GCCGCCGAGACCCCAGGACCC 296 1 0 0 0 0.03 0 0 0 GCAGCCGTGCTTTTA 297 0
1 0 0 0 0.03 0 0 GCAAATGATGCCCTCTGATC 298 0 0 0 1 0 0 0 0.04
GAGGGGGGTCAAAAAAA 299 0 0 0 1 0 0 0 0.04 CTTGATGATGAGCAGGATCTGA 300
0 0 0 1 0 0 0 0.04 GT CTGTAGGCACTGAAA 301 0 0 0 1 0 0 0 0.04
CTGTAGGCACCATTAA 302 0 0 0 1 0 0 0 0.04 CTGCTTAAGTCCTGACCAG 303 0 0
1 0 0 0 0.04 0 CTGAGCACCTTTCCCTTCC 304 0 1 0 0 0 0.03 0 0
CTAGCCCCAAACCCA 305 1 0 0 0 0.03 0 0 0 CGGTCACACGATTAACCCA 306 0 0
1 0 0 0 0.04 0 CGGGGGGAGGAAAAAA 307 0 0 0 1 0 0 0 0.04
CGGGGGGAAAAAAAAA 308 0 0 0 1 0 0 0 0.04 CGGGGCCGCACGCGC 309 1 0 0 0
0.03 0 0 0 CGGGAGTGGGGTGGCGCCCAG 310 1 0 0 0 0.03 0 0 0
CGGGAGCCCCGGGTT 311 1 0 0 0 0.03 0 0 0 CGGACCTGATAAATTCCCAC 312 0 0
1 0 0 0 0.04 0 CGCGGCTCTTGCGGT 313 1 0 0 0 0.03 0 0 0
CGCCTGAGTCAGAAC 314 1 0 0 0 0.03 0 0 0 CGCCGCCGCCCCCCCC 315 0 1 0 0
0 0.03 0 0 CCTTCCTTGGATGTCTGAGTGAG 316 0 0 1 0 0 0 0.04 0
CCTCGCTGGGGCCTCCA 317 1 0 0 0 0.03 0 0 0 CCTCACAGGGACGCCA 318 1 0 0
0 0.03 0 0 0 CCTAGGAGTGCGACAATT 319 0 0 0 1 0 0 0 0.04
CCGCTCTGAGACCTA 320 0 1 0 0 0 0.03 0 0 CCGCCCGTCACCCTCCTCAAGTA 321
0 0 1 0 0 0 0.04 0 CCCGGGCGGCACACCA 322 0 1 0 0 0 0.03 0 0
CCCGCGGGCTTGCTGGGCGTC 323 0 1 0 0 0 0.03 0 0 CC CCCCTGCGATTTCCCCA
324 0 1 0 0 0 0.03 0 0 CCCCGGCATCTCCACTA 325 1 0 0 0 0.03 0 0 0
CCCCAGTGAGTGCCCTCTTCC 326 0 1 0 0 0 0.03 0 0 CCCAGAGACGCCGTCCTCGA
327 1 0 0 0 0.03 0 0 0 CCCACCGAGGATGCCA 328 1 0 0 0 0.03 0 0 0
CCATCACTACCCACCA 329 0 1 0 0 0 0.03 0 0 CCACTCCAGCCTAGCCCC 330 0 1
0 0 0 0.03 0 0 CAGTACAGGCACACCTC 331 0 1 0 0 0 0.03 0 0
CACGTCGGGGTCCCCA 332 1 0 0 0 0.03 0 0 0 CACGATTAACCCAAGTC 333 0 0 1
0 0 0 0.04 0 CACCACACCCGGGCCA 334 1 0 0 0 0.03 0 0 0
CAACACAGGCATGCT 335 0 1 0 0 0 0.03 0 0 ATAGGGTTTACGACCTCGATGTT 336
0 0 1 0 0 0 0.04 0 GGATCA ATACCATGATGAACAATAGCTGA 337 0 0 0 1 0 0 0
0.04 GA AGGGTTCAGCTGTCTC 338 1 0 0 0 0.03 0 0 0
AGGCTGTGATGGACCTGGCTGA 339 0 0 0 1 0 0 0 0.04 GCCTG
AGAGAGTAGGGGGAGGT 340 0 1 0 0 0 0.03 0 0 ACTGTCCCTGTCTACTA 341 0 0
0 1 0 0 0 0.04 ACCGCATCTGGCCTATTTTT 342 0 0 0 1 0 0 0 0.04
ACCAGACCTCCTGTGCGAAG 343 0 0 0 1 0 0 0 0.04 ACAGCCCGGATCCCAGCCCACT
344 0 0 0 1 0 0 0 0.04 TA ACACTGAGCCACAACCCA 345 0 0 1 0 0 0 0.04 0
AAGGGCTTGGCTTAATTA 346 0 0 1 0 0 0 0.04 0 AACCCGGAAGGCGGAGGTTGC 347
0 0 0 1 0 0 0 0.04 GG AACCCCACACCAACC 348 0 0 0 1 0 0 0 0.04
AACAAGCTTCTTTGACGTCCCAT 349 0 0 0 1 0 0 0 0.04 CCAC
TCCCCGGCATCTCCACCA 350 116.53 275.18 104.72 59 3.38 9.22 4.11 2.42
CTGATTGCTCCTGTCTGATT 351 0 0 6 1 0 0 0.24 0.04
TCTAGAGGAGCCTGTTCTGTA 352 0 1 3 0 0 0.03 0.12 0
TCGATTCCCGGTCAGGGAACCA 353 0 0 0 4 0 0 0 0.16
ATAGGTTTGGTCCTAGCCTTTCT 354 0 0 3 1 0 0 0.12 0.04
CGTTCGCGCTTTCCCCTG 355 0 1 2 0 0 0.03 0.08 0 TAAGTGTTTGTGGGTTA 356
1 1 0 0 0.03 0.03 0 0 GGCGGCGGGAGACCCA 357 1 1 0 0 0.03 0.03 0 0
CCCCGGCAGGTTTGA 358 0 2 0 0 0 0.07 0 0 TGCCGTGATCGTATAGTGGTTA 359 0
0 1 0 0 0 0.04 0 TCAGACTACTCTCCTCCGCCCATT 360 0 0 1 0 0 0 0.04 0
GGACACAGAGGCTTCG 361 0 1 0 0 0 0.03 0 0
CTGACAGCCGGGGTTTTGGA 362 0 0 0 1 0 0 0 0.04 CGGCGGGGCCTGGAGTCTG 363
1 0 0 0 0.03 0 0 0 CCTGGCTCGCTGCGCCA 364 1 0 0 0 0.03 0 0 0
CCGCCCCACCCCGCGCGC 365 0 1 0 0 0 0.03 0 0 CCCGAACGCTGCCAACCC 366 0
1 0 0 0 0.03 0 0 AGACCCGCGGGCGCTCTCCAGTC 367 0 0 1 0 0 0 0.04 0
CCCCCACAACCGCGCTTGACTA 368 12 11 7 9 0.35 0.37 0.27 0.37 GC
CCCTGCTCGCTGCGCCA 369 7 20 5 1 0.2 0.67 0.2 0.04
CTCCCACTGCTTCACTTGACTAGC 370 2 2 18 9 0.06 0.07 0.71 0.37
CCCATCCTCGTCGCCA 371 16 11 1 1 0.46 0.37 0.04 0.04
TCACGTCGGGGTCACCA 372 16 4 5 1 0.46 0.13 0.2 0.04
TCCCTGGTGGTCTAGTGGTTAG 373 0 1 10 6 0 0.03 0.39 0.25 GATTCG
GGTAGCGTGGCCGAG 374 10 6 0 0 0.29 0.2 0 0 TCCTGCCGCGGTCGCCA 375 6 8
0 1 0.17 0.27 0 0.04 GGAGAGAACGCGGTCTGAGTG 376 3 7 1 0 0.09 0.23
0.04 0 GT TCGGGTGCGAGAGGTCCCGGGT 377 0 0 0 10 0 0 0 0.41
GGCTGGTCCGATGGTAGTGGGTT 378 4 3 3 0 0.12 0.1 0.12 0
CGGAAGCGTGCTGGGCCC 379 1 5 0 4 0.03 0.17 0 0.16 CCCGGGCGGCGCACCA
380 5 4 0 0 0.14 0.13 0 0 GCGGGTGATGCGAACTGGAGTC 381 0 0 6 1 0 0
0.24 0.04 TGAGC GACGAGGTGGCCGAGTGG 382 2 3 2 0 0.06 0.1 0.08 0
GGGGGTGTAGCTCAG 383 4 2 0 0 0.12 0.07 0 0 CTCCTGGCTGGCTCGCCA 384 0
0 3 3 0 0 0.12 0.12 CGGGAGGCCCGGGTT 385 3 3 0 0 0.09 0.1 0 0
GGCTGGTCCGAGTGCAGTGGTG 386 0 1 4 0 0 0.03 0.16 0 TTTA
CTGCTGTGATGACATTC 387 1 2 2 0 0.03 0.07 0.08 0 TGTCACGCGGGAGACC 388
0.5 0 1 1.4 0.01 0 0.04 0.06 TCCTCGTTAGTATAGTGGTGAGT 389 0 1 3 0 0
0.03 0.12 0 ATCCC GGCCGGTTAGCTCAG 390 2 2 0 0 0.06 0.07 0 0
GCATTGGTGGTTCAGTGGTAGA 391 0 0 3 1 0 0 0.12 0.04 CTGTCACGCGGGAGA
392 0.5 0 0 2.6 0.01 0 0 0.11 CTACGGGGATGATTTT 393 3 1 0 0 0.09
0.03 0 0 CCAGGGGCTGAGGGCA 394 1 3 0 0 0.03 0.1 0 0
TTCTCACTACTGCACTTGACTA 395 0 0 2 1 0 0 0.08 0.04 TGGTTATCACGTTCGCC
396 0 2 0 1 0 0.07 0 0.04 TAGGGGTATGATTCTCGCT 397 1 0 0 2 0.03 0 0
0.08 CCACGAGGAAGAGAGGTAGC 398 2 1 0 0 0.06 0.03 0 0
GTCAGGATGGCCGAGCGGTCT 399 0 1 1 0 0 0.03 0.04 0 GGGGATGTAGCTCAG 400
1 1 0 0 0.03 0.03 0 0 GCAGCGATGGCCGAG 401 0 2 0 0 0 0.07 0 0
[0227] Three hundred and thirty five sequences aligned to genomic
regions which did not fulfill the criteria for miRNA precursors
(FIG. 11). About 30% of these non-miRNA sequences were annotated
and may represent degradation products originating from other RNA
species (FIG. 11 and Table 2).
TABLE-US-00018 TABLE 2 Characterization of short-RNA libraries.
Number of non-redundant short-RNAs cloned in each library (naive,
memory, and centroblast B cells, and Ramos cell line) and overall
(Total). RNA species Naive Memory Centroblasts Ramos Total Total
(non redundant) 683 710 744 765 2115 miRNA 498 485 564 590 1453
miRNA other* 5 3 7 4 19 tRNA 27 33 32 29 108 tRNA 61 99 34 16 174
mRNA 76 72 25 34 176 yRNA 11 11 31 21 53 piRNA 46 54 70 62 148
Repeats 1 1 0 1 2 Mitochondrial genome 12 36 54 11 101 Human
viruses 1 4 0 0 5 E. Coli 5 4 0 0 7 Not Annotated 66 64 74 113 262
*miRNA other includes fragments of miRNA precursors, not mature
[0228] Each short-RNA is annotated according to the listed RNA
species. Results shown in Table 2 refer only to short-RNAs with
good-qulaity matches to the human genome. The same short-RNA may
match to multiple databases and therefore the overall sum does not
correspond to the total number of short-RNAs. The databeses used in
the analysis depicted in Table 2 is detailed in the Supplementary
Methods section.
[0229] The remaining (236 sequences), however, mapped to genomic
regions that lack annotations and may therefore represent a part of
the transcriptome whose functions are unknown (Table 3A-3B and
Table 4A-4B).
TABLE-US-00019 TABLE 3A List of short-RNA lacking genomic locations
with appropriate RNA secondary structures to be defined miRNAs. SEQ
ID ID NO: Short-RNA sequence Annotations CU-5016 402
AATGACACGATCACTCCCGTTGAG Mature:hsa-miR-425:MIMAT0003393 CU-5019
403 GGAGGGGGGGTAAAAAAAA NEW CU-5020 404 CCCCGGCATCTCCACC NEW
CU-5004 405 GAAGCGGGTGCTCTTATTTT NEW CU-5021 406 ACCGGGCGGAAACACCA
NEW CU-5022 407 TCCCGGGTTCAAATCCCGGACGAGCCCCCA NEW CU-5008 408
GTGTAAGCAGGGTCGTTTT NEW CU-6003 409 ATCCCACCGCTGCTACCA NEW CU-5023
410 GGGAAGGTGACCTGAC NEW CU-5007 411 CTCCCGCCTTTTTTCCC NEW CU-5024
412 CGGAGCAAGAGCGT NEW CU-5025 413 CCCCGTACTGGCCACCA NEW CU-5026
414 CCCCCGGCACCATCAATA NEW CU-5027 415 CAGCCTAGCCCCTACCC NEW
CU-5005 416 CAGAAGGTCTCACTTTT NEW CU-5006 417 AGTATTCTCTGTGGCTTT
NEW CU-5028 418 TGGAGTGACTATATGGATGCCCCC NEW CU-5029 419
TCTGATAGCTTACTTT NEW CU-5030 420 TCGAGCCCCAGTGGAACCAC NEW CU-5031
421 TCGAATCCTGTTCGTGACGCCA NEW CU-5032 422
TCCTCCCCACACTCATCGCCCTTACCA NEW CU-5033 423 TATACTACAAGGACACCA NEW
CU-5034 424 TAGTGGGTGAAAAAAAAAAAA NEW CU-5035 425
TACCACACATTCGAAGAACCCGTA NEW CU-5036 426 TACAAAACCCACCCCATTCCTCCCCA
NEW CU-5037 427 GCCCTCCTAATGACCTCC NEW CU-5038 428
CTTCCCTCTACACTTATCATC NEW CU-5039 429 CGGGCGGCCTGCGCTCTCA NEW
CU-5040 430 CCCGAGGCCGTGTGCAAATGCAT NEW CU-5041 431
CCCCCAGTACCTCCACCA NEW CU-5042 432 CCCCCACTGCTAAACTTGACTGGCTTT NEW
CU-5043 433 CCCACTCCACCTTACTACCA NEW CU-5044 434
CCCAAGAACAGGGTGACCA NEW CU-5045 435 CCAGTCGCGGCCAAATCA NEW CU-5046
436 CCAGCTTCACCAAGGTATTGGTTA NEW CU-5047 437 CCAGAAAAAACAGGCCTC NEW
CU-5048 438 CATCATAATCGGAGGCTTTGGCAAC NEW CU-5049 439
CAGCAGGGGTAATAAGTGAAATCAAA NEW CU-5050 440
CAATGGTGCAGCCGCTATTAAAGGTTCA NEW CU-5051 441 CAACTCCTACATACTTCCCCC
NEW CU-5052 442 ATTCAAAAAAGAGTACCA NEW CU-5053 443
ATGCATCTCATATGCGAATAGGAATGC NEW CU-5054 444 ATCCCACTTCTGTACCA NEW
CU-5055 445 ATAACACTAGAAAGTTGGGGCAGATTGC NEW CU-5056 446
ACGTGGGCACATTACCCGTCTGACCTGA NEW CU-5057 447 ACCCCTTATTAACCCA NEW
CU-5058 448 ACAAGGCACACCTACACCCCTTATCCC NEW CU-5059 449
AAAAGACACCCCCCCACCA NEW CU-5060 450 AAAACCCCTACGCATTTATAT NEW
CU-5061 451 AAAAAGACACCCCCCACCA NEW CU-5003 452 ACCCCACTCCTGGTACCA
refseqGeneIntron-annotate CU-5009 453 TGCCCCCATGTCTAACAACATGGCTA
refseqGeneIntron-annotate; rnaGene-annotate CU-5013 454
GGCCGGTGATGAGAACT mRNAall-annotate; refseqGeneIntron-annotate;
wgRNA-annotate; snoRNA-annotate CU-5062 455 CCCCGCCTGTTTACC
refseqGeneIntron-annotate CU-5063 456 CCCACTTCTGACACCA
computGene-annotate; refseqGeneIntron-annotate; exEID-annotate
CU-5064 457 CACCACCTCTTGCTCAGCC mRNA-annotate;
refseqGeneIntron-annotate CU-5014 458 CTGGAAAGTGCACTTGGACGAACA
refseqGeneIntron-annotate CU-5065 459 TGACCGCTCTGACCAC
refseqGeneIntron-annotate CU-5066 460 TGAAGTCCCTTTGCTTTGTT
refseqGeneIntron-annotate CU-5067 461 TGAACACACAATAGCTAAGACCC
mRNA-annotate; refseqGeneIntron-annotate CU-5068 462
TCGCCTTACCCCCCACTA refseqGeneIntron-annotate CU-5069 463
TCGATAAACCCCGATCAACCT mRNA-annotate; refseqGeneIntron-annotate
CU-5070 464 TCCCCGTCACCTCCACCA refseqGeneIntron-annotate CU-5071
465 TCCCCGGCACTCCACCA refseqGeneIntron-annotate CU-5072 466
TCCCCCCGCTGCCACCA refseqGeneIntron-annotate CU-5073 467
TCCCCCCCATCTCCACCA refseqGeneIntron-annotate CU-5074 468
TACACACCGCCCGTCACCC mRNA-annotate; refseqGeneIntron-annotate
CU-5075 469 GGCCGGTGATGAGAACTTCTCCC mRNAall-annotate;
refseqGeneIntron-annotate; wgRNA-annotate; snoRNA-annotate CU-5076
470 GCTTAGCCTAGCCACACCCCCACG mRNA-annotate;
refseqGeneIntron-annotate CU-5077 471 GCTCGCCAGAACACTACGA
mRNA-annotate; refseqGeneIntron-annotate CU-5078 472
GCCGGGGGGCGGGCGCA refseqGeneIntron-annotate CU-5079 473
GAACCGGGCGGGAACACCA refseqGeneIntron-annotate CU-5080 474
CGCCGCAGTACTGATCATTC refseqGeneIntron-annotate CU-5081 475
CCGCACCAATAGGATCCTCC refseqGeneIntron-annotate CU-5082 476
CCCGGCCGACGCACCA refseqGeneIntron-annotate CU-5083 477
CCACCCCATCATACTCTTTC refseqGeneIntron-annotate CU-5084 478
CACCCCCCAGCTCCTCCTTT refseqGeneIntron-annotate CU-5085 479
ATAAGTAACATGAAAACATTCTCCTC refseqGeneIntron-annotate CU-5086 480
ACTGCTCGCCAGAACAC mRNA-annotate; refseqGeneIntron-annotate CU-5087
481 ACCCTGGTGTGGGATCTGCCCGATC refseqGeneIntron-annotate CU-5088 482
AACCTCACCACCTCTTTCT refseqGeneIntron-annotate CU-5089 483
AAAAGACACCCCCCACACCA refseqGeneIntron-annotate CU-5011 484
GCTAAACCTAGCCCCAAACCC piRNA-annotate CU-5010 485 GGCCGTGATCGTATA
piRNA-annotate CU-5090 486 TGGGATGCGAGAGGTCCCGGGT rnaGene-annotate
CU-5091 487 CTGAACTCCTCACACCC piRNA-annotate CU-5092 488
ATTAATCCCCTGGCCCAACCCG computGene-annotate CU-5093 489
AGCCCCAAACCCACTCCAC piRNA-annotate CU-5094 490 CGCGACCTCAGATCAGAC
rRNA-eliminate; piRNA-annotate; refseqGeneIntron-annotate CU-5015
491 TCAAGTGATGTCATCTTACTACTGAGA mRNAall-annotate; snoRNA-annotate;
snoRNA-eliminate; wgRNA- annotate; rnaGene-annotate CU-5095 492
TTGGGTGCGAGAGGTCCCGGGT tRNAcomputational-annotate; tRNA-eliminate;
HStRNA-eliminate; rnaGene-annotate CU-5096 493 TCTCGGTGGGACCTCCA
refseqGeneExon-eliminate CU-5097 494 CCGCCCCCCGTTCCCCC
rRNA-eliminate CU-5098 495 CCCACTGCTAAATTTGACTGGCTT
mRNAall-annotate; yRNA-eliminate; refseqGeneIntron-annotate;
rnaGene-annotate CU-5099 496 ACAGACCAAGAGCCTTC tRNA-eliminate;
rnaGene-annotate CU-5100 497 TGTAGTAGTCAATTAATGGATATTA
refseqGeneExon-eliminate CU-5101 498 TGGTTATCACGTTCGCCTCACACGCGA
tRNAcomputational-annotate; tRNA-eliminate; HStRNA-eliminate;
rnaGene-annotate CU-5102 499 TGGGAATACCGGGTG rRNA-eliminate;
rnaGene-annotate; piRNA-annotate; refseqGeneIntron-annotate CU-5103
500 TGGCGGCCAAGCGTTCATAGCGACGTC rRNA-eliminate;
refseqGeneIntron-annotate; rnaGene-annotate CU-5104 501
TCGTCATCCAGCTAAGGGCTCAGA mRNAall-annotate;
refseqGeneExon-eliminate; exEID-annotate CU-5105 502
TCGCCTGCCACGCGGGAGGCCCGGGT rnaGene-annotate;
tRNAcomputational-annotate; tRNA- eliminate;
refseqGeneIntron-annotate; mRNA-annotate; HStRNA-eliminate CU-5106
503 TCCCACTGCTTCACTTGA yRNA-eliminate; refseqGeneIntron-annotate;
rnaGene-annotate CU-5107 504 GTTTAGACGGGCTCACATCACCCCA
tRNA-eliminate; piRNA-annotate; refseqGeneIntron-annotate CU-5108
505 GCTAACTCATGCCCCCATGTC tRNA-eliminate;
refseqGeneIntron-annotate; rnaGene-annotate CU-5109 506
GACTGTGGTGGTTGAATATA mRNAall-annotate; computGene-annotate;
refseqGeneExon-eliminate; exEID-annotate CU-5110 507
CGCGACCTCAGATCAGACGTGGCGACC rRNA-eliminate; piRNA-annotate;
refseqGeneIntron-annotate CU-5111 508 CGCCGCCGCCCCCCC
mRNAall-annotate; refseqGeneExon-eliminate;
refseqGeneIntron-annotate; exEID-annotate CU-5112 509
CGCCCGACTACCACCACATCCA mRNAall-annotate; computGene-annotate;
refseqGeneExon-eliminate; exEID-annotate CU-5113 510
CCCCCCTCCACGCGCCC rRNA-eliminate; refseqGeneIntron-annotate CU-5114
511 CCCCACCCCGCGCCCTC rRNA-eliminate; refseqGeneIntron-annotate
CU-5115 512 CAGAGTGTAGCTTAACACAAAGCACCCAA tRNA-eliminate;
piRNA-annotate; rnaGene-annotate CU-5116 513
CAATCTTGGCATGTTGGTCTGGTCACCCA mRNAall-annotate;
refseqGeneExon-eliminate; exEID-annotate CU-5117 514
CAAAGCATCGCGAAGGCCC mRNAall-annotate; rRNA-eliminate;
piRNA-annotate; rnaGene-annotate CU-5118 515
AACACCCTGATTGCTCCTGTCTGAT mRNAall-annotate; exEID-annotate;
snoRNA-annotate; refseqGeneExon-eliminate; rnaGene-annotate;
snoRNA-eliminate; wgRNA-annotate CU-5119 516
AAAAAGGGCCTAAAGAAGATGCA mRNAall-annotate; computGene-annotate;
refseqGeneExon- eliminate; refseqGeneIntron-annotate;
exEID-annotate
TABLE-US-00020 TABLE 3B List of short-RNA lacking genomic locations
with appropriate RNA secondary structures to be defined miRNAs
including information on frequencies. Corrected Counts Frequencies
SEQ ID Naive Memory Centroblasts Ramos Naive Memory Centroblasts
Ramos NO: Short-RNA sequence (N) (M) (CB) (RA) (N) (M) (CB) (RA)
525 AATGACACGATCACTCCCG 0 0 7 0 0 0 3.98 0 TTGAG 526
GGAGGGGGGGTAAAAAAAA 0 0 1 0 0 0 0.57 0 527 CCCCGGCATCTCCACC 1 0 0 0
1.72 0 0 0 528 GAAGCGGGTGCTCTTATTTT 5 23 25 224 8.62 20.35 14.2
65.31 529 ACCGGGCGGAAACACCA 9 14 60 20 15.52 12.39 34.09 5.83 530
TCCCGGGTTCAAATCCCGG 0 0 4 37 0 0 2.27 10.79 ACGAGCCCCCA 531
GTGTAAGCAGGGTCGTTTT 0 0 0 7 0 0 0 2.04 532 ATCCCACCGCTGCTACCA 0 1 0
2 0 0.88 0 0.58 533 GGGAAGGTGACCTGAC 2 0 0 0 3.45 0 0 0 534
CTCCCGCCTTTTTTCCC 0 2 0 0 0 1.77 0 0 535 CGGAGCAAGAGCGT 2 0 0 0
3.45 0 0 0 536 CCCCGTACTGGCCACCA 2 0 0 0 3.45 0 0 0 537
CCCCCGGCACCATCAATA 0 0 1 1 0 0 0.57 0.29 538 CAGCCTAGCCCCTACCC 0 2
0 0 0 1.77 0 0 539 CAGAAGGTCTCACTTTT 0 1 0 1 0 0.88 0 0.29 540
AGTATTCTCTGTGGCTTT 0 0 0 2 0 0 0 0.58 541 TGGAGTGACTATATGGATG 0 0 1
0 0 0 0.57 0 CCCCC 542 TCTGATAGCTTACTTT 0 1 0 0 0 0.88 0 0 543
TCGAGCCCCAGTGGAACCAC 0 0 1 0 0 0 0.57 0 544 TCGAATCCTGTTCGTGACG 0 0
0 1 0 0 0 0.29 CCA 545 TCCTCCCCACACTCATCGC 0 0 1 0 0 0 0.57 0
CCTTACCA 546 TATACTACAAGGACACCA 0 0 0 1 0 0 0 0.29 547
TAGTGGGTGAAAAAAAAAA 0 0 0 1 0 0 0 0.29 AA 548 TACCACACATTCGAAGAAC 0
0 1 0 0 0 0.57 0 CCGTA 549 TACAAAACCCACCCCATTC 0 1 0 0 0 0.88 0 0
CTCCCCA 550 GCCCTCCTAATGACCTCC 0 0 1 0 0 0 0.57 0 551
CTTCCCTCTACACTTATCATC 0 0 1 0 0 0 0.57 0 552 CGGGCGGCCTGCGCTCTCA 1
0 0 0 1.72 0 0 0 553 CCCGAGGCCGTGTGCAAAT 0 0 1 0 0 0 0.57 0 GCAT
554 CCCCCAGTACCTCCACCA 0 1 0 0 0 0.88 0 0 555 CCCCCACTGCTAAACTTGA 0
0 1 0 0 0 0.57 0 CTGGCTTT 556 CCCACTCCACCTTACTACCA 0 0 0 1 0 0 0
0.29 557 CCCAAGAACAGGGTGACCA 0 0 0 1 0 0 0 0.29 558
CCAGTCGCGGCCAAATCA 0 1 0 0 0 0.88 0 0 559 CCAGCTTCACCAAGGTATT 0 0 1
0 0 0 0.57 0 GGTTA 560 CCAGAAAAAACAGGCCTC 0 0 0 1 0 0 0 0.29 561
CATCATAATCGGAGGCTTT 0 0 1 0 0 0 0.57 0 GGCAAC 562
CAGCAGGGGTAATAAGTGA 0 0 1 0 0 0 0.57 0 AATCAAA 563
CAATGGTGCAGCCGCTATT 0 0 0 1 0 0 0 0.29 AAAGGTTCA 564
CAACTCCTACATACTTCCC 1 0 0 0 1.72 0 0 0 CC 565 ATTCAAAAAAGAGTACCA 0
0 1 0 0 0 0.57 0 566 ATGCATCTCATATGCGAAT 0 0 1 0 0 0 0.57 0
AGGAATGC 567 ATCCCACTTCTGTACCA 0 1 0 0 0 0.88 0 0 568
ATAACACTAGAAAGTTGGG 0 0 1 0 0 0 0.57 0 GCAGATTGC 569
ACGTGGGCACATTACCCGT 0 0 0 1 0 0 0 0.29 CTGACCTGA 570
ACCCCTTATTAACCCA 0 1 0 0 0 0.88 0 0 571 ACAAGGCACACCTACACCC 0 0 1 0
0 0 0.57 0 CTTATCCC 572 AAAAGACACCCCCCCACCA 0 0 0 1 0 0 0 0.29 573
AAAACCCCTACGCATTTATAT 0 0 1 0 0 0 0.57 0 574 AAAAAGACACCCCCCACCA 0
0 0 1 0 0 0 0.29 575 ACCCCACTCCTGGTACCA 1 11 5 6 1.72 9.73 2.84
1.75 576 TGCCCCCATGTCTAACAAC 7 4 1 1 12.07 3.54 0.57 0.29 ATGGCTA
577 GGCCGGTGATGAGAACT 4 3 0 0 6.9 2.65 0 0 578 CCCCGCCTGTTTACC 0 5
2 0 0 4.42 1.14 0 579 CCCACTTCTGACACCA 3 4 0 0 5.17 3.54 0 0 580
CACCACCTCTTGCTCAGCC 1 3 0 0 1.72 2.65 0 0 581 CTGGAAAGTGCACTTGGAC 0
2 0 0 0 1.77 0 0 GAACA 582 TGACCGCTCTGACCAC 0 1 0 0 0 0.88 0 0 583
TGAAGTCCCTTTGCTTTGTT 1 0 0 0 1.72 0 0 0 584 TGAACACACAATAGCTAAG 0 0
1 0 0 0 0.57 0 ACCC 585 TCGCCTTACCCCCCACTA 0 1 0 0 0 0.88 0 0 586
TCGATAAACCCCGATCAAC 0 0 1 0 0 0 0.57 0 CT 587 TCCCCGTCACCTCCACCA 0
0 1 0 0 0 0.57 0 588 TCCCCGGCACTCCACCA 0 0 1 0 0 0 0.57 0 589
TCCCCCCGCTGCCACCA 1 0 0 0 1.72 0 0 0 590 TCCCCCCCATCTCCACCA 0 0 1 0
0 0 0.57 0 591 TACACACCGCCCGTCACCC 0 0 1 0 0 0 0.57 0 592
GGCCGGTGATGAGAACTTC 1 0 0 0 1.72 0 0 0 TCCC 593 GCTTAGCCTAGCCACACCC
0 0 1 0 0 0 0.57 0 CCACG 594 GCTCGCCAGAACACTACGA 0 0 1 0 0 0 0.57 0
595 GCCGGGGGGCGGGCGCA 0 1 0 0 0 0.88 0 0 596 GAACCGGGCGGGAACACCA 0
0 0 1 0 0 0 0.29 597 CGCCGCAGTACTGATCATTC 0 0 1 0 0 0 0.57 0 598
CCGCACCAATAGGATCCTCC 0 1 0 0 0 0.88 0 0 599 CCCGGCCGACGCACCA 1 0 0
0 1.72 0 0 0 600 CCACCCCATCATACTCTTTC 0 0 1 0 0 0 0.57 0 601
CACCCCCCAGCTCCTCCTTT 1 0 0 0 1.72 0 0 0 602 ATAAGTAACATGAAAACATT 0
0 1 0 0 0 0.57 0 CTCCTC 603 ACTGCTCGCCAGAACAC 0 0 1 0 0 0 0.57 0
604 ACCCTGGTGTGGGATCTGC 0 0 1 0 0 0 0.57 0 CCGATC 605
AACCTCACCACCTCTTTCT 0 0 1 0 0 0 0.57 0 606 AAAAGACACCCCCCACACCA 0 0
0 1 0 0 0 0.29 607 GCTAAACCTAGCCCCAAAC 9 16 13 18 15.52 14.16 7.39
5.25 CC 608 GGCCGTGATCGTATA 2 0 0 0 3.45 0 0 0 609
TGGGATGCGAGAGGTCCC 0 0 0 1 0 0 0 0.29 GGGT 610 CTGAACTCCTCACACCC 0
1 0 0 0 0.88 0 0 611 ATTAATCCCCTGGCCCAAC 0 0 0 1 0 0 0 0.29 CCG 612
AGCCCCAAACCCACTCCAC 0 0 1 0 0 0 0.57 0 613 CGCGACCTCAGATCAGAC 1 5 8
1 1.72 4.42 4.55 0.29 614 TCAAGTGATGTCATCTTACT 0 0 3 1 0 0 1.7 0.29
ACTGAGA 615 TTGGGTGCGAGAGGTCCC 0 0 0 3 0 0 0 0.87 GGGT 616
TCTCGGTGGGACCTCCA 0 2 0 0 0 1.77 0 0 617 CCGCCCCCCGTTCCCCC 1 1 0 0
1.72 0.88 0 0 618 CCCACTGCTAAATTTGACT 0 0 1 1 0 0 0.57 0.29 GGCTT
619 ACAGACCAAGAGCCTTC 0 0 2 0 0 0 1.14 0 620 TGTAGTAGTCAATTAATGG 0
0 1 0 0 0 0.57 0 ATATTA 621 TGGTTATCACGTTCGCCTC 0 0 0 1 0 0 0 0.29
ACACGCGA 622 TGGGAATACCGGGTG 0 0 1 0 0 0 0.57 0 623
TGGCGGCCAAGCGTTCATA 0 0 0 1 0 0 0 0.29 GCGACGTC 624
TCGTCATCCAGCTAAGGGC 0 0 1 0 0 0 0.57 0 TCAGA 625 TCGCCTGCCACGCGGGAG
0 0 1 0 0 0 0.57 0 GCCCGGGT 626 TCCCACTGCTTCACTTGA 0 0 0 1 0 0 0
0.29
627 GTTTAGACGGGCTCACATC 0 0 1 0 0 0 0.57 0 ACCCCA 628
GCTAACTCATGCCCCCATG 0 0 1 0 0 0 0.57 0 TC 629 GACTGTGGTGGTTGAATATA
0 0 0 1 0 0 0 0.29 630 CGCGACCTCAGATCAGACG 0 0 1 0 0 0 0.57 0
TGGCGACC 631 CGCCGCCGCCCCCCC 0 1 0 0 0 0.88 0 0 632
CGCCCGACTACCACCACAT 1 0 0 0 1.72 0 0 0 CCA 633 CCCCCCTCCACGCGCCC 0
1 0 0 0 0.88 0 0 634 CCCCACCCCGCGCCCTC 0 1 0 0 0 0.88 0 0 635
CAGAGTGTAGCTTAACACA 0 0 1 0 0 0 0.57 0 AAGCACCCAA 636
CAATCTTGGCATGTTGGTC 0 0 1 0 0 0 0.57 0 TGGTCACCCA 637
CAAAGCATCGCGAAGGCCC 0 0 1 0 0 0 0.57 0 638 AACACCCTGATTGCTCCTG 0 0
1 0 0 0 0.57 0 TCTGAT 639 AAAAAGGGCCTAAAGAAGA 0 0 1 0 0 0 0.57 0
TGCA
TABLE-US-00021 TABLE 4A List of short-RNA consensus with maximum 1
mismatch to the human genome. SEQ ID ID NO: Short-RNA sequence
Annotations CU-6232 640 TGGCTCAGTTCAGCAGGAACAGT
Mature:hsa-miR-24:MIMAT0000080 CU-6180 641 GTGGGGGAGAGGCTGTCGA
Mature:hsa-miR-1275:MIMAT0005929 CU-6130 642 CGGGGCAGCTCAGTACAGGATT
Mature:hsa-miR-486-3p:MIMAT0004762 CU-6044 643
AATTGCACGGTATCCATCTGTAT Mature:hsa-miR-363:MIMAT0000707 CU-6133 644
CGGGGGAGCGCCGCGTA NEW CU-6215 645 TCGATCCCGGGTTTCGGCACCA NEW
CU-6072 646 ATCGTATCCCACTTCTGACACCA NEW CU-6030 647
ATCCTGCCGACTACGCCA NEW CU-6210 648 TCGAATCCCACTCCTGACACCA NEW
CU-6069 649 ATCCCATCCTCGTCGCCA NEW CU-6216 650
TCGATTCCCCGACGGGGAGCCA NEW CU-6071 651 ATCCGGGTGCCCCCTCCA NEW
CU-6202 652 TCCCGGGCGGCGCACCA NEW CU-6066 653 ATCCCACCAGAGTCGCCA
NEW CU-6192 654 TCAAATCACGTCGGGGTCACCA NEW CU-6239 655
TGTCAGTTTGTTAATTGACCCAA NEW CU-6214 656 TCGATCCCCGTACGGGCCACCA NEW
CU-6213 657 TCGAGCCTCACCTGGAGCACCA NEW CU-6206 658
TCCGGCTCGAAGGACCA NEW CU-6006 659 GGCAATACGAGCACCCTG NEW CU-6004
660 CCGGGGCGTCTCGTAC NEW CU-6056 661 AGCGGCTGTGCACAAA NEW CU-6242
662 TGTCAGTTTGTTTAATCCAA NEW CU-6241 663 TGTCAGTTTGTTATTACCAA NEW
CU-6237 664 TGTCAGGCACCATCAATAA NEW CU-6225 665
TGATCTTGACACTTAAAGCC NEW CU-6219 666 TCGTAGGCACCATCAAT NEW CU-6211
667 TCGACTCCCGGTATGGGAACCA NEW CU-6187 668 TAGGGAGGTTATGATTAACTTTT
NEW CU-6183 669 TAAAGTGCTTAGTGCAGGTA NEW CU-6181 670
GTTTATGTTGCTTACCTCC NEW CU-6176 671 GTAGATAAAATATTGGCG NEW CU-6163
672 GGCGGGGACGACGTCAG NEW CU-6162 673 GGCGGCGTCGCGGCGGGTC NEW
CU-6161 674 GGAGGGGGTGAACAAAAAGAAAAA NEW CU-6159 675
GCTAAACCTAGCCCCAAACCCACTCCACA NEW CU-6142 676 CTGGATAGCGCACTTCGTT
NEW CU-6129 677 CGGGCGAGGGGCGGACGTTCG NEW CU-6123 678
CGGACCTATACCGGA NEW CU-6096 679 CCCCGGGTTCAATCCCCGGCACCTCCAC NEW CA
CU-6088 680 CCCCCCACAACCGCGAA NEW CU-6087 681 CCCAGCATCTCCTGTGTTTA
NEW CU-6086 682 CCCACGTTGGGACGCCA NEW CU-6064 683
ATCACGTCCGTGCCTCCA NEW CU-6063 684 ATAGCAATGTCAGCAGTACCT NEW
CU-6051 685 ACCCTGCTCGCTGCGCCA refseqGeneIntron-annotate CU-6198
686 TCCCACCCAGGGACGCCA refseqGeneIntron-annotate CU-6218 687
TCGTAGGCACATCAATA refseqGeneIntron-annotate CU-6007 688
CCCCCACAACCGCGTA refseqGeneIntron-annotate CU-6001 689
ACCCCGTCCGTGCCTCCA refseqGeneIntron-annotate CU-6039 690
AAAAAAGACACCCCCCACA refseqGeneIntron-annotate CU-6005 691
TGTCAGTTTGTTAACCCAA refseqGeneIntron-annotate CU-6204 692
TCCCTGTGGTCTAGTGGTTAGG refseqGeneIntron-annotate CU-6172 693
GGGGGGGTAAAAAAA refseqGeneIntron-annotate CU-6171 694
GGGGGGGGAAAAAAAA refseqGeneIntron-annotate CU-6128 695
CGGGCCCGGGTCTTCCC refseqGeneIntron-annotate CU-6002 696
CCGCCCCCCGTTCCCCCCA refseqGeneIntron-annotate CU-6050 697
ACCCCCGGCTCCTCCACCA refseqGeneIntron-annotate CU-6244 698
TTTGGTGGAAATTTTTTGA refseqGeneIntron-annotate CU-6240 699
TGTCAGTTTGTTATACCAA refseqGeneIntron-annotate CU-6238 700
TGTCAGTTTGTAATTATCCCAA refseqGeneIntron-annotate CU-6236 701
TGTCAATTTTTAACCCAA refseqGeneIntron-annotate CU-6227 702
TGCTAGGGTAAAAAAAAAA refseqGeneIntron-annotate CU-6226 703
TGCAACTCCAAATAAAAGTACCA refseqGeneIntron-annotate CU-6224 704
TGAGGTAACGGGGAATTA refseqGeneIntron-annotate CU-6209 705
TCCTCGGCATCTCCACCA refseqGeneIntron-annotate CU-6197 706
TCATATGAAGTCACCCTAGCCATC mitochondrion-annotate;
refseqGeneIntron-annotate CU-6196 707 TCAGTTTGTTTATTAACCCAA
refseqGeneIntron-annotate CU-6195 708 TCAGCGTGTCTTTGCCCT
refseqGeneIntron-annotate CU-6194 709 TCACTGGTGGTCTAGTGGT
refseqGeneIntron-annotate; rnaGene-annotate CU-6193 710
TCACAATGCTGCCACCA refseqGeneIntron-annotate CU-6189 711
TAGTTGTTAATTAACCCAA refseqGeneIntron-annotate CU-6188 712
TAGTCCTCATCGCCCTCC mitochondrion-annotate;
refseqGeneIntron-annotate CU-6184 713 TAAAGTGCTTATAGTGCGGGTAA
refseqGeneIntron-annotate CU-6179 714 GTCCCACCAGAGTCGCCA
refseqGeneIntron-annotate CU-6170 715 GGGGGAGGGGCCAAAAAAA
refseqGeneIntron-annotate CU-6167 716 GGGACGCCGCGGTGTCG
refseqGeneIntron-annotate CU-6166 717 GGGAATACCGGGTGCTTTAGGCTT
refseqGeneIntron-annotate; rnaGene-annotate CU-6160 718
GGAAGAAGGTGGTGGTATA refseqGeneIntron-annotate CU-6156 719
GCGGTGAAATGCGTA computGene-annotate; Ecoli-annotate;
refseqGeneIntron- annotate CU-6154 720 GCGGGGAAGGTGGCAAA
refseqGeneIntron-annotate CU-6152 721 GCGACGACCTCGCGCCCACCTGGTCA
refseqGeneIntron-annotate CU-6151 722 GCCACCCGATACTGCTGT
refseqGeneIntron-annotate CU-6150 723 GATGTATGCTTTGTTTCTGTT
refseqGeneIntron-annotate CU-6148 724 GAGGGGGATTTAGAAAAAAA
refseqGeneIntron-annotate CU-6147 725 GAAGGAAAGTTCTATAGT
refseqGeneIntron-annotate CU-6146 726 GAAGCGGCTCTCTTATTT
refseqGeneIntron-annotate CU-6145 727 GAACGAGACTCTGGCATGCTGA
refseqGeneIntron-annotate; rnaGene-annotate CU-6143 728
CTGGTAGGCCCATCAAT refseqGeneIntron-annotate CU-6132 729
CGGGGCCGATCGCGCGC computGene-annotate; refseqGeneIntron-annotate
CU-6125 730 CGGCCCCGGGTTCCTCCC computGene-annotate;
refseqGeneIntron-annotate CU-6118 731 CGAGCCCGGTTAGTA
refseqGeneIntron-annotate; rnaGene-annotate CU-6117 732
CGACTCTTAGCGGTGGA piRNA-annotate; refseqGeneIntron-annotate CU-6116
733 CGAATCCCACTTCTGACACCA refseqGeneIntron-annotate CU-6113 734
CGAAAGGGAATCGGGTC refseqGeneIntron-annotate CU-6112 735
CCTTAGGTCGCTGGTAAA refseqGeneIntron-annotate CU-6108 736
CCGTGCGAGAATACCA refseqGeneIntron-annotate CU-6107 737
CCGGTCTCTCAAGCGGCC refseqGeneIntron-annotate CU-6099 738
CCCGGCCCTCGCGCGTCC computGene-annotate; refseqGeneIntron-annotate
CU-6094 739 CCCCGGCATTTCCACCA computGene-annotate;
refseqGeneIntron-annotate CU-6090 740 CCCCCCCGGCTCCTCCACCA
refseqGeneIntron-annotate CU-6089 741 CCCCCCACAACCGCTA
refseqGeneIntron-annotate CU-6085 742 CCCAAGTATTGACTCACCC
mitochondrion-annotate; refseqGeneIntron-annotate CU-6084 743
CCAGTAAGCGCGAGTC refseqGeneIntron-annotate CU-6082 744
CCAAAGAAAGCACGTAGAG refseqGeneIntron-annotate CU-6081 745
CATGTTTAACGGCCGCGGT mitochondrion-annotate;
refseqGeneIntron-annotate CU-6080 746 CAGTTTGTAATTAACCCAA
refseqGeneIntron-annotate CU-6079 747 CAGGAACGGCGCACCA
computGene-annotate; refseqGeneIntron-annotate CU-6078 748
CAGAACCCTCTAAATCCCC mitochondrion-annotate;
refseqGeneIntron-annotate CU-6076 749 CACCCGGCTGTGTGCACATGTGT
miRBASE-annotate; computGene-annotate; refseqGeneIntron- annotate;
wgRNA-annotate CU-6075 750 CAATTGGACCAATCTATC
mitochondrion-annotate; refseqGeneIntron-annotate CU-6074 751
ATTCCTGTACTGCGATA refseqGeneIntron-annotate CU-6070 752
ATCCCTGCGGCGTCTCCA refseqGeneIntron-annotate
CU-6067 753 ATCCCACCGCTGCCATCA refseqGeneIntron-annotate CU-6062
754 AGTCAATAGAAGCCGGCGTA mitochondrion-annotate;
refseqGeneIntron-annotate CU-6061 755 AGGTTCGTTTGTAAAAA
refseqGeneIntron-annotate CU-6060 756 AGGTCCTGGGTTTAAGTGT
computGene-annotate; refseqGeneIntron-annotate CU-6058 757
AGGGGGAAGTTCTATAGTC refseqGeneIntron-annotate CU-6057 758
AGGCTGTGATGCTCTCNTGAGCCCT refseqGeneIntron-annotate CU-6055 759
AGCCCCTCTCCGGCCCTTA refseqGeneIntron-annotate CU-6054 760
ACTACCACCTACCTCCC mitochondrion-annotate; refseqGeneIntron-annotate
CU-6052 761 ACGCCCTTCCCCCCCTTCTTT miRBASE-annotate;
refseqGeneIntron-annotate CU-6049 762 ACCCCACTCCTGGTGCAC
refseqGeneIntron-annotate CU-6048 763 ACCACCTGATCCCTTCCC
refseqGeneIntron-annotate CU-6047 764 ACAGCTAAGCACCCACCA
refseqGeneIntron-annotate CU-6045 765 ACACATGTTTAACGGCC
mitochondrion-annotate; refseqGeneIntron-annotate CU-6043 766
AATTAGGGACCTGTATG refseqGeneIntron-annotate CU-6042 767
AATGGCCCATTTGGGCAAACA computGene-annotate;
refseqGeneIntron-annotate CU-6041 768 AAAGCGGCTGTGCAAACA
refseqGeneIntron-annotate CU-6212 769 TCGACTCCTGGCTGGCTCGCCA
wgRNA-annotate CU-6200 770 TCCCCGGCATCTCCACCAA computGene-annotate
CU-6157 771 GCGGTGGATCACTCGGCTCGTGCGT rnaGene-annotate CU-6105 772
CCGGGTGTTGTAGA mRNAall-annotate; exEID-annotate CU-6235 773
TGTAGCGTGGCCGAGCGGT rnaGene-annotate CU-6234 774
TGGGGCGACCTCGGAGCAG mitochondrion-annotate CU-6230 775
TGGCGTCCTAAGCCAGGGATTGTGGGT rnaGene-annotate CU-6229 776
TGGCAGGGGAGATACCATGATTT rnaGene-annotate CU-6222 777
TCTGATCAGGGTGAGCATC mitochondrion-annotate CU-6220 778
TCGTAGGCACCATCCAT computGene-annotate CU-6165 779
GGGAAACGGGGCGCGGCTG rnaGene-annotate CU-6137 780
CTACTCCTGCTCGCATCTGCTATA mitochondrion-annotate CU-6135 781
CGGGTGGGTTTTTACCGG computGene-annotate CU-6120 782
CGAGGAATTCCCAGTAAG rnaGene-annotate CU-6115 783 CGAACGCACTTGCGGCCCC
rnaGene-annotate CU-6093 784 CCCCGCGCGGGTTCGAATC rnaGene-annotate
CU-6059 785 AGGGGTATGATTCCCGCTT rnaGene-annotate CU-6131 786
CGGGGCCACGCGCGCGTC mRNA-annotate; rRNA-eliminate CU-6032 787
TGGCGCTGCGGGATGAAC rRNA-eliminate; refseqGeneIntron-annotate;
rnaGene-annotate CU-1153 788 CCCCCCACTGCTAAATTTGACTGGCTT
yRNA-eliminate; refseqGeneIntron-annotate; rnaGene-annotate CU-6182
789 TAAAGGTTCGTTTGTAAAA computGene-annotate;
refseqGeneExon-eliminate CU-6033 790 CGGGGCCGAGGGAGCGA
rRNA-eliminate; refseqGeneExon-eliminate; refseqGeneIntron-
annotate CU-6174 791 GGGTTAGGCCTCTTTT tRNA-eliminate;
rnaGene-annotate CU-6141 792 CTGCGGAAGGATCATTA rRNA-eliminate;
rnaGene-annotate CU-6101 793 CCCTACCCCCCCGG rRNA-eliminate;
refseqGeneIntron-annotate CU-6034 794 CCCGCCGGGTCCGCCC
computGene-annotate; rRNA-eliminate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate; rnaGene-annotate CU-6035 795
CCCCGCGCCCTCTCTCTCTC rRNA-eliminate; refseqGeneIntron-annotate
CU-6028 796 CAGGCCTCCCTGGAATC computGene-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6029 797
AGTCCCACCCGGGGTACCA computGene-annotate; refseqGeneExon-eliminate
CU-6243 798 TTGACACGCCCCAGTGCCCTGT refseqGeneExon-eliminate CU-6233
799 TGGGAGCGGGCGGGCGGTC rRNA-eliminate; rnaGene-annotate CU-6231
800 TGGCGTGGAGCCGGGCGT rRNA-eliminate; refseqGeneIntron-annotate
CU-6228 801 TGGAGGTCCGTAGCGGT rRNA-eliminate; mRNA-annotate;
refseqGeneIntron- annotate; rnaGene-annotate CU-6223 802
TGAAGAAGGTCTCGAACA computGene-annotate; refseqGeneExon-eliminate
CU-6221 803 TCTCGCCGGGGCTTCCA computGene-annotate;
refseqGeneExon-eliminate; rnaGene- annotate CU-6217 804
TCGTAGCACCATCAATAA computGene-annotate; refseqGeneExon-eliminate
CU-6208 805 TCCGGGTCCCCCCTCCA computGene-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6207 806
TCCGGGGCTGCACGCGCGCT rRNA-eliminate; rnaGene-annotate CU-6205 807
TCCGGCCGTGTCGGT computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6203 808 TCCCTGTCCTCCAGGAGT
miRBASE-annotate; computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate; wgRNA-annotate CU-6201 809
TCCCCTCCTCGTCGCCA refseqGeneExon-eliminate;
refseqGeneIntron-annotate CU-6199 810 TCCCAGGTAGTCTAGTGGT
refseqGeneExon-eliminate; refseqGeneIntron- annotate;
rnaGene-annotate CU-6191 811 TATTCATTTATCCCCAGCCTAT
miRBASE-annotate; snoRNA-eliminate; refseqGeneIntron- annotate;
wgRNA-annotate; rnaGene-annotate CU-6190 812 TAGTTGTTATAACCCAA
refseqGeneExon-eliminate; refseqGeneIntron-annotate CU-6186 813
TAGATCACCCCCTCCCC mitochondrion-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6185 814 TACCGGCACCTGGCGCC
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6178 815 GTATAGGGGCGAAAGAC
rRNA-eliminate; mRNA-annotate; refseqGeneIntron- annotate;
rnaGene-annotate CU-6177 816 GTAGCTGGTTCCCTCCGAA rRNA-eliminate;
mRNA-annotate; refseqGeneIntron- annotate; rnaGene-annotate CU-6175
817 GGTAAGAAGCCCGGCTC computGene-annotate; rRNA-eliminate;
refseqGeneExon- eliminate; refseqGeneIntron-annotate;
rnaGene-annotate CU-6173 818 GGGGGGGTTTAAAAAAAAA
refseqGeneExon-eliminate; refseqGeneIntron-annotate CU-6169 819
GGGGCGCACTACCGGCC refseqGeneExon-eliminate CU-6168 820
GGGAGAGGCTGTCGCTGCG computGene-annotate; refseqGeneExon-eliminate
CU-6164 821 GGCGGGTGAAGCGGCG computGene-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6158 822 GCGGTTCCGGCGGCGTC
rRNA-eliminate; refseqGeneExon-eliminate; refseqGeneIntron-
annotate CU-6155 823 GCGGGGCGCCTAGGCCTGGTTTGT
refseqGeneExon-eliminate CU-6153 824 GCGGCGGTCGGCGGGCGGCGGG
rRNA-eliminate; refseqGeneExon-eliminate; refseqGeneIntron-
annotate CU-6149 825 GAGGGGGGGGGTGGGGGGGGA
refseqGeneExon-eliminate; refseqGeneIntron-annotate CU-6144 826
CTGTCGGCCACCATCAT computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6140 827 CTGCAACTCGACCCCA
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6139 828 CTCCTCTCCCCGCCCGCCG
refseqGeneExon-eliminate; refseqGeneIntron-annotate CU-6138 829
CTCAAAGATTAAGCCATGCATGTCTA rRNA-eliminate; rnaGene-annotate CU-6136
830 CTACGCCGCGACGAG computGene-annotate; rRNA-eliminate CU-6134 831
CGGGTGACGGGGAATCAGGGTT rRNA-eliminate; rnaGene-annotate CU-6127 832
CGGGCAGCTTCCGGGA computGene-annotate; rRNA-eliminate;
refseqGeneExon- eliminate; refseqGeneIntron-annotate CU-6126 833
CGGGAGGCCCGGGTCCTG refseqGeneExon-eliminate;
refseqGeneIntron-annotate CU-6124 834 CGGCCCCGCATCCTCCC
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6122 835 CGCGGGTAAACGGCGGGAGTAACTAT
mRNAall-annotate; rRNA-eliminate; refseqGeneIntron- annotate;
rnaGene-annotate CU-6121 836 CGCCCCCCGTTCCCCCCTCC rRNA-eliminate
CU-6119 837 CGAGCGGAAACACCA computGene-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6114 838 CGAACCCGGCACCGC
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6111 839 CCTCGGGCCGATCGCAC
rRNA-eliminate; rnaGene-annotate CU-6110 840 CCTATATATCTTACCA
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6109 841 CCGTGGCGGCGACGACC
computGene-annotate; rRNA-eliminate; refseqGeneExon- eliminate
CU-6106 842 CCGGGTTCCGGCACCA computGene-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6104 843 CCGCGAGGGGGGCCCG
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6103 844 CCGCCTCACGGGACCA
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6102 845 CCGCCCGTCCCCGCCCCTTG
rRNA-eliminate;
refseqGeneIntron-annotate; rnaGene-annotate CU-6100 846
CCCGGGGCCGCGGTTCCG computGene-annotate; rRNA-eliminate;
refseqGeneIntron- annotate CU-6098 847 CCCGAGCCGCCTGGAT
computGene-annotate; rRNA-eliminate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate; rnaGene-annotate CU-6097 848
CCCGACGGCCGAACT computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6095 849 CCCCGGGGAGCCCGGCGGG
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6092 850 CCCCCTCGCGGCCCTCCCC
rRNA-eliminate; refseqGeneIntron-annotate CU-6091 851
CCCCCCGTGGCGGCGAC rRNA-eliminate; refseqGeneIntron-annotate CU-6083
852 CCACCCAGGGCACGCCA refseqGeneExon-eliminate;
refseqGeneIntron-annotate CU-6077 853 CACGGGTGACGGGGAA
computGene-annotate; rnaGene-annotate; refseqGeneIntron- annotate;
rRNA-eliminate; refseqGeneExon-eliminate; piRNA- annotate CU-6073
854 ATGGGGAGGAAAAAAAAAAAAAA refseqGeneExon-eliminate;
refseqGeneIntron-annotate CU-6068 855 ATCCCACCGCTGCCCCCA
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6065 856 ATCACGTCGGTCACCA
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6053 857 ACGGGAAACCTCACCCGGCCCGG
rRNA-eliminate; piRNA-annotate; rnaGene-annotate CU-6046 858
ACAGAGGCTTACGACCCCTTATTT mitochondrion-annotate; tRNA-eliminate;
refseqGeneIntron- annotate; rnaGene-annotate CU-6040 859
AAAAAGGCATAATTAAACTT mitochondrion-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate
TABLE-US-00022 TABLE 4B List of short-RNA consensus with maximum 1
mismatch to the human genome. Table includes information on genomic
frequencies. SEQ Corrected Counts Frequencies ID Naive Memory
Centroblasts Ramos Naive Memory Centroblasts Ramos NO: Short-RNA
sequence (N) (M) (CB) (RA) (N) (M) (CB) (RA) 860
TGGCTCAGTTCAGCAGGAA 0 0 1 0 0 0 1.05 0 CAGT 861 GTGGGGGAGAGGCTGTCGA
0 0 0 1 0 0 0 0.81 862 CGGGGCAGCTCAGTACAGG 0 0 1 0 0 0 1.05 0 ATT
863 AATTGCACGGTATCCATCTG 0 0 1 0 0 0 1.05 0 TAT 864
CGGGGGAGCGCCGCGTA 2 0 0 0 2.04 0 0 0 865 TCGATCCCGGGTTTCGGCA 0 0 1
0 0 0 1.05 0 CCA 866 ATCGTATCCCACTTCTGACA 0 0 0 1 0 0 0 0.81 CCA
867 ATCCTGCCGACTACGCCA 13 15 13 6 13.27 13.76 13.68 4.88 868
TCGAATCCCACTCCTGACAC 1 2 7 7 1.02 1.83 7.37 5.69 CA 869
ATCCCATCCTCGTCGCCA 0 0 10 3 0 0 10.53 2.44 870 TCGATTCCCCGACGGGGAG
1 1 1 9 1.02 0.92 1.05 7.32 CCA 871 ATCCGGGTGCCCCCTCCA 2 4 0 1 2.04
3.67 0 0.81 872 TCCCGGGCGGCGCACCA 2 2 1 0 2.04 1.83 1.05 0 873
ATCCCACCAGAGTCGCCA 0 0 2 3 0 0 2.11 2.44 874 TCAAATCACGTCGGGGTCAC 0
1 2 0 0 0.92 2.11 0 CA 875 TGTCAGTTTGTTAATTGACC 0 0 1 1 0 0 1.05
0.81 CAA 876 TCGATCCCCGTACGGGCCA 0 0 1 1 0 0 1.05 0.81 CCA 877
TCGAGCCTCACCTGGAGCA 0 0 2 0 0 0 2.11 0 CCA 878 TCCGGCTCGAAGGACCA 0
0 2 0 0 0 2.11 0 879 GGCAATACGAGCACCCTG 2 0 0 0 2.04 0 0 0 880
CCGGGGCGTCTCGTAC 2 0 0 0 2.04 0 0 0 881 AGCGGCTGTGCACAAA 0 0 0 2 0
0 0 1.63 882 TGTCAGTTTGTTTAATCCAA 0 0 0 1 0 0 0 0.81 883
TGTCAGTTTGTTATTACCAA 0 0 0 1 0 0 0 0.81 884 TGTCAGGCACCATCAATAA 0 0
0 1 0 0 0 0.81 885 TGATCTTGACACTTAAAGCC 0 0 0 1 0 0 0 0.81 886
TCGTAGGCACCATCAAT 0 0 0 1 0 0 0 0.81 887 TCGACTCCCGGTATGGGAA 0 0 0
1 0 0 0 0.81 CCA 888 TAGGGAGGTTATGATTAACT 0 0 0 1 0 0 0 0.81 TTT
889 TAAAGTGCTTAGTGCAGGTA 0 0 0 1 0 0 0 0.81 890 GTTTATGTTGCTTACCTCC
0 0 1 0 0 0 1.05 0 891 GTAGATAAAATATTGGCG 1 0 0 0 1.02 0 0 0 892
GGCGGGGACGACGTCAG 0 0 0 1 0 0 0 0.81 893 GGCGGCGTCGCGGCGGGTC 0 1 0
0 0 0.92 0 0 894 GGAGGGGGTGAACAAAAAG 0 0 0 1 0 0 0 0.81 AAAAA 895
GCTAAACCTAGCCCCAAACC 0 0 0 1 0 0 0 0.81 CACTCCACA 896
CTGGATAGCGCACTTCGTT 0 0 0 1 0 0 0 0.81 897 CGGGCGAGGGGCGGACGTT 0 0
1 0 0 0 1.05 0 CG 898 CGGACCTATACCGGA 1 0 0 0 1.02 0 0 0 899
CCCCGGGTTCAATCCCCGG 0 0 1 0 0 0 1.05 0 CACCTCCACCA 900
CCCCCCACAACCGCGAA 0 1 0 0 0 0.92 0 0 901 CCCAGCATCTCCTGTGTTTA 0 1 0
0 0 0.92 0 0 902 CCCACGTTGGGACGCCA 1 0 0 0 1.02 0 0 0 903
ATCACGTCCGTGCCTCCA 0 1 0 0 0 0.92 0 0 904 ATAGCAATGTCAGCAGTACCT 0 0
1 0 0 0 1.05 0 905 ACCCTGCTCGCTGCGCCA 9 17 4 7 9.18 15.6 4.21 5.69
906 TCCCACCCAGGGACGCCA 8 2 1 0 8.16 1.83 1.05 0 907
TCGTAGGCACATCAATA 0 0 0 4 0 0 0 3.25 908 CCCCCACAACCGCGTA 0 4 0 0 0
3.67 0 0 909 ACCCCGTCCGTGCCTCCA 2 1 1 0 2.04 0.92 1.05 0 910
AAAAAAGACACCCCCCACA 0 0 0 3 0 0 0 2.44 911 TGTCAGTTTGTTAACCCAA 0 0
0 2 0 0 0 1.63 912 TCCCTGTGGTCTAGTGGTTA 0 0 1 1 0 0 1.05 0.81 GG
913 GGGGGGGTAAAAAAA 0 0 0 1 0 0 0 0.81 914 GGGGGGGGAAAAAAAA 0 0 0 1
0 0 0 0.81 915 CGGGCCCGGGTCTTCCC 1 1 0 0 1.02 0.92 0 0 916
CCGCCCCCCGTTCCCCCCA 0 2 0 0 0 1.83 0 0 917 ACCCCCGGCTCCTCCACCA 0 1
0 1 0 0.92 0 0.81 918 TTTGGTGGAAATTTTTTGA 0 0 0 1 0 0 0 0.81 919
TGTCAGTTTGTTATACCAA 0 0 0 1 0 0 0 0.81 920 TGTCAGTTTGTAATTATCCC 0 0
0 1 0 0 0 0.81 AA 921 TGTCAATTTTTAACCCAA 0 0 0 1 0 0 0 0.81 922
TGCTAGGGTAAAAAAAAAA 0 0 0 1 0 0 0 0.81 923 TGCAACTCCAAATAAAAGTA 0 0
0 1 0 0 0 0.81 CCA 924 TGAGGTAACGGGGAATTA 0 0 0 1 0 0 0 0.81 925
TCCTCGGCATCTCCACCA 0 0 1 0 0 0 1.05 0 926 TCATATGAAGTCACCCTAGC 0 0
1 0 0 0 1.05 0 CATC 927 TCAGTTTGTTTATTAACCCAA 0 0 0 1 0 0 0 0.81
928 TCAGCGTGTCTTTGCCCT 1 0 0 0 1.02 0 0 0 929 TCACTGGTGGTCTAGTGGT 0
1 0 0 0 0.92 0 0 930 TCACAATGCTGCCACCA 1 0 0 0 1.02 0 0 0 931
TAGTTGTTAATTAACCCAA 0 0 0 1 0 0 0 0.81 932 TAGTCCTCATCGCCCTCC 0 1 0
0 0 0.92 0 0 933 TAAAGTGCTTATAGTGCGGG 0 0 0 1 0 0 0 0.81 TAA 934
GTCCCACCAGAGTCGCCA 0 0 1 0 0 0 1.05 0 935 GGGGGAGGGGCCAAAAAAA 0 0 0
1 0 0 0 0.81 936 GGGACGCCGCGGTGTCG 1 0 0 0 1.02 0 0 0 937
GGGAATACCGGGTGCTTTA 0 1 0 0 0 0.92 0 0 GGCTT 938
GGAAGAAGGTGGTGGTATA 0 0 0 1 0 0 0 0.81 939 GCGGTGAAATGCGTA 1 0 0 0
1.02 0 0 0 940 GCGGGGAAGGTGGCAAA 0 0 0 1 0 0 0 0.81 941
GCGACGACCTCGCGCCCAC 0 1 0 0 0 0.92 0 0 CTGGTCA 942
GCCACCCGATACTGCTGT 0 1 0 0 0 0.92 0 0 943 GATGTATGCTTTGTTTCTGTT 0 0
1 0 0 0 1.05 0 944 GAGGGGGATTTAGAAAAAAA 0 0 0 1 0 0 0 0.81 945
GAAGGAAAGTTCTATAGT 0 0 0 1 0 0 0 0.81 946 GAAGCGGCTCTCTTATTT 0 0 0
1 0 0 0 0.81 947 GAACGAGACTCTGGCATGC 0 0 1 0 0 0 1.05 0 TGA 948
CTGGTAGGCCCATCAAT 0 0 0 1 0 0 0 0.81 949 CGGGGCCGATCGCGCGC 0 1 0 0
0 0.92 0 0 950 CGGCCCCGGGTTCCTCCC 1 0 0 0 1.02 0 0 0 951
CGAGCCCGGTTAGTA 1 0 0 0 1.02 0 0 0 952 CGACTCTTAGCGGTGGA 0 0 1 0 0
0 1.05 0 953 CGAATCCCACTTCTGACACCA 0 0 0 1 0 0 0 0.81 954
CGAAAGGGAATCGGGTC 1 0 0 0 1.02 0 0 0 955 CCTTAGGTCGCTGGTAAA 0 0 1 0
0 0 1.05 0 956 CCGTGCGAGAATACCA 0 1 0 0 0 0.92 0 0 957
CCGGTCTCTCAAGCGGCC 1 0 0 0 1.02 0 0 0 958 CCCGGCCCTCGCGCGTCC 0 1 0
0 0 0.92 0 0 959 CCCCGGCATTTCCACCA 0 0 1 0 0 0 1.05 0 960
CCCCCCCGGCTCCTCCACCA 0 0 0 1 0 0 0 0.81 961 CCCCCCACAACCGCTA 0 1 0
0 0 0.92 0 0 962 CCCAAGTATTGACTCACCC 0 1 0 0 0 0.92 0 0 963
CCAGTAAGCGCGAGTC 1 0 0 0 1.02 0 0 0 964 CCAAAGAAAGCACGTAGAG 0 0 0 1
0 0 0 0.81 965 CATGTTTAACGGCCGCGGT 0 0 1 0 0 0 1.05 0 966
CAGTTTGTAATTAACCCAA 0 0 0 1 0 0 0 0.81 967 CAGGAACGGCGCACCA 0 0 1 0
0 0 1.05 0 968 CAGAACCCTCTAAATCCCC 0 0 1 0 0 0 1.05 0
969 CACCCGGCTGTGTGCACAT 1 0 0 0 1.02 0 0 0 GTGT 970
CAATTGGACCAATCTATC 0 0 1 0 0 0 1.05 0 971 ATTCCTGTACTGCGATA 0 0 0 1
0 0 0 0.81 972 ATCCCTGCGGCGTCTCCA 0 0 0 1 0 0 0 0.81 973
ATCCCACCGCTGCCATCA 0 1 0 0 0 0.92 0 0 974 AGTCAATAGAAGCCGGCGTA 0 0
1 0 0 0 1.05 0 975 AGGTTCGTTTGTAAAAA 0 0 0 1 0 0 0 0.81 976
AGGTCCTGGGTTTAAGTGT 0 0 0 1 0 0 0 0.81 977 AGGGGGAAGTTCTATAGTC 0 0
0 1 0 0 0 0.81 978 AGGCTGTGATGCTCTCNTGA 0 0 1 0 0 0 1.05 0 GCCCT
979 AGCCCCTCTCCGGCCCTTA 0 1 0 0 0 0.92 0 0 980 ACTACCACCTACCTCCC 1
0 0 0 1.02 0 0 0 981 ACGCCCTTCCCCCCCTTCTTT 0 0 0 1 0 0 0 0.81 982
ACCCCACTCCTGGTGCAC 1 0 0 0 1.02 0 0 0 983 ACCACCTGATCCCTTCCC 1 0 0
0 1.02 0 0 0 984 ACAGCTAAGCACCCACCA 0 0 1 0 0 0 1.05 0 985
ACACATGTTTAACGGCC 1 0 0 0 1.02 0 0 0 986 AATTAGGGACCTGTATG 0 0 1 0
0 0 1.05 0 987 AATGGCCCATTTGGGCAAACA 0 0 0 1 0 0 0 0.81 988
AAAGCGGCTGTGCAAACA 0 0 0 1 0 0 0 0.81 989 TCGACTCCTGGCTGGCTCG 0 2 2
1 0 1.83 2.11 0.81 CCA 990 TCCCCGGCATCTCCACCAA 0 1 2 0 0 0.92 2.11
0 991 GCGGTGGATCACTCGGCTC 0 0 0 3 0 0 0 2.44 GTGCGT 992
CCGGGTGTTGTAGA 2 0 0 0 2.04 0 0 0 993 TGTAGCGTGGCCGAGCGGT 0 1 0 0 0
0.92 0 0 994 TGGGGCGACCTCGGAGCAG 0 0 1 0 0 0 1.05 0 995
TGGCGTCCTAAGCCAGGGA 0 0 0 1 0 0 0 0.81 TTGTGGGT 996
TGGCAGGGGAGATACCATG 0 0 1 0 0 0 1.05 0 ATTT 997 TCTGATCAGGGTGAGCATC
0 1 0 0 0 0.92 0 0 998 TCGTAGGCACCATCCAT 0 0 0 1 0 0 0 0.81 999
GGGAAACGGGGCGCGGCTG 0 1 0 0 0 0.92 0 0 1000 CTACTCCTGCTCGCATCTGC 0
0 1 0 0 0 1.05 0 TATA 1001 CGGGTGGGTTTTTACCGG 1 0 0 0 1.02 0 0 0
1002 CGAGGAATTCCCAGTAAG 0 0 1 0 0 0 1.05 0 1003 CGAACGCACTTGCGGCCCC
1 0 0 0 1.02 0 0 0 1004 CCCCGCGCGGGTTCGAATC 1 0 0 0 1.02 0 0 0 1005
AGGGGTATGATTCCCGCTT 0 0 0 1 0 0 0 0.81 1006 CGGGGCCACGCGCGCGTC 3 6
0 0 3.06 5.5 0 0 1007 TGGCGCTGCGGGATGAAC 0 3 1 0 0 2.75 1.05 0 1008
CCCCCCACTGCTAAATTTGA 0 0 2 2 0 0 2.11 1.63 CTGGCTT 1009
TAAAGGTTCGTTTGTAAAA 0 0 0 3 0 0 0 2.44 1010 CGGGGCCGAGGGAGCGA 1 2 0
0 1.02 1.83 0 0 1011 GGGTTAGGCCTCTTTT 0 1 1 0 0 0.92 1.05 0 1012
CTGCGGAAGGATCATTA 1 0 1 0 1.02 0 1.05 0 1013 CCCTACCCCCCCGG 0 2 0 0
0 1.83 0 0 1014 CCCGCCGGGTCCGCCC 2 0 0 0 2.04 0 0 0 1015
CCCCGCGCCCTCTCTCTCTC 0 2 0 0 0 1.83 0 0 1016 CAGGCCTCCCTGGAATC 2 0
0 0 2.04 0 0 0 1017 AGTCCCACCCGGGGTACCA 0 0 0 2 0 0 0 1.63 1018
TTGACACGCCCCAGTGCCC 1 0 0 0 1.02 0 0 0 TGT 1019 TGGGAGCGGGCGGGCGGTC
0 1 0 0 0 0.92 0 0 1020 TGGCGTGGAGCCGGGCGT 0 1 0 0 0 0.92 0 0 1021
TGGAGGTCCGTAGCGGT 1 0 0 0 1.02 0 0 0 1022 TGAAGAAGGTCTCGAACA 0 0 0
1 0 0 0 0.81 1023 TCTCGCCGGGGCTTCCA 0 1 0 0 0 0.92 0 0 1024
TCGTAGCACCATCAATAA 0 0 0 1 0 0 0 0.81 1025 TCCGGGTCCCCCCTCCA 0 1 0
0 0 0.92 0 0 1026 TCCGGGGCTGCACGCGCGCT 0 1 0 0 0 0.92 0 0 1027
TCCGGCCGTGTCGGT 1 0 0 0 1.02 0 0 0 1028 TCCCTGTCCTCCAGGAGT 0 0 0 1
0 0 0 0.81 1029 TCCCCTCCTCGTCGCCA 1 0 0 0 1.02 0 0 0 1030
TCCCAGGTAGTCTAGTGGT 1 0 0 0 1.02 0 0 0 1031 TATTCATTTATCCCCAGCCT 0
1 0 0 0 0.92 0 0 AT 1032 TAGTTGTTATAACCCAA 0 0 0 1 0 0 0 0.81 1033
TAGATCACCCCCTCCCC 0 1 0 0 0 0.92 0 0 1034 TACCGGCACCTGGCGCC 1 0 0 0
1.02 0 0 0 1035 GTATAGGGGCGAAAGAC 0 0 1 0 0 0 1.05 0 1036
GTAGCTGGTTCCCTCCGAA 0 0 0 1 0 0 0 0.81 1037 GGTAAGAAGCCCGGCTC 0 0 1
0 0 0 1.05 0 1038 GGGGGGGTTTAAAAAAAAA 0 0 0 1 0 0 0 0.81 1039
GGGGCGCACTACCGGCC 1 0 0 0 1.02 0 0 0 1040 GGGAGAGGCTGTCGCTGCG 0 0 0
1 0 0 0 0.81 1041 GGCGGGTGAAGCGGCG 0 1 0 0 0 0.92 0 0 1042
GCGGTTCCGGCGGCGTC 0 1 0 0 0 0.92 0 0 1043 GCGGGGCGCCTAGGCCTGG 1 0 0
0 1.02 0 0 0 TTTGT 1044 GCGGCGGTCGGCGGGCGG 1 0 0 0 1.02 0 0 0 CGGG
1045 GAGGGGGGGGGTGGGGGG 0 0 0 1 0 0 0 0.81 GGA 1046
CTGTCGGCCACCATCAT 0 0 0 1 0 0 0 0.81 1047 CTGCAACTCGACCCCA 0 1 0 0
0 0.92 0 0 1048 CTCCTCTCCCCGCCCGCCG 0 0 1 0 0 0 1.05 0 1049
CTCAAAGATTAAGCCATGCA 0 0 1 0 0 0 1.05 0 TGTCTA 1050 CTACGCCGCGACGAG
1 0 0 0 1.02 0 0 0 1051 CGGGTGACGGGGAATCAGG 1 0 0 0 1.02 0 0 0 GTT
1052 CGGGCAGCTTCCGGGA 0 0 0 1 0 0 0 0.81 1053 CGGGAGGCCCGGGTCCTG 1
0 0 0 1.02 0 0 0 1054 CGGCCCCGCATCCTCCC 1 0 0 0 1.02 0 0 0 1055
CGCGGGTAAACGGCGGGAG 0 0 1 0 0 0 1.05 0 TAACTAT 1056
CGCCCCCCGTTCCCCCCTCC 0 1 0 0 0 0.92 0 0 1057 CGAGCGGAAACACCA 1 0 0
0 1.02 0 0 0 1058 CGAACCCGGCACCGC 1 0 0 0 1.02 0 0 0 1059
CCTCGGGCCGATCGCAC 0 0 1 0 0 0 1.05 0 1060 CCTATATATCTTACCA 0 1 0 0
0 0.92 0 0 1061 CCGTGGCGGCGACGACC 0 1 0 0 0 0.92 0 0 1062
CCGGGTTCCGGCACCA 1 0 0 0 1.02 0 0 0 1063 CCGCGAGGGGGGCCCG 1 0 0 0
1.02 0 0 0 1064 CCGCCTCACGGGACCA 1 0 0 0 1.02 0 0 0 1065
CCGCCCGTCCCCGCCCCTTG 0 1 0 0 0 0.92 0 0 1066 CCCGGGGCCGCGGTTCCG 1 0
0 0 1.02 0 0 0 1067 CCCGAGCCGCCTGGAT 0 1 0 0 0 0.92 0 0 1068
CCCGACGGCCGAACT 0 1 0 0 0 0.92 0 0 1069 CCCCGGGGAGCCCGGCGGG 1 0 0 0
1.02 0 0 0 1070 CCCCCTCGCGGCCCTCCCC 0 1 0 0 0 0.92 0 0 1071
CCCCCCGTGGCGGCGAC 0 1 0 0 0 0.92 0 0 1072 CCACCCAGGGCACGCCA 1 0 0 0
1.02 0 0 0 1073 CACGGGTGACGGGGAA 1 0 0 0 1.02 0 0 0 1074
ATGGGGAGGAAAAAAAAAAA 0 0 0 1 0 0 0 0.81 AAA 1075 ATCCCACCGCTGCCCCCA
0 0 0 1 0 0 0 0.81 1076 ATCACGTCGGTCACCA 0 0 0 1 0 0 0 0.81 1077
ACGGGAAACCTCACCCGGC 0 0 1 0 0 0 1.05 0 CCGG 1078
ACAGAGGCTTACGACCCCTT 0 0 1 0 0 0 1.05 0 ATTT 1079
AAAAAGGCATAATTAAACTT 0 0 1 0 0 0 1.05 0
[0230] Interestingly, several of these non-annotated sequences
(i.e. CU-5004, CU-5021, CU-6030, CU-6069) were cloned multiple
times and showed differential expression across libraries,
suggesting they may represent short-RNAs with characteristics
distinct from those currently recognized in "classic" miRNAs.
[0231] In conclusion, the generation of short-RNA libraries from
normal and neoplastic B cells led to the identification of 401 bona
fide miRNAs as well as other short-RNA species of unknown
function.
[0232] Abundance and Evolutionary Conservation
[0233] Previously reported miRNAs appeared to be more abundant than
newly discovered miRNAs (FIG. 13A). Approximately 21% of previously
reported miRNAs appeared in the libraries as single occurrences
compared to 57% of the newly discovered miRNAs. Approximately 42%
of known miRNAs were expressed at all stages of mature B cell
development, while newly identified miRNAs showed a more distinct
stage-specificity (FIG. 13B), consistent with the notion that
presently known miRNAs are mostly representative of ubiquitously
expressed miRNAs.
[0234] Regardless of their novelty, stage-specific miRNAs were
observed with frequencies (defined as the fraction of the total
pool of cloned miRNAs represented by a given miRNA) ranging between
0.03 and 0.6% of their respective libraries. The most abundant
GC-associated miRNAs showed restricted expression in GC B cells
and, if unaffected by transformation, in Ramos cells. However, in
naive and memory B cell libraries only the rarest miRNAs were truly
exclusive in their expression and most of the non-GC-specific
miRNAs were expressed in both naive and memory cells albeit at
different levels.
[0235] In order to investigate the presence of orthologous miRNA in
other mammalian species, we relied on UCSC-provided Blastz pairwise
alignments between human and target species and investigated
conservation using two complementary methods, detailed in
Supplementary Methods. The analysis was performed on the complete
set of miRNAs deposited in the miRBase database and on the miRNAs
(known and new) represented in the B cell libraries. Alignments of
the human mature miRNA to its target species were required to have
either perfect conservation of the entire mature miRNA sequence
(FIG. 13C) or conservation of seeds composed of seven bases
starting from the second position of the human mature sequence
followed by conservation of 3 bases starting from the 12th, 13th or
14th position as suggested by.sup.21. The majority of miRBase
miRNAs showed conservation across mammalian genomes, from primates
to rodents. Conservation frequency mimicked known phylogenetic
distances to human, with the highest conservation in chimp and
lowest in rat. The conservation frequencies of known and new miRNAs
in B cells were similar in chimp (Pan troglodytes) and monkey
(Macacus rhesus), especially when conservation requirements were
restricted to the seed region of miRNAs. However, conservation
frequencies in dog, mouse and rat were significantly divergent,
with known miRNAs more likely to exhibit conservation than new
candidate miRNAs (FIG. 13C). In summary, new miRNAs expressed at
specific stages of B cell differentiation were less abundant and
showed a lower level of conservation across species.
[0236] Validation of Newly Discovered miRNA
[0237] The newly identified miRNAs were investigated by Northern
Blot analysis in order to validate their existence in vivo.
Northern Blot analyses were performed using B cell lines and cells
isolated from tonsil tissue obtained from multiple donors. Among 23
candidate miRNAs that have been cloned in any of the four libraries
with 1-100 occurrences, 13 were detectable by Northern Blot (FIG.
14A). Detection of several miRNAs represented by low number of
occurrences in the libraries was successful only upon enrichment
for the short-RNA fraction, suggesting that low-abundance miRNA
could be below the level of detection by Northern blotting.
Overall, approximately 55% of the newly cloned and computationally
validated miRNAs were detectable by Northern Blot.
[0238] Transcriptional and Post-Transcriptional Regulation
[0239] Most newly identified miRNAs showed a long abundant
transcript (>150 nt) that might correspond to the primary miRNA
transcript and a second transcript (.about.60-80 nt) consistent
with the precursor miRNA. As shown in FIG. 14B (top panel), the
precursor miRNA and the correspondent mature miRNA may be produced
in some cell type but not in others, suggesting transcriptional
regulation. Conversely in some cases the miRNA precursor species
may be present in cell types that lack expression of the mature
form (FIG. 14B, bottom panel) suggesting the existence of a second
level of regulation targeting the Dicer-dependent pre-miRNA
processing.sup.22-24.
[0240] Distinct miRNA Signatures in Normal B Cells
[0241] miRNA representation in the four constructed libraries
suggested differential expression of miRNAs during B cell
differentiation and GC transit (FIG. 13B). The correlation among
miRNA profiles from normal B cells and Ramos cell line was further
investigated by hierarchical clustering using miRNA frequencies
(defined as the fraction of the total pool of cloned miRNAs
represented by a given miRNA in a library) obtained from the
cloning data (FIG. 15A). Naive and memory B cells appeared similar,
sharing a large fraction of the most abundant miRNA. Conversely,
centroblasts and Ramos cells showed more distinct miRNA profiles
with a sizeable fraction of abundant miRNA being specifically
expressed in each library.
[0242] We also performed miRNA expression profiling of
centroblasts, naive and memory B cells (six donors/each) using a
microarray representative of 723 known human miRNAs (miRBase
v.10.1). Each B cell population showed a distinct miRNA expression
profile. Consistent with the cloning data (FIGS. 13B and 15A) GC B
cells appeared to be quite distinct from naive and memory B cells
which instead shared expression of a large fraction of miRNAs (FIG.
15A). The main differences between naive and memory B cells resided
in the level of miRNA expression. The expression of several miRNAs
was tested by qRT-PCR analysis which confirmed that the microarray
data were accurate for the relative quantification.
[0243] miRNA Signatures can Identify Subtypes of B Cell
Malignancies
[0244] The miRNA library generated from Ramos BL cell line
demonstrated that tumors can display specific miRNA expression
signatures. To investigate whether these signatures can identify
subtypes of B cell malignancies, miRNA expression profiling was
performed using the same microarray platform on a panel of
GC-derived malignancies including BL (8), DLBCL (16) and FL (10).
Unsupervised clustering analysis of the tumor miRNA profiles was
able to identify three major clusters enriched for samples
belonging to each malignant phenotype (FIG. 16). These tumors can
be discriminated as well by gene expression profiling however it
requires the use of a higher number of features. These results show
that tumors deriving from the same stage of B cell differentiation
acquire distinct miRNA expression profiles as consequence of
malignant transformation.
DISCUSSION
[0245] The combination of cloning procedures and computational
tools led us to the identification of a large fraction of known as
well as newly discovered miRNA expressed during B cell
differentiation. These findings have general implications for the
understanding of the total miRNA content of the human genome as
well as for future studies on the role of miRNAs in B cell
differentiation, function and lymphomagenesis.
[0246] The discovery of >250 new miRNAs and of their
tissue-specific pattern of expression are in sharp contrast with
previous reports that suggested, based on the discovery of only 12
new human miRNA.sup.7 from an analysis of 26 different organ
systems and cell types, that most miRNAs are ubiquitously expressed
and that most miRNAs have already been identified.sup.7. These
discordant results and conclusions may be partially due to the
significantly higher number of clones per library sequenced in this
study (3500 versus 1300 on average in.sup.7) which allowed the
detection of low abundant miRNA species and to the criteria applied
in the miRNA prediction (see Supplementary Methods).
[0247] The relatively lower degree of evolutionary conservation of
tissue-specifc miRNAs (FIG. 13C) may have prevented the
cross-species identification of miRNAs using murine
libraries.sup.18,25. Consistent with these observations, a recent
report on short-RNAs in mouse embryonic stem cells discovered new
Dicer-dependent miRNAs characterized by both low abundance and low
level of conservation.sup.26. Thus, a large number of
low-abundance, recently evolved, tissue-specific miRNAs remain to
be discovered.
[0248] Two categories of short-RNAs were identified that could not
be annotated as bona fide miRNAs. The first category is represented
by those short-RNAs that could not be accurately mapped to the
genome. Considering that a fraction of these RNAs were cloned
multiple times and showed a stage-specific behavior, such
short-RNAs do actually exist and that the lack of a match to the
human genome may be due to polymorphisms, editing and other
post-transcriptional modifications or to an incomplete/inaccurate
sequencing of the corresponding genomic regions. The second
category is represented by short-RNAs for which classic pre-miRNA
structures could not be identified in the genome and no similarity
to other non-coding RNA was found in the available databases. These
short-RNAs may either be miRNA for which RNA secondary structure
prediction algorithms failed to predict the correct hairpin
structure or may represent new miRNA species of presently unknown
mechanism of generation or other not yet described types of
short-RNAs.
[0249] The stage specific expression of various miRNAs, especially
in GC B cells, suggests highly specialized regulatory functions in
B cell biology. The role of miRNAs that show cell type-specific
functions in lymphocytes has just begun to be
elucidated.sup.8-10,27. The miRNAs specifically associated to GC or
non-GC B cells by either cloning or miRNA expression profiling
(FIG. 15) have not been previously reported in B cell
differentiation with the exception of miR-150.sup.10. The miR-17-92
cluster, previously reported as a potential oncogene.sup.11, was
found over-expressed in Ramos cell line compared to GC B cells
possibly as a consequence of the transformation process.
[0250] Specificity in mature miRNA expression may be regulated at
the transcriptional as well as at the post-transcriptional, i.e.
pre-miRNA processing, level. Pre-miRNA accumulation in absence of a
mature miRNA can occur in a cell type-restricted manner, suggesting
the presence of a regulation mechanism at the pre-miRNA processing
step. Both regulatory mechanisms may act during normal
differentiation and may also be dysregulated during transformation
as a consequence of genetic or epigenetic alterations.sup.22-24.
The expanded B cell miRNome described here can be used to identify
specific differences in miRNA expression in normal versus lymphoma
cells that can guide searches for these tumor alterations.
[0251] miRNA expression profile differences between GC and non-GC B
cells resembled those observed by expression profiling of coding
genes.sup.28, consistent with the previous observation that miRNA
profiling may be equally or more informative in discriminating cell
phenotypes.sup.29. miRNA expression profiling, especially if
including new B-cell specific miRNAs, may be useful in the
differential diagnosis of lymphoid malignancies.
[0252] Materials and Methods
[0253] Generation of Short-RNA Libraries
[0254] Purification of naive, memory and GC B cells was performed
as previously reported.sup.28 using magnetic cell sorting of
mononucleated cells obtained from human tonsils. Total RNA was
purified using the Trizol Reagent (Invitrogen) following the
manufacturer's indications. The short-RNA libraries were generated
using an established protocol described in detail in.sup.30.
Briefly, total RNA was separated on 15% polyacrylamide gel and the
fragment corresponding to 18-28 nucleotides length was excised. The
purified small RNAs were linked to adaptor oligonucleotides and gel
purified. Upon adaptor ligation, RNA was reverse transcribed and
cDNA was PCR amplified and cloned into pCR2.1-TOPO vector
(Invitrogen). Sequencing was performed on colony PCR amplicons.
[0255] Computational Identification of Mature and Precursor
miRNAs
[0256] The bioinformatics miRNA analysis pipeline (FIG. 18)
includes: (a) identification of short-RNAs from each library, (b)
identification of exact and partial matches of the short-RNA
sequences to the human genome, (c) testing each short-RNA genomic
region for compatibility with hairpin secondary structures, (d)
clustering genomic regions to predict mature miRNAs, (e) annotating
and filtering short-RNAs and miRNAs candidates, (f) estimation of
predicted miRNA frequencies in the libraries and (g) clustering
short-RNAs that do not support miRNA candidates. The details are
reported in the Supplementary Methods.
[0257] Orthology Analysis
[0258] The identification of putative orthologous sequences of
known and predicted precursor and mature human miRNAs in chimp
(panTro2), monkey (rheMac2), dog (canFam2) mouse (mm8) and rat (m4)
was performed using UCSC-provided Blastz.sup.31 pairwise alignments
between human and target species. The details are reported in the
Supplementary Methods.
[0259] miRNA Expression Profiling
[0260] The miRNA expression profiles were generated using the Human
miRNA Microarray kit (Agilent Technologies) that allows detection
of 723 known human (miRBase v.10.1) and 76 human viral miRNAs
following the manufacturer's indications. Analysis of raw data was
performed using the Feature Extraction Software 9.5.3.1 (Agilent
Technologies). The dendrograms (FIG. 15) were generated using a
hierarchical clustering algorithm based on the average-linkage
method.sup.32,33 and Spearman's correlation as provided by the
geWorkbench platform (http://www.geworkbench.org).
[0261] Northern Blot
[0262] Total RNA and small RNA fractions were purified using the
Trizol Reagent (Invitrogen) and the PureLink miRNA Isolation Kit
(Invitrogen), respectively, following the manufacturer's
indications. Electrophoresis was performed on 15% denaturing
polyacrylamide gel and then RNA was transferred on Duralon UV
membrane (Stratagene) using a semidry transfer apparatus.
Pre-hybridization and hybridization were performed in 5.times.SSC,
20 mM Na.sub.2HPO.sub.4 pH 7.2, 7% SDS, 3.times.Denhardt's
Solution. Oligonucleotide probes were [.gamma.-.sup.32P]-ATP
labeled by polynucleotide kinase (Fermentas). The list of
oligonucleotides is reported in Table 5.
TABLE-US-00023 TABLE 5 Listing of Oligonucleotide Probe Sequences
mature miRNA SEQ ID sequence (5'-3') ID NO: Probe sequence (5'-3')
SEQ ID NO: CU-1303 ATCCCACTTCTGAC 237 TGGTGTCAGAAGTGGGAT 1080 ACCA
CU-1403 GCATTGGTGGTTCA 391 TCTACCACTGAACCACCAATGC 1081 GTGGTAGA
CU-1253 GTGAAGCGTTCCAT 281 AAAAATATGGAACGCTTCAC 1082 ATTTTT CU-1513
GCGGGTGATGCGA 381 GCTCAGACTCCAGTTCGCATCAC 1083 ACTGGAGTCTGAGC CCGC
CU-1173 ATCCCACTCCTGAC 145 TGGTGTCAGGAGTGGGAT 1084 ACCA CU-1276
TCGATTCCCGGCCA 236 TGGTGCATTGGCCGGGAATCGA 1085 ATGCACCA CU-1368
GACGAGGTGGCCG 382 AACCACTCGGCCACCTCGTC 1086 AGTGG CU-1254
TCCCCGGCACCTC 233 TGGTGGAGGTGCCGGGGA 1087 CACCA CU-1137
GCTAAGGAAGTCCT 132 AAAACTGAGCACAGGACTTCCTT 1088 GTGCTCAGTTTT AGC
CU-1153 CCCCCCACTGCTAA 142 AAGCCAGTCAAATTTAGCAGTGG 1089
ATTTGACTGGCTT GGGG CU-1241 AGTCCCATCTGGGT 243 TGGCGACCCAGATGGGACT
1090 CGCCA CU-1351 CCTTCCTTGGATGT 316 CTCACTCAGACATCCAAGGAAGG 1091
CTGAGTGAG CU-1142 TCGATTCCCGGCCC 149 TGGTGCATGGGCCGGGAATCGA 1092
ATGCACCA
[0263] After over-night hybridization, membranes were washed at the
same temperature in 3.times.SSC, 25 mM NaH.sub.2PO.sub.4 pH 7.5, 5%
SDS, 10.times.Denhardt's Solution for 15-20' and in 1.times.SSC, 1%
SDS for 5'. Images were obtained by exposure to phosphoimager
cassette and acquisition by Storm 840 Phosphoimager (Molecular
Dynamics) and by film exposure for approximately 2 weeks.
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[0264] 1. Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism,
and function. Cell 116, 281-97 (2004). [0265] 2. Kim, V. N.
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Cell Biol 6, 376-85 (2005). [0266] 3. Griffiths-Jones, S. miRBase:
the microRNA sequence database. Methods Mol Biol 342, 129-38
(2006). [0267] 4. Griffiths-Jones, S., Grocock, R. J., van Dongen,
S., Bateman, A. & Enright, A. J. [0268] miRBase: microRNA
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D140-4 (2006). [0269] 5. Miranda, K. C. et al. A pattern-based
method for the identification of MicroRNA binding sites and their
corresponding heteroduplexes. Cell 126, 1203-17 (2006). [0270] 6.
Bentwich, I. et al. Identification of hundreds of conserved and
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7. Landgraf, P. et al. A mammalian microRNA expression atlas based
on small RNA library sequencing. Cell 129, 1401-14 (2007). [0272]
8. Thai, T. H. et al. Regulation of the germinal center response by
microRNA-155. Science 316, 604-8 (2007). [0273] 9. Rodriguez, A. et
al. Requirement of bic/microRNA-155 for normal immune function.
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Controls B Cell Differentiation by Targeting the Transcription
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microRNA polycistron as a potential human oncogene. Nature 435,
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[0300] Supplementary Methods
[0301] Bioinformatics Analysis of Short-RNA Libraries
[0302] The bioinformatics microRNA (miRNA) analysis pipeline
includes (a) identification of short-RNAs from each library, (b)
identification of exact and partial matches of the short-RNA
sequences to the human genome, (c) testing each short-RNA genomic
region for compatibility with hairpin secondary structures, (d)
clustering genomic regions to predict mature miRNAs, (e) annotating
and filtering short-RNAs and miRNAs candidates, (f) estimation of
predicted miRNA frequencies in the libraries, (g) clustering
short-RNAs that do not support miRNAs candidates.
[0303] a. Identification of Short-RNAs from Cloned cDNA
Sequences:
[0304] Short-RNA sequences of length 15-30 bp were recovered from
within cloned cDNA sequences using 8 bp adaptor oligonucleotides as
oriented markers. An exact .gtoreq.6 bp match to the suffix of the
5' daptor oligonucleotide and the prefix of the 3' adaptor
oligonucleotide were required. All short-RNAs of length 17 to 27 nt
(length range of miRNAs deposited in the miRBase database v11.0)
that are bounded by adaptors were reported, and short-RNAs
containing adaptor fragments were tagged as lower confidence
observations. miRNA candidates supported by low confidence
short-RNAs were later evaluated individually and discarded by
expert decision. The remaining ones are listed here: CU-1153 is
supported by 29 short-RNAs including 1 low confidence; CU-1293 and
CU-1079 are supported by low confidence short-RNAs including
sequence fragments that could not originate from linkers.
[0305] b. Mapping to the Human Genome:
[0306] Each short-RNA was aligned to the human genome assembly from
March 2006 (hg18) using WU-Blast. WU-Blast was ran locally optimal,
with default word length 6, maximum allowed separation 2, no gaps,
and no high scoring pair consistency. All WU-Blast reported matches
were retrieved and mismatches marked. Only the genomic matches with
the smallest number of mismatches were recorded, and we refer to
them as short-RNA genomic locations.
[0307] c. Testing Short-RNA Genomic Locations for Hairpin Secondary
Structures:
[0308] Short-RNA genomic locations were tested for compatibility
with hairpin secondary structures. The criteria were established
upon investigation of the characteristics of mammalian miRNA
precursors deposited in the miRBase database (v.11.0).sup.s1,s2.
Only short-RNAs that have genomic locations compatible with a
hairpin structure were used to define putative miRNAs and their
precursors. A short-RNA genomic location was considered if the
following criteria were satisfied: i) one or more hairpin
structures were predicted in the genomic region starting at most 90
bases upstream and ending at most 90 bases downstream of the
short-RNA genomic location; ii) the lowest free-energy predicted
secondary structure for the containing region was a hairpin with
maximum fold free energy of -8 joules, which is the maximum fold
free energy observed for miRBase miRNAs; iii) the short-RNA genomic
location could not overlap the predicted hairpin loop, which was
required to be 3-20 bp long (the range of hairpin-loop lengths
observed in the miRBase database); iv) the ratio between the number
of complementary base pairs and the total number of base pairs in
the stem was larger than 0.645, which is the minimum ratio observed
in miRBase database. We used RNAfold 1.6, a part of the ViennaRNA
package (http://www.tbi.univie.ac.at/.about.ivo/RNA/), with
temperature set to 37.degree. C. to predict the lowest energy
secondary RNA structure for each candidate genomic sequence.
[0309] d. Prediction of Mature miRNA:
[0310] Short-RNA genomic locations consistent with hairpin
secondary structures (smirREGs) were clustered based on genomic
region overlap, and smirREG clusters were pruned, split, merged,
accepted, or eliminated iteratively. Clusters were first
constructed from smirREGs corresponding to: (1) regions perfectly
aligned to short-RNAs; (2) regions aligned to short-RNAs with
1-mismatch, represented by an `A` in the last position; and (3)
regions aligned to short-RNAs with 1-mismatch, where the associated
short-RNAs had no perfect matches, were not used in (1) or (2) and
were 1-mismatch away from short RNAs associated with smirREGs
defined in (1) or (2). These smirREGs are major contributors to
each region cluster. Regions associated with perfectly matching
short-RNAs and 1-mismatch short-RNAs that were not used to define
smirREG clusters, but overlapped 5 or fewer such clusters were
tagged as minor contributors and added to the overlapping smirREG
clusters. Each cluster was pruned or divided by identifying regions
corresponding to short-RNAs where more than 25% of the region is
supported by no more than 50% of the observations. For each
cluster, all such regions were identified and first minor then
major contributors with the largest ratio of unsupported portions
to total length were iteratively removed until at least 75% of
every contributing region was supported by more than 50% of the
observations.
[0311] One exception is represented by CU-1088 cluster where a
short-RNA was included despite the fact that only 70% of its
sequence contributed to the majority observation. This exception
was made because this short-RNA was the only one matching a known
mature miRNA (miR-320a) and it was left out by the 75% rule.
[0312] Pruned smirREGs were merged and used to construct new and
possibly overlapping clusters, but minor contributors were
discarded. Finally, smirREG clusters were used to define putative
mature miRNAs. The mature sequence was defined as the majority
nucleotide in each position supported by more than 50% of the
observations, with the genomic sequence allowed to break ties.
SmirREG clusters were matched based on mature sequence containment.
Clusters corresponding to a short-RNA set that is fully contained
in a set corresponding to a matched cluster were eliminated, and
matching clusters with partial containment were merged. The process
was repeated until no elimination or merging was needed. Finally, a
putative precursor was identified for each smirREG cluster
following the procedure described in (c) with the added restriction
that no more than 5 positions in the mature sequence were allowed
to dangle off of the precursor region encapsulated by complimentary
base pairs. When the mature region dangled off of the precursor
region (but no more than 5 bases), the precursor was extended with
non complimentary bases to include the mature region.
[0313] The mature miRNA prediction was followed by the elimination
of incompatible predictions. Putative miRNAs whose predicted
locations overlapped loops of known miRNAs or precursors of other
higher-confidence predictions that could not form mature-star pairs
were eliminated. Predicted miRNAs that were entirely composed of
low confidence single-observation short-RNAs that contained linker
fragments were also eliminated, with the exception of CU-1293 as
described in (a). Mature miRNA predictions of length shorter than
17 nt or longer than 28 nt were discarded. Candidate miRNAs that
were supported by a single observation were tagged as lower
confidence predictions; some of these are likely to be miRNA, but
others may be degradation products of previously unannotated
RNA.
[0314] e. Annotation and Filtering of Candidate miRNA and sRNA:
[0315] Putative miRNAs and short RNAs were matched to several RNA
databases (see below) via regular expression scans (for sequence
databases) or genomic region containment (for databases that
specify genomic regions). Databases identifying validated human
mRNA, tRNA, snoRNA and yRNA were used to eliminate putative miRNA
candidates with one observation and to annotate putative miRNAs
with multiple observations. All putative miRNAs matching rRNAs were
eliminated regardless of the number of observations because of the
extreme abundance of rRNAs. Other RNA databases were used for
annotation purposes only.
[0316] Precursor and mature miRNA as well as sRNA sequences were
aligned to several sequence databases (see below) using the BLAST
and MEGABLAST programs from NCBI. Candidate miRNA precursors
showing a full match to non-coding RNAs (tRNA, rRNA, snoRNA, other
nc-RNA) or to mRNA were disregarded. Predicted precursor and mature
miRNAs were further classified as either "known" or "new" based on
whether exact matches can be found in miRBAse database. Short-RNA
sequences included in miRNA precursor, but not overlapping the
mature miRNA, were considered as degradation products of miRNA
precursor processing and marked as "miRNA other" (Table 6). All
cloned short-RNA were annotated using the databases reported below
and results are showed in Table 2.
TABLE-US-00024 TABLE 6 Databases used for annotation of short-RNA
and miRNA. Name/Description Source Version/Date miRBASE Sanger
Institute, version 11.0 http://microrna.sanger.ac.uk/sequences
Human fraction of GIRI, http://www.girinst.org/Repbase_Update.html
version 12.02 REPBASE Human tRNA EMBL,
http://www.trna.uni-bayreuth.de, September Bayreuth Univ., Germany
2007 edition Human snoRNA The University of Queensland, Australia,
September IMB, http://imb.uq.edu.au 2006 edition Human rRNA NCBI,
ftp://ftp.ncbi.nlm/nih.gov, compiled Downloaded manually January
2007 Human yRNA NCBI, ftp://ftp.ncbi.nlm/nih.gov, compiled
Downloaded manually January 2007 Non coding RNA Compiled manually
combining resources Compiled in October from NCBI,
ftp://ftp.ncbi.nlm/nih.gov and 2006 using IMB http://imb.uq.edu.au
current ENTREZ and September 2006 edition of Univ. of Queensland
database VECTOR databases NCBI, ftp://ftp.ncbi.nlm/nih.gov
Downloaded January 2007 Human protein coding NCBI annotation for
human genome, Downloaded genes and mRNA ftp://ftp.ncbi.nlm/nih.gov
January 2007 mRNA dataset NCBI, ftp://ftp.ncbi.nlm/nih.gov compiled
Downloaded manually using ENTRES NR database January 2007 exEID
(exon subset of University of Toledo, Ohio, September EID database)
http://hsc.utoledo.edu/bioinfo/eid/ 2005 (hs35p1) Human
mitochondrial NCBI, ftp://ftp.ncbi.nlm/nih.gov Downloaded genome
January 2007 Human EST database NCBI, ftp://ftp.ncbi.nlm/nih.gov
Human viral genomes NCBI, http://www.ncbi.nlm.nih.gov, viral
Compiled in genomes section March 2007 E. coli genomes NCBI,
ftp://ftp.ncbi.nlm/nih.gov Downloaded August 2007 RefGene Intron
UCSC, http://genome.ucsc.edu, annotation annotation track track for
hg18 for hg18 RefGene Exon UCSC, http://genome.ucsc.edu, annotation
annotation track track for hg18 for hg18 rnaGenes UCSC,
http://genome.ucsc.edu, annotation annotation track track for hg18
for hg18 wgRNA UCSC, http://genome.ucsc.edu, annotation annotation
track track for hg18 for hg18 snoRNA database EMBL,
http://www-snorna.biotoul.fr/ Version 3 Genscan MIT,
http://genes.mit.edu/GENSCAN.html Version 1.0 Computational tRNA
UCSC, http://genome.ucsc.edu, annotation annotation track prdiction
track for hg18 for hg18 piRNA The University of Queensland,
Australia, September IMB, http://imb.uq.edu.au 2006 edition Morozov
database Manually curated Version 1.0
[0317] f. Estimation of Mature miRNA Frequencies:
[0318] Short-RNAs may contribute to more than one miRNA. In order
to compare observation frequencies of predicted miRNAs we
normalized the contribution of each supporting short-RNA to its
associated predicted miRNA in each library. Short-RNAs supporting a
single miRNA prediction were not affected, but the level of support
of short-RNAs associated with several miRNAs was prorated. The
normalization procedure was performed iteratively. First, for each
library, we assigned an observation frequency to each miRNA, taken
to be the sum of the library-specific observations across all of
its supporting short-RNAs. Second, for each short-RNA observed in
this library, we computed sum, the sum of the observation
frequencies of the predicted miRNAs it supports. Then, short-RNA
support for each miRNA was adjusted to be the number of its
observations multiplied by the ratio between the observation
frequency of this miRNA and sum. Finally, the frequency of each
predicted miRNA was recalculated to be the sum of the adjusted
frequencies of the short-RNAs supporting it. To compare the
abundance of predicted miRNAs across libraries we normalized the
frequencies of observations in each library to sum to 100%,
comparing frequencies of observations in each library rather than
raw observations. This normalization step was necessary due to the
variability between the total number of observations across
libraries.
[0319] g. Clustering Short-RNAs.
[0320] Short-RNAs that did not support predicted miRNAs were
categorized according to the quality of their best alignments to
hg18. These short-RNA were clustered following the procedure
described in (c) but with no secondary structure requirements
(Table 2 and Tables 9-10). Table 3 and Tables 9-10 were constructed
from perfect matches and single mismatches, respectively, as
described in (c). Tables 4 and 5 smirREGs were constructed from
single-mismatches, double mismatches and three or more mismatches,
respectively.
[0321] Estimation of Libraries Complexity
[0322] A bootstrap technique was used to estimate the total number
of miRNAs expressed in each library and the number of short-RNAs
must be sequenced to achieve a complete coverage. Bootstrapping is
a statistical technique for estimating properties of an "estimator"
by measuring those properties in multiple subsets of the
samples.sup.s3,s4. Specifically, we estimated the distribution of
mature miRNAs obtained by random sub-sampling different size
short-RNA libraries from each complete library. For each size N=10,
20, . . . N.sub.t, where N.sub.t is the total number of short-RNAs
in the library, we randomly sampled 1000 libraries of size N and
computed the number r(N) of inferred miRNAs, resulting in a
distribution p(r(N)) for which we could compute standard
statistical parameters such as average, variance, mode and median.
Based on this sampling, we can extrapolate p(r(N)) for increasing
values of N to determine at which point it is no longer efficient
to use larger values of N to increase miRNA coverage. To achieve
this, we fitted the data to the parametric function
f(x)=K*(1-e.sup.-mx). Since we include both experimentally
confirmed and putative mature miRNAs and since bootstrapping can
produce optimistic results we expect that the estimated values
constitute an upper boundary on the real library complexity.
[0323] Based on this analysis, we estimated that the total numbers
of mature miRNAs are: 188 (naive), 211 (memory), 219 (centroblasts)
and 225 (Ramos). Thus, the libraries sequenced in this study cover
respectively 84.0% (naive), 87.2% (memory), 86.8% (centroblasts),
and 85.8% (Ramos) of the expressed miRNAs in these cellular
phenotypes. FIG. 17 gives the 95% confidence intervals for p(r(N))
at each sampling point, in addition to the curve of the associated
extrapolated function for each library. Clearly, the bootstrap
analysis estimate of the total number of miRNA is correct only if
the abundance of the miRNAs expressed in the sampled populations
closely matches that of known miRNA in miRBase. This is not
unreasonable if, as was done here, only miRNAs that are specific to
a B cell differentiation stage or transformation are considered.
Thus, this does not estimate the total number of miRNA expressed
across all human cell types, stages of differentiation and
neoplastic transformations, which could be several fold larger than
what was estimated from the B cell clone libraries.
[0324] Orthology and Conservation Analysis
[0325] We investigated conservation of known and predicted
precursor and mature human miRNA in chimp (panTro2), monkey
(rheMac2), dog (canFam2) mouse (mm8) and rat (rn4). We obtained 678
miRNA precursor sequences from miRBase (v.11.0); 677 (672 unique)
mature miRNAs; and 170 (167 unique) star sequences. In total, we
obtained 947 locations for mature and star mirBase sequences. We
predicted 926 precursors of which 146 match miRBase precursors and
780 are newly predicted. Categorizing these by their corresponding
mature sequences, 762 precursors correspond to mature miRNAs that
are not included in the miRBase and 164 precursors are associated
with 129 predicted miRNAs that match miRBase miRNAs. Of the 762
newly predicted precursors, one overlaps with a miRBase precursor
and its corresponding predicted miRNA is a candidate star sequence;
19 precursors associated with 8 mature sequences listed in miRBase
database.
[0326] Here, we predicted 762 miRNA genomic locations associated
with unique mature miRNA sequences not included in miRBase. Of
these 762 predicted miRNA genomic locations, one overlaps with a
miRBase precursor and is a candidate star sequence. We identified
164 precursors associated with 129 predicted miRNAs matching the
sequence of known miRNAs; 19 of the 164 precursors, associated with
9 known miRNAs, do not match known precursors. miRNA conservation
has been repeatedly used to help identify putative miRNA mappings
to genomes. To identify putative ortholog miRNAs we relied on
UCSC-provided Blastz pairwise alignments between human and target
species.sup.s5. We used two related but complementary methods: (1)
map the mature human miRNA to its ortholog location as specified by
pairwise alignment; and (2) map the precursor of the human miRNA to
its ortholog location as specified by pairwise alignment, expanding
the human region to include at least 80 bases from both sides of
the mature region, and identifying regions in the target that match
the sequence of the mature human miRNA.
[0327] Method 1 is the simplest but fails to account for alignment
inaccuracies and local mutations that may shift the position of the
mature sequence in the target species. Method 2 accounts for
locally imperfect Blastz mapping, but relies on conservation of
larger regions that may not be subject to the same selective
pressure as the mature miRNA. Alignment-based mapping of the human
mature miRNA to its target were required to have either perfect
conservation of the entire mature miRNA sequence or conservation of
seeds composed of seven bases starting from the second position of
the human mature sequence followed by conservation of 3 bases
starting from the 12th, 13.sup.th, or 14th position as suggested
by.sup.s6. We scanned the entire mapped ortholog region for a match
to the human mature sequence or to its seed.
[0328] Comparison with Previously Reported miRNA Prediction from
Short-RNA Libraries
[0329] Landgraf et al..sup.s7 used more restrictive miRNA
charachterizations for mature miRNA prediction, annotation and
conservation. They required that at least 60% of the observations
associated with a predicted miRNA align at the 5' end. We made no
such restriction, and some of the miRNAs with the highest number of
observations in our libraries, such as CU-1026 and CU-1018, are
supported by a high proportion of 5'-misaligned cloned sequences.
Landgraf et al. eliminated predictions that can be derived from
repeat sequences by excluding precursors that contain more than 30%
repetitive elements and that match hg18 more than 10 times with at
least 75% identity. We annotated mature sequences that match known
repeats but did not eliminate them. Finally, Landgraf et al.
formulated extensive criteria for sequence orthology, requiring
sequence conservation greater than 75% in multiple alignments
across vertebrates and either restricting the 20 5'-most misaligned
nucleotides to be transitions or requiring 100% conservation in
positions 2 through 8 and 90% conservation overall. We, as
described above, simply considered full conservation and seed-based
conservation, mapping human to primates, dog and rodents.
REFERENCES
[0330] s1. Griffiths-Jones, S. miRBase: the microRNA sequence
database. Methods Mol Biol 342, 129-38 (2006). [0331] s2.
Griffiths-Jones, S., Grocock, R. J., van Dongen, S., Bateman, A.
& Enright, A. J. miRBase: microRNA sequences, targets and gene
nomenclature. Nucleic Acids Res 34, D140-4 (2006). [0332] s3.
Harrell, F. E. Regression modeling strategies: with applications to
linear models, logistic regression, and survival analysis
(Springer, New York, 2001). [0333] s4. Hinkley, A. C. D. a. D. V.
Bootstrap Methods and their Applications (Cambridge University
Press, New York, 1997). [0334] s5. Schwartz, S. et al. Human-mouse
alignments with BLASTZ. Genome Res 13, 103-7 (2003). [0335] s6.
Grimson, A. et al. MicroRNA targeting specificity in mammals:
determinants beyond seed pairing. Mol Cell 27, 91-105 (2007).
[0336] s7. Landgraf, P. et al. A mammalian microRNA expression
atlas based on small RNA library sequencing. Cell 129, 1401-14
(2007).
Example 4
miRNome of Human Mature B Cells
[0337] Summary:
[0338] The full set of microRNAs (miRNAs) in the human genome is
not known. Because presently known miRNAs have been identified by
virtue of their abundant expression in a few cell types, many
tissue-specific miRNAs remain unrevealed. To understand the role of
miRNAs in B cell function and lymphomagenesis, we generated
short-RNA libraries from normal human B cells at different stages
of development (naive, germinal center, memory) and from a Burkitt
lymphoma cell line. A combination of cloning and computational
analysis identified 178 miRNAs (miRNome) expressed in normal and/or
transformed B cell libraries. Most notably, the B cell miRNome
included 75 miRNAs which to our knowledge have not been previously
reported and of which 66 have been validated by RNA blot and/or
RT-PCR analyses. Numerous miRNAs were expressed in a stage- or
transformation-specific fashion in B cells, suggesting specific
functional or pathologic roles. These results provide a resource
for studying the role of miRNAs in B cell development, immune
function, and lymphomagenesis.
[0339] A new mechanism of post-transcriptional regulation has been
revealed with the discovery of microRNAs (miRNAs), a class of short
RNAs that impair translation or induce mRNA degradation by binding
to the 3' untranslated region of target mRNA ([Bartel, 2004] and
[Kim, 2005]). A recent release of the miRBase database (v.11.0)
([Griffiths-Jones, 2006] and [Griffiths-Jones et al., 2006])
reports 847 human miRNAs. However, the discovery of miRNAs is still
an on-going process with variable predictions about the total
number of miRNAs expressed in mammalian cells ranging from one
thousand to several thousands ([Bentwich et al., 2005] and [Miranda
et al., 2006]). The reported miRNAs have been identified from a
limited number of cell types or from tissues whose cellular
heterogeneity may favor the identification of ubiquitous and
abundant miRNA. In fact, a recent report aiming for the
identification of miRNA expression profiles from a large panel of
different mammalian tissues and cell types led to the discovery of
only 12 previously unreported human miRNA (Landgraf et al., 2007).
These findings led to the conclusion that most miRNAs are known and
that most of them are ubiquitously expressed (Landgraf et al.,
2007). Nonetheless, additional analyses of purified cell
populations have led to the identification of tissue- and stage of
differentiation-specific miRNAs in a few tissues, suggesting the
existence of tissue-specific miRNA expression ([Calabrese et al.,
2007] and [Cummins et al., 2006]).
[0340] The role of miRNAs in B lymphocyte development and B cell
lymphomagenesis is largely unknown. A critical stage of the
differentiation process leading to effector B cells is represented
by the germinal centers (GC), the structures that develop when
mature naive B cells encounter the antigen in the secondary
lymphoid organs and are stimulated to proliferate and differentiate
into GC centroblasts (CB). During the GC reaction, B cells undergo
somatic hypermutation of their immunoglobulin-variable regions and
class switch recombination. B cells that have acquired the ability
to express high-affinity immunoglobulins are then positively
selected and further differentiate into the final effectors of the
humoral immune response, i.e., memory B cells and plasma cells
(Klein and Dalla-Favera, 2008). Naive, GC, and memory B cells are
also relevant targets of disease because each of these B cell
subpopulations can be affected by malignant transformation leading
to different types of lymphomas and leukemias ([Klein and
Dalla-Favera, 2008] and [Kuppers and Dalla-Favera, 2001]).
[0341] Several initial observations suggest an important role of
specific miRNAs in B cell function and malignancy. Via mouse
models, miR-155 has been demonstrated to affect regulation of the
GC response through modulation of cytokine production ([Rodriguez
et al., 2007] and [Thai et al., 2007]) and by direct
post-transcriptional regulation of the activation-induced cytidine
deaminase (AID) ([Dorsett et al., 2008] and [Teng et al., 2008]).
Recently, miR-150 has been shown to target MYB, a critical
transcription factor involved in the control of B cell
differentiation (Xiao et al., 2007). In B cell lymphomas, 13q31
amplification has been associated with the overexpression of the
miR-17-92 cluster and its enforced expression in a murine B cell
lymphoma model showed a role in accelerating tumor development (He
et al., 2005). Furthermore, miR-15a and miR-16 have been implicated
in the pathogenesis of B cell chronic lymphocytic leukemia (CLL)
([Calin et al., 2002] and [Calin et al., 2005]).
[0342] As a basis for a comprehensive analysis of the role of
miRNAs in B cell function and lymphomagenesis, this study was aimed
at identifying the miRNAs expressed (miRNome) in the human mature B
cell compartment, including naive, GC, and memory B cells. By using
a combination of cloning and computational analysis, we report the
identification of 178 miRNAs representing the mature B cell
miRNome, including 75 previously unreported miRNAs. The results
show that normal B cell subpopulations are characterized by
specific miRNA "signatures," suggesting functional roles of miRNAs
in B cell differentiation and transformation.
[0343] Results
[0344] Construction of Short-RNA Libraries from Human B Cell
Subpopulations.
[0345] Short-RNA libraries were generated by cloning RNA fractions
of 15-30 nt from human centroblasts, naive, and memory B cells
purified from tonsils, as well as from the Burkitt lymphoma cell
line Ramos, which is representative of malignant transformation of
GC B cells. Approximately 3,500 sequences were analyzed from each
library, corresponding to 13,788 total short-RNAs (2,632
nonredundant sequences). By using a bootstrap approach ([Harrell,
2001] and [Davison and Hinkley, 1997]), we estimated that more than
85% of the complexity of the libraries has been examined (FIG.
23).
[0346] Mapping of Short-RNA Sequences to the Human Genome.
[0347] The cloned sequences were subjected to a computational
analysis (see Supplemental Experimental Procedures described in
Example 3) summarized in the flowchart illustrated in FIG. 24. Each
cloned sequence was first matched to the human genome assembly
(March 2006, hg18) to retrieve the genomic regions from which the
short RNAs originated. One or more genomic locations were
identified for 2086 (80%) of the cloned sequences considering both
perfect matches and single mismatches (FIG. 24). Consistent with
previous observations, 3'-end mismatches were the most common and
showed a clear preference for A in the last position (Neilson et
al., 2007). The failure of 546 short-RNA sequences to align with
the human genome is likely due, at least in part, to errors
introduced by PCR during the cloning procedure (FIG. 24). However,
a small subset of these short RNAs lacking a corresponding genomic
region in Homo sapiens have been cloned with high frequencies in
multiple libraries and showed differential expression during B cell
differentiation, suggesting that they may represent bona fide
short-RNA species, which cannot be mapped on the current reference
genome probably because of polymorphisms and/or
post-transcriptional modifications. However, given the difficulty
of assigning genomic coordinates to these sequences, they were
omitted from further analyses.
[0348] Computational Prediction of Precursor and Mature miRNAs.
[0349] In order to identify candidate miRNAs among the cloned
short-RNA sequences, we developed a computational pipeline aiming
at the identification of potential miRNA precursors based on the
investigation of their genomic location and folding characteristics
(FIG. 18 and Supplemental Experimental Procedures in Example 3). In
brief, short RNA sequences were mapped to the human genome and
their respective candidate genomic precursors (.+-.90 nt) were
retrieved and analyzed for secondary structure, size and energy of
the loop, and number of complimentary base pairs in the stem of the
loop. The prediction was performed on the full set of nonredundant
short RNAs (2632 sequences) for which one or more genomic locations
could be identified (FIG. 24). The analysis led to the
identification of candidate miRNA precursors for 1646 short-RNA
sequences, which were then clustered allowing for (1) the
variability observed at the mature miRNA 3' ends (and less
dramatically at the 5' ends) including nucleotide substitutions and
deletions, and (2) the possibility of miRNA editing as previously
reported ([Kawahara et al., 2007] and [Luciano et al., 2004])
(Supplemental Experimental Procedures in Example 3). After
annotating each candidate mature miRNA, those which matched mRNA,
rRNA, tRNA, post-transcriptionally modified t-RNA, and other ncRNA
(yRNA, sn/snoRNA) sequences, and were present only once in the
libraries were not considered further. The remaining sequences were
still considered miRNAs based on criteria (identification of
genomic loci consistent with a pre-miRNA, length, recurrence,
differential expression, detection in the Ago complex) that suggest
their existence as bona fide miRNA. Moreover, consistent with the
miRNA length of the Homo sapiens miRBase database (v11.0), only
mature candidate miRNAs of length 17-28 nt were considered.
[0350] Overall, the analysis identified 178 mature miRNAs, of which
103 were known and 75 were not previously reported, to our
knowledge (Table 7 and FIG. 24). Computational prediction of
precursor miRNAs (pre-miRNA) identified 114 precursors already
reported to potentially code for the 103 known mature miRNA, and
274 genomic locations containing new candidate pre-miRNA associated
with the 75 previously unreported and 8 known mature miRNAs (FIG.
19 and Table 7).
TABLE-US-00025 TABLE 7 (PART A) List of known and newly identified
bona fide and candidate mature miRNAs and their predicted
precursors. Genomic locations are provided for all candidate miRNA.
Frequencies have been calculated only for bona fide miRNA (cloned
at least 2 times in the B cell libraries). SEQ ID ID NO. Mature
miRNA sequence Annotations CU-1026 1 TGTAGTGTTTCCTACTTTATGGA
Mature:hsa-miR-142-3p:MIMAT0000434 CU-1064 2 TAGCTTATCAGACTGATGTTGA
Mature:hsa-miR-21:MIMAT0000076 CU-1061 3 TAAAGTGCTTATAGTGCAGGTAG
Mature:hsa-miR-20a:MIMAT0000075 CU-1035 4 TAGCAGCACATCATGGTTTACA
Mature:hsa-miR-15b:MIMAT0000417 CU-1037 5 TAGCAGCACGTAAATATTGGCG
Mature:hsa-miR-16:MIMAT0000069 CU-1001 6 TGAGGTAGTAGGTTGTATAGTT
Mature:hsa-let-7a:MIMAT0000062 CU-1116 7 TATTGCACTTGTCCCGGCCTGT
Mature:hsa-miR-92a:MIMAT0000092 CU-1018 8 TCCCACCGCTGCCACCA
Mature:hsa-miR-1280:MIMAT0005946 CU-1006 9 TGAGGTAGTAGATTGTATAGTT
Mature:hsa-let-7f:MIMAT0000067 CU-1079 10 TAGCACCATCTGAAATCGGTTA
Mature:hsa-miR-29a:MIMAT0000086 CU-1033 11 TAGCAGCACATAATGGTTTGT
Mature:hsa-miR-15a:MIMAT0000068 CU-1124 12 CCCATAAAGTAGAAAGCACTA
Mature:hsa-miR-142-5p:MIMAT0000433 CU-1007 13
TGAGGTAGTAGTTTGTACAGTT Mature:hsa-let-7g:MIMAT0000414 CU-1008 14
TGAGGTAGTAGTTTGTGCTGTT Mature:hsa-let-7i:MIMAT0000415 CU-1082 15
TAGCACCATTTGAAATCGGTTA Mature:hsa-miR-29c:MIMAT0000681 CU-1085 16
TGTAAACATCCTACACTCTCAGC Mature:hsa-miR-30c:MIMAT0000244 CU-1039 17
CAAAGTGCTTACAGTGCAGGTAG Mature:hsa-miR-17:MIMAT0000070 CU-1071 18
CATTGCACTTGTCTCGGTCTGA Mature:hsa-miR-25:MIMAT0000081 CU-1046 19
CAACGGAATCCCAAAAGCAGCTG Mature:hsa-miR-191:MIMAT0000440 CU-1057 20
TGTGCAAATCCATGCAAAACTGA Mature:hsa-miR-19b:MIMAT0000074 CU-1024 21
TACCACAGGGTAGAACCACGGA Mature:hsa-miR-140-3p:MIMAT0004597 CU-1084
22 TGTAAACATCCTACACTCAGCT Mature:hsa-miR-30b:MIMAT0000420 CU-1003
23 TGAGGTAGTAGGTTGTGTGGTT Mature:hsa-let-7b:MIMAT0000063 CU-1080 24
TAGCACCATTTGAAATCAGTGTT Mature:hsa-miR-29b:MIMAT0000100 CU-1012 25
TAAAGTGCTGACAGTGCAGAT Mature:hsa-miR-106b:MIMAT0000680 CU-1092 26
TCCCTGTCCTCCAGGAGCTC Mature:hsa-miR-339-5p:MIMAT0000764 CU-1072 27
TTCAAGTAATCCAGGATAGGCT Mature:hsa-miR-26a:MIMAT0000082 CU-1118 28
CAAAGTGCTGTTCGTGCAGGTAG Mature:hsa-miR-93:MIMAT0000093 CU-1067 29
TGTCAGTTTGTCAAATACCCCA Mature:hsa-miR-223:MIMAT0000280 CU-1027 30
TGAGAACTGAATTCCATGGGTT Mature:hsa-miR-146a:MIMAT0000449 CU-1029 31
TCTCCCAACCCTTGTACCAGT Mature:hsa-miR-150:MIMAT0000451 CU-1015 32
TCCCTGAGACCCTAACTTGTGA Mature:hsa-miR-125b:MIMAT0000423 CU-1093 33
TCTCACACAGAAATCGCACCCGTC Mature:hsa-miR-342-3p:MIMAT0000753 CU-1016
34 GTCCCTGTTCGGGCGCCA Mature:hsa-miR-1274b:MIMAT0005938 CU-1056 35
TGTGCAAATCTATGCAAAACTGA Mature:hsa-miR-19a:MIMAT0000073 CU-1086 36
TGTAAACATCCCCGACTGGAAG Mature:hsa-miR-30d:MIMAT0000245 CU-1065 37
AGCTACATTGTCTGCTGGGTT Mature:hsa-miR-221:MIMAT0000278 CU-1004 38
AGAGGTAGTAGGTTGCATAGTT Mature:hsa-let-7d:MIMAT0000065 CU-1011 39
CCGCACTGTGGGTACTTGCT Star:hsa-miR-106b*:MIMAT0004672 CU-1010 40
AGCAGCATTGTACAGGGCTATGA Mature:hsa-miR-103:MIMAT0000101 CU-1050 41
AACTGGCCCTCAAAGTCCCGCT Mature:hsa-miR-193b:MIMAT0002819 CU-1091 42
GCCCCTGGGCCTATCCTAGAA Mature:hsa-miR-331-3p:MIMAT0000760 CU-1023 43
AGCTGGTGTTGTGAATCAGGCCGT Mature:hsa-miR-138:MIMAT0000430 CU-1101 44
TGAGGGGCAGAGAGCGAGACTT Mature:hsa-miR-423-5p:MIMAT0004748 CU-1066
45 AGCTACATCTGGCTACTGGGTCT Mature:hsa-miR-222:MIMAT0000279 CU-1017
46 GTGGGGGAGAGGCTGTA Mature:hsa-miR-1275:MIMAT0005929 CU-5001 47
CTATACGACCTGCTGCCTTTC Star:hsa-let-7d*:MIMAT0004484 CU-1032 48
TTAATGCTAATCGTGATAGGGGT Mature:hsa-miR-155:MIMAT0000646 CU-1108 49
AGGGGGAAAGTTCTATAGTC Mature:hsa-miR-625:MIMAT0003294 CU-1055 50
ACAGTAGTCTGCACATTGGTT Mature:hsa-miR-199b-3p:MIMAT0004563 CU-1042
51 AACATTCAACGCTGTCGGTGAGTT Mature:hsa-miR-181a:MIMAT0000256
CU-1113 52 TGGAAGACTAGTGATTTTGTTGT Mature:hsa-miR-7:MIMAT0000252
CU-1098 53 TAATGCCCCTAAAAATCCTTAT Mature:hsa-miR-365:MIMAT0000710
CU-1052 54 TAGCAGCACAGAAATATTGGCA Mature:hsa-miR-195:MIMAT0000461
CU-1568 55 TGAGGTAGTAGGTTGTAT Mature:hsa-let-7c:MIMAT0000064
CU-1103 56 TCCTGTACTGAGCTGCCCCGAG
Mature:hsa-miR-486-5p:MIMAT0002177 CU-1014 57
TCCCTGAGACCCTTTAACCTGTGA Mature:hsa-miR-125a-5p:MIMAT0000443
CU-1068 58 ATCACATTGCCAGGGATTTCCA Mature:hsa-miR-23a:MIMAT0000078
CU-1019 59 TCACAGTGAACCGGTCTCTTT Mature:hsa-miR-128:MIMAT0000424
CU-1076 60 CACTAGATTGTGAGCTCCTGGA Mature:hsa-miR-28-3p:MIMAT0004502
CU-1111 61 CAACAAATCACAGTCTGCCAT Star:hsa-miR-7-1*:MIMAT0004553
CU-1062 62 CAAAGTGCTTATAGTGCAGGTAG
Mature:hsa-miR-20b-mm:MIMAT0001413 CU-1115 63
AGGTTGGGATCGGTTGCAATGCT Star:hsa-miR-92a-1*:MIMAT0004507 CU-1126 64
ACATTCATTGCTGTCGGTGGGTT Mature:hsa-miR-181b:MI0000270 CU-5016 1093
AATGACACGATCACTCCCGTTGAG Mature:hsa-miR-425:MIMAT0003393 CU-1096 65
TCCCCCAGGTGTGATTCTGATT Mature:hsa-miR-361-3p:MIMAT0004682 CU-1054
66 CCCAGTGTTCAGACTACCTGTTC Mature:hsa-miR-199a-5p:MIMAT0000231
CU-1125 67 ACCAATATTACTGTGCTGCTT Star:hsa-miR-16-2*:MIMAT0004518
CU-1087 68 TGTAAACATCCTTGACTGGAAGCT Mature:hsa-miR-30e:MIMAT0000692
CU-1045 69 TAAGGTGCATCTAGTGCAGATA Mature:hsa-miR-18a:MIMAT0000072
CU-1069 70 ATCACATTGCCAGGGATTACCA Mature:hsa-miR-23b:MIMAT0000418
CU-1044 71 ACTGCCCTAAGTGCTCCTTCTG Star:hsa-miR-18a*:MIMAT0002891
CU-1083 72 TGTAAACATCCTCGACTGGA Mature:hsa-miR-30a:MIMAT0000087
CU-1009 73 TACAGTACTGTGATAACTGAAG Mature:hsa-miR-101:MIMAT0000099
CU-1030 74 CTAGACTGAAGCTCCTTGAGG Mature:hsa-miR-151-3p:MIMAT0000757
CU-1088 1094 TGGGTTGAGAGGGCGAA Mature:hsa-miR-320a:MIMAT0000510
CU-1095 75 TGGCAGTGTCTTAGCTGGTTGTT Mature:hsa-miR-34a:MIMAT0000255
CU-1119 76 TGAGGTAGTAAGTTGTATTGTT Mature:hsa-miR-98:MIMAT0000096
CU-1028 77 TGAGAACTGAATTCCATAGGCTGT
Mature:hsa-miR-146b-5p:MIMAT0002809 CU-1031 78
TCGAGGAGCTCACAGTCTAGTA Mature:hsa-miR-151-5p:MIMAT0004697 CU-1100
79 AGCTCGGTCTGAGGCCCCTCAG Mature:hsa-miR-423-3p:MIMAT0001340
CU-1038 80 ACTGCAGTGAAGGCACTTGTAG Star:hsa-miR-17*:MIMAT0000071
CU-1040 81 ACCATCGACCGTTGATTGTA Star:hsa-miR-181a*:MIMAT0000270
CU-1053 82 TTCACCACCTTCTCCACCCAG Mature:hsa-miR-197:MIMAT0000227
CU-1075 83 TTCACAGTGGCTAAGTTCTG Mature:hsa-miR-27b:MIMAT0000419
CU-1073 84 TTCAAGTAATTCAGGATAGGTT Mature:hsa-miR-26b:MIMAT0000083
CU-1110 85 TGGGTTTACGTTGGGAGAACT Mature:hsa-miR-629:MIMAT0004810
CU-1005 87 TGAGGTAGGAGGTTGTATAGTT Mature:hsa-let-7e:MIMAT0000066
CU-1081 88 TGACCGATTTCTCCTGGTGTT Star:hsa-miR-29c*:MIMAT0004673
CU-1117 89 TATTGCACTCGTCCCGGCC Mature:hsa-miR-92b:MIMAT0003218
CU-1094 90 GGGGTGCTATCTGTGATTGA Mature:hsa-miR-342-5p:MIMAT0004694
CU-1021 91 GCATGGGTGGTTCAGTGGTAGAA Mature:hsa-miR-1308:MIMAT0005947
CU-1089 92 CTGGCCCTCTCTGCCCTT Mature:hsa-miR-328:MIMAT0000752
CU-1047 93 CTGACCTATGAATTGACAGC Mature:hsa-miR-192:MIMAT0000222
CU-1099 94 CTCCTGACTCCAGGTCCTGTG Star:hsa-miR-378*:MIMAT0000731
CU-1105 95 CGTCAACACTTGCTGGTT Mature:hsa-miR-505:MIMAT0002876
CU-1034 96 CGAATCATTATTTGCTGCTCT Star:hsa-miR-15b*:MIMAT0004586
CU-5002 97 CATCGGGAATGTCGTGTCCGCC Star:hsa-miR-425*:MI0001448
CU-1025 98 CAGTGGTTTTACCCTATGGTA Mature:hsa-miR-140-5p:MIMAT0000431
CU-1022 99 CAGTGCAATGATGAAAGGGCAT Mature:hsa-miR-130b:MIMAT0000691
CU-1104 100 CAGCAGCACACTGTGGTTTGT Mature:hsa-miR-497:MIMAT0002820
CU-1106 101 CACGCTCATGCACACACCCAC
Mature:hsa-miR-574-3p:MIMAT0003239 CU-1077 102
AAGGAGCTCACAGTCTATTGAG Mature:hsa-miR-28-5p:MIMAT0000085 CU-1132
131 GCCGGGTACTTTCGTATTTT NEW CU-1137 132 GCTAAGGAAGTCCTGTGCTCAGTTTT
NEW CU-1178 148 AGGGTGTGCGTGTTTTT NEW CU-1164 150 GAGAGCGCTCGGTTTTT
NEW CU-1148 151 TGGTGTGGTCTGTTGTTTT NEW CU-1221 152
TGTGCTCCGGAGTTACCTCGTTT NEW CU-1180 155
AACCGAGCGTCCAAGCTCTTTCCATTTT NEW CU-1155 156 TCCCCGCACCTCCACCA NEW
CU-1175 162 GGCGTGATTCATACCTTTT NEW CU-1197 169 ATGTGGTGGCTTACTTTT
NEW CU-1146 172 AGAAAGGCCGAATTTTA NEW CU-1212 157
TCCCCGGCACTTCCACCA NEW CU-1251 232 CCCACCCAGGGACGCCA
tRNAprefix-annotate; refseqGeneIntron-annotate; CU-1254 233
TCCCCGGCACCTCCACCA tRNAprefix-annotate; refseqGeneIntron-annotate;
CU-1298 234 ATCCCGGACGAGCCCCCA tRNAprefix-annotate;
refseqGeneIntron-annotate;
CU-1153 142 CCCCCCACTGCTAAATTTGACTGGCTT refseqGeneIntron-annotate;
rnaGene-annotate CU-1276 236 TCGATTCCCGGCCAATGCACCA
tRNAprefix-annotate; refseqGeneIntron-annotate; CU-1303 237
ATCCCACTTCTGACACCA computGene-annotate; refseqGeneIntron-annotate;
tRNAprefix-annotate CU-1242 239 TCCCCGTACGGGCCACCA
tRNAprefix-annotate; refseqGeneIntron-annotate; CU-1241 243
AGTCCCATCTGGGTCGCCA tRNAprefix-annotate; refseqGeneIntron-annotate;
CU-1575 244 CCCCCCACTGCTAAATTTGACTGGA refseqGeneIntron-annotate;
rnaGene-annotate CU-1243 246 GTCCCTTCGTGGTCGCCA
tRNAprefix-annotate; refseqGeneIntron-annotate; CU-1300 248
TCCTCACACGGGGCACCA tRNAprefix-annotate; refseqGeneIntron-annotate;
CU-1278 249 TAACGGCCGCGGTACCC refseqGeneIntron-annotate CU-1264 250
GAGGGGGACCAAAAAAAA refseqGeneIntron-annotate CU-1130 133
CCCGGGTTTCGGCACCA tRNAprefix-annotate; refseqGeneIntron-annotate;
CU-1380 354 ATAGGTTTGGTCCTAGCCTTTCT piRNA-annotate;
refseqGeneIntron-annotate CU-1246 252 AGGGGGGTAAAAAAAAA
refseqGeneIntron-annotate CU-1277 254 GAGCCATGATGATACCACTGAGC
refseqGeneIntron-annotate CU-1345 257 AGAACACTACGAGCCACA
mRNA-annotate; refseqGeneIntron-annotate CU-1352 258
ACCCCACTTCTGGTACCA tRNAprefix-annotate; refseqGeneIntron-annotate;
CU-1324 260 TCTCGGTGGAACCTCCA tRNAprefix-annotate;
refseqGeneIntron-annotate; CU-1269 262 TACCGAGCCTGGTGATAGC
refseqGeneIntron-annotate CU-1281 263 GCAGCGCCAGCCTCCCGCCCTAC
refseqGeneIntron-annotate CU-1339 265 ATCCCCAGCACCTCCACCA
tRNAprefix-annotate; refseqGeneIntron-annotate; CU-1293 266
AGCAGTGATGTCCTGAAAATTCTGAAG refseqGeneIntron-annotate CU-1307 267
ACCCCACTATGCTTAGCCCT mRNA-annotate; refseqGeneIntron-annotate
CU-1294 268 AAAGGACCTGGCGGTGCTTC mRNA-annotate;
refseqGeneIntron-annotate CU-1369 350 TCCCCGGCATCTCCACCA
computGene-annotate; tRNAprefix-annotate CU-1191 143
GCCCGCATCCTCCACCA tRNAprefix-annotate; CU-1173 145
ATCCCACTCCTGACACCA tRNAprefix-annotate; CU-1142 149
TCGATTCCCGGCCCATGCACCA tRNAprefix-annotate; CU-1186 153
TCCCCGACACCTCCACCA tRNAprefix-annotate; CU-1371 352
TCTAGAGGAGCCTGTTCTGTA mRNA-annotate CU-1381 353
TCGATTCCCGGTCAGGGAACCA repeats-annotate; tRNAprefix-annotate
CU-1213 158 TCACCCCATAAACACCA tRNAprefix-annotate; CU-1363 355
CGTTCGCGCTTTCCCCTG rnaGene-annotate CU-1220 161 TTCCCCGACGGGGAGCCA
tRNAprefix-annotate; CU-1396 356 TAAGTGTTTGTGGGTTA rnaGene-annotate
CU-1570 171 ATCCCCAGCATCTCCACCA tRNAprefix-annotate; CU-1524 368
CCCCCACAACCGCGCTTGACTAGC mRNAall-annotate; yRNA-eliminate;
rnaGene-annotate CU-1453 369 CCCTGCTCGCTGCGCCA tRNAprefix-annotate;
refseqGeneExon-eliminate; CU-1477 370 CTCCCACTGCTTCACTTGACTAGC
yRNA-eliminate; refseqGeneIntron-annotate; rnaGene-annotate CU-1222
372 TCACGTCGGGGTCACCA refseqGeneExon-eliminate; tRNAprefix-annotate
CU-1388 373 TCCCTGGTGGTCTAGTGGTTAGGATTCG
tRNAcomputational-annotate; refseqGeneIntron-annotate;
rnaGene-annotate; HStRNA-eliminate; piRNA-annotate CU-1488 375
TCCTGCCGCGGTCGCCA tRNAprefix-annotate; refseqGeneExon-eliminate;
CU-1557 376 GGAGAGAACGCGGTCTGAGTGGT snoRNA-eliminate;
wgRNA-annotate; rnaGene-annotate CU-1379 377 TCGGGTGCGAGAGGTCCCGGGT
tRNAcomputational-annotate; HStRNA-eliminate; rnaGene-annotate
CU-1542 378 GGCTGGTCCGATGGTAGTGGGTT mRNAall-annotate;
yRNA-eliminate; refseqGeneIntron-annotate; rnaGene-annotate CU-1550
379 CGGAAGCGTGCTGGGCCC tRNAcomputational-annotate; tRNA-eliminate;
rnaGene-annotate; HStRNA-eliminate; piRNA-annotate CU-1513 381
GCGGGTGATGCGAACTGGAGTCTGAGC computGene-annotate; snoRNA-annotate;
refseqGeneExon-eliminate; rnaGene- annotate; snoRNA-eliminate;
wgRNA-annotate CU-1368 382 GACGAGGTGGCCGAGTGG
tRNAcomputational-annotate; rnaGene-annotate; HStRNA-eliminate;
piRNA-annotate CU-1370 351 CTGATTGCTCCTGTCTGATT mRNAall-annotate;
refseqGeneExon-eliminate; wgRNA-annotate; exEID-annotate;
rnaGene-annotate CU-1470 384 CTCCTGGCTGGCTCGCCA mRNAall-annotate;
computGene-annotate; exEID-annotate; tRNAprefix-annotate;
refseqGeneIntron-annotate; refseqGeneExon-eliminate; CU-1538 386
GGCTGGTCCGAGTGCAGTGGTGTTTA yRNA-eliminate;
refseqGeneIntron-annotate; rnaGene-annotate CU-1486 387
CTGCTGTGATGACATTC computGene-annotate; snoRNA-annotate;
refseqGeneExon-eliminate; rnaGene- annotate; snoRNA-eliminate;
wgRNA-annotate CU-1382 389 TCCTCGTTAGTATAGTGGTGAGTATCCC
tRNAcomputational-annotate; rnaGene-annotate; HStRNA-eliminate;
piRNA-annotate CU-1403 391 GCATTGGTGGTTCAGTGGTAGA rnaGene-annotate;
tRNAcomputational-annotate; piRNA-annotate; tRNA-eliminate;
refseqGeneIntron-annotate; HStRNA-eliminate CU-1457 395
TTCTCACTACTGCACTTGACTA mRNAall-annotate; exEID-annotate;
yRNA-eliminate; rnaGene-annotate; refseqGeneIntron-annotate;
refseqGeneExon-eliminate CU-1440 396 TGGTTATCACGTTCGCC
tRNAcomputational-annotate; tRNA-eliminate; rnaGene-annotate;
HStRNA- eliminate; piRNA-annotate CU-1528 397 TAGGGGTATGATTCTCGCT
tRNAcomputational-annotate; tRNA-eliminate; HStRNA-eliminate;
rnaGene-annotate CU-1288 255 CGTCCATGATGTTCCGCAA mRNAall-annotate;
snoRNA-annotate; refseqGeneIntron-annotate; refseqGeneExon-
eliminate; piRNA-annotate; wgRNA-annotate CU-1545 398
CCACGAGGAAGAGAGGTAGC snoRNA-annotate; snoRNA-eliminate;
wgRNA-annotate; rnaGene-annotate CU-1323 259 TGTATTGTGAGACATTC
mRNAall-annotate; refseqGeneExon-eliminate;
refseqGeneIntron-annotate; wgRNA-annotate; rnaGene-annotate CU-1244
399 GTCAGGATGGCCGAGCGGTCT tRNAcomputational-annotate;
rnaGene-annotate; HStRNA-eliminate; refseqGeneIntron- annotate
Candidate miRNAs observed only once in any of the four libraries
CU-1123 103 TTGGTCCCCTTCAACCAGCTGT Mature:hsa-miR-133a:MIMAT0000427
CU-1074 104 TTCACAGTGGCTAAGTTCCGA Mature:hsa-miR-27a:MIMAT0000084
CU-1097 105 TTATCAGAATCTCCAGGGGTAA
Mature:hsa-miR-361-5p:MIMAT0000703 CU-1043 106
TGGAGAGAAAGGCAGTTCCTGAT Mature:hsa-miR-185:MIMAT0000455 CU-1112 107
TGAGACCTCTGGGTTCTGAGCT Mature:hsa-miR-769-5p:MIMAT0003886 CU-1122
108 TCTTTGGTTATCTAGCTGTATGA Mature:hsa-miR-9:MIMAT0000441 CU-1109
109 TCTAGTAAGAGTGGCAGTCGA Mature:hsa-miR-628-3p:MIMAT0003297
CU-1090 110 TATTGCACATTACTAAGTTGA Mature:hsa-miR-32:MIMAT0000090
CU-1013 111 TAAGGCACGCGGTGAATGCCA Mature:hsa-miR-124:MIMAT0000422
CU-1058 112 TAACACTGTCTGGTAACGATGTT
Mature:hsa-miR-200a:MIMAT0000682 CU-1059 113 GTGAAATGTTTAGGACCACTAG
Mature:hsa-miR-203:MIMAT0000264 CU-1102 114 GCAGTCCATGGGCATATACACA
Mature:hsa-miR-455-3p:MIMAT0004784 CU-1107 115
GAGCTTATTCATAAAAGTGCAG Mature:hsa-miR-590-5p:MIMAT0003258 CU-1114
116 CTGCCCTGGCCCGAGGGACCGA Mature:hsa-miR-874:MIMAT0004911 CU-1002
117 CTATACAACCTACTGCCTTC Star:hsa-let-7b*:MIMAT0004482 CU-1049 118
CGGGGTTTTGAGGGCGAGATGA Star:hsa-miR-193b*:MIMAT0004767 CU-1051 119
CCAGTGGGGCTGCTGTTATCTG Star:hsa-miR-194*:MIMAT0004671 CU-1036 120
CCAGTATTAACTGTGCTGCTGA Star:hsa-miR-16-1*:MIMAT0004489 CU-1121 121
CACCCGTAGAACCGACCTTGCG Mature:hsa-miR-99b:MIMAT0000689 CU-1120 122
CAAGCTCGTGTCTGTGGGTCCG Star:hsa-miR-99b*:MIMAT0004678 CU-1063 123
CAACACCAGTCGATGGGCTGTA Star:hsa-miR-21*:MIMAT0004494 CU-1070 124
AGGCGGAGACTTGGGCAATT Star:hsa-miR-25*:MIMAT0004498 CU-1060 125
ACTGCATTATGAGCACTTAAAGT Star:hsa-miR-20a*:MIMAT0004493 CU-1078 126
ACTGATTTCTTTTGGTGTTCA Star:hsa-miR-29a*:MIMAT0004503 CU-1020 127
ACTCGGCGTGGCGTCGGTCGTGG Mature:hsa-miR-1307:MIMAT0005951 CU-1041
128 ACCACTGACCGTTGACTGTAC Star:hsa-miR-181a-2*:MIMAT0004558 CU-1048
129 AACTGGCCTACAAAGTCCCAGT Mature:hsa-miR-193a-3p:MIMAT0000459
CU-1136 134 TCGGGCGGGAGTGGTGGCTTT NEW CU-1383 135
TAGAGGCACCGCCTGCCCA NEW CU-1131 136 CGGGGCGCGGCCTCGCTG NEW CU-1135
137 CCCACGGGGGTCTCCGGGCGAG NEW CU-1133 139 CAGCCCGGCCTGGCTCCTCCAT
NEW CU-1134 140 CACGGAAGGTGGCCCGG NEW CU-1160 174 TGTCAGTTTGAACCCAA
NEW CU-1189 175 TGTAGTGTTTCTTACTTTA NEW
CU-1219 176 TGGCGAAGGTCGGCCGCG NEW CU-1190 179
TCGGCTTTCCCTGCTAACTGGGCTTTTT NEW CU-1144 180 TCAGAGCGCGGGCCGACCCC
NEW CU-1384 183 TAACCCCAGGGTTGGTCA NEW CU-1171 185
GGGCGTGGGTGTGATGATTC NEW CU-1199 186 GGGAGGTGAGTAGGTCTG NEW CU-1226
187 GGAGACGTGGCCGAGAG NEW CU-1572 188 GCGGAATACCACGGGGA NEW CU-1151
189 GCAGGCGGGGGATTAGCTA NEW CU-1227 190 GCAGCGGAACGTCGGCGCGC NEW
CU-1152 192 CTTGGACTAACCTGGTGTA NEW CU-1207 197
CGGTGGAACCTGCATTGGTTT NEW CU-1181 198 CGGGGCCGGGGCTAGGGT NEW
CU-1185 199 CGGGCCGCCCCCGCCCACCG NEW CU-1366 201
CGGCCTATCCGGAATGCCCC NEW CU-1145 203 CGCGGCCAGTGTCCCCTTGTA NEW
CU-1201 204 CGACACACGGCCCGTGGCGC NEW CU-1172 206 CCTCACTGGGGGCTCCA
NEW CU-1217 210 CCGCCCCGACCTTAGCTA NEW CU-1177 214
CCCCGGCATCTCCATCA NEW CU-1360 218 CCACCCTGGAGCCTCCGT NEW CU-1179
221 ATGGCCTGGACCCCACTCCT NEW CU-1161 222 ATGGCCGCATATATTTT NEW
CU-1168 225 AGCGAGGGTTCCGCCGGCC NEW CU-1195 226
ACTGGGGAGGGGGAGGAGCCTCGAGG NEW CU-1215 227 ACCCCGAGGGGACGGGCG NEW
CU-1208 228 ACAGCGCTGTGTTCCCGT NEW CU-1373 230 AACTAAAACCCCTACGCA
NEW CU-1196 231 AAAGGAGCCGAATCTTT NEW CU-1204 224
ATCCTGCTCACAGCCCCA NEW CU-1325 269 TTTGCCACACTGCAACACCTT
refseqGeneIntron-annotate CU-1310 271 TTAAACCACCAAGATCGCTGATGCAC
refseqGeneIntron-annotate CU-1299 272 TGTTCGCCGACCGTTGA
refseqGeneIntron-annotate CU-1165 173 TGTCAGTTTTTACCCAA
refseqGeneIntron-annotate CU-1322 274 TGGGAGAGCAGGGTATTGT
refseqGeneIntron-annotate CU-1203 177 TGCAGGGCCGGCGGGGAGG
refseqGeneIntron-annotate CU-1308 277 TCCGAAAGGCCTCCCGCACCG
refseqGeneIntron-annotate CU-1376 181 TCAACACCCACTCCCTC
refseqGeneIntron-annotate CU-1138 182 TATCAATGATGCTTCTGAGA
refseqGeneIntron-annotate CU-1297 279 TAGATGAATAGGTAAAGAG
refseqGeneIntron-annotate CU-1235 280 GTGTATGATGACCTCATGTAGCCTGAAC
refseqGeneIntron-annotate CU-1253 281 GTGAAGCGTTCCATATTTTT
mRNAall-annotate; refseqGeneIntron-annotate; rnaGene-annotate
CU-1337 283 GGGGGGAGGGAAGGCAA refseqGeneIntron-annotate CU-1316 284
GGGGGCTGGGCTGGGTA refseqGeneIntron-annotate CU-1343 285
GGGGCCGCCGCCTGTGT refseqGeneIntron-annotate CU-1326 286
GGGAGTCCGCGGCGAGC refseqGeneIntron-annotate CU-1286 288
GGCTTGGTCTAGGGGTA refseqGeneIntron-annotate CU-1332 289
GGCTGGGACCCTGGACAC refseqGeneIntron-annotate CU-1262 290
GGCGACCTGCGACTCCTT refseqGeneIntron-annotate CU-1317 292
GGAGGGGGGAAAAAAAAAA computGene-annotate; refseqGeneIntron-annotate
CU-1266 295 GCCGGGCGTGGTGGTCTG refseqGeneIntron-annotate CU-1261
296 GCCGCCGAGACCCCAGGACCC refseqGeneIntron-annotate CU-1259 298
GCAAATGATGCCCTCTGATC refseqGeneIntron-annotate CU-1349 299
GAGGGGGGTCAAAAAAA refseqGeneIntron-annotate CU-1272 300
CTTGATGATGAGCAGGATCTGAGT refseqGeneIntron-annotate CU-1313 303
CTGCTTAAGTCCTGACCAG refseqGeneIntron-annotate CU-1157 196
CTGATGTTGATGCATATGATGACA refseqGeneIntron-annotate CU-1296 304
CTGAGCACCTTTCCCTTCC refseqGeneIntron-annotate CU-1245 306
CGGTCACACGATTAACCCA mRNA-annotate; refseqGeneIntron-annotate
CU-1319 310 CGGGAGTGGGGTGGCGCCCAG refseqGeneIntron-annotate CU-1569
312 CGGACCTGATAAATTCCCAC refseqGeneIntron-annotate CU-1351 316
CCTTCCTTGGATGTCTGAGTGAG mRNAall-annotate;
refseqGeneIntron-annotate; wgRNA-annotate; rnaGene-annotate CU-1354
317 CCTCGCTGGGGCCTCCA tRNAprefix-annotate;
refseqGeneIntron-annotate; CU-1228 321 CCGCCCGTCACCCTCCTCAAGTA
mRNA-annotate; refseqGeneIntron-annotate CU-1271 323
CCCGCGGGCTTGCTGGGCGTCCC refseqGeneIntron-annotate CU-1166 213
CCCCGGCCCATGCACCA refseqGeneIntron-annotate; CU-1285 325
CCCCGGCATCTCCACTA refseqGeneIntron-annotate CU-1571 326
CCCCAGTGAGTGCCCTCTTCC refseqGeneIntron-annotate CU-1353 327
CCCAGAGACGCCGTCCTCGA refseqGeneIntron-annotate CU-1347 330
CCACTCCAGCCTAGCCCC refseqGeneIntron-annotate CU-1295 331
CAGTACAGGCACACCTC refseqGeneIntron-annotate CU-1250 333
CACGATTAACCCAAGTC mRNA-annotate; refseqGeneIntron-annotate CU-1311
337 ATACCATGATGAACAATAGCTGAGA refseqGeneIntron-annotate CU-1350 339
AGGCTGTGATGGACCTGGCTGAGCCTG refseqGeneIntron-annotate CU-1252 340
AGAGAGTAGGGGGAGGT refseqGeneIntron-annotate CU-1334 341
ACTGTCCCTGTCTACTA refseqGeneIntron-annotate CU-1340 342
ACCGCATCTGGCCTATTTTT refseqGeneIntron-annotate CU-1342 343
ACCAGACCTCCTGTGCGAAG refseqGeneIntron-annotate CU-1304 344
ACAGCCCGGATCCCAGCCCACTTA refseqGeneIntron-annotate CU-1230 345
ACACTGAGCCACAACCCA refseqGeneIntron-annotate CU-1192 229
ACAAAAAAAAAAGCCCAACCCT refseqGeneIntron-annotate CU-1312 346
AAGGGCTTGGCTTAATTA refseqGeneIntron-annotate CU-1255 347
AACCCGGAAGGCGGAGGTTGCGG computGene-annotate;
refseqGeneIntron-annotate CU-1346 349 AACAAGCTTCTTTGACGTCCCATCCAC
refseqGeneIntron-annotate CU-1573 359 TGCCGTGATCGTATAGTGGTTA
piRNA-annotate CU-1395 362 CTGACAGCCGGGGTTTTGGA computGene-annotate
CU-1365 363 CGGCGGGGCCTGGAGTCTG mRNAall-annotate;
computGene-annotate; exEID-annotate CU-1375 364 CCTGGCTCGCTGCGCCA
computGene-annotate CU-1209 207 CCTCACCTGGAGCACCA
tRNAprefix-annotate; CU-1174 366 CCCGAACGCTGCCAACCC exEID-annotate
CU-1214 215 CCCCAGTACCTCCACCA tRNAprefix-annotate; CU-1218 223
ATCCTGTTCGTGACGCCA tRNAprefix-annotate; CU-1385 367
AGACCCGCGGGCGCTCTCCAGTC rnaGene-annotate
TABLE-US-00026 TABLE 7 (PART B) List of known and newly identified
bona fide and candidate mature miRNAs. Counts and annotations are
provided for all candidate miRNA. Frequencies have been calculated
only for bona fide miRNA (cloned at least 2 times in the B cell
libraries). SEQ Corrected Counts Frequencies ID Naive Memory
Centroblasts Ramos Memory Centroblasts Ramos Mature miRNA sequence
NO. (N) (M) (CB) (RA) Naive (N) (M) (CB) (RA)
TGTAGTGTTTCCTACTTTATGGA 1 1329 592 635 391 40.74 21.5 25.55 17.89
TAGCTTATCAGACTGATGTTGA 2 196 353 144 13 6.01 12.82 5.79 0.59
TAAAGTGCTTATAGTGCAGGTAG 3 54 19 49.82 257.89 1.66 0.69 2 11.8
TAGCAGCACATCATGGTTTACA 4 38 61 176.84 105 1.16 2.21 7.12 4.8
TAGCAGCACGTAAATATTGGCG 5 131 97 53 35 4.02 3.52 2.13 1.6
TGAGGTAGTAGGTTGTATAGTT 6 62.84 78.99 92.19 63.25 1.93 2.87 3.71
2.89 TATTGCACTTGTCCCGGCCTGT 7 17 21 46 207 0.52 0.76 1.85 9.47
TCCCACCGCTGCCACCA 8 68 97 25 28 2.08 3.52 1.01 1.28
TGAGGTAGTAGATTGTATAGTT 9 41.28 44 64 51.38 1.27 1.6 2.58 2.35
TAGCACCATCTGAAATCGGTTA 10 78 60 42 22 2.39 2.18 1.69 1.01
TAGCAGCACATAATGGTTTGT 11 90 39 32.16 8 2.76 1.42 1.29 0.37
CCCATAAAGTAGAAAGCACTA 12 88 53 7 10 2.7 1.92 0.28 0.46
TGAGGTAGTAGTTTGTACAGTT 13 41.28 47 30.77 21.16 1.27 1.71 1.24 0.97
TGAGGTAGTAGTTTGTGCTGTT 14 23 24 32 42 0.71 0.87 1.29 1.92
TAGCACCATTTGAAATCGGTTA 15 44 41 16 1 1.35 1.49 0.64 0.05
TGTAAACATCCTACACTCTCAGC 16 27 25 26 20 0.83 0.91 1.05 0.91
CAAAGTGCTTACAGTGCAGGTAG 17 9 6 10.18 65.04 0.28 0.22 0.41 2.98
CATTGCACTTGTCTCGGTCTGA 18 11 9 34 39 0.34 0.33 1.37 1.78
CAACGGAATCCCAAAAGCAGCTG 19 17 21 36 18 0.52 0.76 1.45 0.82
TGTGCAAATCCATGCAAAACTGA 20 0 1 25 65 0 0.04 1.01 2.97
TACCACAGGGTAGAACCACGGA 21 31 22 17 21 0.95 0.8 0.68 0.96
TGTAAACATCCTACACTCAGCT 22 31 11 27 16 0.95 0.4 1.09 0.73
TGAGGTAGTAGGTTGTGTGGTT 23 19.48 19 29 5.08 0.6 0.69 1.17 0.23
TAGCACCATTTGAAATCAGTGTT 24 22 14 12 4 0.67 0.51 0.48 0.18
TAAAGTGCTGACAGTGCAGAT 25 7 6 13 26 0.21 0.22 0.52 1.19
TCCCTGTCCTCCAGGAGCTC 26 6 3 3 32 0.18 0.11 0.12 1.46
TTCAAGTAATCCAGGATAGGCT 27 2 8 13 16 0.06 0.29 0.52 0.73
CAAAGTGCTGTTCGTGCAGGTAG 28 9 2 13 14 0.28 0.07 0.52 0.64
TGTCAGTTTGTCAAATACCCCA 29 25 10 1 0 0.77 0.36 0.04 0
TGAGAACTGAATTCCATGGGTT 30 4 7 21 4 0.12 0.25 0.85 0.18
TCTCCCAACCCTTGTACCAGT 31 12 18 2 0 0.37 0.65 0.08 0
TCCCTGAGACCCTAACTTGTGA 32 0 1 28 2 0 0.04 1.13 0.09
TCTCACACAGAAATCGCACCCG 33 10 8 8 3 0.31 0.29 0.32 0.14 TC
GTCCCTGTTCGGGCGCCA 34 12 10 6 1 0.37 0.36 0.24 0.05
TGTGCAAATCTATGCAAAACTGA 35 0 0 9 19 0 0 0.36 0.87
TGTAAACATCCCCGACTGGAAG 36 7 3 14 3 0.21 0.11 0.56 0.14
AGCTACATTGTCTGCTGGGTT 37 17 6 4 0 0.52 0.22 0.16 0
AGAGGTAGTAGGTTGCATAGTT 38 2 4 10 10 0.06 0.15 0.4 0.46
CCGCACTGTGGGTACTTGCT 39 8 6 2 8 0.25 0.22 0.08 0.37
AGCAGCATTGTACAGGGCTATGA 40 1 1 10 11 0.03 0.04 0.4 0.5
AACTGGCCCTCAAAGTCCCGCT 41 0 0 2 21 0 0 0.08 0.96
GCCCCTGGGCCTATCCTAGAA 42 1 0 10 10 0.03 0 0.4 0.46
AGCTGGTGTTGTGAATCAGGCC 43 0 0 15 5 0 0 0.6 0.23 GT
TGAGGGGCAGAGAGCGAGACTT 44 5 1 7 4 0.15 0.04 0.28 0.18
AGCTACATCTGGCTACTGGGTCT 45 6 6 5 0 0.18 0.22 0.2 0
GTGGGGGAGAGGCTGTA 46 2 6 3 5 0.06 0.22 0.12 0.23
CTATACGACCTGCTGCCTTTC 47 6 3 4 1 0.18 0.11 0.16 0.05
TTAATGCTAATCGTGATAGGGGT 48 3 4 5 1 0.09 0.15 0.2 0.05
AGGGGGAAAGTTCTATAGTC 49 0 2 0 11 0 0.07 0 0.5 ACAGTAGTCTGCACATTGGTT
50 0 0 13 0 0 0 0.52 0 AACATTCAACGCTGTCGGTGAG 51 0 0 7 6 0 0 0.28
0.27 TT TGGAAGACTAGTGATTTTGTTGT 52 1 1 1 8 0.03 0.04 0.04 0.37
TAATGCCCCTAAAAATCCTTAT 53 0 0 6 4 0 0 0.24 0.18
TAGCAGCACAGAAATATTGGCA 54 4 0 5 0 0.12 0 0.2 0 TGAGGTAGTAGGTTGTAT
55 0.11 0.01 0.01 0.13 0 0 0 0.01 TCCTGTACTGAGCTGCCCCGAG 56 0 0 7 1
0 0 0.28 0.05 TCCCTGAGACCCTTTAACCTGTGA 57 0 0 8 0 0 0 0.32 0
ATCACATTGCCAGGGATTTCCA 58 0 0.5 7 0 0 0.02 0.28 0
TCACAGTGAACCGGTCTCTTT 59 1 0 0 6 0.03 0 0 0.27
CACTAGATTGTGAGCTCCTGGA 60 2 0 4 1 0.06 0 0.16 0.05
CAACAAATCACAGTCTGCCAT 61 3 0 1 3 0.09 0 0.04 0.14
CAAAGTGCTTATAGTGCAGGTAG 62 0 1 1 0.08 0 0.04 0.04 0
AGGTTGGGATCGGTTGCAATGCT 63 0 0 0 7 0 0 0 0.32
ACATTCATTGCTGTCGGTGGGTT 64 0 0 1 6 0 0 0.04 0.27
AATGACACGATCACTCCCGTTG 1095 0 0 7 0 0 0 0.28 0 AG
TCCCCCAGGTGTGATTCTGATT 65 4 1 0 1 0.12 0.04 0 0.05
CCCAGTGTTCAGACTACCTGTTC 66 0 0 6 0 0 0 0.24 0 ACCAATATTACTGTGCTGCTT
67 1 1 2 2 0.03 0.04 0.08 0.09 TGTAAACATCCTTGACTGGAAGCT 68 2 0 3 0
0.06 0 0.12 0 TAAGGTGCATCTAGTGCAGATA 69 0 0 1 4 0 0 0.04 0.18
ATCACATTGCCAGGGATTACCA 70 0 0.5 3 1 0 0.02 0.12 0.05
ACTGCCCTAAGTGCTCCTTCTG 71 0 0 0 5 0 0 0 0.23 TGTAAACATCCTCGACTGGA
72 1 0 3 0 0.03 0 0.12 0 TACAGTACTGTGATAACTGAAG 73 1 0 0 3 0.03 0 0
0.14 CTAGACTGAAGCTCCTTGAGG 74 2 1 1 0 0.06 0.04 0.04 0
TGGGTTGAGAGGGCGAA 1094 1 0 1 1 0.03 0 0.04 0.05
TGGCAGTGTCTTAGCTGGTTGTT 75 0 1 2 0 0 0.04 0.08 0
TGAGGTAGTAAGTTGTATTGTT 76 0 1 1 1 0 0.04 0.04 0.05
TGAGAACTGAATTCCATAGGCT 77 1 0 2 0 0.03 0 0.08 0 GT
TCGAGGAGCTCACAGTCTAGTA 78 1 0 1 1 0.03 0 0.04 0.05
AGCTCGGTCTGAGGCCCCTCAG 79 0 0 2 1 0 0 0.08 0.05
ACTGCAGTGAAGGCACTTGTAG 80 0 0 0 3 0 0 0 0.14 ACCATCGACCGTTGATTGTA
81 0 1 0 2 0 0.04 0 0.09 TTCACCACCTTCTCCACCCAG 82 0 0 0 2 0 0 0
0.09 TTCACAGTGGCTAAGTTCTG 83 0 0 2 0 0 0 0.08 0
TTCAAGTAATTCAGGATAGGTT 84 0 0 1 1 0 0 0.04 0.05
TGGGTTTACGTTGGGAGAACT 85 0 0 0 2 0 0 0 0.09 TGAGGTAGGAGGTTGTATAGTT
87 0 0 1.02 0 0 0 0.04 0 TGACCGATTTCTCCTGGTGTT 88 2 0 0 0 0.06 0 0
0 TATTGCACTCGTCCCGGCC 89 0 0 1 1 0 0 0.04 0.05 GGGGTGCTATCTGTGATTGA
90 2 0 0 0 0.06 0 0 0 GCATGGGTGGTTCAGTGGTAGAA 91 0 0 2 0 0 0 0.08 0
CTGGCCCTCTCTGCCCTT 92 0 0 1 1 0 0 0.04 0.05 CTGACCTATGAATTGACAGC 93
0 0 0 2 0 0 0 0.09 CTCCTGACTCCAGGTCCTGTG 94 0 0 0 2 0 0 0 0.09
CGTCAACACTTGCTGGTT 95 0 0 1 1 0 0 0.04 0.05 CGAATCATTATTTGCTGCTCT
96 0 0 1 1 0 0 0.04 0.05 CATCGGGAATGTCGTGTCCGCC 97 0 2 0 0 0 0.07 0
0 CAGTGGTTTTACCCTATGGTA 98 0 0 1 1 0 0 0.04 0.05
CAGTGCAATGATGAAAGGGCAT 99 0 0 2 0 0 0 0.08 0 CAGCAGCACACTGTGGTTTGT
100 0 0 2 0 0 0 0.08 0 CACGCTCATGCACACACCCAC 101 0 0 2 0 0 0 0.08 0
AAGGAGCTCACAGTCTATTGAG 102 0 0 2 0 0 0 0.08 0 GCCGGGTACTTTCGTATTTT
131 3 3 0 34 0.09 0.11 0 1.56 GCTAAGGAAGTCCTGTGCTCAG 132 0 0 1 19 0
0 0.04 0.87 TTTT AGGGTGTGCGTGTTTTT 148 0 0 0 20 0 0 0 0.91
GAGAGCGCTCGGTTTTT 150 0 0 1 9 0 0 0.04 0.41 TGGTGTGGTCTGTTGTTTT 151
0 0 0 9 0 0 0 0.41 TGTGCTCCGGAGTTACCTCGTTT 152 0 0 0 8 0 0 0 0.37
AACCGAGCGTCCAAGCTCTTTC 155 0 0 0 5 0 0 0 0.23 CATTTT
TCCCCGCACCTCCACCA 156 0 2 1 1 0 0.07 0.04 0.05 GGCGTGATTCATACCTTTT
162 0 0 0 2 0 0 0 0.09 ATGTGGTGGCTTACTTTT 169 0 0 0 2 0 0 0 0.09
AGAAAGGCCGAATTTTA 172 0 0 1 1 0 0 0.04 0.05 TCCCCGGCACTTCCACCA 157
0 3 0 0 0 0.11 0 0 CCCACCCAGGGACGCCA 232 223 218 6 2 6.84 7.92 0.24
0.09
TCCCCGGCACCTCCACCA 233 60.47 101.82 40.28 34 1.85 3.7 1.62 1.56
ATCCCGGACGAGCCCCCA 234 48 60 80 45 1.47 2.18 3.22 2.06
CCCCCCACTGCTAAATTTGACTG 142 18 8 61 22 0.55 0.29 2.45 1.01 GCTT
TCGATTCCCGGCCAATGCACCA 236 4 18 36 4 0.12 0.65 1.45 0.18
ATCCCACTTCTGACACCA 237 11 9 26.69 14 0.34 0.33 1.07 0.64
TCCCCGTACGGGCCACCA 239 11 6 3 2 0.34 0.22 0.12 0.09
AGTCCCATCTGGGTCGCCA 243 4 2 3 6 0.12 0.07 0.12 0.27
CCCCCCACTGCTAAATTTGACTG 244 1 1 6 2 0.03 0.04 0.24 0.09 GA
GTCCCTTCGTGGTCGCCA 246 1 2 1 2 0.03 0.07 0.04 0.09
TCCTCACACGGGGCACCA 248 2 1 2 0 0.06 0.04 0.08 0 TAACGGCCGCGGTACCC
249 0 3 1 0 0 0.11 0.04 0 GAGGGGGACCAAAAAAAA 250 0 0 0 4 0 0 0 0.18
CCCGGGTTTCGGCACCA 133 0 3 0 1 0 0.11 0 0.05 ATAGGTTTGGTCCTAGCCTTTCT
354 0 0 3 1 0 0 0.12 0.05 AGGGGGGTAAAAAAAAA 252 0 0 0 4 0 0 0 0.18
GAGCCATGATGATACCACTGAGC 254 0 1 0 2 0 0.04 0 0.09
AGAACACTACGAGCCACA 257 3 0 0 0 0.09 0 0 0 ACCCCACTTCTGGTACCA 258 0
0 1 2 0 0 0.04 0.09 TCTCGGTGGAACCTCCA 260 0 0 1 1 0 0 0.04 0.05
TACCGAGCCTGGTGATAGC 262 0 1 1 0 0 0.04 0.04 0
GCAGCGCCAGCCTCCCGCCCTAC 263 2 0 0 0 0.06 0 0 0 ATCCCCAGCACCTCCACCA
265 0 0 0 2 0 0 0 0.09 AGCAGTGATGTCCTGAAAATTCT 266 0 0 0 2 0 0 0
0.09 GAAG ACCCCACTATGCTTAGCCCT 267 0 0 2 0 0 0 0.08 0
AAAGGACCTGGCGGTGCTTC 268 1 0 1 0 0.03 0 0.04 0 TCCCCGGCATCTCCACCA
350 116.53 275.18 104.72 59 3.57 9.99 4.21 2.7 GCCCGCATCCTCCACCA
143 38 61 2 4 1.16 2.21 0.08 0.18 ATCCCACTCCTGACACCA 145 7 13 11.31
3 0.21 0.47 0.46 0.14 TCGATTCCCGGCCCATGCACCA 149 1 2 10 4 0.03 0.07
0.4 0.18 TCCCCGACACCTCCACCA 153 2 2 2 1 0.06 0.07 0.08 0.05
TCTAGAGGAGCCTGTTCTGTA 352 0 1 3 0 0 0.04 0.12 0
TCGATTCCCGGTCAGGGAACCA 353 0 0 0 4 0 0 0 0.18 TCACCCCATAAACACCA 158
2 1 0 0 0.06 0.04 0 0 CGTTCGCGCTTTCCCCTG 355 0 1 2 0 0 0.04 0.08 0
TTCCCCGACGGGGAGCCA 161 1 0 0 1 0.03 0 0 0.05 TAAGTGTTTGTGGGTTA 356
1 1 0 0 0.03 0.04 0 0 ATCCCCAGCATCTCCACCA 171 0 0 2 0 0 0 0.08 0
CCCCCACAACCGCGCTTGACTA 368 12 11 7 9 0.37 0.4 0.28 0.41 GC
CCCTGCTCGCTGCGCCA 369 7 20 5 1 0.21 0.73 0.2 0.05
CTCCCACTGCTTCACTTGACTAGC 370 2 2 18 9 0.06 0.07 0.72 0.41
TCACGTCGGGGTCACCA 372 16 4 5 1 0.49 0.15 0.2 0.05
TCCCTGGTGGTCTAGTGGTTAG 373 0 1 10 6 0 0.04 0.4 0.27 GATTCG
TCCTGCCGCGGTCGCCA 375 6 8 0 1 0.18 0.29 0 0.05
GGAGAGAACGCGGTCTGAGTG 376 3 7 1 0 0.09 0.25 0.04 0 GT
TCGGGTGCGAGAGGTCCCGGGT 377 0 0 0 10 0 0 0 0.46
GGCTGGTCCGATGGTAGTGGGTT 378 4 3 3 0 0.12 0.11 0.12 0
CGGAAGCGTGCTGGGCCC 379 1 5 0 4 0.03 0.18 0 0.18
GCGGGTGATGCGAACTGGAGTC 381 0 0 6 1 0 0 0.24 0.05 TGAGC
GACGAGGTGGCCGAGTGG 382 2 3 2 0 0.06 0.11 0.08 0
CTGATTGCTCCTGTCTGATT 351 0 0 6 1 0 0 0.24 0.05 CTCCTGGCTGGCTCGCCA
384 0 0 3 3 0 0 0.12 0.14 GGCTGGTCCGAGTGCAGTGGTG 386 0 1 4 0 0 0.04
0.16 0 TTTA CTGCTGTGATGACATTC 387 1 2 2 0 0.03 0.07 0.08 0
TCCTCGTTAGTATAGTGGTGAGT 389 0 1 3 0 0 0.04 0.12 0 ATCCC
GCATTGGTGGTTCAGTGGTAGA 391 0 0 3 1 0 0 0.12 0.05
TTCTCACTACTGCACTTGACTA 395 0 0 2 1 0 0 0.08 0.05 TGGTTATCACGTTCGCC
396 0 2 0 1 0 0.07 0 0.05 TAGGGGTATGATTCTCGCT 397 1 0 0 2 0.03 0 0
0.09 CGTCCATGATGTTCCGCAA 255 1 0 2 0 0.03 0 0.08 0
CCACGAGGAAGAGAGGTAGC 398 2 1 0 0 0.06 0.04 0 0 TGTATTGTGAGACATTC
259 0 1 1 0 0 0.04 0.04 0 GTCAGGATGGCCGAGCGGTCT 399 0 1 1 0 0 0.04
0.04 0
[0351] A sizeable number of sequences (334) aligned to genomic
regions that did not fulfill the criteria for miRNA precursors
(FIG. 24). About 80% of these sequences were annotated or cloned
only once and may represent degradation products originating from
other RNA species (FIG. 24 and Table 8). The remaining (58
sequences), however, mapped to genomic regions that lack
annotations and may therefore represent a part of the transcriptome
whose functions are unknown (Table 9 and Table 10). Interestingly,
several of these nonannotated sequences (i.e., CU-5004, CU-5021,
CU-6030, CU-6069) were cloned multiple times and showed
differential expression across libraries (Table 9 and Table 10),
suggesting that they may represent short RNAs with characteristics
distinct from those currently recognized in "classic" miRNAs.
[0352] In conclusion, the generation of short-RNA libraries from
normal and neoplastic B cells led to the identification of 178
mature miRNAs cloned multiple times as well as other short-RNA
species of unknown function.
TABLE-US-00027 TABLE 8 Characterization of short-RNA libraries.
Number of not redundant short-RNAs cloned in each library (naive B
cells, memory B cells, centroblasts and Ramos cell line) and
overall (total). Each short-RNA is annotated according to the
listed RNA species. Results shown here refer only to short-RNA with
matches to the human genome. The same short-RNA might match to
multiple databases and therefore the overall sum does not
correspond to the total number of short-RNAs. RNA species Naive
Memory Centroblasts Ramos Total Total (non redundant) 680 709 740
740 2086 miRNA 424 408 528 538 1259 miRNA other* 1 0 3 0 4 tRNA 27
33 32 29 108 rRNA 61 99 34 16 174 mRNA 76 72 25 34 176 snoRNA 8 13
15 6 40 yRNA 11 11 31 21 53 piRNA 46 54 70 62 148 Repeats 1 1 0 1 2
Mitochondrial genome 12 36 54 11 101 Human viruses 1 4 0 0 5 E.
Coli 5 4 0 0 7 Not Annotated 111 119 97 134 375 *miRNA other:
includes fragments of miRNA precursors, not mature. The databases
used in this analysis are detailed in Supplementary Methods.
TABLE-US-00028 TABLE 9 (PART A) List of short-RNA lacking genomic
locations with appropriate RNA secondary structures to be defined
miRNAs. Table includes information on genomic locations and
annotations. SEQ ID ID NO: Short-RNA sequence Annotations CU-5004
1096 GAAGCGGGTGCTCTTATTTT NEW CU-5008 1097 GTGTAAGCAGGGTCGTTTT NEW
CU-6003 1098 ATCCCACCGCTGCTACCA NEW CU-5023 1099 GGGAAGGTGACCTGAC
NEW CU-5007 1100 CTCCCGCCTTTTTTCCC NEW CU-5024 1101 CGGAGCAAGAGCGT
NEW CU-5026 1102 CCCCCGGCACCATCAATA NEW CU-5027 1103
CAGCCTAGCCCCTACCC NEW CU-5005 1104 CAGAAGGTCTCACTTTT NEW CU-5006
1105 AGTATTCTCTGTGGCTTT NEW CU-5028 1106 TGGAGTGACTATATGGATGCCCCC
NEW CU-5029 1107 TCTGATAGCTTACTTT NEW CU-5030 1108
TCGAGCCCCAGTGGAACCAC NEW CU-5032 1109 TCCTCCCCACACTCATCGCCCTTACCA
NEW CU-5033 1110 TATACTACAAGGACACCA NEW CU-5034 1111
TAGTGGGTGAAAAAAAAAAAA NEW CU-5035 1112 TACCACACATTCGAAGAACCCGTA NEW
CU-5036 1113 TACAAAAoGGGGTAAAAAAAA NEW CU-5037 1115
GCCCTCCTAATGACCTCC NEW CU-5038 1116 CTTCCCTCTACACTTATCATC NEW
CU-5039 1117 CGGGCGGCCTGCGCTCTCA NEW CU-5040 1118
CCCGAGGCCGTGTGCAAATGCAT NEW CU-5020 1119 CCCCGGCATCTCCACC NEW
CU-5041 1120 CCCCCAGTACCTCCACCA NEW CU-5042 1121
CCCCCACTGCTAAACTTGACTGGCTTT NEW CU-5043 1122 CCCACTCCACCTTACTACCA
NEW CU-5044 1123 CCCAAGAACAGGGTGACCA NEW CU-5045 1124
CCAGTCGCGGCCAAATCA NEW CU-5046 1125 CCAGCTTCACCAAGGTATTGGTTA NEW
CU-5047 1126 CCAGAAAAAACAGGCCTC NEW CU-5048 1127
CATCATAATCGGAGGCTTTGGCAAC NEW CU-5049 1128
CAGCAGGGGTAATAAGTGAAATCAAA NEW CU-5050 1129
CAATGGTGCAGCCGCTATTAAAGGTTCA NEW CU-5051 1130 CAACTCCTACATACTTCCCCC
NEW CU-5053 1131 ATGCATCTCATATGCGAATAGGAATGC NEW CU-5054 1132
ATCCCACTTCTGTACCA NEW CU-5055 1133 ATAACACTAGAAAGTTGGGGCAGATTGC NEW
CU-5056 1134 ACGTGGGCACATTACCCGTCTGACCTGA NEW CU-5057 1135
ACCCCTTATTAACCCA NEW CU-5058 1136 ACAAGGCACACCTACACCCCTTATCCC NEW
CU-5059 1137 AAAAGACACCCCCCCACCA NEW CU-5060 1138
AAAACCCCTACGCATTTATAT NEW CU-5061 1139 AAAAAGACACCCCCCACCA NEW
CU-5011 1140 GCTAAACCTAGCCCCAAACCC piRNA-annotate;
refseqGeneIntron-annotate CU-5003 1141 ACCCCACTCCTGGTACCA
refseqGeneIntron-annotate CU-5009 1142 TGCCCCCATGTCTAACAACATGGCTA
refseqGeneIntron-annotate; rnaGene-annotate CU-5062 1143
CCCCGCCTGTTTACC refseqGeneIntron-annotate CU-5063 1144
CCCACTTCTGACACCA computGene-annotate; refseqGeneIntron-annotate;
exEID- annotate CU-5064 1145 CACCACCTCTTGCTCAGCC mRNA-annotate;
refseqGeneIntron-annotate CU-5014 1146 CTGGAAAGTGCACTTGGACGAACA
refseqGeneIntron-annotate CU-5065 1147 TGACCGCTCTGACCAC
refseqGeneIntron-annotate CU-5066 1148 TGAAGTCCCTTTGCTTTGTT
refseqGeneIntron-annotate CU-5067 1149 TGAACACACAATAGCTAAGACCC
mRNA-annotate; refseqGeneIntron-annotate CU-5068 1150
TCGCCTTACCCCCCACTA refseqGeneIntron-annotate CU-5069 1151
TCGATAAACCCCGATCAACCT mRNA-annotate; refseqGeneIntron-annotate
CU-5070 1152 TCCCCGTCACCTCCACCA refseqGeneIntron-annotate CU-5071
1153 TCCCCGGCACTCCACCA refseqGeneIntron-annotate CU-5072 1154
TCCCCCCGCTGCCACCA refseqGeneIntron-annotate CU-5073 1155
TCCCCCCCATCTCCACCA refseqGeneIntron-annotate CU-5074 1156
TACACACCGCCCGTCACCC mRNA-annotate; refseqGeneIntron-annotate
CU-5076 1157 GCTTAGCCTAGCCACACCCCCACG mRNA-annotate;
refseqGeneIntron-annotate CU-5077 1158 GCTCGCCAGAACACTACGA
mRNA-annotate; refseqGeneIntron-annotate CU-5078 1159
GCCGGGGGGCGGGCGCA refseqGeneIntron-annotate CU-5079 1160
GAACCGGGCGGGAACACCA refseqGeneIntron-annotate CU-5080 1161
CGCCGCAGTACTGATCATTC refseqGeneIntron-annotate CU-5081 1162
CCGCACCAATAGGATCCTCC refseqGeneIntron-annotate CU-5082 1163
CCCGGCCGACGCACCA refseqGeneIntron-annotate CU-5083 1164
CCACCCCATCATACTCTTTC refseqGeneIntron-annotate CU-5084 1165
CACCCCCCAGCTCCTCCTTT refseqGeneIntron-annotate CU-5085 1166
ATAAGTAACATGAAAACATTCTCCTC refseqGeneIntron-annotate CU-5086 1167
ACTGCTCGCCAGAACAC mRNA-annotate; refseqGeneIntron-annotate CU-5087
1168 ACCCTGGTGTGGGATCTGCCCGATC refseqGeneIntron-annotate CU-5088
1169 AACCTCACCACCTCTTTCT refseqGeneIntron-annotate CU-5089 1170
AAAAGACACCCCCCACACCA refseqGeneIntron-annotate CU-5021 1171
ACCGGGCGGAAACACCA tRNAprefix-annotate CU-5022 1172
TCCCGGGTTCAAATCCCGGACGAGCCCC tRNAprefix-annotate CA CU-5010 1173
GGCCGTGATCGTATA piRNA-annotate CU-5025 1174 CCCCGTACTGGCCACCA
tRNAprefix-annotate CU-5090 1175 TGGGATGCGAGAGGTCCCGGGT
rnaGene-annotate CU-5031 1176 TCGAATCCTGTTCGTGACGCCA
tRNAprefix-annotate CU-5091 1177 CTGAACTCCTCACACCC piRNA-annotate
CU-5052 1178 ATTCAAAAAAGAGTACCA tRNAprefix-annotate CU-5092 1179
ATTAATCCCCTGGCCCAACCCG computGene-annotate CU-5093 1180
AGCCCCAAACCCACTCCAC piRNA-annotate CU-5094 1181 CGCGACCTCAGATCAGAC
rRNA-eliminate; piRNA-annotate; refseqGeneIntron-annotate CU-5013
1182 GGCCGGTGATGAGAACT mRNAall-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate; wgRNA- annotate; snoRNA-annotate CU-5015
1183 TCAAGTGATGTCATCTTACTACTGAGA mRNAall-annotate; snoRNA-annotate;
refseqGeneExon- eliminate; rnaGene-annotate; refseqGeneIntron-
annotate; snoRNA-eliminate; wgRNA-annotate CU-5095 1184
TTGGGTGCGAGAGGTCCCGGGT tRNAcomputational-annotate; tRNA-eliminate;
HStRNA- eliminate; rnaGene-annotate CU-5096 1185 TCTCGGTGGGACCTCCA
tRNAprefix-annotate; refseqGeneExon-eliminate CU-5097 1186
CCGCCCCCCGTTCCCCC rRNA-eliminate CU-5098 1187
CCCACTGCTAAATTTGACTGGCTT mRNAall-annotate; yRNA-eliminate;
refseqGeneIntron- annotate; rnaGene-annotate CU-5099 1188
ACAGACCAAGAGCCTTC tRNA-eliminate; rnaGene-annotate CU-5100 1189
TGTAGTAGTCAATTAATGGATATTA refseqGeneExon-eliminate CU-5101 1190
TGGTTATCACGTTCGCCTCACACGCGA tRNAcomputational-annotate;
tRNA-eliminate; HStRNA- eliminate; rnaGene-annotate CU-5102 1191
TGGGAATACCGGGTG rRNA-eliminate; rnaGene-annotate; piRNA- annotate;
refseqGeneIntron-annotate CU-5103 1192 TGGCGGCCAAGCGTTCATAGCGACGTC
rRNA-eliminate; refseqGeneIntron-annotate; rnaGene-annotate CU-5104
1193 TCGTCATCCAGCTAAGGGCTCAGA mRNAall-annotate;
refseqGeneExon-eliminate; exEID-annotate CU-5105 1194
TCGCCTGCCACGCGGGAGGCCCGGGT rnaGene-annotate;
tRNAcomputational-annotate; tRNA- eliminate;
refseqGeneIntron-annotate; mRNA-annotate; HStRNA- eliminate CU-5106
1195 TCCCACTGCTTCACTTGA yRNA-eliminate; refseqGeneIntron-annotate;
rnaGene-annotate CU-5107 1196 GTTTAGACGGGCTCACATCACCCCA
tRNA-eliminate; piRNA-annotate; refseqGeneIntron-annotate CU-5075
1197 GGCCGGTGATGAGAACTTCTCCC mRNAall-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate; wgRNA- annotate;
snoRNA-annotate CU-5108 1198 GCTAACTCATGCCCCCATGTC tRNA-eliminate;
refseqGeneIntron-annotate; rnaGene-annotate CU-5109 1199
GACTGTGGTGGTTGAATATA mRNAall-annotate; computGene-annotate;
refseqGeneExon- eliminate; exEID-annotate
CU-5110 1200 CGCGACCTCAGATCAGACGTGGCGACC rRNA-eliminate;
piRNA-annotate; refseqGeneIntron-annotate CU-5111 1201
CGCCGCCGCCCCCCC mRNAall-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate; exEID-annotate CU-5112 1202
CGCCCGACTACCACCACATCCA mRNAall-annotate; computGene-annotate;
refseqGeneExon- eliminate; exEID-annotate CU-5113 1203
CCCCCCTCCACGCGCCC rRNA-eliminate; refseqGeneIntron-annotate CU-5114
1204 CCCCACCCCGCGCCCTC rRNA-eliminate; refseqGeneIntron-annotate
CU-5115 1205 CAGAGTGTAGCTTAACACAAAGCACCCAA tRNA-eliminate;
piRNA-annotate; rnaGene-annotate CU-5116 1206
CAATCTTGGCATGTTGGTCTGGTCACCCA mRNAall-annotate;
refseqGeneExon-eliminate; exEID-annotate CU-5117 1207
CAAAGCATCGCGAAGGCCC mRNAall-annotate; rRNA-eliminate;
piRNA-annotate; rnaGene- annotate CU-5118 1208
AACACCCTGATTGCTCCTGTCTGAT mRNAall-annotate; exEID-annotate; snoRNA-
annotate; refseqGeneExon-eliminate; rnaGene- annotate;
snoRNA-eliminate; wgRNA-annotate CU-5119 1209
AAAAAGGGCCTAAAGAAGATGCA mRNAall-annotate; computGene-annotate;
refseqGeneExon- eliminate; refseqGeneIntron-annotate;
exEID-annotate
TABLE-US-00029 TABLE 9 (PART B) List of short-RNA lacking genomic
locations with appropriate RNA secondary structures to be defined
miRNAs. Table includes information on counts. Corrected Counts SEQ
ID Naive Memory Centroblasts Ramos NO: Short-RNA sequence (N) (M)
(CB) (RA) 1210 GAAGCGGGTGCTCTTATTTT 5 23 25 224 1211
GTGTAAGCAGGGTCGTTTT 0 0 0 7 1212 ATCCCACCGCTGCTACCA 0 1 0 2 1213
GGGAAGGTGACCTGAC 2 0 0 0 1214 CTCCCGCCTTTTTTCCC 0 2 0 0 1215
CGGAGCAAGAGCGT 2 0 0 0 1216 CCCCCGGCACCATCAATA 0 0 1 1 1217
CAGCCTAGCCCCTACCC 0 2 0 0 1218 CAGAAGGTCTCACTTTT 0 1 0 1 1219
AGTATTCTCTGTGGCTTT 0 0 0 2 1220 TGGAGTGACTATATGGATGCCC 0 0 1 0 CC
1221 TCTGATAGCTTACTTT 0 1 0 0 1222 TCGAGCCCCAGTGGAACCAC 0 0 1 0
1223 TCCTCCCCACACTCATCGCCCTT 0 0 1 0 ACCA 1224 TATACTACAAGGACACCA 0
0 0 1 1225 TAGTGGGTGAAAAAAAAAAAA 0 0 0 1 1226
TACCACACATTCGAAGAACCCG 0 0 1 0 TA 1227 TACAAAACCCACCCCATTCCTCC 0 1
0 0 CCA 1228 GGAGGGGGGGTAAAAAAAA 0 0 1 0 1229 GCCCTCCTAATGACCTCC 0
0 1 0 1230 CTTCCCTCTACACTTATCATC 0 0 1 0 1231 CGGGCGGCCTGCGCTCTCA 1
0 0 0 1232 CCCGAGGCCGTGTGCAAATGCAT 0 0 1 0 1233 CCCCGGCATCTCCACC 1
0 0 0 1234 CCCCCAGTACCTCCACCA 0 1 0 0 1235 CCCCCACTGCTAAACTTGACTG 0
0 1 0 GCTTT 1236 CCCACTCCACCTTACTACCA 0 0 0 1 1237
CCCAAGAACAGGGTGACCA 0 0 0 1 1238 CCAGTCGCGGCCAAATCA 0 1 0 0 1239
CCAGCTTCACCAAGGTATTGGTTA 0 0 1 0 1240 CCAGAAAAAACAGGCCTC 0 0 0 1
1241 CATCATAATCGGAGGCTTTGGC 0 0 1 0 AAC 1242 CAGCAGGGGTAATAAGTGAAAT
0 0 1 0 CAAA 1243 CAATGGTGCAGCCGCTATTAAA 0 0 0 1 GGTTCA 1244
CAACTCCTACATACTTCCCCC 1 0 0 0 1245 ATGCATCTCATATGCGAATAGGA 0 0 1 0
ATGC 1246 ATCCCACTTCTGTACCA 0 1 0 0 1247 ATAACACTAGAAAGTTGGGGCA 0 0
1 0 GATTGC 1248 ACGTGGGCACATTACCCGTCTG 0 0 0 1 ACCTGA 1249
ACCCCTTATTAACCCA 0 1 0 0 1250 ACAAGGCACACCTACACCCCTT 0 0 1 0 ATCCC
1251 AAAAGACACCCCCCCACCA 0 0 0 1 1252 AAAACCCCTACGCATTTATAT 0 0 1 0
1253 AAAAAGACACCCCCCACCA 0 0 0 1 1254 GCTAAACCTAGCCCCAAACCC 9 16 13
18 1255 ACCCCACTCCTGGTACCA 1 11 5 6 1256 TGCCCCCATGTCTAACAACATG 7 4
1 1 GCTA 1257 CCCCGCCTGTTTACC 0 5 2 0 1258 CCCACTTCTGACACCA 3 4 0 0
1259 CACCACCTCTTGCTCAGCC 1 3 0 0 1260 CTGGAAAGTGCACTTGGACGAA 0 2 0
0 CA 1261 TGACCGCTCTGACCAC 0 1 0 0 1262 TGAAGTCCCTTTGCTTTGTT 1 0 0
0 1263 TGAACACACAATAGCTAAGACCC 0 0 1 0 1264 TCGCCTTACCCCCCACTA 0 1
0 0 1265 TCGATAAACCCCGATCAACCT 0 0 1 0 1266 TCCCCGTCACCTCCACCA 0 0
1 0 1267 TCCCCGGCACTCCACCA 0 0 1 0 1268 TCCCCCCGCTGCCACCA 1 0 0 0
1269 TCCCCCCCATCTCCACCA 0 0 1 0 1270 TACACACCGCCCGTCACCC 0 0 1 0
1271 GCTTAGCCTAGCCACACCCCCA 0 0 1 0 CG 1272 GCTCGCCAGAACACTACGA 0 0
1 0 1273 GCCGGGGGGCGGGCGCA 0 1 0 0 1274 GAACCGGGCGGGAACACCA 0 0 0 1
1275 CGCCGCAGTACTGATCATTC 0 0 1 0 1276 CCGCACCAATAGGATCCTCC 0 1 0 0
1277 CCCGGCCGACGCACCA 1 0 0 0 1278 CCACCCCATCATACTCTTTC 0 0 1 0
1279 CACCCCCCAGCTCCTCCTTT 1 0 0 0 1280 ATAAGTAACATGAAAACATTCTC 0 0
1 0 CTC 1281 ACTGCTCGCCAGAACAC 0 0 1 0 1282 ACCCTGGTGTGGGATCTGCCCG
0 0 1 0 ATC 1283 AACCTCACCACCTCTTTCT 0 0 1 0 1284
AAAAGACACCCCCCACACCA 0 0 0 1 1285 ACCGGGCGGAAACACCA 9 14 60 20 1286
TCCCGGGTTCAAATCCCGGACG 0 0 4 37 AGCCCCCA 1287 GGCCGTGATCGTATA 2 0 0
0 1288 CCCCGTACTGGCCACCA 2 0 0 0 1289 TGGGATGCGAGAGGTCCCGGGT 0 0 0
1 1290 TCGAATCCTGTTCGTGACGCCA 0 0 0 1 1291 CTGAACTCCTCACACCC 0 1 0
0 1292 ATTCAAAAAAGAGTACCA 0 0 1 0 1293 ATTAATCCCCTGGCCCAACCCG 0 0 0
1 1294 AGCCCCAAACCCACTCCAC 0 0 1 0 1295 CGCGACCTCAGATCAGAC 1 5 8 1
1296 GGCCGGTGATGAGAACT 4 3 0 0 1297 TCAAGTGATGTCATCTTACTACT 0 0 3 1
GAGA 1298 TTGGGTGCGAGAGGTCCCGGGT 0 0 0 3 1299 TCTCGGTGGGACCTCCA 0 2
0 0 1300 CCGCCCCCCGTTCCCCC 1 1 0 0 1301 CCCACTGCTAAATTTGACTGGCTT 0
0 1 1 1302 ACAGACCAAGAGCCTTC 0 0 2 0 1303 TGTAGTAGTCAATTAATGGATAT 0
0 1 0 TA 1304 TGGTTATCACGTTCGCCTCACAC 0 0 0 1 GCGA 1305
TGGGAATACCGGGTG 0 0 1 0 1306 TGGCGGCCAAGCGTTCATAGCG 0 0 0 1 ACGTC
1307 TCGTCATCCAGCTAAGGGCTCA 0 0 1 0 GA 1308 TCGCCTGCCACGCGGGAGGCC 0
0 1 0 CGGGT 1309 TCCCACTGCTTCACTTGA 0 0 0 1 1310
GTTTAGACGGGCTCACATCACC 0 0 1 0 CCA 1311 GGCCGGTGATGAGAACTTCTCCC 1 0
0 0 1312 GCTAACTCATGCCCCCATGTC 0 0 1 0 1313 GACTGTGGTGGTTGAATATA 0
0 0 1 1314 CGCGACCTCAGATCAGACGTGG 0 0 1 0 CGACC 1315
CGCCGCCGCCCCCCC 0 1 0 0 1316 CGCCCGACTACCACCACATCCA 1 0 0 0 1317
CCCCCCTCCACGCGCCC 0 1 0 0
1318 CCCCACCCCGCGCCCTC 0 1 0 0 1319 CAGAGTGTAGCTTAACACAAAG 0 0 1 0
CACCCAA 1320 CAATCTTGGCATGTTGGTCTGGT 0 0 1 0 CACCCA 1321
CAAAGCATCGCGAAGGCCC 0 0 1 0 1322 AACACCCTGATTGCTCCTGTCTG 0 0 1 0 AT
1323 AAAAAGGGCCTAAAGAAGATGCA 0 0 1 0
TABLE-US-00030 TABLE 10 (PART A) List of short-RNA consensus with
maximum 1 mismatch to the human genome. Table includes information
on genomic locations and annotations. SEQ ID ID NO: Short-RNA
sequence Annotations CU-6232 1324 TGGCTCAGTTCAGCAGGAACAGT
Mature:hsa-miR-24:MIMAT0000080 CU-6180 1325 GTGGGGGAGAGGCTGTCGA
Mature:hsa-miR-1275:MIMAT0005929 CU-6130 1326
CGGGGCAGCTCAGTACAGGATT Mature:hsa-miR-486-3p:MIMAT0004762 CU-6044
1327 AATTGCACGGTATCCATCTGTAT Mature:hsa-miR-363:MIMAT0000707
CU-6239 1328 TGTCAGTTTGTTAATTGACCCAA NEW CU-6006 1329
GGCAATACGAGCACCCTG NEW CU-6133 1330 CGGGGGAGCGCCGCGTA NEW CU-6004
1331 CCGGGGCGTCTCGTAC NEW CU-6056 1332 AGCGGCTGTGCACAAA NEW CU-6242
1333 TGTCAGTTTGTTTAATCCAA NEW CU-6241 1334 TGTCAGTTTGTTATTACCAA NEW
CU-6237 1335 TGTCAGGCACCATCAATAA NEW CU-6225 1336
TGATCTTGACACTTAAAGCC NEW CU-6219 1337 TCGTAGGCACCATCAAT NEW CU-6215
1338 TCGATCCCGGGTTTCGGCACCA NEW CU-6211 1339 TCGACTCCCGGTATGGGAACCA
NEW CU-6187 1340 TAGGGAGGTTATGATTAACTTTT NEW CU-6183 1341
TAAAGTGCTTAGTGCAGGTA NEW CU-6181 1342 GTTTATGTTGCTTACCTCC NEW
CU-6176 1343 GTAGATAAAATATTGGCG NEW CU-6163 1344 GGCGGGGACGACGTCAG
NEW CU-6162 1345 GGCGGCGTCGCGGCGGGTC NEW CU-6161 1346
GGAGGGGGTGAACAAAAAGAAAAA NEW CU-6159 1347
GCTAAACCTAGCCCCAAACCCACTCCACA NEW CU-6142 1348 CTGGATAGCGCACTTCGTT
NEW CU-6129 1349 CGGGCGAGGGGCGGACGTTCG NEW CU-6123 1350
CGGACCTATACCGGA NEW CU-6096 1351 CCCCGGGTTCAATCCCCGGCACCTCCAC NEW
CA CU-6088 1352 CCCCCCACAACCGCGAA NEW CU-6087 1353
CCCAGCATCTCCTGTGTTTA NEW CU-6086 1354 CCCACGTTGGGACGCCA NEW CU-6072
1355 ATCGTATCCCACTTCTGACACCA NEW CU-6064 1356 ATCACGTCCGTGCCTCCA
NEW CU-6063 1357 ATAGCAATGTCAGCAGTACCT NEW CU-6051 1358
ACCCTGCTCGCTGCGCCA tRNAprefix-annotate; refseqGeneIntron-annotate
CU-6198 1359 TCCCACCCAGGGACGCCA tRNAprefix-annotate;
refseqGeneIntron-annotate CU-6218 1360 TCGTAGGCACATCAATA
refseqGeneIntron-annotate CU-6007 1361 CCCCCACAACCGCGTA
refseqGeneIntron-annotate CU-6001 1362 ACCCCGTCCGTGCCTCCA
tRNAprefix-annotate; refseqGeneIntron-annotate CU-6039 1363
AAAAAAGACACCCCCCACA refseqGeneIntron-annotate CU-6005 1364
TGTCAGTTTGTTAACCCAA refseqGeneIntron-annotate CU-6204 1365
TCCCTGTGGTCTAGTGGTTAGG refseqGeneIntron-annotate CU-6172 1366
GGGGGGGTAAAAAAA refseqGeneIntron-annotate CU-6171 1367
GGGGGGGGAAAAAAAA refseqGeneIntron-annotate CU-6128 1368
CGGGCCCGGGTCTTCCC refseqGeneIntron-annotate CU-6002 1369
CCGCCCCCCGTTCCCCCCA refseqGeneIntron-annotate CU-6050 1370
ACCCCCGGCTCCTCCACCA tRNAprefix-annotate; refseqGeneIntron-annotate
CU-6244 1371 TTTGGTGGAAATTTTTTGA refseqGeneIntron-annotate CU-6240
1372 TGTCAGTTTGTTATACCAA refseqGeneIntron-annotate CU-6238 1373
TGTCAGTTTGTAATTATCCCAA refseqGeneIntron-annotate CU-6236 1374
TGTCAATTTTTAACCCAA refseqGeneIntron-annotate CU-6227 1375
TGCTAGGGTAAAAAAAAAA refseqGeneIntron-annotate CU-6226 1376
TGCAACTCCAAATAAAAGTACCA tRNAprefix-annotate;
refseqGeneIntron-annotate CU-6224 1377 TGAGGTAACGGGGAATTA
refseqGeneIntron-annotate CU-6209 1378 TCCTCGGCATCTCCACCA
refseqGeneIntron-annotate CU-6197 1379 TCATATGAAGTCACCCTAGCCATC
mitochondrion-annotate; refseqGeneIntron-annotate CU-6196 1380
TCAGTTTGTTTATTAACCCAA refseqGeneIntron-annotate CU-6195 1381
TCAGCGTGTCTTTGCCCT refseqGeneIntron-annotate CU-6194 1382
TCACTGGTGGTCTAGTGGT refseqGeneIntron-annotate; rnaGene-annotate
CU-6193 1383 TCACAATGCTGCCACCA refseqGeneIntron-annotate CU-6189
1384 TAGTTGTTAATTAACCCAA refseqGeneIntron-annotate CU-6188 1385
TAGTCCTCATCGCCCTCC mitochondrion-annotate;
refseqGeneIntron-annotate CU-6184 1386 TAAAGTGCTTATAGTGCGGGTAA
refseqGeneIntron-annotate CU-6179 1387 GTCCCACCAGAGTCGCCA
tRNAprefix-annotate; refseqGeneIntron-annotate CU-6170 1388
GGGGGAGGGGCCAAAAAAA refseqGeneIntron-annotate CU-6167 1389
GGGACGCCGCGGTGTCG refseqGeneIntron-annotate CU-6166 1390
GGGAATACCGGGTGCTTTAGGCTT refseqGeneIntron-annotate;
rnaGene-annotate CU-6160 1391 GGAAGAAGGTGGTGGTATA
refseqGeneIntron-annotate CU-6156 1392 GCGGTGAAATGCGTA
computGene-annotate; Ecoli-annotate; refseqGeneIntron- annotate
CU-6154 1393 GCGGGGAAGGTGGCAAA refseqGeneIntron-annotate CU-6152
1394 GCGACGACCTCGCGCCCACCTGGTCA refseqGeneIntron-annotate CU-6151
1395 GCCACCCGATACTGCTGT refseqGeneIntron-annotate CU-6150 1396
GATGTATGCTTTGTTTCTGTT refseqGeneIntron-annotate CU-6148 1397
GAGGGGGATTTAGAAAAAAA refseqGeneIntron-annotate CU-6147 1398
GAAGGAAAGTTCTATAGT refseqGeneIntron-annotate CU-6146 1399
GAAGCGGCTCTCTTATTT refseqGeneIntron-annotate CU-6145 1400
GAACGAGACTCTGGCATGCTGA refseqGeneIntron-annotate; rnaGene-annotate
CU-6143 1401 CTGGTAGGCCCATCAAT refseqGeneIntron-annotate CU-6132
1402 CGGGGCCGATCGCGCGC computGene-annotate;
refseqGeneIntron-annotate CU-6125 1403 CGGCCCCGGGTTCCTCCC
computGene-annotate; refseqGeneIntron-annotate CU-6118 1404
CGAGCCCGGTTAGTA refseqGeneIntron-annotate; rnaGene-annotate CU-6117
1405 CGACTCTTAGCGGTGGA piRNA-annotate; refseqGeneIntron-annotate
CU-6116 1406 CGAATCCCACTTCTGACACCA tRNAprefix-annotate;
refseqGeneIntron-annotate CU-6113 1407 CGAAAGGGAATCGGGTC
refseqGeneIntron-annotate CU-6112 1408 CCTTAGGTCGCTGGTAAA
refseqGeneIntron-annotate CU-6108 1409 CCGTGCGAGAATACCA
tRNAprefix-annotate; refseqGeneIntron-annotate CU-6107 1410
CCGGTCTCTCAAGCGGCC refseqGeneIntron-annotate CU-6099 1411
CCCGGCCCTCGCGCGTCC computGene-annotate; refseqGeneIntron-annotate
CU-6094 1412 CCCCGGCATTTCCACCA computGene-annotate;
refseqGeneIntron-annotate CU-6090 1413 CCCCCCCGGCTCCTCCACCA
refseqGeneIntron-annotate CU-6089 1414 CCCCCCACAACCGCTA
refseqGeneIntron-annotate CU-6085 1415 CCCAAGTATTGACTCACCC
mitochondrion-annotate; refseqGeneIntron-annotate CU-6084 1416
CCAGTAAGCGCGAGTC refseqGeneIntron-annotate CU-6082 1417
CCAAAGAAAGCACGTAGAG refseqGeneIntron-annotate CU-6081 1418
CATGTTTAACGGCCGCGGT mitochondrion-annotate;
refseqGeneIntron-annotate CU-6080 1419 CAGTTTGTAATTAACCCAA
refseqGeneIntron-annotate CU-6079 1420 CAGGAACGGCGCACCA
computGene-annotate; refseqGeneIntron-annotate CU-6078 1421
CAGAACCCTCTAAATCCCC mitochondrion-annotate;
refseqGeneIntron-annotate CU-6076 1422 CACCCGGCTGTGTGCACATGTGT
miRBASE-annotate; computGene-annotate; refseqGeneIntron- annotate;
wgRNA-annotate CU-6075 1423 CAATTGGACCAATCTATC
mitochondrion-annotate; refseqGeneIntron-annotate CU-6074 1424
ATTCCTGTACTGCGATA refseqGeneIntron-annotate CU-6070 1425
ATCCCTGCGGCGTCTCCA refseqGeneIntron-annotate CU-6067 1426
ATCCCACCGCTGCCATCA refseqGeneIntron-annotate CU-6062 1427
AGTCAATAGAAGCCGGCGTA mitochondrion-annotate;
refseqGeneIntron-annotate CU-6061 1428 AGGTTCGTTTGTAAAAA
refseqGeneIntron-annotate CU-6060 1429 AGGTCCTGGGTTTAAGTGT
computGene-annotate; refseqGeneIntron-annotate CU-6058 1430
AGGGGGAAGTTCTATAGTC refseqGeneIntron-annotate
CU-6057 1431 AGGCTGTGATGCTCTCNTGAGCCCT refseqGeneIntron-annotate
CU-6055 1432 AGCCCCTCTCCGGCCCTTA refseqGeneIntron-annotate CU-6054
1433 ACTACCACCTACCTCCC mitochondrion-annotate;
refseqGeneIntron-annotate CU-6052 1434 ACGCCCTTCCCCCCCTTCTTT
miRBASE-annotate; refseqGeneIntron-annotate CU-6049 1435
ACCCCACTCCTGGTGCAC refseqGeneIntron-annotate CU-6048 1436
ACCACCTGATCCCTTCCC refseqGeneIntron-annotate CU-6047 1437
ACAGCTAAGCACCCACCA refseqGeneIntron-annotate CU-6045 1438
ACACATGTTTAACGGCC mitochondrion-annotate; refseqGeneIntron-annotate
CU-6043 1439 AATTAGGGACCTGTATG refseqGeneIntron-annotate CU-6042
1440 AATGGCCCATTTGGGCAAACA computGene-annotate;
refseqGeneIntron-annotate CU-6041 1441 AAAGCGGCTGTGCAAACA
refseqGeneIntron-annotate CU-6030 1442 ATCCTGCCGACTACGCCA
tRNAprefix-annotate CU-6210 1443 TCGAATCCCACTCCTGACACCA
tRNAprefix-annotate CU-6069 1444 ATCCCATCCTCGTCGCCA
tRNAprefix-annotate CU-6216 1445 TCGATTCCCCGACGGGGAGCCA
tRNAprefix-annotate CU-6071 1446 ATCCGGGTGCCCCCTCCA
tRNAprefix-annotate CU-6212 1447 TCGACTCCTGGCTGGCTCGCCA
tRNAprefix-annotate; wgRNA-annotate CU-6202 1448 TCCCGGGCGGCGCACCA
tRNAprefix-annotate CU-6066 1449 ATCCCACCAGAGTCGCCA
tRNAprefix-annotate CU-6200 1450 TCCCCGGCATCTCCACCAA
computGene-annotate CU-6192 1451 TCAAATCACGTCGGGGTCACCA
tRNAprefix-annotate CU-6157 1452 GCGGTGGATCACTCGGCTCGTGCGT
rnaGene-annotate CU-6214 1453 TCGATCCCCGTACGGGCCACCA
tRNAprefix-annotate CU-6213 1454 TCGAGCCTCACCTGGAGCACCA
tRNAprefix-annotate CU-6206 1455 TCCGGCTCGAAGGACCA
tRNAprefix-annotate CU-6105 1456 CCGGGTGTTGTAGA mRNAall-annotate;
exEID-annotate CU-6235 1457 TGTAGCGTGGCCGAGCGGT rnaGene-annotate
CU-6234 1458 TGGGGCGACCTCGGAGCAG mitochondrion-annotate CU-6230
1459 TGGCGTCCTAAGCCAGGGATTGTGGGT rnaGene-annotate CU-6229 1460
TGGCAGGGGAGATACCATGATTT rnaGene-annotate CU-6222 1461
TCTGATCAGGGTGAGCATC mitochondrion-annotate CU-6220 1462
TCGTAGGCACCATCCAT computGene-annotate CU-6165 1463
GGGAAACGGGGCGCGGCTG rnaGene-annotate CU-6137 1464
CTACTCCTGCTCGCATCTGCTATA mitochondrion-annotate CU-6135 1465
CGGGTGGGTTTTTACCGG computGene-annotate CU-6120 1466
CGAGGAATTCCCAGTAAG rnaGene-annotate CU-6115 1467
CGAACGCACTTGCGGCCCC rnaGene-annotate CU-6093 1468
CCCCGCGCGGGTTCGAATC rnaGene-annotate CU-6059 1469
AGGGGTATGATTCCCGCTT rnaGene-annotate CU-6131 1470
CGGGGCCACGCGCGCGTC mRNA-annotate; rRNA-eliminate CU-6032 1471
TGGCGCTGCGGGATGAAC rRNA-eliminate; refseqGeneIntron-annotate;
rnaGene-annotate CU-1153 1472 CCCCCCACTGCTAAATTTGACTGGCTT
yRNA-eliminate; refseqGeneIntron-annotate; rnaGene-annotate CU-6182
1473 TAAAGGTTCGTTTGTAAAA computGene-annotate;
refseqGeneExon-eliminate CU-6033 1474 CGGGGCCGAGGGAGCGA
rRNA-eliminate; refseqGeneExon-eliminate; refseqGeneIntron-
annotate CU-6174 1475 GGGTTAGGCCTCTTTT tRNA-eliminate;
rnaGene-annotate CU-6141 1476 CTGCGGAAGGATCATTA rRNA-eliminate;
rnaGene-annotate CU-6101 1477 CCCTACCCCCCCGG rRNA-eliminate;
refseqGeneIntron-annotate CU-6034 1478 CCCGCCGGGTCCGCCC
computGene-annotate; rRNA-eliminate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate; rnaGene-annotate CU-6035 1479
CCCCGCGCCCTCTCTCTCTC rRNA-eliminate; refseqGeneIntron-annotate
CU-6028 1480 CAGGCCTCCCTGGAATC computGene-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6029 1481
AGTCCCACCCGGGGTACCA computGene-annotate; refseqGeneExon-eliminate;
tRNAprefix- annotate CU-6243 1482 TTGACACGCCCCAGTGCCCTGT
refseqGeneExon-eliminate CU-6233 1483 TGGGAGCGGGCGGGCGGTC
rRNA-eliminate; rnaGene-annotate CU-6231 1484 TGGCGTGGAGCCGGGCGT
rRNA-eliminate; refseqGeneIntron-annotate CU-6228 1485
TGGAGGTCCGTAGCGGT rRNA-eliminate; mRNA-annotate; refseqGeneIntron-
annotate; rnaGene-annotate CU-6223 1486 TGAAGAAGGTCTCGAACA
computGene-annotate; refseqGeneExon-eliminate CU-6221 1487
TCTCGCCGGGGCTTCCA computGene-annotate; refseqGeneExon-eliminate;
rnaGene- annotate CU-6217 1488 TCGTAGCACCATCAATAA
computGene-annotate; refseqGeneExon-eliminate CU-6208 1489
TCCGGGTCCCCCCTCCA computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6207 1490 TCCGGGGCTGCACGCGCGCT
rRNA-eliminate; rnaGene-annotate CU-6205 1491 TCCGGCCGTGTCGGT
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6203 1492 TCCCTGTCCTCCAGGAGT
miRBASE-annotate; computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate; wgRNA-annotate CU-6201 1493
TCCCCTCCTCGTCGCCA refseqGeneExon-eliminate;
refseqGeneIntron-annotate CU-6199 1494 TCCCAGGTAGTCTAGTGGT
refseqGeneExon-eliminate; refseqGeneIntron- annotate;
rnaGene-annotate CU-6191 1495 TATTCATTTATCCCCAGCCTAT
miRBASE-annotate; snoRNA-eliminate; refseqGeneIntron- annotate;
wgRNA-annotate; rnaGene-annotate CU-6190 1496 TAGTTGTTATAACCCAA
refseqGeneExon-eliminate; refseqGeneIntron-annotate CU-6186 1497
TAGATCACCCCCTCCCC mitochondrion-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6185 1498 TACCGGCACCTGGCGCC
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6178 1499 GTATAGGGGCGAAAGAC
rRNA-eliminate; mRNA-annotate; refseqGeneIntron- annotate;
rnaGene-annotate CU-6177 1500 GTAGCTGGTTCCCTCCGAA rRNA-eliminate;
mRNA-annotate; refseqGeneIntron- annotate; rnaGene-annotate CU-6175
1501 GGTAAGAAGCCCGGCTC computGene-annotate; rRNA-eliminate;
refseqGeneExon- eliminate; refseqGeneIntron-annotate;
rnaGene-annotate CU-6173 1502 GGGGGGGTTTAAAAAAAAA
refseqGeneExon-eliminate; refseqGeneIntron-annotate CU-6169 1503
GGGGCGCACTACCGGCC refseqGeneExon-eliminate CU-6168 1504
GGGAGAGGCTGTCGCTGCG computGene-annotate; refseqGeneExon-eliminate
CU-6164 1505 GGCGGGTGAAGCGGCG computGene-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6158 1506 GCGGTTCCGGCGGCGTC
rRNA-eliminate; refseqGeneExon-eliminate; refseqGeneIntron-
annotate CU-6155 1507 GCGGGGCGCCTAGGCCTGGTTTGT
refseqGeneExon-eliminate CU-6153 1508 GCGGCGGTCGGCGGGCGGCGGG
rRNA-eliminate; refseqGeneExon-eliminate; refseqGeneIntron-
annotate CU-6149 1509 GAGGGGGGGGGTGGGGGGGGA
refseqGeneExon-eliminate; refseqGeneIntron-annotate CU-6144 1510
CTGTCGGCCACCATCAT computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6140 1511 CTGCAACTCGACCCCA
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6139 1512 CTCCTCTCCCCGCCCGCCG
refseqGeneExon-eliminate; refseqGeneIntron-annotate CU-6138 1513
CTCAAAGATTAAGCCATGCATGTCTA rRNA-eliminate; rnaGene-annotate CU-6136
1514 CTACGCCGCGACGAG computGene-annotate; rRNA-eliminate CU-6134
1515 CGGGTGACGGGGAATCAGGGTT rRNA-eliminate; rnaGene-annotate
CU-6127 1516 CGGGCAGCTTCCGGGA computGene-annotate; rRNA-eliminate;
refseqGeneExon- eliminate; refseqGeneIntron-annotate CU-6126 1517
CGGGAGGCCCGGGTCCTG refseqGeneExon-eliminate;
refseqGeneIntron-annotate CU-6124 1518 CGGCCCCGCATCCTCCC
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6122 1519 CGCGGGTAAACGGCGGGAGTAACTAT
mRNAall-annotate; rRNA-eliminate; refseqGeneIntron- annotate;
rnaGene-annotate CU-6121 1520 CGCCCCCCGTTCCCCCCTCC rRNA-eliminate
CU-6119 1521 CGAGCGGAAACACCA computGene-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate; tRNAprefix-annotate CU-6114
1522 CGAACCCGGCACCGC computGene-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6111 1523 CCTCGGGCCGATCGCAC
rRNA-eliminate; rnaGene-annotate CU-6110 1524 CCTATATATCTTACCA
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate; tRNAprefix-annotate CU-6109 1525
CCGTGGCGGCGACGACC computGene-annotate; rRNA-eliminate;
refseqGeneExon- eliminate
CU-6106 1526 CCGGGTTCCGGCACCA computGene-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate CU-6104 1527 CCGCGAGGGGGGCCCG
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6103 1528 CCGCCTCACGGGACCA
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6102 1529 CCGCCCGTCCCCGCCCCTTG
rRNA-eliminate; refseqGeneIntron-annotate; rnaGene-annotate CU-6100
1530 CCCGGGGCCGCGGTTCCG computGene-annotate; rRNA-eliminate;
refseqGeneIntron- annotate CU-6098 1531 CCCGAGCCGCCTGGAT
computGene-annotate; rRNA-eliminate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate; rnaGene-annotate CU-6097 1532
CCCGACGGCCGAACT computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6095 1533 CCCCGGGGAGCCCGGCGGG
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6092 1534 CCCCCTCGCGGCCCTCCCC
rRNA-eliminate; refseqGeneIntron-annotate CU-6091 1535
CCCCCCGTGGCGGCGAC rRNA-eliminate; refseqGeneIntron-annotate CU-6083
1536 CCACCCAGGGCACGCCA refseqGeneExon-eliminate;
refseqGeneIntron-annotate CU-6077 1537 CACGGGTGACGGGGAA
computGene-annotate; rnaGene-annotate; refseqGeneIntron- annotate;
rRNA-eliminate; refseqGeneExon-eliminate; piRNA- annotate CU-6073
1538 ATGGGGAGGAAAAAAAAAAAAAA refseqGeneExon-eliminate;
refseqGeneIntron-annotate CU-6068 1539 ATCCCACCGCTGCCCCCA
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6065 1540 ATCACGTCGGTCACCA
computGene-annotate; refseqGeneExon- eliminate;
refseqGeneIntron-annotate CU-6053 1541 ACGGGAAACCTCACCCGGCCCGG
rRNA-eliminate; piRNA-annotate; rnaGene-annotate CU-6046 1542
ACAGAGGCTTACGACCCCTTATTT mitochondrion-annotate; tRNA-eliminate;
refseqGeneIntron- annotate; rnaGene-annotate CU-6040 1543
AAAAAGGCATAATTAAACTT mitochondrion-annotate; refseqGeneExon-
eliminate; refseqGeneIntron-annotate
TABLE-US-00031 TABLE 10 (PART B) List of short-RNA consensus with
maximum 1 mismatch to the human genome, including count
information. Corrected Counts SEQ ID Naive Memory Centroblasts
Ramos NO: Short-RNA sequence (N) (M) (CB) (RA) 1544
TGGCTCAGTTCAGCAGGAACAGT 0 0 1 0 1545 GTGGGGGAGAGGCTGTCGA 0 0 0 1
1546 CGGGGCAGCTCAGTACAGGATT 0 0 1 0 1547 AATTGCACGGTATCCATCTGTAT 0
0 1 0 1548 TGTCAGTTTGTTAATTGACCCAA 0 0 1 1 1549 GGCAATACGAGCACCCTG
2 0 0 0 1550 CGGGGGAGCGCCGCGTA 2 0 0 0 1551 CCGGGGCGTCTCGTAC 2 0 0
0 1552 AGCGGCTGTGCACAAA 0 0 0 2 1553 TGTCAGTTTGTTTAATCCAA 0 0 0 1
1554 TGTCAGTTTGTTATTACCAA 0 0 0 1 1555 TGTCAGGCACCATCAATAA 0 0 0 1
1556 TGATCTTGACACTTAAAGCC 0 0 0 1 1557 TCGTAGGCACCATCAAT 0 0 0 1
1558 TCGATCCCGGGTTTCGGCACCA 0 0 1 0 1559 TCGACTCCCGGTATGGGAACCA 0 0
0 1 1560 TAGGGAGGTTATGATTAACTTTT 0 0 0 1 1561 TAAAGTGCTTAGTGCAGGTA
0 0 0 1 1562 GTTTATGTTGCTTACCTCC 0 0 1 0 1563 GTAGATAAAATATTGGCG 1
0 0 0 1564 GGCGGGGACGACGTCAG 0 0 0 1 1565 GGCGGCGTCGCGGCGGGTC 0 1 0
0 1566 GGAGGGGGTGAACAAAAAGAAAAA 0 0 0 1 1567
GCTAAACCTAGCCCCAAACCCAC 0 0 0 1 TCCACA 1568 CTGGATAGCGCACTTCGTT 0 0
0 1 1569 CGGGCGAGGGGCGGACGTTCG 0 0 1 0 1570 CGGACCTATACCGGA 1 0 0 0
1571 CCCCGGGTTCAATCCCCGGCACC 0 0 1 0 TCCACCA 1572 CCCCCCACAACCGCGAA
0 1 0 0 1573 CCCAGCATCTCCTGTGTTTA 0 1 0 0 1574 CCCACGTTGGGACGCCA 1
0 0 0 1575 ATCGTATCCCACTTCTGACACCA 0 0 0 1 1576 ATCACGTCCGTGCCTCCA
0 1 0 0 1577 ATAGCAATGTCAGCAGTACCT 0 0 1 0 1578 ACCCTGCTCGCTGCGCCA
9 17 4 7 1579 TCCCACCCAGGGACGCCA 8 2 1 0 1580 TCGTAGGCACATCAATA 0 0
0 4 1581 CCCCCACAACCGCGTA 0 4 0 0 1582 ACCCCGTCCGTGCCTCCA 2 1 1 0
1583 AAAAAAGACACCCCCCACA 0 0 0 3 1584 TGTCAGTTTGTTAACCCAA 0 0 0 2
1585 TCCCTGTGGTCTAGTGGTTAGG 0 0 1 1 1586 GGGGGGGTAAAAAAA 0 0 0 1
1587 GGGGGGGGAAAAAAAA 0 0 0 1 1588 CGGGCCCGGGTCTTCCC 1 1 0 0 1589
CCGCCCCCCGTTCCCCCCA 0 2 0 0 1590 ACCCCCGGCTCCTCCACCA 0 1 0 1 1591
TTTGGTGGAAATTTTTTGA 0 0 0 1 1592 TGTCAGTTTGTTATACCAA 0 0 0 1 1593
TGTCAGTTTGTAATTATCCCAA 0 0 0 1 1594 TGTCAATTTTTAACCCAA 0 0 0 1 1595
TGCTAGGGTAAAAAAAAAA 0 0 0 1 1596 TGCAACTCCAAATAAAAGTACCA 0 0 0 1
1597 TGAGGTAACGGGGAATTA 0 0 0 1 1598 TCCTCGGCATCTCCACCA 0 0 1 0
1599 TCATATGAAGTCACCCTAGCCATC 0 0 1 0 1600 TCAGTTTGTTTATTAACCCAA 0
0 0 1 1601 TCAGCGTGTCTTTGCCCT 1 0 0 0 1602 TCACTGGTGGTCTAGTGGT 0 1
0 0 1603 TCACAATGCTGCCACCA 1 0 0 0 1604 TAGTTGTTAATTAACCCAA 0 0 0 1
1605 TAGTCCTCATCGCCCTCC 0 1 0 0 1606 TAAAGTGCTTATAGTGCGGGTAA 0 0 0
1 1607 GTCCCACCAGAGTCGCCA 0 0 1 0 1608 GGGGGAGGGGCCAAAAAAA 0 0 0 1
1609 GGGACGCCGCGGTGTCG 1 0 0 0 1610 GGGAATACCGGGTGCTTTAGGCTT 0 1 0
0 1611 GGAAGAAGGTGGTGGTATA 0 0 0 1 1612 GCGGTGAAATGCGTA 1 0 0 0
1613 GCGGGGAAGGTGGCAAA 0 0 0 1 1614 GCGACGACCTCGCGCCCACCTG 0 1 0 0
GTCA 1615 GCCACCCGATACTGCTGT 0 1 0 0 1616 GATGTATGCTTTGTTTCTGTT 0 0
1 0 1617 GAGGGGGATTTAGAAAAAAA 0 0 0 1 1618 GAAGGAAAGTTCTATAGT 0 0 0
1 1619 GAAGCGGCTCTCTTATTT 0 0 0 1 1620 GAACGAGACTCTGGCATGCTGA 0 0 1
0 1621 CTGGTAGGCCCATCAAT 0 0 0 1 1622 CGGGGCCGATCGCGCGC 0 1 0 0
1623 CGGCCCCGGGTTCCTCCC 1 0 0 0 1624 CGAGCCCGGTTAGTA 1 0 0 0 1625
CGACTCTTAGCGGTGGA 0 0 1 0 1626 CGAATCCCACTTCTGACACCA 0 0 0 1 1627
CGAAAGGGAATCGGGTC 1 0 0 0 1628 CCTTAGGTCGCTGGTAAA 0 0 1 0 1629
CCGTGCGAGAATACCA 0 1 0 0 1630 CCGGTCTCTCAAGCGGCC 1 0 0 0 1631
CCCGGCCCTCGCGCGTCC 0 1 0 0 1632 CCCCGGCATTTCCACCA 0 0 1 0 1633
CCCCCCCGGCTCCTCCACCA 0 0 0 1 1634 CCCCCCACAACCGCTA 0 1 0 0 1635
CCCAAGTATTGACTCACCC 0 1 0 0 1636 CCAGTAAGCGCGAGTC 1 0 0 0 1637
CCAAAGAAAGCACGTAGAG 0 0 0 1 1638 CATGTTTAACGGCCGCGGT 0 0 1 0 1639
CAGTTTGTAATTAACCCAA 0 0 0 1 1640 CAGGAACGGCGCACCA 0 0 1 0 1641
CAGAACCCTCTAAATCCCC 0 0 1 0 1642 CACCCGGCTGTGTGCACATGTGT 1 0 0 0
1643 CAATTGGACCAATCTATC 0 0 1 0 1644 ATTCCTGTACTGCGATA 0 0 0 1 1645
ATCCCTGCGGCGTCTCCA 0 0 0 1 1646 ATCCCACCGCTGCCATCA 0 1 0 0 1647
AGTCAATAGAAGCCGGCGTA 0 0 1 0 1648 AGGTTCGTTTGTAAAAA 0 0 0 1 1649
AGGTCCTGGGTTTAAGTGT 0 0 0 1 1650 AGGGGGAAGTTCTATAGTC 0 0 0 1 1651
AGGCTGTGATGCTCTCNTGAGCC 0 0 1 0 CT 1652 AGCCCCTCTCCGGCCCTTA 0 1 0 0
1653 ACTACCACCTACCTCCC 1 0 0 0 1654 ACGCCCTTCCCCCCCTTCTTT 0 0 0 1
1655 ACCCCACTCCTGGTGCAC 1 0 0 0 1656 ACCACCTGATCCCTTCCC 1 0 0 0
1657 ACAGCTAAGCACCCACCA 0 0 1 0 1658 ACACATGTTTAACGGCC 1 0 0 0 1659
AATTAGGGACCTGTATG 0 0 1 0 1660 AATGGCCCATTTGGGCAAACA 0 0 0 1 1661
AAAGCGGCTGTGCAAACA 0 0 0 1 1662 ATCCTGCCGACTACGCCA 13 15 13 6
1663 TCGAATCCCACTCCTGACACCA 1 2 7 7 1664 ATCCCATCCTCGTCGCCA 0 0 10
3 1665 TCGATTCCCCGACGGGGAGCCA 1 1 1 9 1666 ATCCGGGTGCCCCCTCCA 2 4 0
1 1667 TCGACTCCTGGCTGGCTCGCCA 0 2 2 1 1668 TCCCGGGCGGCGCACCA 2 2 1
0 1669 ATCCCACCAGAGTCGCCA 0 0 2 3 1670 TCCCCGGCATCTCCACCAA 0 1 2 0
1671 TCAAATCACGTCGGGGTCACCA 0 1 2 0 1672 GCGGTGGATCACTCGGCTCGTGC 0
0 0 3 GT 1673 TCGATCCCCGTACGGGCCACCA 0 0 1 1 1674
TCGAGCCTCACCTGGAGCACCA 0 0 2 0 1675 TCCGGCTCGAAGGACCA 0 0 2 0 1676
CCGGGTGTTGTAGA 2 0 0 0 1677 TGTAGCGTGGCCGAGCGGT 0 1 0 0 1678
TGGGGCGACCTCGGAGCAG 0 0 1 0 1679 TGGCGTCCTAAGCCAGGGATTGT 0 0 0 1
GGGT 1680 TGGCAGGGGAGATACCATGATTT 0 0 1 0 1681 TCTGATCAGGGTGAGCATC
0 1 0 0 1682 TCGTAGGCACCATCCAT 0 0 0 1 1683 GGGAAACGGGGCGCGGCTG 0 1
0 0 1684 CTACTCCTGCTCGCATCTGCTATA 0 0 1 0 1685 CGGGTGGGTTTTTACCGG 1
0 0 0 1686 CGAGGAATTCCCAGTAAG 0 0 1 0 1687 CGAACGCACTTGCGGCCCC 1 0
0 0 1688 CCCCGCGCGGGTTCGAATC 1 0 0 0 1689 AGGGGTATGATTCCCGCTT 0 0 0
1 1690 CGGGGCCACGCGCGCGTC 3 6 0 0 1691 TGGCGCTGCGGGATGAAC 0 3 1 0
1692 CCCCCCACTGCTAAATTTGACTG 0 0 2 2 GCTT 1693 TAAAGGTTCGTTTGTAAAA
0 0 0 3 1694 CGGGGCCGAGGGAGCGA 1 2 0 0 1695 GGGTTAGGCCTCTTTT 0 1 1
0 1696 CTGCGGAAGGATCATTA 1 0 1 0 1697 CCCTACCCCCCCGG 0 2 0 0 1698
CCCGCCGGGTCCGCCC 2 0 0 0 1699 CCCCGCGCCCTCTCTCTCTC 0 2 0 0 1700
CAGGCCTCCCTGGAATC 2 0 0 0 1701 AGTCCCACCCGGGGTACCA 0 0 0 2 1702
TTGACACGCCCCAGTGCCCTGT 1 0 0 0 1703 TGGGAGCGGGCGGGCGGTC 0 1 0 0
1704 TGGCGTGGAGCCGGGCGT 0 1 0 0 1705 TGGAGGTCCGTAGCGGT 1 0 0 0 1706
TGAAGAAGGTCTCGAACA 0 0 0 1 1707 TCTCGCCGGGGCTTCCA 0 1 0 0 1708
TCGTAGCACCATCAATAA 0 0 0 1 1709 TCCGGGTCCCCCCTCCA 0 1 0 0 1710
TCCGGGGCTGCACGCGCGCT 0 1 0 0 1711 TCCGGCCGTGTCGGT 1 0 0 0 1712
TCCCTGTCCTCCAGGAGT 0 0 0 1 1713 TCCCCTCCTCGTCGCCA 1 0 0 0 1714
TCCCAGGTAGTCTAGTGGT 1 0 0 0 1715 TATTCATTTATCCCCAGCCTAT 0 1 0 0
1716 TAGTTGTTATAACCCAA 0 0 0 1 1717 TAGATCACCCCCTCCCC 0 1 0 0 1718
TACCGGCACCTGGCGCC 1 0 0 0 1719 GTATAGGGGCGAAAGAC 0 0 1 0 1720
GTAGCTGGTTCCCTCCGAA 0 0 0 1 1721 GGTAAGAAGCCCGGCTC 0 0 1 0 1722
GGGGGGGTTTAAAAAAAAA 0 0 0 1 1723 GGGGCGCACTACCGGCC 1 0 0 0 1724
GGGAGAGGCTGTCGCTGCG 0 0 0 1 1725 GGCGGGTGAAGCGGCG 0 1 0 0 1726
GCGGTTCCGGCGGCGTC 0 1 0 0 1727 GCGGGGCGCCTAGGCCTGGTTT 1 0 0 0 GT
1728 GCGGCGGTCGGCGGGCGGCGGG 1 0 0 0 1729 GAGGGGGGGGGTGGGGGGGGA 0 0
0 1 1730 CTGTCGGCCACCATCAT 0 0 0 1 1731 CTGCAACTCGACCCCA 0 1 0 0
1732 CTCCTCTCCCCGCCCGCCG 0 0 1 0 1733 CTCAAAGATTAAGCCATGCATGTC 0 0
1 0 TA 1734 CTACGCCGCGACGAG 1 0 0 0 1735 CGGGTGACGGGGAATCAGGGTT 1 0
0 0 1736 CGGGCAGCTTCCGGGA 0 0 0 1 1737 CGGGAGGCCCGGGTCCTG 1 0 0 0
1738 CGGCCCCGCATCCTCCC 1 0 0 0 1739 CGCGGGTAAACGGCGGGAGTAA 0 0 1 0
CTAT 1740 CGCCCCCCGTTCCCCCCTCC 0 1 0 0 1741 CGAGCGGAAACACCA 1 0 0 0
1742 CGAACCCGGCACCGC 1 0 0 0 1743 CCTCGGGCCGATCGCAC 0 0 1 0 1744
CCTATATATCTTACCA 0 1 0 0 1745 CCGTGGCGGCGACGACC 0 1 0 0 1746
CCGGGTTCCGGCACCA 1 0 0 0 1747 CCGCGAGGGGGGCCCG 1 0 0 0 1748
CCGCCTCACGGGACCA 1 0 0 0 1749 CCGCCCGTCCCCGCCCCTTG 0 1 0 0 1750
CCCGGGGCCGCGGTTCCG 1 0 0 0 1751 CCCGAGCCGCCTGGAT 0 1 0 0 1752
CCCGACGGCCGAACT 0 1 0 0 1753 CCCCGGGGAGCCCGGCGGG 1 0 0 0 1754
CCCCCTCGCGGCCCTCCCC 0 1 0 0 1755 CCCCCCGTGGCGGCGAC 0 1 0 0 1756
CCACCCAGGGCACGCCA 1 0 0 0 1757 CACGGGTGACGGGGAA 1 0 0 0 1758
ATGGGGAGGAAAAAAAAAAAAAA 0 0 0 1 1759 ATCCCACCGCTGCCCCCA 0 0 0 1
1760 ATCACGTCGGTCACCA 0 0 0 1 1761 ACGGGAAACCTCACCCGGCCCGG 0 0 1 0
1762 ACAGAGGCTTACGACCCCTTATTT 0 0 1 0 1763 AAAAAGGCATAATTAAACTT 0 0
1 0
[0353] Abundance and Evolutionary Conservation.
[0354] Previously reported miRNAs appeared to be generally more
abundant than newly discovered miRNAs. Approximately 50% of
previously reported miRNAs appeared in the libraries with more than
10 occurrences compared to 29% of the newly discovered miRNAs (FIG.
20A). Moreover, 48% of known miRNAs were expressed at all stages of
mature B-cell development, while newly identified miRNAs showed a
more distinct stage-specificity (FIG. 20B), consistent with the
notion that presently known miRNAs are mostly representative of
ubiquitously expressed miRNAs.
[0355] In order to investigate the presence of orthologous miRNA in
other mammalian species, we relied on UCSC-provided Blastz pairwise
alignments between human and target species and investigated
conservation using two complementary methods, detailed in
Supplemental Experimental Procedures. The analysis was performed on
the complete set of miRNAs deposited in the miRBase database and on
the miRNAs (known and new) represented in the B-cell libraries.
Alignments of the human mature miRNA to its target species were
required to have either perfect conservation of the entire mature
miRNA sequence or conservation of seeds composed of seven bases
starting from the second position of the human mature sequence
followed by conservation of 3 bases starting from the 12th, 13th or
14th position as suggested by (Grimson et al., 2007) (FIG. 20C and
Appendix Table 11).
[0356] The majority of miRBase-miRNAs showed conservation across
mammalian genomes, from primates to rodents. Conservation frequency
mimicked known phylogenetic distances to human, with the highest
conservation in chimp and lowest in rat. The conservation
frequencies of known and newly identified miRNAs in B cells were
similar in chimp (Pan troglodytes) and monkey (Macacus rhesus),
especially when conservation requirements were restricted to the
seed region of miRNAs. However, conservation frequencies in dog,
mouse and rat were significantly divergent, with known miRNAs more
likely to exhibit conservation than new candidate miRNAs (FIG. 20C
and Appendix Table 11). In summary, previously unreported miRNAs
expressed at specific stages of B-cell differentiation were
generally less abundant and showed a lower degree of conservation
across species, as shown for other tissue-specific miRNAs.
[0357] Validation of Previously Unreported miRNAs.
[0358] All 75 newly identified miRNAs were investigated by RT-PCR
analysis in order to independently validate their existence in vivo
in B-cell lines and cells isolated from tonsils. Positive results
were obtained in 66 of the cases (see FIG. 21A for representative
results and Table 12). Eighteen previously unreported miRNAs were
also tested by RNA blot analysis and 11 were detectable (FIG. 21B
and Table 12), either using total cellular RNA or upon enrichment
for the short-RNA fraction. Overall, 88% of the newly cloned and
computationally validated miRNAs were detectable by RNA blot and/or
RT-PCR. The validation process also led to the identification of
numerous miRNA which are differentially regulated either in normal
versus transformed cells (see examples CU-1440, CU-1241, CU-1276
and CU-1137 in FIG. 21) as well as during the GC reaction (FIG.
22).
TABLE-US-00032 TABLE 12 Summary of results obtained from the
Northern Blot and/or RT-PCR analyses performed on newly identified
mature miRNAs cloned multiple times in the B-cell libraries. Seq ID
Northern ID No. Mature miRNA sequence Blot RT-PCR CU-1369 1764
TCCCCGGCATCTCCACCA negative positive CU-1254 1765
TCCCCGGCACCTCCACCA positive positive CU-1298 1766
ATCCCGGACGAGCCCCCA not tested positive CU-1303 1767
ATCCCACTTCTGACACCA positive positive CU-1173 1768
ATCCCACTCCTGACACCA positive positive CU-1242 1769
TCCCCGTACGGGCCACCA not tested positive CU-1550 1770
CGGAAGCGTGCTGGGCCC not tested positive CU-1186 1771
TCCCCGACACCTCCACCA not tested positive CU-1368 1772
GACGAGGTGGCCGAGTGG positive positive CU-1243 1773
GTCCCTTCGTGGTCGCCA not tested positive CU-1470 1774
CTCCTGGCTGGCTCGCCA not tested positive CU-1300 1775
TCCTCACACGGGGCACCA not tested positive CU-1264 1776
GAGGGGGACCAAAAAAAA not tested negative CU-1212 1777
TCCCCGGCACTTCCACCA not tested positive CU-1345 1778
AGAACACTACGAGCCACA not tested positive CU-1352 1779
ACCCCACTTCTGGTACCA negative positive CU-1363 1780
CGTTCGCGCTTTCCCCTG not tested negative CU-1220 1781
TTCCCCGACGGGGAGCCA not tested positive CU-1197 1782
ATGTGGTGGCTTACTTTT not tested positive CU-1241 1783
AGTCCCATCTGGGTCGCCA positive positive CU-1148 1784
TGGTGTGGTCTGTTGTTTT not tested positive CU-1288 1785
CGTCCATGATGTTCCGCAA not tested positive CU-1528 1786
TAGGGGTATGATTCTCGCT not tested negative CU-1175 1787
GGCGTGATTCATACCTTTT not tested positive CU-1570 1788
ATCCCCAGCATCTCCACCA not tested positive CU-1269 1789
TACCGAGCCTGGTGATAGC not tested positive CU-1339 1790
ATCCCCAGCACCTCCACCA not tested positive CU-1132 1791
GCCGGGTACTTTCGTATTTT not tested negative CU-1370 1792
CTGATTGCTCCTGTCTGATT not tested positive CU-1545 1793
CCACGAGGAAGAGAGGTAGC not tested negative CU-1307 1794
ACCCCACTATGCTTAGCCCT not tested positive CU-1294 1795
AAAGGACCTGGCGGTGCTTC not tested positive CU-1371 1796
TCTAGAGGAGCCTGTTCTGTA not tested positive CU-1244 1797
GTCAGGATGGCCGAGCGGTCT not tested positive CU-1276 1798
TCGATTCCCGGCCAATGCAC positive positive CA CU-1142 1799
TCGATTCCCGGCCCATGCAC positive positive CA CU-1379 1800
TCGGGTGCGAGAGGTCCCG negative positive GGT CU-1381 1801
TCGATTCCCGGTCAGGGAAC not tested positive CA CU-1403 1802
GCATTGGTGGTTCAGTGGTA positive positive GA CU-1457 1803
TTCTCACTACTGCACTTGACTA not tested positive CU-1557 1804
GGAGAGAACGCGGTCTGAGT not tested positive GGT CU-1542 1805
GGCTGGTCCGATGGTAGTGG not tested positive GTT CU-1221 1806
TGTGCTCCGGAGTTACCTCG not tested negative TTT CU-1380 1807
ATAGGTTTGGTCCTAGCCTTT not tested positive CT CU-1277 1808
GAGCCATGATGATACCACTG not tested positive AGC CU-1281 1809
GCAGCGCCAGCCTCCCGCCC not tested positive TAC CU-1524 1810
CCCCCACAACCGCGCTTGAC not tested positive TAGC CU-1477 1811
CTCCCACTGCTTCACTTGACT not tested positive AGC CU-1575 1812
CCCCCCACTGCTAAATTTGAC not tested positive TGGA CU-1137 1813
GCTAAGGAAGTCCTGTGCTC positive positive AGTTTT CU-1538 1814
GGCTGGTCCGAGTGCAGTGG not tested positive TGTTTA CU-1153 1815
CCCCCCACTGCTAAATTTGAC positive positive TGGCTT CU-1513 1816
GCGGGTGATGCGAACTGGAG positive positive TCTGAGC CU-1293 1817
AGCAGTGATGTCCTGAAAATT not tested negative CTGAAG CU-1388 1818
TCCCTGGTGGTCTAGTGGTT negative positive AGGATTCG CU-1180 1819
AACCGAGCGTCCAAGCTCTT not tested positive TCCATTTT CU-1382 1820
TCCTCGTTAGTATAGTGGTGA negative positive GTATCCC CU-1251 1821
CCCACCCAGGGACGCCA negative positive CU-1191 1822 GCCCGCATCCTCCACCA
negative positive CU-1453 1823 CCCTGCTCGCTGCGCCA not tested
positive CU-1222 1824 TCACGTCGGGGTCACCA not tested positive CU-1178
1825 AGGGTGTGCGTGTTTTT not tested positive CU-1488 1826
TCCTGCCGCGGTCGCCA not tested positive CU-1164 1827
GAGAGCGCTCGGTTTTT not tested negative CU-1486 1828
CTGCTGTGATGACATTC not tested positive CU-1130 1829
CCCGGGTTTCGGCACCA not tested positive CU-1155 1830
TCCCCGCACCTCCACCA not tested positive CU-1278 1831
TAACGGCCGCGGTACCC not tested positive CU-1246 1832
AGGGGGGTAAAAAAAAA not tested positive CU-1440 1833
TGGTTATCACGTTCGCC not tested positive CU-1213 1834
TCACCCCATAAACACCA not tested positive CU-1146 1835
AGAAAGGCCGAATTTTA not tested positive CU-1323 1836
TGTATTGTGAGACATTC not tested positive CU-1324 1837
TCTCGGTGGAACCTCCA not tested positive CU-1396 1838
TAAGTGTTTGTGGGTTA not tested negative
[0359] In order to gain preliminary evidence of the functionality
of the previously unreported miRNAs, a small subset of these miRNAs
which were fully validated at the expression level was tested for
incorporation in the functional miRNA-mRNA complex by
co-immunoprecipitation with Ago2 proteins (Mourelatos et al.,
2002). The results showed that the RNA fraction associated with the
Ago complex was indeed enriched for each of the four tested
previously unreported miRNAs (FIG. 25), confirming that the
identified sequences enter the expected miRNA functional
pathway.
[0360] Indirect clues on the functionality of miRNAs may also be
obtained analyzing the effect of stage-specific miRNAs on the
corresponding transcriptome since most miRNAs have been showed to
affect the expression of their targets albeit to a modest degree
(Filipowicz et al., 2008). Toward this end, the targets of 15
previously unreported GC-over-expressed miRNAs were predicted by
two algorithms (miRanda and RNA22) (John et al., 2004; Miranda et
al., 2006) and were tested for enrichment in genes down-regulated
in GC versus naive B cells. Eleven out of 15 miRNA showed an
increase (and only two a decrease) in their candidate target
enrichment p-value for GC down-regulated genes compared to control
populations (FIG. 26 and Table 13). These results suggest that
indeed miRNAs associated with GC B cells specifically affect the GC
transcriptome.
TABLE-US-00033 TABLE 13 Enrichment for predicted miRNA targets in
genes down regulated in CB and in memory compared to naive B cells.
CB Targets enrichment in genes Targets enrichment in genes
over-expressed downregulated in CB vs N downregulated in M vs N
miRNA (p-value) (p-value) CU-1380 0.0001 0.4079 CU-1388 0.0002
0.2699 CU-1477 0.0002 0.0514 CU-1538 0.0014 0.1609 CU-1142 0.0016
0.0012 CU-1382 0.0016 0.0242 CU-1403 0.0026 0.0032 CU-1470 0.0029
0.5392 CU-1276 0.0193 0.0187 CU-1371 0.0413 0.2252 CU-1153 0.091 1
CU-1575 0.1598 1 CU-1370 0.1708 0.4595 CU-1303 1 1 CU-1513 1 1
[0361] In summary, previously unreported miRNAs identified by
cloning and computational analysis were validated at the expression
level by multiple detection methods. For a small subset tested,
their incorporation in the Ago complex and their activity on the GC
transcriptome suggests biological functionality.
[0362] Transcriptional and Post-Transcriptional Regulation.
[0363] Most newly identified miRNAs tested by RNA blot showed a
long abundant transcript (>150 nt) likely corresponding to the
primary miRNA transcript and a second transcript (.about.60-80 nt)
consistent with the precursor miRNA. As shown in FIG. 21C (top
panel), the precursor miRNA and the correspondent mature miRNA may
be produced in some cell type but not in others, suggesting
transcriptional regulation. Conversely, the relative abundance of
precursor and mature miRNA was different is some cell types (FIG.
21C, bottom panel) suggesting the existence of post-transcriptional
regulation most likely targeting the Dicer-dependent pre-miRNA
processing (Lee et al., 2007; Michael et al., 2003; Thomson et al.,
2006).
[0364] Taken together, these observations suggest that the
expression of mature miRNAs may be affected by both transcriptional
and post-transcriptional regulatory mechanisms.
[0365] Distinct miRNA Signatures in Normal B-Cell
Subpopulations.
[0366] In order to further investigate whether specific miRNA
regulation occurred in normal B-cell development or in transformed
cells, miRNA representation was examined in libraries constructed
from naive, GC and memory B cells, as well as from the Ramos BL
cell line. Differential expression of numerous known and newly
identified miRNAs was evident during B-cell differentiation and GC
transit as shown by hierarchical clustering using miRNA frequencies
(defined as the fraction of the total pool of cloned miRNAs
represented by a given miRNA in a library) obtained from the
cloning data (FIG. 22A). Naive and memory B cells appeared similar,
sharing a large fraction of the most abundant miRNAs. Conversely,
centroblasts showed a more distinct miRNA profile with a sizeable
fraction of abundant miRNAs being specifically expressed in the CB
library, suggesting specific functions. Some miRNAs were expressed
in the GC-derived Ramos cells, but not in normal GC B cells, or
vice versa in the normal but not in the tumor cells, suggesting
that malignant transformation affects miRNA expression.
[0367] To independently validate results of the cloning experiment,
miRNA expression profiling was performed of centroblasts, naive and
memory B cells (six donors/each) using a commercial microarray
representative of 723 known human miRNAs (miRBase v.10.1). The
Spearman correlation between cloning and microarray data is 0.7
corresponding to a p-value<3.9e-28 (FIG. 27). Each B-cell
population showed a distinct miRNA expression profile. Consistent
with the cloning data (FIG. 22A), GC B cells appeared to be quite
distinct from naive and memory B cells, which instead shared
expression of a large fraction of miRNAs (FIG. 22B). The expression
of several miRNAs was tested by qRT-PCR analysis, which confirmed
that the microarray data were quantitatively accurate. Overall,
these results show that the GC reaction is characterized by the
specific expression of multiple miRNAs.
[0368] Discussion
[0369] The combination of cloning procedures and computational
tools used in this study led to the identification of a large
fraction of miRNA expressed during B-cell differentiation. These
included 75 previously unreported miRNAs, as well as a potentially
distinct class of short-RNAs not fulfilling current criteria for
miRNAs. These findings have general implications for the
understanding of the total miRNA content of the human genome as
well as for future studies on the role of miRNAs in B-cell
differentiation, function and lymphomagenesis.
[0370] The discovery of 75 previously unreported miRNAs expressed
in normal and/or malignant B cells is in contrast with a previous
study that reported the discovery of only 12 new human miRNA
(Landgraf et al., 2007) from an analysis of a large panel of
different organ systems and cell types and suggested that most
miRNAs have already been identified and are ubiquitously expressed
(Landgraf et al., 2007). These discordant results and conclusions
may be due i) to the higher number of clones per library sequenced
in this study (3500 versus 1300 on average in (Landgraf et al.,
2007)), which allowed the detection of low-abundance miRNA species
and ii) to the criteria applied in the miRNA identification which
do not include conservation and allow consideration of repetitive
elements (see Supplemental Experimental Procedures in Example 3).
Moreover, the relatively lower degree of evolutionary conservation
of previously unreported miRNAs may have prevented the
cross-species identification of miRNAs using murine libraries (Chen
et al., 2004; Neilson et al., 2007). Consistent with these
observations, a recent report on short-RNAs in mouse embryonic stem
cells discovered Dicer-dependent miRNAs characterized by both low
abundance and low degree of conservation (Calabrese et al., 2007).
Since 88% of the previously unreported miRNAs have been
independently detected by RT-PCR and/or RNA blot analyses, our
cloning and computational approach is largely validated.
[0371] We note that a fraction of the validated miRNAs display
similarity to the 3'-end of post-transcriptionally modified tRNAs,
raising the possibility that they may derive from loci with t-RNA
homology or by direct processing of t-RNAs. We also identified a
large set of candidate miRNAs (101 unreported, to our knowledge,
and 27 known) that have been cloned as single occurrences in the
B-cell libraries (Table 7). This group of candidate miRNAs has not
yet been fully investigated, but nevertheless they may include bona
fide miRNAs because 3 out of 3 tested were detectable by RNA blot
or RT-PCR analyses. Thus, our data in B cells suggest that a large
number of low-abundance, recently evolved, tissue-specific miRNAs
remain to be discovered.
[0372] Two categories of short-RNAs were identified that could not
be annotated as bona fide miRNAs. The first category is represented
by short-RNAs which display all features required by the
computational pipeline to be defined as candidate miRNAs, but
nevertheless have an atypical length (<17 nt or >28 nt; 75
candidate miRNAs). Sequences belonging to this first category may
include bona fide miRNAs since 2 out of 2 tested were detectable by
RT-PCR. The second category is represented by those short-RNAs for
which classic pre-miRNA structures could not be identified in the
genome and no similarity to other non-coding RNA was found in the
available databases. These short-RNAs may either be miRNA for which
RNA secondary structure prediction algorithms failed to predict the
correct hairpin structure or may represent new miRNA species of
presently unknown mechanism of generation or other not yet
described types of short-RNAs.
[0373] Finally, this analysis led to the discovery of short-RNAs
that could not be accurately mapped to the genome. Considering that
a fraction of these RNAs were cloned multiple times and showed a
stage-specific behavior, we suggest that such short-RNAs do
actually exist and that the lack of a match to the human genome may
be due to polymorphisms, editing and other post-transcriptional
modifications or to an incomplete or inaccurate sequencing of the
corresponding genomic regions.
[0374] The specificity in mature miRNA expression appears to be
regulated at the transcriptional as well as at the
post-transcriptional, i.e. pre-miRNA processing, level. Indeed, the
accumulation of pre-miRNA in absence of a mature miRNA can occur in
a cell type-restricted manner, suggesting the presence of a
mechanism of regulation at the pre-miRNA processing step. Both
regulatory mechanisms may act during normal differentiation and may
also be dysregulated during transformation as a consequence of
genetic or epigenetic alterations (Lee et al., 2007; Michael et
al., 2003; Thomson et al., 2006). Indeed, miRNAs CU-1137 and
CU-1368 represent examples of transcriptional activation and
post-transcriptional silencing associated with malignant
transformation, respectively.
[0375] The stage-specific expression of various miRNAs strongly
suggests highly specialized regulatory functions in B-cell biology.
The role of miRNAs that show cell type-specific functions in
lymphocytes has just begun to be elucidated (Dorsett et al., 2008;
Li et al., 2007; Rodriguez et al., 2007; Teng et al., 2008; Thai et
al., 2007; Xiao et al., 2007). The miRNAs specifically associated
with GC or non-GC B cells by either cloning or miRNA expression
profiling have not been previously reported in B-cell
differentiation with the exception of miR-150 (Xiao et al., 2007).
For example the miR-199 and miR-125 families as well as miR-138
show a distinct expression in GC B cells although none of these
miRNAs has been investigated for a role in this cell compartment.
The extent of post-transcriptional regulation added by miRNAs will
be fully uncovered only in the context of the complex network of
cellular interactions (Basso et al., 2005), which will require the
integration of large scale gene and miRNA expression data.
[0376] miRNA expression can be affected by malignant
transformation. For instance, the miR-17-92 cluster, previously
reported as a potential oncogene (He et al., 2005), was found
over-expressed in Ramos cell line compared to GC B cells. Moreover,
several miRNAs (i.e. CU-1137, CU-1148) show expression in Ramos
cells and in several additional BL cell lines, but not in their
normal GC counterpart. Vice versa, as observed for the miR-199
family, the expression of some miRNAs is lost in the tumor cells.
The data herein represents a useful basis to investigate whether
lymphoma-associated chromosomal lesions affect genomic regions
associated with miRNA expression.
[0377] Finally, the differences in miRNA expression profile between
GC and non-GC B cells resembled those observed by expression
profiling of coding genes (Klein et al., 2003), consistent with the
previous observation that miRNA profiling may be equally or more
informative in discriminating tumor phenotypes (Calin et al., 2005;
Lu et al., 2005). This suggests that miRNA expression profiling,
especially if including new B-cell specific miRNAs, may be useful
in the differential diagnosis of lymphoid malignancies.
[0378] The expanded B-cell miRNome described here represents a
resource which can be used to identify miRNAs expressed during the
GC transit as well as specific differences in miRNA expression in
normal versus lymphoma cells, and which can guide studies to unveil
the function of miRNAs in normal B cell development and
lymphomagenesis.
[0379] Experimental Procedures
[0380] Generation of Short-RNA Libraries.
[0381] Purification of naive, memory and GC B cells was performed
as previously reported (Klein et al., 2003) using magnetic cell
sorting of mononucleated cells obtained from human tonsils. Total
RNA was purified using the Trizol Reagent (Invitrogen) following
the manufacturer's indications. The short-RNA libraries were
generated using an established protocol described in detail in (Lau
et al., 2001). Briefly, total RNA was separated on 15%
polyacrylamide gel and the fragment corresponding to 15-30
nucleotides length was excised. The purified small RNAs were linked
to adaptor oligonucleotides and gel purified. Upon adaptor
ligation, RNA was reverse transcribed and cDNA was PCR amplified
and cloned into pCR2.1-TOPO vector (Invitrogen). Sequencing was
performed on colony PCR amplicons.
[0382] Computational Identification of Precursor and Mature
miRNAs.
[0383] The bioinformatics miRNA analysis pipeline (FIG. 18)
includes: (a) identification of short-RNAs from each library, (b)
identification of exact and partial matches of the short-RNA
sequences to the human genome, (c) testing each short-RNA genomic
region for compatibility with hairpin secondary structures, (d)
clustering genomic regions to predict mature miRNAs, (e) annotating
and filtering short-RNAs and miRNAs candidates, (f) estimation of
predicted miRNA frequencies in the libraries and (g) clustering
short-RNAs that do not support miRNA candidates. The details are
reported in the Supplemental Experimental Procedures in
Example.
[0384] Orthology Analysis.
[0385] The identification of putative orthologous sequences of
known and predicted precursor and mature human miRNAs in chimp
(panTro2), monkey (rheMac2), dog (canFam2), mouse (mm8) and rat
(rn4) was performed using UCSC-provided Blastz (Schwartz et al.,
2003) pairwise alignments between human and target species. The
details are reported below.
[0386] miRNA Expression Profiling.
[0387] The miRNA expression profiles were generated using the Human
miRNA Microarray kit (Agilent Technologies) that allows detection
of 723 known human (miRBase v.10.1) and 76 human viral miRNAs,
following the manufacturer's indications. Analysis of raw data was
performed using the Feature Extraction Software 9.5.3.1 (Agilent
Technologies). The dendrograms (FIG. 22) were generated using a
hierarchical clustering algorithm based on the average-linkage
method (Eisen et al., 1998; Hartigan, 1975) and Spearman's
correlation as provided by the geWorkbench platform
(http://www.geworkbench.org).
[0388] RT-PCR Analysis.
[0389] Small RNA fractions were purified using the Trizol Reagent
(Invitrogen) and the PureLink miRNA Isolation Kit (Invitrogen),
following the manufacturer's indications. RT-PCR was performed as
previously described (Sharbati-Tehrani et al., 2008). Briefly,
miRNA sequences were reverse-transcribed from 50 ng short-RNA using
Superscript III First Strand Synthesis Kit (Invitrogen), in the
presence of 0.2 .mu.M RTFS primer (miRNA-specific primers, see
Table 14). 1/10.sup.th of the cDNA volume was then used as template
for 34 cycles of PCR amplification in the presence of 4 nM SS
primer (miRNA-specific primers, see Table 14) and 0.4 .mu.M each of
MPF and MPR universal primers (Table 14). PCR products were
separated on 12% non-denaturing polyacrylamide gel, detected by
SybrGold (1:10,000 dilution; Invitrogen) and visualized under UV
light.
TABLE-US-00034 TABLE 14 List of probes and primers used for
Northern Blot and RT-PCR analyses, respectively. mature miRNA Seq
sequence Seq ID Probe sequence Hybridization ID ID No. (5'-3') No.
(5'-3') Temperature [.degree. C.] CU- 1839 GCTAAGGAA 1926
AAAACTGAGCACAG 60 1137 GTCCTGTGCT GACTTCCTTAGC CAGTTTT CU- 1840
TCGATTCCCG 1927 TGGTGCATGGGCCG 55 1142 GCCCATGCA GGAATCGA CCA CU-
1841 CCCCCCACT 1928 AAGCCAGTCAAATTT 50 1153 GCTAAATTTG AGCAGTGGGGGG
ACTGGCTT CU- 1842 ATCCCACTCC 1929 TGGTGTCAGGAGTG 50 1173 TGACACCA
GGAT CU- 1843 AGTCCCATCT 1930 TGGCGACCCAGATG 55 1241 GGGTCGCCA
GGACT CU- 1844 TCCCCGGCA 1931 TGGTGGAGGTGCCG 55 1254 CCTCCACCA GGGA
CU- 1845 TCGATTCCCG 1932 TGGTGCATTGGCCG 60 1276 GCCAATGCA GGAATCGA
CCA CU- 1846 ATCCCACTTC 1933 TGGTGTCAGAAGTG 50 1303 TGACACCA GGAT
CU- 1847 GACGAGGTG 1934 AACCACTCGGCCAC 60 1368 GCCGAGTGG CTCGTC CU-
1848 GCATTGGTG 1935 TCTACCACTGAACCA 60 1403 GTTCAGTGGT CCAATGC AGA
CU- 1849 GCGGGTGAT 1936 GCTCAGACTCCAGT 50 1513 GCGAACTGG
TCGCATCACCCGC AGTCTGAGC mature miRNA Seq SS Seq sequence (5'- ID
RTFS primer primer ID ID No. 3') No. sequence (5'-3') sequence
(5'-3') CU- 1850 CCCGGGTTT 1937 TGTCAGGCAACCGT SEQ ID NO: 2013 1130
CGGCACCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGTGC GTAGAGGGGGAAC
GGCGCCCGGGTTT CG CU- 1851 GCCGGGTAC 1938 TGTCAGGCAACCGT SEQ ID NO:
2014 1132 TTTCGTATTTT ATTCACCGTGAGTG CGTCAGATGTCCGA GTAAAATACG
GTAGAGGGGGAAC GGCGGCCGGGTAC TTT CU- 1852 GCTAAGGAA 1939
TGTCAGGCAACCGT SEQ ID NO: 2015 1137 GTCCTGTGCT ATTCACCGTGAGTG
CGTCAGATGTCCGA CAGTTTT GTAAAACTGAGC GTAGAGGGGGAAC GGCGGCTAAGGAA
GTCCTGT CU- 1853 TATCAATGAT 1940 TGTCAGGCAACCGT SEQ ID NO: 2016
1138 GCTTCTGAGA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTCTCAG
GTAGAGGGGGAAC GGCGTATCAATGAT GCTT CU- 1854 TCGATTCCCG 1941
TGTCAGGCAACCGT SEQ ID NO: 2017 1142 GCCCATGCA ATCACCGTGAGTGG
CGTCAGATGTCCGA CCA TTTGGTGC GTAGAGGGGGAAC GGCGTCGATTCCCG GCCCAT CU-
1855 AGAAAGGCC 1942 TGTCAGGCAACCGT SEQ ID NO: 2018 1146 GAATTTTA
ATTCACCGTGAGTG[ CGTCAGATGTCCGA GTTAAAATTCGG GTAGAGGGGGAAC
GGCGAGAAAGGCCG CU- 1856 TGGTGTGGT 1943 TGTCAGGCAACCGT SEQ ID NO:
2019 1148 CTGTTGTTTT ATTCACCGTGAGTG CGTCAGATGTCCGA GTAAAACAACAG
GTAGAGGGGGAAC GGCGTGGTGTGGT CTG CU- 1857 CCCCCCACT 1944
TGTCAGGCAACCGT SEQ ID NO: 2020 1153 GCTAAATTTG ATTCACCGTGAGTG
CGTCAGATGTCCGA ACTGGCTT GTAAGCCA GTAGAGGGGGAAC GGCGCCCCCCACT
GCTAAATTTG CU- 1858 TCCCCGCAC 1945 TGTCAGGCAACCGT SEQ ID NO: 2021
1155 CTCCACCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGTGG GTAGAGGGGGAAC
GGCGTCCCCGCAC CT CU- 1859 GAGAGCGCT 1946 TGTCAGGCAACCGT SEQ ID NO:
2022 1164 CGGTTTTT ATTCACCGTGAGTG CGTCAGATGTCCGA GTAAAAACCG
GTAGAGGGGGAAC GGCGGAGAGCGCT CU- 1860 ATCCCACTCC 1947 TGTCAGGCAACCGT
SEQ ID NO: 2023 1173 TGACACCA ATTCACCGTGAGTG CGTCAGATGTCCGA
GTTGGTGT GTAGAGGGGGAAC GGCGATCCCACTCC TG CU- 1861 GGCGTGATT 1948
TGTCAGGCAACCGT SEQ ID NO: 2024 1175 CATACCTTTT ATTCACCGTGAGTG
CGTCAGATGTCCGA GTAAAAGGTATG GTAGAGGGGGAAC GGCGGGCGTGATT CAT CU-
1862 AGGGTGTGC 1949 TGTCAGGCAACCGT SEQ ID NO: 2025 1178 GTGTTTTT
ATTCACCGTGAGTG[ CGTCAGATGTCCGA GTAAAAACACGC GTAGAGGGGGAAC
GGCGAGGGTGTGC GT CU- 1863 AACCGAGCG 1950 TGTCAGGCAACCGT SEQ ID NO:
2026 1180 TCCAAGCTCT ATTCACCGTGAGTG CGTCAGATGTCCGA TTCCATTTT
GTAAAATG GTAGAGGGGGAAC GGCGAACCGAGCG TCCAAGCTCT CU- 1864 TCCCCGACA
1951 TGTCAGGCAACCGT SEQ ID NO: 2027 1186 CCTCCACCA ATTCACCGTGAGTG
CGTCAGATGTCCGA GTTGGTGG GTAGAGGGGGAAC GGCGTCCCCGACA CCT CU- 1865
GCCCGCATC 1952 TGTCAGGCAACCGT SEQ ID NO: 2028 1191 CTCCACCA
ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGTGG GTAGAGGGGGAAC GGCGGCCCGCATC
CT CU- 1866 ATGTGGTGG 1953 TGTCAGGCAACCGT SEQ ID NO: 2029 1197
CTTACTTTT ATTCACCGTGAGTG CGTCAGATGTCCGA GTAAAAGTAAGC GTAGAGGGGGAAC
GGCGATGTGGTGG CTT CU- 1867 TCCCCGGCA 1954 TGTCAGGCAACCGT SEQ ID NO:
2030 1212 CTTCCACCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGTGG
GTAGAGGGGGAAC GGCGTCCCCGGCA CTT CU- 1868 TCACCCCATA 1955
TGTCAGGCAACCGT SEQ ID NO: 2031 1213 AACACCA ATTCACCGTGAGTG
CGTCAGATGTCCGA GTTGGTGT GTAGAGGGGGAAC GGCGTCACCCCATAA CU- 1869
TTCCCCGAC 1956 TGTCAGGCAACCGT SEQ ID NO: 2032 1220 GGGGAGCCA
ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGCTC GTAGAGGGGGAAC GGCGTTCCCCGAC
GGG CU- 1870 TGTGCTCCG 1957 TGTCAGGCAACCGT SEQ ID NO: 2033 1221
GAGTTACCTC ATTCACCGTGAGTG CGTCAGATGTCCGA GTTT GTAAACGAGG
GTAGAGGGGGAAC GGCGTGTGCTCCG GAGTTA CU- 1871 TCACGTCGG 1958
TGTCAGGCAACCGT SEQ ID NO: 2034 1222 GGTCACCA ATTCACCGTGAGTG
CGTCAGATGTCCGA GTTGGTGA GTAGAGGGGGAAC GGCGTCACGTCGG GG CU- 1872
AGTCCCATCT 1959 TGTCAGGCAACCGT SEQ ID NO: 2035 1241 GGGTCGCCA
ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGCGA GTAGAGGGGGAAC GGCGAGTCCCATCT
GGG CU- 1873 TCCCCGTAC 1960 TGTCAGGCAACCGT SEQ ID NO: 2036 1242
GGGCCACCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGTGG GTAGAGGGGGAAC
GGCGTCCCCGTAC GGG CU- 1874 GTCCCTTCGT 1961 TGTCAGGCAACCGT SEQ ID
NO: 2037 1243 GGTCGCCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGCGA
GTAGAGGGGGAAC GGCGGTCCCTTCGT GG CU- 1875 GTCAGGATG 1962
TGTCAGGCAACCGT SEQ ID NO: 2038 1244 GCCGAGCGG ATTCACCGTGAGTG
CGTCAGATGTCCGA TCT GTAGACCG GTAGAGGGGGAAC GGCGGTCAGGATG GCCGAG CU-
1876 AGGGGGGTA 1963 TGTCAGGCAACCGT SEQ ID NO: 2039 1246 AAAAAAAA
ATTCACCGTGAGTG CGTCAGATGTCCGA GTTTTTTT GTAGAGGGGGAAC GGCGAGGGGGGTA
AA CU- 1877 CCCACCCAG 1964 TGTCAGGCAACCGT SEQ ID NO: 2040 1251
GGACGCCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGCGT GTAGAGGGGGAAC
GGCGCCCACCCAG GG CU- 1878 TCCCCGGCA 1965 TGTCAGGCAACCGT SEQ ID NO:
2041 1254 CCTCCACCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGTGG
GTAGAGGGGGAAC GGCGTCCCCGGCA CCT CU- 1879 GAGGGGGAC 1966
TGTCAGGCAACCGT SEQ ID NO: 2042 1264 CAAAAAAAA ATTCACCGTGAGTG
CGTCAGATGTCCGA GTTTTTTTTTGG GTAGAGGGGGAAC GGCGGAGGGGGA CU- 1880
TACCGAGCC 1967 TGTCAGGCAACCGT SEQ ID NO: 2043 1269 TGGTGATAGC
ATTCACCGTGAGTG CGTCAGATGTCCGA GTGCTATC GTAGAGGGGGAAC GGCGTACCGAGCC
TGGT CU- 1881 TCGATTCCCG 1968 TGTCAGGCAACCGT SEQ ID NO: 2044 1276
GCCAATGCA ATTCACCGTGAGTG CGTCAGATGTCCGA CCA GTTGGTGCATTG
GTAGAGGGGGAAC GGCGTCGATTCCCG GC CU- 1882 GAGCCATGA 1969
TGTCAGGCAACCGT SEQ ID NO: 2045 1277 TGATACCACT ATTCACCGTGAGTG
CGTCAGATGTCCGA GAGC GTGCTCAG GTAGAGGGGGAAC GGCGGAGCCATGA TGATACCA
CU- 1883 TAACGGCCG 1970 TGTCAGGCAACCGT SEQ ID NO: 2046 1278
CGGTACCC ATTCACCGTGAGTG CGTCAGATGTCCGA GTGGGTAC GTAGAGGGGGAAC
GGCGTAACGGCCG CG CU- 1884 GCAGCGCCA 1971 TGTCAGGCAACCGT SEQ ID NO:
2047 1281 GCCTCCCGC ATTCACCGTGAGTG CGTCAGATGTCCGA CCTAC GTGTAGGG
GTAGAGGGGGAAC GGCGGCAGCGCCA GCCTCCCG CU- 1885 CGTCCATGAT 1972
TGTCAGGCAACCGT SEQ ID NO: 2048 1288 GTTCCGCAA ATTCACCGTGAGTG
CGTCAGATGTCCGA GTTTGCGG GTAGAGGGGGAAC GGCGCGTCCATGAT GTT CU- 1886
AGCAGTGAT 1973 TGTCAGGCAACCGT SEQ ID NO: 2049 1293 GTCCTGAAA
ATTCACCGTGAGTG CGTCAGATGTCCGA ATTCTGAAG GTCTTCAGAATTT GTAGAGGGGGAAC
GGCGAGCAGTGAT GTCCTGA CU- 1887 AAAGGACCT 1974 TGTCAGGCAACCGT SEQ ID
NO: 2050 1294 GGCGGTGCT ATTCACCGTGAGTG CGTCAGATGTCCGA TC GTGAAGCA
GTAGAGGGGGAAC GGCGAAAGGACCT GGCGG CU- 1888 ATCCCGGAC 1975
TGTCAGGCAACCGT SEQ ID NO: 2051 1298 GAGCCCCCA ATTCACCGTGAGTG
CGTCAGATGTCCGA GTTGGGGG GTAGAGGGGGAAC GGCGATCCCGGAC GAG CU- 1889
TCCTCACAC 1976 TGTCAGGCAACCGT SEQ ID NO: 2052 1300 GGGGCACCA
ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGTGC GTAGAGGGGGAAC GGCGTCCTCACAC
GGG CU- 1890 ATCCCACTTC 1977 TGTCAGGCAACCGT SEQ ID NO: 2053 1303
TGACACCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGTGT GTAGAGGGGGAAC
GGCGATCCCACTTC TG CU- 1891 ACCCCACTAT 1978 TGTCAGGCAACCGT SEQ ID
NO: 2054 1307 GCTTAGCCCT ATTCACCGTGAGTG CGTCAGATGTCCGA GTAGGGCT
GTAGAGGGGGAAC GGCGACCCCACTAT GCTT CU- 1892 TGTATTGTGA 1979
TGTCAGGCAACCGT SEQ ID NO: 2055 1323 GACATTC ATTCACCGTGAGTG
CGTCAGATGTCCGA GTGAATGT GTAGAGGGGGAAC GGCGTGTATTGTGAG CU- 1893
TCTCGGTGG 1980 TGTCAGGCAACCGT SEQ ID NO: 2056 1324 AACCTCCA
ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGAGG GTAGAGGGGGAAC GGCGTCTCGGTGG
AA CU- 1894 ATCCCCAGC 1981 TGTCAGGCAACCGT SEQ ID NO: 2057 1339
ACCTCCACCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGTGG GTAGAGGGGGAAC
GGCGATCCCCAGC ACCT CU- 1895 AGAACACTA 1982 TGTCAGGCAACCGT SEQ ID
NO: 2058 1345 CGAGCCACA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGTGGC
GTAGAGGGGGAAC GGCGAGAACACTA CGA CU- 1896 ACCCCACTTC 1983
TGTCAGGCAACCGT SEQ ID NO: 2059 1352 TGGTACCA ATTCACCGTGAGTG
CGTCAGATGTCCGA GTTGGTACCA GTAGAGGGGGAAC GGCGACCCCACTTC CU- 1897
CGTTCGCGC 1984 TGTCAGGCAACCGT SEQ ID NO: 2060 1363 TTTCCCCTG
ATTCACCGTGAGTG CGTCAGATGTCCGA GTCAGGGGAAAG GTAGAGGGGGAAC
GGCGCGTTCGCG CU- 1898 GACGAGGTG 1985 TGTCAGGCAACCGT SEQ ID NO: 2061
1368 GCCGAGTGG ATTCACCGTGAGTG CGTCAGATGTCCGA GTCCACTC GTAGAGGGGGAAC
GGCGGACGAGGTG GCC CU- 1899 TCCCCGGCA 1986 TGTCAGGCAACCGT SEQ ID NO:
2062 1369 TCTCCACCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGTGG
GTAGAGGGGGAAC GGCGTCCCCGGCA TCT CU- 1900 CTGATTGCTC 1987
TGTCAGGCAACCGT SEQ ID NO: 2063 1370_MOD CTATCTGATT ATTCACCGTGAGTG
CGTCAGATGTCCGA GTAATCAG GTAGAGGGGGAAC GGCGCTGATTGCTC CTAT CU- 1901
TCTAGAGGA 1988 TGTCAGGCAACCGT SEQ ID NO: 2064 1371 GCCTGTTCTG
ATTCACCGTGAGTG CGTCAGATGTCCGA TA GTTACAGA GTAGAGGGGGAAC
GGCGTCTAGAGGA GCCTGT CU- 1902 TCGGGTGCG 1989 TGTCAGGCAACCGT SEQ ID
NO: 2065 1379 AGAGGTCCC ATTCACCGTGAGTG CGTCAGATGTCCGA GGGT
GTACCCGGGACC GTAGAGGGGGAAC GGCGTCGGGTGCG AGA CU- 1903 ATAGGTTTGG
1990 TGTCAGGCAACCGT SEQ ID NO: 2066 1380 TCCTAGCCTT ATTCACCGTGAGTG
CGTCAGATGTCCGA TCT GTAGAAAG GTAGAGGGGGAAC GGCGATAGGTTTGG TCCTAGC
CU- 1904 TCGATTCCCG 1991 TGTCAGGCAACCGT SEQ ID NO: 2067 1381
GTCAGGGAA ATTCACCGTGAGTG CGTCAGATGTCCGA CCA GTTGGTTC GTAGAGGGGGAAC
GGCGTCGATTCCCG GTCAGG CU- 1905 TCCTCGTTAG 1992 TGTCAGGCAACCGT SEQ
ID NO: 2068 1382 TATAGTGGTG ATTCACCGTGAGTG CGTCAGATGTCCGA AGTATCCC
GTGGGATA GTAGAGGGGGAAC GGCGTCCTCGTTAG TATAGTGGT CU- 1906 TCCCTGGTG
1993 TGTCAGGCAACCGT SEQ ID NO: 2069 1388 GTCTAGTGGT ATTCACCGTGAGTG
CGTCAGATGTCCGA TAGGATTCG GTCGAATC GTAGAGGGGGAAC GGCGTCCCTGGTG
GTCTAGTGGT CU- 1907 TAAGTGTTTG 1994 TGTCAGGCAACCGT SEQ ID NO: 2070
1396 TGGGTTA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTAACCCACA
GTAGAGGGGGAAC GGCGTAAGTGTT CU- 1908 GCATTGGTG 1995 TGTCAGGCAACCGT
SEQ ID NO: 2071 1403 GTTCAGTGGT ATTCACCGTGAGTG CGTCAGATGTCCGA AGA
GTTCTACC GTAGAGGGGGAAC GGCGGCATTGGTG GTTCAGT CU- 1909 TGGTTATCAC
1996 TGTCAGGCAACCGT SEQ ID NO: 2072 1440 GTTCGCC ATTCACCGTGAGTG
CGTCAGATGTCCGA GTGGCGAACGT GTAGAGGGGGAAC GGCGTGGTTATC CU- 1910
CCGTGCTCG 1997 TGTCAGGCAACCGT SEQ ID NO: 2073 1453 CTGCGCCA
ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGCGC GTAGAGGGGGAAC GGCGCCCTGCTCG
CT CU- 1911 TTCTCACTAC 1998 TGTCAGGCAACCGT SEQ ID NO: 2074 1457
TGCACTTGAC ATTCACCGTGAGTG CGTCAGATGTCCGA TA GTTAGTCA GTAGAGGGGGAAC
GGCGTTCTCACTAC TGCACT CU- 1912 CTGCTGGCT 1999 TGTCAGGCAACCGT SEQ ID
NO: 2075 1470 GGGTCGCCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGCGA
GTAGAGGGGGAAC GGCGCTCCTGGCT GGC CU- 1913 CTGCCACTG 2000
TGTCAGGCAACCGT SEQ ID NO: 2076 1477 CTTCACTTGA ATTCACCGTGAGTG
CGTCAGATGTCCGA CTAGC GTGCTAGT GTAGAGGGGGAAC GGCGCTCCCACTG CTTCACTTG
CU- 1914 CTGCTGTGAT 2001 TGTCAGGCAACCGT SEQ ID NO: 2077 1486
GACATTC ATTCACCGTGAGTG CGTCAGATGTCCGA GTGAATGT GTAGAGGGGGAAC
GGCGCTGCTGTGATG CU- 1915 TCCTGCCGC 2002 TGTCAGGCAACCGT SEQ ID NO:
2078 1488 GGTCGCCA ATTCACCGTGAGTG CGTCAGATGTCCGA GTTGGCGA
GTAGAGGGGGAAC GGCGTCCTGCCGC GG CU- 1916 GCGGGTGAT 2003
TGTCAGGCAACCGT SEQ ID NO: 2079 1513 GGGAACTGG ATTCACCGTGAGTG
CGTCAGATGTCCGA AGTCTGAGC GTGCTCAG GTAGAGGGGGAAC GGCGGCGGGTGAT
GCGAACTGGA CU- 1917 CCCCCACAA 2004 TGTCAGGCAACCGT SEQ ID NO: 2080
1524 CCGCGCTTG ATTCACCGTGAGTG CGTCAGATGTCCGA ACTAGC GTGCTAGT
GTAGAGGGGGAAC GGCGCCCCCACAA CCGCGCTTG CU- 1918 TAGGGGTAT 2005
TGTCAGGCAACCGT SEQ ID NO: 2081 1528 GATTCTCGCT ATTCACCGTGAGTG
CGTCAGATGTCCGA GTAGCGAG GTAGAGGGGGAAC GGCGTAGGGGTAT GATT CU- 1919
GGCTGGTCC 2006 TGTCAGGCAACCGT SEQ ID NO: 2082 1538 GAGTGCAGT
ATTCACCGTGAGTG CGTCAGATGTCCGA GGTGTTTA GTTAAACACCAC GTAGAGGGGGAAC
GGCGGGCTGGTCC GAGTGCAGTG CU- 1920 GGCTGGTCC 2007 TGTCAGGCAACCGT SEQ
ID NO: 2083 1542 GATGGTAGT ATTCACCGTGAGTG CGTCAGATGTCCGA GGGTT
GTAACCCA GTAGAGGGGGAAC GGCGGGCTGGTCC GATGGTAG CU- 1921 CCACGAGGA
2008 TGTCAGGCAACCGT SEQ ID NO: 2084 1545 AGAGAGGTA ATTCACCGTGAGTG
CGTCAGATGTCCGA GC GTGCTACCTCT GTAGAGGGGGAAC GGCGCCACGAGGA AG CU-
1922 CGGAAGGGT 2009 TGTCAGGCAACCGT SEQ ID NO: 2085 1550 GCTGGGCCC
ATTCACCGTGAGTG CGTCAGATGTCCGA GTGGGCCC GTAGAGGGGGAAC GGCGCGGAAGCGT
GCT CU- 1923 GGAGAGAAC 2010 TGTCAGGCAACCGT SEQ ID NO: 2086 1557
GCGGTCTGA ATTCACCGTGAGTG CGTCAGATGTCCGA GTGGT GTACCACT
GTAGAGGGGGAAC GGCGGGAGAGAAC GCGGTCTG CU- 1924 ATCCCCAGC 2011
TGTCAGGCAACCGT SEQ ID NO: 2087 1570 ATCTCCACCA ATTCACCGTGAGTG
CGTCAGATGTCCGA GTTGGTGG GTAGAGGGGGAAC GGCGATCCCCAGC ATCT CU- 1925
CCCCCCACT 2012 TGTCAGGCAACCGT SEQ ID NO: 2088 1575 GGTAAATTTG
ATTCACCGTGAGTG CGTCAGATGTCCGA ACTGGA GTTCCAGT GTAGAGGGGGAAC
GGCGCCCCCCACT GCTAAATTTG Universal primer ID Universal primer
sequences (5'-3')
MPF SEQ ID NO: 2089 TGTCAGGCAACCGTATTC ACC MPR SEQ ID NO: 2090
CGTCAGATGTCCGAGTAG AGG Control primer sequences Control Primer ID
(5'-3') 5s_rRNA_FWD SEQ ID NO: 2091 GCCCGATCTCGTCTGATCT 5s_rRNA_REV
SEQ ID NO: 2092 AGCCTACAGCACCCGGTA TT
[0390] RNA Blot.
[0391] Total RNA and small RNA fractions were purified using the
Trizol Reagent (Invitrogen) and the PureLink miRNA Isolation Kit
(Invitrogen), respectively, following the manufacturer's
indications. Electrophoresis was performed on 15% denaturing
polyacrylamide gel and then RNA was transferred on Duralon UV
membrane (Stratagene) using a semidry transfer apparatus.
Pre-hybridization and hybridization were performed in 5.times.SSC,
20 mM Na.sub.2HPO.sub.4 pH7.2, 7% SDS, 3.times.Denhardt's Solution.
Oligonucleotide probes were [.gamma.-.sup.32P]-ATP labeled by
polynucleotide kinase (Fermentas). The list of oligonucleotides and
their hybridization temperature is reported in Table S8. After
over-night hybridization, membranes were washed at the same
temperature in 3.times.SSC, 25 mM NaH.sub.2PO.sub.4 pH 7.5, 5% SDS,
10.times.Denhardt's Solution for 15-20' and in 1.times.SSC, 1% SDS
for 5'. Images were obtained by exposure to phosphoimager cassette
and acquisition by Storm 840 Phosphoimager (Molecular Dynamics) and
by film exposure for approximately 2 weeks.
[0392] Estimation of Library Complexity.
[0393] A bootstrap technique was used to estimate the total number
of miRNAs expressed in each library and the number of short-RNAs
must be sequenced to achieve a complete coverage. Bootstrapping is
a statistical technique for estimating properties of an "estimator"
by measuring those properties in multiple subsets of the samples
(Harrell, 2001; Hinkley, 1997). Specifically, we estimated the
distribution of mature miRNAs obtained by random sub-sampling
different size short-RNA libraries from each complete library. For
each size N=10, 20, . . . N.sub.t, where N.sub.t is the total
number of short-RNAs in the library, we randomly sampled 1000
libraries of size N and computed the number r(N) of inferred
miRNAs, resulting in a distribution p(r(N)) for which we could
compute standard statistical parameters such as average, variance,
mode and median. Based on this sampling, we can extrapolate
p(r(1V)) for increasing values of N to determine at which point it
is no longer efficient to use larger values of N to increase miRNA
coverage. To achieve this, we fitted the data to the parametric
function f(x)=K*(1-e.sup.-mx).
[0394] Since we include both experimentally confirmed and putative
mature miRNAs and since bootstrapping can produce optimistic
results we expect that the estimated values constitute an upper
boundary on the real library complexity. Based on this analysis, we
estimated that the total numbers of mature miRNAs are: 129 (naive),
154 (memory), 204 (centroblasts) and 189 (Ramos). Thus, the
libraries sequenced in this study cover respectively 90.7% (naive),
88.3% (memory), 85.8% (centroblasts), and 91% (Ramos) of the
expressed miRNAs in these cellular phenotypes. FIG. 23 gives the
95% confidence intervals for p(r(N)) at each sampling point, in
addition to the curve of the associated extrapolated function for
each library. Clearly, the bootstrap analysis estimate of the total
number of miRNA is correct only if the abundance of the miRNAs
expressed in the sampled populations closely matches that of known
miRNA in miRBase. This is not unreasonable if, as done here, only
miRNAs that are specific to a B cell differentiation stage or
transformation are considered. Thus, this does not estimate the
total number of miRNA expressed across all human cell types, stages
of differentiation and neoplastic transformations, which could be
several fold larger than what was estimated from the B cell
libraries.
[0395] Orthology and Conservation Analysis.
[0396] We investigated conservation of known and predicted
precursor and mature human miRNA in chimp (panTro2), monkey
(rheMac2), dog (canFam2) mouse (mm8) and rat (rn4). We obtained 678
miRNA precursor sequences from miRBase (v.11.0), 666 mature miRNAs
and 167 star sequences. In total, we obtained 947 locations for
mature and star mirBase sequences. We predicted 388 precursors of
which 114 match miRBase precursors and 274 are newly predicted.
Categorizing these by their corresponding mature sequences, 255
precursors correspond to mature miRNAs that are not included in the
miRBase and 133 precursors are associated with 103 predicted miRNAs
that match miRBase miRNAs. Of the 274 newly predicted precursors,
19 associated with 8 mature sequences listed in miRBase
database.
[0397] miRNA conservation has been repeatedly used to help identify
putative miRNA mappings to genomes. To identify putative ortholog
miRNAs we relied on UCSC-provided Blastz pairwise alignments
between human and target species (Schwartz et al., 2003). We used
two related but complementary methods: (1) map the mature human
miRNA to its ortholog location as specified by pairwise alignment;
and (2) map the precursor of the human miRNA to its ortholog
location as specified by pairwise alignment, expanding the human
region to include at least 80 bases from both sides of the mature
region, and identifying regions in the target that match the
sequence of the mature human miRNA.
[0398] Method 1 is the simplest but fails to account for alignment
inaccuracies and local mutations that may shift the position of the
mature sequence in the target species. Method 2 accounts for
locally imperfect Blastz mapping, but relies on conservation of
larger regions that may not be subject to the same selective
pressure as the mature miRNA. Alignment-based mapping of the human
mature miRNA to its target were required to have either perfect
conservation of the entire mature miRNA sequence or conservation of
seeds composed of seven bases starting from the second position of
the human mature sequence followed by conservation of 3 bases
starting from the 12th, 13th or 14th position as suggested by
(Grimson et al., 2007) (Appendix Table 11). We scanned the entire
mapped ortholog region for a match to the human mature sequence or
to its seed.
[0399] miRNA Target Prediction and Analysis.
[0400] Target predictions for not previously reported miRNAs were
performed by miRanda v1.0 (John et al., 2004) and RNA22 (Miranda et
al., 2006) using recommended parameters with the exception of RNA22
energy threshold that was changed from default -25.0 kcal/mol to
-20.0 kcal/mol.
[0401] In order to investigate the potential effect of miRNAs on
the transcriptome, predicted targets were tested for enrichment in
genes down-regulated in the same population over-expressing the
tested miRNA. Over-expressed miRNA were selected based on a minimum
frequency value>0.08 and a three-fold increase in their cloning
frequency comparing CB vs. naive or memory B cell libraries. Genes
differentially expressed across normal B cell populations were
identified based on intensity fold change greater than 1.5, and
p-value under 0.01 according to a non-parametric U test applied to
six biological replicates per cell type (gene expression data are
available from GEO database; GSE2350).
[0402] For each miRNA, using a Fisher exact test, we compared the
numbers of down- and up-regulated predicted targets to down- and
up-regulated genes that are not predicted targets. Setting a
p-value threshold of 0.01, targets of most GC-specific miRNAs were
significantly down regulated in CB. Conversely, targets of naive-
and memory-specific miRNAs were not significantly differentially
regulated. Therefore the analysis was focused on targets of the 15
GC-specific miRNAs. Predicted targets of 8 out of 15 miRNAs showed
significant enrichment (p-value<0.001) in genes down-regulated
in GC compared to naive B cells and 2 of them showed enrichment for
genes down-regulated in a control population (memory compared to
naive) (Table 13). We can conclude that targets of GC-specific
miRNAs are significantly more likely to be down regulated in CB
than in naive B cells with p<0.05 according to a Fisher exact
test. Moreover, down-regulation p-values in CB were systematically
lower than in memory (FIG. 26 and Table 13). Of the target sets for
the 15 GC-specific miRNAs, 11 were more significantly down
regulated in CB, 2 were more significantly down regulated in the
control population (memory), and 2 were not down regulated in
either (FIG. 26). Using down-regulation in memory as control, we
therefore conclude that down-regulation p-values are lower for CB
with p<0.05 according to a binomial test with an 11/15 rate
under a null hypothesis of equally likely odds for greater down
regulation. In summary, while targets of naive and memory specific
miRNAs were not found differentially expressed in our data, we were
able to demonstrate that predicted targets of GC-specific miRNAs
are enriched in genes that are down regulated in GC.
[0403] Correlation Between Cloning and Microarray miRNA
Profiling.
[0404] In order to compare cloning and microarray data, we focused
on the 89 miRNAs for which both types of data were available. A
significant correlation (p-value.ltoreq.3.9e-28) was shown between
cloning and miRNA microarray data as measured by Spearman
correlation. The corresponding scatter plot is shown in FIG. 27.
Furthermore, to investigate if miRNA cloning counts were predictive
of differential expression as measured by miRNA microarray, we
identified 39 miRNAs whose cloning frequency was at least 2 fold
greater in one normal B cell subset relative to each of the
remaining two subsets. Of these, 25 (64.1%) miRNAs were found to be
over-expressed in the same B cell subset according to miRNA
microarray profiling. Over-expression was measured using a one
sided U test, with threshold corresponding to p<0.01. We used
permutation testing to estimate the significance of the success
rate, randomly shuffling expression labels while keeping clone
frequencies unchanged. The distribution of confirmed clone
predictions using the shuffled expression data had mean of 1.2% and
standard deviation of 5.1%, corresponding to 12.2 standard
deviations away from our prediction success rate and a p-value near
zero. We conclude that miRNA cloning counts are predictive of
miRNAs concentration levels and differential expression.
[0405] Immunoprecipitation.
[0406] Immunoprecipitations were performed from Ramos cells grown
in IMDM, 10% fetal bovine serum, 1% Penicillin/Streptomycin.
1-2.times.10 8 cells were collected and resuspended in 1 ml lysis
buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 10 mM KCl, 2.5 mM DTT,
1.times. protease inhibitors, 40 U/ul Ambion Superase-IN). Lysate
supernatant was mixed with 500 ul ATP depletion mix (450 mM KCl,
100 mM glucose, 0.5 U/ul Sigma-Aldrich hexokinase). Cleared
supernatant was divided equally between paramagnetic protein G
beads (New England Biolabs) bound to either a monoclonal rat
antibody raised against human Ago2 protein (Rudel et al., 2008) or
total purified rat IgG (Sigma-Aldrich). Beads were incubated with
lysate under rotation for 2 hours at 4.degree. C., then washed
three times with ice-cold lysis buffer and collected in Trizol
(Invitrogen) for RNA extraction. RNA from three sequential
immunoprecipitations was pooled and 1/10.sup.th of yield was used
for reverse transcription of each miRNA species using Superscript
III First Strand Synthesis Kit (Invitrogen), in the presence of 0.2
.mu.M RTFS primer (miRNA-specific primers, see Table S8). cDNA was
also generated from reverse transcription in the presence of random
hexamers to test expression of 5s rRNA. 1/10.sup.th of the cDNA
volume was used as template for SYBR (Applied Biosystems) qPCR
amplification in the presence of 4 nM SS primer (miRNA-specific
primers, see Table 14) and 0.4 .mu.M each of MPF and MPR universal
or 0.4 .mu.M each of 5sRNA primers (Table 14). Each qPCR reaction
was performed in triplicate. The tested miRNA were selected based
on the availability of optimized qRT-PCR conditions among the ones
detectable both by RNA blot and RT-PCR.
[0407] Accession numbers. The miRNA array profiles data are
available from the GEO repository (GSE15144).
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A., Farh, K. K., Johnston, W. K., Garrett-Engele, P., Lim, L. P.,
and Bartel, D. P. (2007). MicroRNA targeting specificity in
mammals: determinants beyond seed pairing. Mol Cell 27, 91-105.
[0453] Harrell, F. E. (2001). Regression modeling strategies: with
applications to linear models, logistic regression, and survival
analysis (New York, Springer). [0454] Hinkley, A. C. D. a. D. V.
(1997). Bootstrap Methods and their Applications (New York,
Cambridge University Press). [0455] John, B., Enright, A. J.,
Aravin, A., Tuschl, T., Sander, C., and Marks, D. S. (2004). Human
MicroRNA targets. PLoS Biol 2, e363. [0456] Landgraf, P., Rusu, M.,
Sheridan, R., Sewer, A., Iovino, N., Aravin, A., Pfeffer, S., Rice,
A., Kamphorst, A. O., Landthaler, M., et al. (2007). A mammalian
microRNA expression atlas based on small RNA library sequencing.
Cell 129, 1401-1414. [0457] Miranda, K. C., Huynh, T., Tay, Y.,
Ang, Y. S., Tam, W. L., Thomson, A. M., Lim, B., and Rigoutsos, I.
(2006). A pattern-based method for the identification of MicroRNA
binding sites and their corresponding heteroduplexes. Cell 126,
1203-1217. [0458] Rudel, S., Flatley, A., Weinmann, L, Kremmer, E.,
and Meister, G. (2008). A multifunctional human Argonaute2-specific
monoclonal antibody. Rna 14, 1244-1253. [0459] Schwartz, S., Kent,
W. J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C.,
Haussler, D., and Miller, W. (2003). Human-mouse alignments with
BLASTZ. Genome Res 13, 103-107.
TABLE-US-00035 [0459] TABLE 11 Analysis of cross-species
conservation for miRNAs. Table displays results for conservation of
(1) full-lenght mature miRNA sequences, (2) seed of the mature
sequence. (1) Conservation of full-length mature miRNA sequence
miRNA identified in B cell libraries and deposited in miRBase
database Seq ID Conservation ID Genomic Coordinates No. Sequence
Chimp Monkey Dog Mouse Rat CU-1001 chr11: 121522485-121522507 2093
TGAGGTAGTAGGTTGTATAGTT Yes Yes Yes Yes Yes CU-1001 chr9:
95978064-95978086 2094 TGAGGTAGTAGGTTGTATAGTT Yes Yes Yes Yes Yes
CU-1003 chr22: 44888234-44888256 2095 TGAGGTAGTAGGTTGTGTGGTT Yes
Yes Yes Yes Yes CU-1004 chr9: 95980943-95980965 2096
AGAGGTAGTAGGTTGCATAGTT Yes Yes Yes Yes Yes CU-1005 chr19:
56887857-56887879 2097 TGAGGTAGGAGGTTGTATAGTT Yes Yes Yes Yes Yes
CU-1006 chrX: 53600931-53600953 2098 TGAGGTAGTAGATTGTATAGTT Yes Yes
Yes Yes Yes CU-1007 chr3: 52277391-52277413 2099
TGAGGTAGTAGTTTGTACAGTT Yes Yes Yes Yes No CU-1008 chr12:
61283737-61283759 2100 TGAGGTAGTAGTTTGTGCTGTT Yes Yes Yes Yes Yes
CU-1009 chr1: 65296711-65296733 2101 TACAGTACTGTGATAACTGAAG Yes Yes
Yes Yes Yes CU-1009 chr9: 4840344-4840366 2102
TACAGTACTGTGATAACTGAAG Yes Yes Yes No No CU-1010 chr20:
3846187-3846210 2103 AGCAGCATTGTACAGGGCTATGA Yes Yes Yes Yes Yes
CU-1011 chr7: 99529562-99529582 2104 CCGCACTGTGGGTACTTGCT Yes Yes
Yes Yes Yes CU-1012 chr7: 99529601-99529622 2105
TAAAGTGCTGACAGTGCAGAT Yes Yes Yes Yes Yes CU-1014 chr19:
56888332-56888356 2106 TCCCTGAGACCCTTTAACCTGTGA Yes Yes Yes Yes Yes
CU-1015 chr21: 16884443-16884465 2107 TCCCTGAGACCCTAACTTGTGA Yes
Yes Yes Yes Yes CU-1016 chr6: 131417431-131417449 2108
GTCCCTGTTCGGGCGCCA No Yes No No No CU-1016 chr19: 62716222-62716240
2109 GTCCCTGTTCGGGCGCCA Yes No No No No CU-1017 chr1:
150066843-150066860 2110 GTGGGGGAGAGGCTGTA No No No No No CU-1018
chr7: 35602718-35602735 2111 TCCCACCGCTGCCACCA No No No No No
CU-1018 chr2: 72555764-72555781 2112 TCCCACCGCTGCCACCA No No No No
No CU-1018 chrX: 55565708-55565725 2113 TCCCACCGCTGCCACCA No No No
No No CU-1018 chr1: 225154598-225154615 2114 TCCCACCGCTGCCACCA No
No No No No CU-1018 chr11: 95714259-95714276 2115 TCCCACCGCTGCCACCA
No No No No No CU-1018 chr7: 5368308-5368325 2116 TCCCACCGCTGCCACCA
No No No No No CU-1018 chr6: 140362954-140362971 2117
TCCCACCGCTGCCACCA No No No No No CU-1019 chr2: 136139485-136139506
2118 TCACAGTGAACCGGTCTCTTT Yes Yes Yes Yes Yes CU-1021 chr1:
159701881-159701904 2119 GCATGGGTGGTTCAGTGGTAGAA Yes Yes No No No
CU-1021 chr1: 159694521-159694544 2120 GCATGGGTGGTTCAGTGGTAGAA Yes
Yes No No No CU-1021 chr1: 159687090-159687113 2121
GCATGGGTGGTTCAGTGGTAGAA Yes Yes No No No CU-1021 chr21:
17749025-17749048 2122 GCATGGGTGGTTCAGTGGTAGAA Yes Yes No No No
CU-1021 chr1: 159679717-159679740 2123 GCATGGGTGGTTCAGTGGTAGAA No
Yes Yes No No CU-1022 chr22: 20337642-20337664 2124
CAGTGCAATGATGAAAGGGCAT Yes Yes Yes Yes Yes CU-1023 chr3:
44130729-44130753 2125 AGCTGGTGTTGTGAATCAGGCCGT No No Yes Yes Yes
CU-1024 chr16: 68524545-68524567 2126 TACCACAGGGTAGAACCACGGA Yes
Yes Yes Yes Yes CU-1025 chr16: 68524506-68524527 2127
CAGTGGTTTTACCCTATGGTA Yes Yes Yes Yes Yes CU-1026 chr17:
53763604-53763627 2128 TGTAGTGTTTCCTACTTTATGGA Yes Yes Yes Yes Yes
CU-1027 chr5: 159844956-159844978 2129 TGAGAACTGAATTCCATGGGTT Yes
Yes Yes Yes Yes CU-1028 chr10: 104186266-104186290 2130
TGAGAACTGAATTCCATAGGCTGT Yes No Yes Yes Yes CU-1029 chr19:
54695901-54695922 2131 TCTCCCAACCCTTGTACCAGT Yes Yes Yes Yes Yes
CU-1030 chr17: 17715007-17715028 2132 CTAGACTGAAGCTCCTTGAGG Yes Yes
No No No CU-1030 chr7: 150838585-150838606 2133
CTAGACTGAAGCTCCTTGAGG Yes No No No No CU-1031 chrX:
53425327-53425349 2134 TCGAGGAGCTCACAGTCTAGTA Yes No No No No
CU-1031 chr8: 141811902-141811924 2135 TCGAGGAGCTCACAGTCTAGTA Yes
Yes Yes No No CU-1032 chr21: 25868165-25868188 2136
TTAATGCTAATCGTGATAGGGGT Yes Yes Yes No No CU-1033 chr13:
49521304-49521325 2137 TAGCAGCACATAATGGTTTGT Yes Yes Yes Yes No
CU-1033 chr7: 3516339-3516360 2138 TAGCAGCACATAATGGTTTGT No No No
No No CU-1034 chr3: 161605126-161605147 2139 CGAATCATTATTTGCTGCTCT
Yes Yes Yes Yes Yes CU-1035 chr3: 161605088-161605110 2140
TAGCAGCACATCATGGTTTACA Yes Yes Yes Yes Yes CU-1037 chr3:
161605235-161605257 2141 TAGCAGCACGTAAATATTGGCG Yes Yes Yes Yes Yes
CU-1037 chr13: 49521163-49521185 2142 TAGCAGCACGTAAATATTGGCG Yes
Yes Yes Yes No CU-1038 chr13: 90800909-90800931 2143
ACTGCAGTGAAGGCACTTGTAG Yes No Yes No No CU-1039 chr13:
90800872-90800895 2144 CAAAGTGCTTACAGTGCAGGTAG Yes No Yes Yes Yes
CU-1040 chr1: 197094822-197094842 2145 ACCATCGACCGTTGATTGTA Yes Yes
Yes Yes Yes CU-1042 chr9: 126494579-126494603 2146
AACATTCAACGCTGTCGGTGAGTT Yes Yes Yes Yes Yes CU-1042 chr1:
197094858-197094882 2147 AACATTCAACGCTGTCGGTGAGTT Yes Yes Yes Yes
Yes CU-1044 chr13: 90801051-90801073 2148 ACTGCCCTAAGTGCTCCTTCTG
Yes No Yes Yes Yes CU-1045 chr13: 90801010-90801032 2149
TAAGGTGCATCTAGTGCAGATA Yes No Yes Yes Yes CU-1046 chr3:
49033108-49033131 2150 CAACGGAATCCCAAAAGCAGCTG Yes Yes Yes Yes Yes
CU-1047 chr11: 64415251-64415271 2151 CTGACCTATGAATTGACAGC Yes Yes
Yes Yes Yes CU-1050 chr16: 14305374-14305396 2152
AACTGGCCCTCAAAGTCCCGCT Yes Yes No No No CU-1052 chr17:
6861708-6861730 2153 TAGCAGCACAGAAATATTGGCA Yes Yes Yes Yes Yes
CU-1053 chr1: 109943084-109943105 2154 TTCACCACCTTCTCCACCCAG Yes
Yes Yes No No CU-1054 chr1: 170380354-170380377 2155
CCCAGTGTTCAGACTACCTGTTC Yes Yes Yes Yes Yes CU-1054 chr19:
10789144-10789167 2156 CCCAGTGTTCAGACTACCTGTTC Yes Yes Yes Yes No
CU-1055 chr19: 10789105-10789126 2157 ACAGTAGTCTGCACATTGGTT Yes Yes
Yes Yes No CU-1055 chr1: 170380317-170380338 2158
ACAGTAGTCTGCACATTGGTT Yes Yes Yes Yes Yes CU-1055 chr9:
130046845-130046866 2159 ACAGTAGTCTGCACATTGGTT Yes Yes Yes Yes No
CU-1056 chr13: 90801193-90801216 2160 TGTGCAAATCTATGCAAAACTGA Yes
No Yes Yes Yes CU-1057 chrX: 133131378-133131401 2161
TGTGCAAATCCATGCAAAACTGA Yes Yes Yes Yes Yes CU-1057 chr13:
90801499-90801522 2162 TGTGCAAATCCATGCAAAACTGA Yes Yes Yes Yes Yes
CU-1061 chr13: 90801326-90801349 2163 TAAAGTGCTTATAGTGCAGGTAG Yes
No Yes Yes Yes CU-1062 chrX: 133131545-133131568 2164
CAAAGTGCTTATAGTGCAGGTAG No No No No No CU-1064 chr17:
55273415-55273437 2165 TAGCTTATCAGACTGATGTTGA Yes Yes Yes Yes Yes
CU-1065 chrX: 45490553-45490574 2166 AGCTACATTGTCTGCTGGGTT Yes Yes
Yes Yes Yes CU-1066 chrX: 45491383-45491406 2167
AGCTACATCTGGCTACTGGGTCT No Yes Yes Yes Yes CU-1067 chrX:
65155503-65155525 2168 TGTCAGTTTGTCAAATACCCCA Yes Yes Yes Yes Yes
CU-1068 chr19: 13808407-13808429 2169 ATCACATTGCCAGGGATTTCCA Yes
Yes Yes Yes Yes CU-1069 chr9: 96887367-96887389 2170
ATCACATTGCCAGGGATTACCA Yes Yes Yes Yes Yes CU-1071 chr7:
99529129-99529151 2171 CATTGCACTTGTCTCGGTCTGA No Yes Yes Yes Yes
CU-1072 chr12: 56504707-56504729 2172 TTCAAGTAATCCAGGATAGGCT Yes
Yes Yes Yes No CU-1072 chr3: 37985907-37985929 2173
TTCAAGTAATCCAGGATAGGCT Yes Yes Yes Yes Yes CU-1073 chr2:
218975623-218975645 2174 TTCAAGTAATTCAGGATAGGTT Yes Yes Yes Yes Yes
CU-1075 chr9: 96887607-96887627 2175 TTCACAGTGGCTAAGTTCTG Yes Yes
Yes Yes
Yes CU-1076 chr3: 189889315-189889337 2176 CACTAGATTGTGAGCTCCTGGA
Yes Yes Yes No Yes CU-1077 chr3: 189889275-189889297 2177
AAGGAGCTCACAGTCTATTGAG Yes Yes Yes Yes Yes CU-1079 chr7:
130212046-130212068 2178 TAGCACCATCTGAAATCGGTTA No Yes Yes Yes Yes
CU-1080 chr1: 206042417-206042440 2179 TAGCACCATTTGAAATCAGTGTT Yes
Yes Yes Yes Yes CU-1081 chr1: 206041871-206041892 2180
TGACCGATTTCTCCTGGTGTT Yes Yes Yes Yes Yes CU-1082 chr1:
206041832-206041854 2181 TAGCACCATTTGAAATCGGTTA Yes Yes Yes Yes Yes
CU-1083 chr6: 72170020-72170040 2182 TGTAAACATCCTCGACTGGA Yes Yes
Yes Yes Yes CU-1084 chr8: 135881994-135882016 2183
TGTAAACATCCTACACTCAGCT Yes Yes Yes Yes Yes CU-1085 chr1:
40995558-40995581 2184 TGTAAACATCCTACACTCTCAGC Yes Yes Yes Yes Yes
CU-1086 chr8: 135886343-135886365 2185 TGTAAACATCCCCGACTGGAAG Yes
Yes Yes Yes Yes CU-1087 chr1: 40992629-40992653 2186
TGTAAACATCCTTGACTGGAAGCT Yes Yes Yes Yes Yes CU-1088 chr8:
22158432-22158448 2187 TGGGTTGAGAGGGCGA Yes Yes Yes Yes Yes CU-1089
chr16: 65793734-65793752 2188 CTGGCCCTCTCTGCCCTT Yes No Yes Yes Yes
CU-1091 chr12: 94226386-94226407 2189 GCCCCTGGGCCTATCCTAGAA Yes Yes
Yes Yes Yes CU-1092 chr7: 1029154-1029174 2190 TCCCTGTCCTCCAGGAGCTC
Yes Yes Yes Yes No CU-1092 chr10: 22978473-22978493 2191
TCCCTGTCCTCCAGGAGCTC No No No No No CU-1093 chr14:
99645804-99645828 2192 TCTCACACAGAAATCGCACCCGTC Yes Yes Yes Yes Yes
CU-1094 chr14: 99645763-99645783 2193 GGGGTGCTATCTGTGATTGA Yes Yes
Yes Yes Yes CU-1095 chr1: 9134379-9134402 2194
TGGCAGTGTCTTAGCTGGTTGTT Yes Yes Yes Yes Yes CU-1096 chrX:
85045302-85045324 2195 TCCCCCAGGTGTGATTCTGATT Yes Yes Yes Yes Yes
CU-1098 chr17: 26926609-26926631 2196 TAATGCCCCTAAAAATCCTTAT Yes
Yes Yes Yes Yes CU-1098 chr16: 14310697-14310719 2197
TAATGCCCCTAAAAATCCTTAT Yes Yes Yes Yes Yes CU-1099 chr5:
149092584-149092605 2198 CTCCTGACTCCAGGTCCTGTG Yes Yes Yes No Yes
CU-1100 chr17: 25468274-25468296 2199 AGCTCGGTCTGAGGCCCCTCAG Yes
Yes Yes Yes Yes CU-1101 chr17: 25468238-25468260 2200
TGAGGGGCAGAGAGCGAGACTT Yes Yes Yes Yes Yes CU-1103 chr8:
41637118-41637140 2201 TCCTGTACTGAGCTGCCCCGAG Yes Yes Yes Yes No
CU-1104 chr17: 6862021-6862042 2202 CAGCAGCACACTGTGGTTTGT Yes Yes
Yes Yes Yes CU-1105 chrX: 138833988-138834006 2203
CGTCAACACTTGCTGGTT Yes Yes Yes Yes Yes CU-1106 chr4:
38546107-38546128 2204 CACGCTCATGCACACACCCAC No No Yes Yes No
CU-1108 chr14: 65007623-65007643 2205 AGGGGGAAAGTTCTATAGTC Yes No
No No No CU-1108 chr14: 65007586-65007606 2206 AGGGGGAAAGTTCTATAGTC
Yes No No No No CU-1110 chr15: 68158819-68158840 2207
TGGGTTTACGTTGGGAGAACT No No No No No CU-1111 chr9:
85774506-85774527 2208 CAACAAATCACAGTCTGCCAT Yes Yes Yes Yes Yes
CU-1113 chr9: 85774546-85774569 2209 TGGAAGACTAGTGATTTTGTTGT Yes
Yes Yes Yes Yes CU-1113 chr15: 86956090-86956113 2210
TGGAAGACTAGTGATTTTGTTGT Yes Yes Yes Yes Yes CU-1113 chr19:
4721711-4721734 2211 TGGAAGACTAGTGATTTTGTTGT Yes Yes Yes No No
CU-1115 chr13: 90801578-90801601 2212 AGGTTGGGATCGGTTGCAATGCT Yes
No Yes No No CU-1116 chrX: 133131239-133131261 2213
TATTGCACTTGTCCCGGCCTGT Yes Yes Yes No No CU-1116 chr13:
90801615-90801637 2214 TATTGCACTTGTCCCGGCCTGT Yes Yes Yes Yes Yes
CU-1117 chr1: 153431651-153431670 2215 TATTGCACTCGTCCCGGCC No Yes
Yes Yes Yes CU-1118 chr7: 99529373-99529396 2216
CAAAGTGCTGTTCGTGCAGGTAG Yes Yes Yes Yes Yes CU-1119 chrX:
53599984-53600006 2217 TGAGGTAGTAAGTTGTATTGTT Yes Yes Yes Yes Yes
CU-1124 chr17: 53763644-53763665 2218 CCCATAAAGTAGAAAGCACTA Yes Yes
Yes Yes Yes CU-1125 chr3: 161605277-161605298 2219
ACCAATATTACTGTGCTGCTT Yes Yes No No No CU-1126 chr9:
126495825-126495848 2220 ACATTCATTGCTGTCGGTGGGTT Yes Yes Yes Yes
Yes CU-1126 chr1: 197094675-197094698 2221 ACATTCATTGCTGTCGGTGGGTT
Yes Yes Yes Yes Yes CU-1568 chr21: 16834028-16834046 2222
TGAGGTAGTAGGTTGTAT Yes Yes Yes Yes Yes CU-5001 chr9:
95980997-95981018 2223 CTATACGACCTGCTGCCTTTC Yes Yes Yes Yes Yes
CU-5002 chr3: 49032596-49032618 2224 CATCGGGAATGTCGTGTCCGCC Yes Yes
Yes Yes No CU-5016 chr3: 49032634-49032658 2225
AATGACACGATCACTCCCGTTGAG Yes Yes Yes Yes Yes new miRNA identified
in B cell libraries Seq. ID Conservation ID Genomic Coordinates NO.
Sequence Chimp Monkey Dog Mouse Rat CU-1130 chr4: 84650562-84650579
2226 CCCGGGTTTCGGCACCA Yes No No No No CU-1130 chr7:
152741807-152741824 2227 CCCGGGTTTCGGCACCA No No No No No CU-1132
chr12: 123990125-123990145 2228 GCCGGGTACTTTCGTATTTT No No No No No
CU-1137 chr17: 8030990-8031016 2229 GCTAAGGAAGTCCTGTGCTCAGTTTT Yes
No No No No CU-1142 chr5: 180625271-180625293 2230
TCGATTCCCGGCCCATGCACCA No No No No No CU-1142 chr21:
17748974-17748996 2231 TCGATTCCCGGCCCATGCACCA No No No No No
CU-1142 chr1: 159687142-159687164 2232 TCGATTCCCGGCCCATGCACCA No No
No No No CU-1142 chr1: 159701933-159701955 2233
TCGATTCCCGGCCCATGCACCA No No No No No CU-1142 chr1:
159679769-159679791 2234 TCGATTCCCGGCCCATGCACCA No No No No No
CU-1142 chr1: 159694573-159694595 2235 TCGATTCCCGGCCCATGCACCA No No
No No No CU-1146 chr16: 3142975-3142992 2236 AGAAAGGCCGAATTTTA No
No No No No CU-1148 chr10: 5935660-5935679 2237 TGGTGTGGTCTGTTGTTTT
Yes No No No No CU-1153 chr14: 22388241-22388268 2238
CCCCCCACTGCTAAATTTGACTGGCTT No No No No No CU-1153 chr17:
35653067-35653094 2239 CCCCCCACTGCTAAATTTGACTGGCTT Yes No No No No
CU-1155 chr20: 58490320-58490337 2240 TCCCCGCACCTCCACCA Yes Yes No
No No CU-1164 chr6: 29057409-29057426 2241 GAGAGCGCTCGGTTTTT No No
No No No CU-1173 chr18: 1681856-1681874 2242 ATCCCACTCCTGACACCA Yes
No No No No CU-1175 chr11: 59075015-59075034 2243
GGCGTGATTCATACCTTTT No No No No No CU-1178 chr6: 28723944-28723961
2244 AGGGTGTGCGTGTTTTT Yes No No No No CU-1180 chr19:
38359877-38359905 2245 AACCGAGCGTCCAAGCTCTTTCCATTTT No No No No No
CU-1186 chr18: 73990174-73990192 2246 TCCCCGACACCTCCACCA No No No
No No CU-1191 chr12: 46439968-46439985 2247 GCCCGCATCCTCCACCA Yes
No No No No CU-1197 chr15: 38673296-38673314 2248
ATGTGGTGGCTTACTTTT No No No No No CU-1212 chr20: 60596937-60596955
2249 TCCCCGGCACTTCCACCA No No No No No CU-1213 chr3:
73875819-73875836 2250 TCACCCCATAAACACCA Yes Yes No No No CU-1220
chr1: 159706825-159706843 2251 TTCCCCGACGGGGAGCCA No No No No No
CU-1220 chr1: 159692034-159692052 2252 TTCCCCGACGGGGAGCCA No No No
No No CU-1220 chr1: 159677235-159677253 2253 TTCCCCGACGGGGAGCCA No
No No No No CU-1220 chr1: 159699444-159699462 2254
TTCCCCGACGGGGAGCCA No No No No No CU-1220 chr1: 159684653-159684671
2255 TTCCCCGACGGGGAGCCA No No No No No CU-1221 chr17:
34564245-34564268 2256 TGTGCTCCGGAGTTACCTCGTTT No No No No No
CU-1222 chrX: 70920902-70920919 2257 TCACGTCGGGGTCACCA Yes No No No
No CU-1241 chr2: 167308360-167308379 2258 AGTCCCATCTGGGTCGCCA No No
No No No CU-1241 chr1: 29814092-29814111 2259 AGTCCCATCTGGGTCGCCA
No No No No No CU-1241 chrX: 51239676-51239695 2260
AGTCCCATCTGGGTCGCCA Yes Yes No No No CU-1241 chr13:
22997399-22997418 2261 AGTCCCATCTGGGTCGCCA Yes No No No No CU-1241
chr6: 70235237-70235256 2262 AGTCCCATCTGGGTCGCCA Yes No No No No
CU-1241 chr6: 141377023-141377042 2263 AGTCCCATCTGGGTCGCCA No No No
No No CU-1241 chr16: 21555749-21555768 2264 AGTCCCATCTGGGTCGCCA Yes
No No No No CU-1241 chr3: 97152533-97152552 2265
AGTCCCATCTGGGTCGCCA Yes No No No No CU-1241 chrX: 70638471-70638490
2266 AGTCCCATCTGGGTCGCCA Yes No No No No CU-1241 chr2:
47181625-47181644 2267 AGTCCCATCTGGGTCGCCA No No No No No
CU-1241 chr3: 114548556-114548575 2268 AGTCCCATCTGGGTCGCCA No No No
No No CU-1241 chr8: 107870541-107870560 2269 AGTCCCATCTGGGTCGCCA No
No No No No CU-1241 chr10: 118251348-118251367 2270
AGTCCCATCTGGGTCGCCA No No No No No CU-1241 chr13:
110648656-110648675 2271 AGTCCCATCTGGGTCGCCA Yes No No No No
CU-1241 chr1: 74982888-74982907 2272 AGTCCCATCTGGGTCGCCA No No No
No No CU-1241 chr1: 74982864-74982883 2273 AGTCCCATCTGGGTCGCCA No
No No No No CU-1241 chrX: 120113204-120113223 2274
AGTCCCATCTGGGTCGCCA Yes No No No No CU-1242 chr7:
148897373-148897391 2275 TCCCCGTACGGGCCACCA Yes No No No No CU-1242
chr6: 159071498-159071516 2276 TCCCCGTACGGGCCACCA Yes No No No No
CU-1243 chr1: 173342843-173342861 2277 GTCCCTTCGTGGTCGCCA No No No
No No CU-1243 chr19: 55148120-55148138 2278 GTCCCTTCGTGGTCGCCA No
No No No No CU-1243 chrX: 117299486-117299504 2279
GTCCCTTCGTGGTCGCCA No No No No No CU-1243 chr8: 4429174-4429192
2280 GTCCCTTCGTGGTCGCCA Yes No No No No CU-1243 chr11:
84485385-84485403 2281 GTCCCTTCGTGGTCGCCA Yes No No No No CU-1243
chr21: 26073725-26073743 2282 GTCCCTTCGTGGTCGCCA Yes No No No No
CU-1243 chr5: 77142069-77142087 2283 GTCCCTTCGTGGTCGCCA Yes No No
No No CU-1243 chr19: 8350798-8350816 2284 GTCCCTTCGTGGTCGCCA No No
No No No CU-1243 chr12: 20827096-20827114 2285 GTCCCTTCGTGGTCGCCA
No No No No No CU-1244 chr1: 159766817-159766838 2286
GTCAGGATGGCCGAGCGGTCT Yes Yes No No No CU-1244 chr1:
159700155-159700176 2287 GTCAGGATGGCCGAGCGGTCT Yes Yes No No No
CU-1244 chr1: 159677946-159677967 2288 GTCAGGATGGCCGAGCGGTCT Yes
Yes Yes No No CU-1244 chr1: 159685364-159685385 2289
GTCAGGATGGCCGAGCGGTCT Yes Yes No No No CU-1244 chr16:
55891954-55891975 2290 GTCAGGATGGCCGAGCGGTCT Yes Yes No No No
CU-1244 chr1: 159692745-159692766 2291 GTCAGGATGGCCGAGCGGTCT Yes
Yes No No No CU-1244 chr1: 159707536-159707557 2292
GTCAGGATGGCCGAGCGGTCT Yes Yes No No No CU-1244 chr1:
240532967-240532988 2293 GTCAGGATGGCCGAGCGGTCT Yes No No No No
CU-1246 chr14: 65014334-65014351 2294 AGGGGGGTAAAAAAAAA Yes No No
No No CU-1246 chr14: 93614119-93614136 2295 AGGGGGGTAAAAAAAAA No No
No No No CU-1251 chr12: 31408926-31408943 2296 CCCACCCAGGGACGCCA No
No No No No CU-1251 chr17: 34161556-34161573 2297 CCCACCCAGGGACGCCA
No No No No No CU-1251 chr1: 146614798-146614815 2298
CCCACCCAGGGACGCCA No No No No No CU-1251 chr19: 33728787-33728804
2299 CCCACCCAGGGACGCCA No No No No No CU-1251 chr9:
136463072-136463089 2300 CCCACCCAGGGACGCCA No No No No No CU-1254
chr4: 2032401-2032419 2301 TCCCCGGCACCTCCACCA No No No No No
CU-1264 chr3: 37897506-37897524 2302 GAGGGGGACCAAAAAAAA Yes No No
No No CU-1269 chr17: 21946878-21946897 2303 TACCGAGCCTGGTGATAGC No
No No No No CU-1269 chr11: 102785624-102785643 2304
TACCGAGCCTGGTGATAGC Yes No No No No CU-1276 chr17: 7969840-7969862
2305 TCGATTCCCGGCCAATGCACCA No No No No No CU-1276 chr19:
39807750-39807772 2306 TCGATTCCCGGCCAATGCACCA No No No No No
CU-1277 chr1: 153990335-153990358 2307 GAGCCATGATGATACCACTGAGC Yes
No No No No CU-1278 chr5: 79981714-79981731 2308 TAACGGCCGCGGTACCC
Yes Yes No No No CU-1278 chr3: 97818860-97818877 2309
TAACGGCCGCGGTACCC Yes Yes No No No CU-1281 chr1:
173235999-173236022 2310 GCAGCGCCAGCCTCCCGCCCTAC Yes No No No No
CU-1288 chr19: 54685975-54685994 2311 CGTCCATGATGTTCCGCAA No No No
No No CU-1293 chr2: 38390703-38390730 2312
AGCAGTGATGTCCTGAAAATTCTGAAG No No No No No CU-1294 chr5:
79983107-79983127 2313 AAAGGACCTGGCGGTGCTTC Yes No No No No CU-1294
chr11: 10487796-10487816 2314 AAAGGACCTGGCGGTGCTTC Yes No No No No
CU-1294 chr13: 108874524-108874544 2315 AAAGGACCTGGCGGTGCTTC Yes No
No No No CU-1298 chr16: 3178151-3178169 2316 ATCCCGGACGAGCCCCCA No
No No No No CU-1298 chr22: 44955360-44955378 2317
ATCCCGGACGAGCCCCCA Yes No No No No CU-1298 chr11: 49720969-49720987
2318 ATCCCGGACGAGCCCCCA Yes No No No No CU-1298 chr16:
3174130-3174148 2319 ATCCCGGACGAGCCCCCA No No No No No CU-1298
chr11: 75624513-75624531 2320 ATCCCGGACGAGCCCCCA No No No No No
CU-1300 chr6: 101499628-101499646 2321 TCCTCACACGGGGCACCA Yes No No
No No CU-1300 chr7: 106814117-106814135 2322 TCCTCACACGGGGCACCA Yes
No No No No CU-1303 chr4: 151694303-151694321 2323
ATCCCACTTCTGACACCA Yes Yes No No No CU-1303 chr1:
212585032-212585050 2324 ATCCCACTTCTGACACCA Yes No No No No CU-1303
chr3: 194813519-194813537 2325 ATCCCACTTCTGACACCA Yes No No No No
CU-1303 chr2: 55018611-55018629 2326 ATCCCACTTCTGACACCA Yes Yes No
No No CU-1303 chr5: 143373194-143373212 2327 ATCCCACTTCTGACACCA No
Yes No No No CU-1303 chr1: 36261536-36261554 2328
ATCCCACTTCTGACACCA Yes No No No No CU-1303 chr12: 67663402-67663420
2329 ATCCCACTTCTGACACCA Yes Yes No No No CU-1303 chr4:
119344866-119344884 2330 ATCCCACTTCTGACACCA No Yes No No No CU-1303
chr12: 70175143-70175161 2331 ATCCCACTTCTGACACCA Yes Yes No No No
CU-1307 chr1: 9557438-9557458 2332 ACCCCACTATGCTTAGCCCT Yes Yes No
No Yes CU-1323 chr2: 232028754-232028771 2333 TGTATTGTGAGACATTC Yes
No No No No CU-1324 chr4: 3167100-3167117 2334 TCTCGGTGGAACCTCCA No
No No No No CU-1324 chr15: 63948450-63948467 2335 TCTCGGTGGAACCTCCA
No No No No No CU-1339 chr8: 141129909-141129928 2336
ATCCCCAGCACCTCCACCA No No No No No CU-1345 chr11: 10487827-10487845
2337 AGAACACTACGAGCCACA Yes No No No No CU-1345 chr5:
79983138-79983156 2338 AGAACACTACGAGCCACA Yes No No No No CU-1345
chr13: 108874555-108874573 2339 AGAACACTACGAGCCACA Yes No No No No
CU-1352 chr12: 12693348-12693366 2340 ACCCCACTTCTGGTACCA Yes Yes No
No No CU-1352 chr5: 119090314-119090332 2341 ACCCCACTTCTGGTACCA No
No No No No CU-1352 chr14: 56457992-56458010 2342
ACCCCACTTCTGGTACCA Yes Yes No No No CU-1352 chr7: 7637279-7637297
2343 ACCCCACTTCTGGTACCA Yes No No No No CU-1352 chr1:
34288353-34288371 2344 ACCCCACTTCTGGTACCA No No No No No CU-1352
chr1: 107581087-107581105 2345 ACCCCACTTCTGGTACCA Yes Yes No No No
CU-1352 chr7: 66011743-66011761 2346 ACCCCACTTCTGGTACCA Yes Yes No
No No CU-1352 chr7: 119683539-119683557 2347 ACCCCACTTCTGGTACCA Yes
No No No No CU-1352 chr18: 16775205-16775223 2348
ACCCCACTTCTGGTACCA Yes Yes No No No CU-1352 chr2: 6916389-6916407
2349 ACCCCACTTCTGGTACCA Yes Yes No No No CU-1352 chr6:
98788231-98788249 2350 ACCCCACTTCTGGTACCA Yes No No No No CU-1352
chr1: 201394394-201394412 2351 ACCCCACTTCTGGTACCA Yes Yes No No No
CU-1352 chrX: 85448496-85448514 2352 ACCCCACTTCTGGTACCA No Yes No
No No CU-1352 chr8: 140073141-140073159 2353 ACCCCACTTCTGGTACCA Yes
Yes No No No CU-1352 chr12: 8391052-8391070 2354 ACCCCACTTCTGGTACCA
Yes No No No No CU-1352 chrX: 77289492-77289510 2355
ACCCCACTTCTGGTACCA No No No No No CU-1352 chr2: 116637798-116637816
2356 ACCCCACTTCTGGTACCA Yes No No No No CU-1352 chr4:
72493755-72493773 2357 ACCCCACTTCTGGTACCA Yes No No No No CU-1352
chr15: 94045767-94045785 2358 ACCCCACTTCTGGTACCA Yes Yes No No No
CU-1352 chrX: 85947724-85947742 2359 ACCCCACTTCTGGTACCA No Yes No
No No CU-1352 chr20: 60081974-60081992 2360 ACCCCACTTCTGGTACCA Yes
No No No No CU-1352 chr18: 31113119-31113137 2361
ACCCCACTTCTGGTACCA Yes No No No No CU-1352 chr11: 8446114-8446132
2362 ACCCCACTTCTGGTACCA No No No No No CU-1352 chr6:
140796063-140796081 2363 ACCCCACTTCTGGTACCA Yes Yes No No No
CU-1352 chr22: 19662967-19662985 2364 ACCCCACTTCTGGTACCA Yes No No
No No CU-1352 chrX: 116622706-116622724 2365 ACCCCACTTCTGGTACCA Yes
No No No No CU-1352 chr22: 43646515-43646533 2366
ACCCCACTTCTGGTACCA Yes No No No No CU-1352 chr11: 3516223-3516241
2367 ACCCCACTTCTGGTACCA No No No No No CU-1352 chr10:
123734159-123734177 2368 ACCCCACTTCTGGTACCA No No No No No CU-1352
chr18: 120806-120824 2369 ACCCCACTTCTGGTACCA Yes Yes No No No
CU-1352 chr1: 174219317-174219335 2370 ACCCCACTTCTGGTACCA Yes Yes
No No No CU-1352 chr7: 156114211-156114229 2371 ACCCCACTTCTGGTACCA
Yes No No No No CU-1352 chr3: 107173811-107173829 2372
ACCCCACTTCTGGTACCA Yes Yes No No No CU-1363 chr1: 17095207-17095225
2373 CGTTCGCGCTTTCCCCTG Yes Yes No No No CU-1363 chr1:
147460729-147460747 2374 CGTTCGCGCTTTCCCCTG No Yes No No No CU-1363
chr14: 34085816-34085834 2375 CGTTCGCGCTTTCCCCTG Yes Yes No No No
CU-1363 chr14: 34095182-34095200 2376 CGTTCGCGCTTTCCCCTG Yes Yes No
No No CU-1368 chr6: 27173063-27173081 2377 GACGAGGTGGCCGAGTGG Yes
Yes Yes No No CU-1368 chr6: 28288793-28288811 2378
GACGAGGTGGCCGAGTGG Yes Yes No No No CU-1368 chr11:
65872166-65872184 2379 GACGAGGTGGCCGAGTGG Yes Yes Yes Yes Yes
CU-1368 chr15: 38673378-38673396 2380 GACGAGGTGGCCGAGTGG Yes Yes
Yes No Yes CU-1368 chr6: 27373753-27373771 2381 GACGAGGTGGCCGAGTGG
Yes Yes No No No CU-1368 chr2: 228333400-228333418 2382
GACGAGGTGGCCGAGTGG Yes No No No No CU-1368 chr6: 28673159-28673177
2383 GACGAGGTGGCCGAGTGG Yes Yes No No No CU-1368 chr17:
8030908-8030926 2384 GACGAGGTGGCCGAGTGG Yes Yes No No Yes CU-1369
chr15: 94627153-94627171 2385 TCCCCGGCATCTCCACCA No No No No No
CU-1370 chr1: 232795752-232795772 2386 CTGATTGCTCCTGTCTGATT No No
No No No CU-1371 chr13: 108874496-108874517 2387
TCTAGAGGAGCCTGTTCTGTA Yes No No No No CU-1379 chr1:
165950616-165950638 2388 TCGGGTGCGAGAGGTCCCGGGT Yes Yes Yes Yes Yes
CU-1380 chr11: 10488308-10488331 2389 ATAGGTTTGGTCCTAGCCTTTCT No No
No No No CU-1381 chr1: 169836691-169836713 2390
TCGATTCCCGGTCAGGGAACCA No No No No No CU-1382 chr6:
27555431-27555459 2391 TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No
No CU-1382 chr1: 159677282-159677310 2392
TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes Yes No No CU-1382 chr17:
8066324-8066352 2393 TCCTCGTTAGTATAGTGGTGAGTATCCC Yes No No No No
CU-1382 chr1: 159699491-159699519 2394 TCCTCGTTAGTATAGTGGTGAGTATCCC
Yes Yes No No No CU-1382 chr1: 159692081-159692109 2395
TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No No CU-1382 chr6:
27579501-27579529 2396 TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No
No CU-1382 chr1: 159684700-159684728 2397
TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No No CU-1382 chr12:
123990189-123990217 2398 TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No
No CU-1382 chr12: 94953929-94953957 2399
TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes Yes Yes No CU-1382 chr12:
123977887-123977915 2400 TCCTCGTTAGTATAGTGGTGAGTATCCC Yes No No No
No CU-1382 chr1: 159706872-159706900 2401
TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No No CU-1388 chr1:
144110633-144110661 2402 TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No
No CU-1388 chr1: 159698476-159698504 2403
TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No No CU-1388 chr1:
159705856-159705884 2404 TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No
No CU-1388 chr1: 159683685-159683713 2405
TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No No CU-1388 chr1:
247135069-247135097 2406 TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No
No CU-1388 chr1: 159691065-159691093 2407
TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No No CU-1388 chr6:
126143129-126143157 2408 TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes No No Yes
Yes CU-1396 chr1: 556086-556103 2409 TAAGTGTTTGTGGGTTA No No No No
No CU-1403 chr17: 7969788-7969810 2410 GCATTGGTGGTTCAGTGGTAGA No
Yes Yes No Yes CU-1403 chr16: 69370491-69370513 2411
GCATTGGTGGTTCAGTGGTAGA Yes Yes Yes No No CU-1403 chr1:
17061002-17061024 2412 GCATTGGTGGTTCAGTGGTAGA No No Yes No No
CU-1403 chr3: 15524502-15524524 2413 GCATTGGTGGTTCAGTGGTAGA Yes No
No No No CU-1403 chr16: 69380097-69380119 2414
GCATTGGTGGTTCAGTGGTAGA Yes Yes Yes Yes Yes CU-1403 chr1:
227740226-227740248 2415 GCATTGGTGGTTCAGTGGTAGA Yes Yes No No No
CU-1403 chr1: 16745069-16745091 2416 GCATTGGTGGTTCAGTGGTAGA Yes No
Yes No No CU-1403 chr1: 159760309-159760331 2417
GCATTGGTGGTTCAGTGGTAGA Yes Yes No No No CU-1403 chr2:
156965953-156965975 2418 GCATTGGTGGTTCAGTGGTAGA Yes Yes No No No
CU-1403 chrX: 64154569-64154591 2419 GCATTGGTGGTTCAGTGGTAGA Yes Yes
No No No CU-1403 chr6: 27978713-27978735 2420
GCATTGGTGGTTCAGTGGTAGA Yes Yes No No No CU-1440 chr5:
180533270-180533287 2421 TGGTTATCACGTTCGCC Yes Yes No No No CU-1440
chr5: 180456690-180456707 2422 TGGTTATCACGTTCGCC Yes Yes No No No
CU-1440 chr6: 27281886-27281903 2423 TGGTTATCACGTTCGCC Yes Yes No
No No CU-1440 chr1: 147565219-147565236 2424 TGGTTATCACGTTCGCC Yes
Yes No No No CU-1440 chr5: 180461899-180461916 2425
TGGTTATCACGTTCGCC Yes Yes No No No CU-1453 chr3:
191522810-191522827 2426 CCCTGCTCGCTGCGCCA No No No No No CU-1457
chr7: 43102939-43102961 2427 TTCTCACTACTGCACTTGACTA Yes No No No No
CU-1457 chr14: 67153778-67153800 2428 TTCTCACTACTGCACTTGACTA Yes No
No No No CU-1457 chr1: 238571371-238571393 2429
TTCTCACTACTGCACTTGACTA No Yes No No No CU-1457 chr2:
147946177-147946199 2430 TTCTCACTACTGCACTTGACTA Yes Yes No No No
CU-1470 chr16: 30675216-30675234 2431 CTCCTGGCTGGCTCGCCA Yes Yes No
No No CU-1470 chr14: 43074235-43074253 2432 CTCCTGGCTGGCTCGCCA Yes
No No No No CU-1477 chr17: 26124435-26124459 2433
CTCCCACTGCTTCACTTGACTAGC No No No No No CU-1477 chr17:
27331095-27331119 2434 CTCCCACTGCTTCACTTGACTAGC No No No No No
CU-1477 chr10: 21810723-21810747 2435 CTCCCACTGCTTCACTTGACTAGC Yes
No No No No CU-1477 chr14: 99119179-99119203 2436
CTCCCACTGCTTCACTTGACTAGC No No No No No CU-1477 chr11:
107460922-107460946 2437 CTCCCACTGCTTCACTTGACTAGC Yes No No No No
CU-1477 chr4: 154407515-154407539 2438 CTCCCACTGCTTCACTTGACTAGC No
Yes No No No CU-1486 chr17: 59577172-59577189 2439
CTGCTGTGATGACATTC No Yes No No No CU-1488 chr1: 4671944-4671961
2440 TCCTGCCGCGGTCGCCA No No No No No CU-1513 chr17:
59577217-59577244 2441 GCGGGTGATGCGAACTGGAGTCTGAGC Yes No No No No
CU-1524 chr7: 148269562-148269586 2442 CCCCCACAACCGCGCTTGACTAGC Yes
Yes No No No CU-1528 chr17: 8066916-8066935 2443
TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528 chr6:
27167511-27167530 2444 TAGGGGTATGATTCTCGCT Yes Yes Yes No No
CU-1528 chr14: 20222026-20222045 2445 TAGGGGTATGATTCTCGCT Yes Yes
No Yes Yes CU-1528 chr14: 20151440-20151459 2446
TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528 chr6:
26663488-26663507 2447 TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528
chr16: 3172676-3172695 2448 TAGGGGTATGATTCTCGCT Yes Yes No No No
CU-1528 chr14: 20147375-20147394 2449 TAGGGGTATGATTCTCGCT Yes Yes
No No No CU-1528 chr5: 180548500-180548519 2450 TAGGGGTATGATTCTCGCT
Yes Yes No No No CU-1528 chr16: 3148935-3148954 2451
TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528 chr16: 3179646-3179665
2452 TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528 chr4:
18668214-18668233 2453 TAGGGGTATGATTCTCGCT Yes No No No No CU-1528
chr1: 165950597-165950616 2454 TAGGGGTATGATTCTCGCT Yes Yes Yes No
Yes CU-1528 chr16: 3182001-3182020 2455 TAGGGGTATGATTCTCGCT Yes No
No No No CU-1528 chr11: 75624216-75624235 2456 TAGGGGTATGATTCTCGCT
Yes Yes Yes No No CU-1528 chr16: 3162061-3162080 2457
TAGGGGTATGATTCTCGCT No Yes No No No CU-1528 chr7:
128210751-128210770 2458 TAGGGGTATGATTCTCGCT Yes Yes Yes Yes Yes
CU-1538 chrX: 16840335-16840361 2459 GGCTGGTCCGAGTGCAGTGGTGTTTA Yes
No No No No CU-1538 chr13: 98986625-98986651 2460
GGCTGGTCCGAGTGCAGTGGTGTTTA Yes No No No No CU-1538 chr10:
128599365-128599391 2461 GGCTGGTCCGAGTGCAGTGGTGTTTA Yes No No No No
CU-1538 chr7: 148311779-148311805 2462 GGCTGGTCCGAGTGCAGTGGTGTTTA
Yes No No No No CU-1538 chr15: 73062744-73062770 2463
GGCTGGTCCGAGTGCAGTGGTGTTTA No No No No No CU-1538 chrX:
116932310-116932336 2464 GGCTGGTCCGAGTGCAGTGGTGTTTA Yes No No No No
CU-1538 chr11: 47705094-47705120 2465 GGCTGGTCCGAGTGCAGTGGTGTTTA
Yes No No No No CU-1542 chr7: 148291339-148291362 2466
GGCTGGTCCGATGGTAGTGGGTT Yes Yes Yes No No CU-1542 chr6:
33275355-33275378 2467 GGCTGGTCCGATGGTAGTGGGTT Yes Yes No No No
CU-1545 chr17: 19031996-19032016 2468 CCACGAGGAAGAGAGGTAGC No No No
No No CU-1550 chr6: 26438546-26438564 2469 CGGAAGCGTGCTGGGCCC Yes
Yes No No No CU-1550 chr6: 27853657-27853675 2470
CGGAAGCGTGCTGGGCCC Yes Yes No No No CU-1550 chr6: 26421369-26421387
2471 CGGAAGCGTGCTGGGCCC Yes Yes No No No CU-1550 chr6:
27408781-27408799 2472 CGGAAGCGTGCTGGGCCC Yes Yes No No No CU-1550
chr6: 27668617-27668635 2473 CGGAAGCGTGCTGGGCCC Yes Yes No No
No
CU-1557 chr17: 19033934-19033957 2474 GGAGAGAACGCGGTCTGAGTGGT Yes
No No No No CU-1557 chr17: 18907957-18907980 2475
GGAGAGAACGCGGTCTGAGTGGT Yes No No No No CU-1557 chr17:
19032115-19032138 2476 GGAGAGAACGCGGTCTGAGTGGT Yes No No No No
CU-1557 chr17: 18956457-18956480 2477 GGAGAGAACGCGGTCTGAGTGGT Yes
No No No No CU-1557 chr17: 18906143-18906166 2478
GGAGAGAACGCGGTCTGAGTGGT Yes No No No No CU-1570 chr17:
36922634-36922653 2479 ATCCCCAGCATCTCCACCA Yes No No No No CU-1575
chr7: 148291405-148291430 2480 CCCCCCACTGCTAAATTTGACTGGA No No No
No No All human miRNA deposited in miRBase database Seq. ID
Conservation ID Genomic Coordinates No. Sequence Chimp Monkey Dog
Mouse Rat hsa-mir-1322 chr8: 10720294-10720313 2481
CAGCATCAGCAGCATCATC Yes No No No No hsa-mir-1323 chr19:
58867043-58867065 2482 TCAAAACTGAGGGGCATTTTCT Yes Yes No No No
hsa-mir-1321 chrX: 84977492-84977510 2483 CAGGGAGGTGAATGTGAT No No
No No No hsa-mir-29c* chr1: 206041870-206041892 2484
GAACACCAGGAGAAATCGGTCA Yes Yes Yes Yes Yes hsa-mir-1324 chr3:
75762663-75762687 2485 CCAGACAGAATTCTATGCACTTTC No No No No No
hsa-mir-675 chr11: 1974605-1974628 2486 CACTGTGGGCCCTCTCCGCACCA No
Yes No No No hsa-mir-183* chr7: 129202003-129202025 2487
TTATGGCCCTTCGGTAATTCAC Yes Yes Yes Yes Yes hsa-mir-335* chr7:
129923238-129923260 2488 TTTTTCATTATTGCTCCTGACC Yes Yes Yes Yes No
hsa-mir-19a* chr13: 90801158-90801180 2489 AGTTTTGCATAGTTGCACTACA
Yes No Yes Yes No hsa-mir-132* chr17: 1900008-1900030 2490
AGTAACAATCGAAAGCCACGGT No Yes Yes Yes Yes hsa-mir-182 chr7:
129197522-129197546 2491 AGTGTGAGTTCTACCATTGCCAAA Yes Yes Yes No No
hsa-mir-122 chr18: 54269299-54269321 2492 TGGAGTGTGACAATGGTGTTTG
Yes Yes Yes Yes Yes hsa-mir-16-2* chr3: 161605278-161605300 2493
CCAATATTACTGTGCTGCTTTA Yes No No No No hsa-mir-124 chr8:
65454320-65454340 2494 TAAGGCACGCGGTGAATGCC Yes Yes Yes Yes Yes
hsa-mir-124 chr8: 9798320-9798340 2495 GGCATTCACCGCGTGCCTTA No Yes
Yes Yes Yes hsa-mir-124 chr20: 61280348-61280368 2496
TAAGGCACGCGGTGAATGCC No Yes Yes Yes Yes hsa-mir-126 chr9:
138684925-138684947 2497 TCGTACCGTGAGTAATAATGCG Yes Yes Yes Yes Yes
hsa-mir-31* chr9: 21502119-21502141 2498 ATGGCAATATGTTGGCATAGCA Yes
Yes Yes Yes Yes hsa-mir-128 chr2: 136139485-136139506 2499
TCACAGTGAACCGGTCTCTTT Yes Yes Yes Yes Yes hsa-mir-128 chr3:
35761022-35761043 2500 TCACAGTGAACCGGTCTCTTT Yes Yes Yes Yes Yes
hsa-mir-19a chr13: 90801193-90801216 2501 TGTGCAAATCTATGCAAAACTGA
Yes No Yes Yes Yes hsa-mir-524-5p chr19: 58906082-58906104 2502
CTACAAAGGGAAGCACTTTCTC Yes No No No No hsa-mir-19b chrX:
133131378-133131401 2503 TCAGTTTTGCATGGATTTGCACA Yes Yes Yes Yes
Yes hsa-mir-19b chr13: 90801499-90801522 2504
TGTGCAAATCCATGCAAAACTGA Yes Yes Yes Yes Yes hsa-mir-148b* chr12:
53017290-53017312 2505 AAGTTCTGTTATACACTCAGGC Yes Yes Yes Yes Yes
hsa-mir-1257 chr20: 59962071-59962092 2506 GGTCAGAACCCATCATTCACT No
No No No No hsa-mir-1254 chr10: 70189097-70189121 2507
AGCCTGGAAGCTGGAGCCTGCAGT Yes No No No No hsa-mir-455-3p chr9:
116011587-116011608 2508 GCAGTCCATGGGCATATACAC Yes Yes Yes No No
hsa-mir-1253 chr17: 2598182-2598203 2509 TGCAGGCTGATCTTCTTCTCT Yes
No No No No hsa-mir-1250 chr17: 76721659-76721680 2510
AAAGGCCACATCCAGCACCGT Yes No No No No hsa-mir-1251 chr12:
96409821-96409842 2511 ACTCTAGCTGCCAAAGGCGCT Yes Yes Yes Yes Yes
hsa-mir-1258 chr2: 180433852-180433873 2512 AGTTAGGATTAGGTCGTGGAA
Yes Yes No No No hsa-mir-1258 chr2: 180433816-180433837 2513
TTCCACGACCTAATCCTAACT Yes Yes No No No hsa-mir-1259 chr20:
47330268-47330289 2514 ATATATGATGACTTAGCTTTT Yes Yes No No No
hsa-mir-1207-3p chr8: 129130630-129130648 2515 TCAGCTGGCCCTCATTTC
Yes No No No No hsa-mir-34c-3p chr11: 110889418-110889440 2516
AATCACTAACCACACGGCCAGG Yes Yes Yes No No hsa-mir-489 chr7:
92951194-92951216 2517 GCTGCCGTATATGTGATGTCAC Yes Yes No No No
hsa-mir-488 chr1: 175265132-175265153 2518 GACCAAGAAATAGCCTTTCAA
Yes Yes Yes No No hsa-mir-556-5p chr1: 160578974-160578996 2519
GATGAGCTCATTGTAATATGAG Yes No No No No hsa-mir-484 chr16:
15644658-15644680 2520 TCAGGCTCAGTCCCCTCCCGAT Yes Yes No Yes Yes
hsa-mir-523* chr19: 58893465-58893487 2521 CTCTAGAGGGAAGCGCTTTCTG
Yes No No No No hsa-mir-125b-1* chr11: 121475686-121475708 2522
AGCTCCCAAGAGCCTAACCCGT Yes Yes Yes Yes Yes hsa-mir-7-2* chr15:
86956130-86956152 2523 CAACAAATCCCAGTCTACCTAA Yes No No No No
hsa-mir-569 chr3: 172307161-172307182 2524 ACTTTCCAGGATTCATTAACT
Yes Yes No No No hsa-mir-574-5p chr4: 38546071-38546094 2525
TGAGTGTGTGTGTGTGAGTGTGT No No Yes Yes No hsa-mir-342-5p chr14:
99645762-99645783 2526 AGGGGTGCTATCTGTGATTGA Yes Yes Yes Yes Yes
hsa-mir-379 chr14: 100558160-100558181 2527 TGGTAGACTATGGAACGTAGG
Yes Yes Yes Yes Yes hsa-mir-520b chr19: 58896332-58896353 2528
AAAGTGCTTCCTTTTAGAGGG Yes Yes No No No hsa-mir-520e chr19:
58870829-58870850 2529 AAAGTGCTTCCTTTTTGAGGG Yes No No No No
hsa-mir-371-5p chr19: 58982745-58982765 2530 ACTCAAACTGTGGGGGCACT
Yes Yes Yes No No hsa-mir-520g chr19: 58917285-58917309 2531
ACAAAGTGCTTCCCTTTAGAGTGT Yes No No No No hsa-mir-520f chr19:
58877278-58877300 2532 AAGTGCTTCCTTTTAGAGGGTT Yes No No No No
hsa-mir-520h chr19: 58937631-58937653 2533 ACAAAGTGCTTCCCTTTAGAGT
Yes No No No No hsa-mir-219-5p chr9: 130194775-130194796 2534
AGAATTGCGTTTGGACAATCA Yes Yes Yes Yes Yes hsa-mir-219-5p chr6:
33283609-33283630 2535 TGATTGTCCAAACGCAATTCT Yes Yes Yes Yes Yes
hsa-mir-140-5p chr16: 68524506-68524528 2536 CAGTGGTTTTACCCTATGGTAG
Yes Yes Yes Yes Yes hsa-mir-423-5p chr17: 25468238-25468261 2537
TGAGGGGCAGAGAGCGAGACTTT Yes Yes Yes Yes Yes hsa-mir-30b* chr8:
135881956-135881978 2538 GAAGTAAACATCCACCTCCCAG Yes Yes Yes No No
hsa-mir-195 chr17: 6861709-6861730 2539 GCCAATATTTCTGTGCTGCTA Yes
Yes Yes Yes Yes hsa-mir-194 chr11: 64415451-64415473 2540
TCCACATGGAGTTGCTGTTACA Yes Yes Yes Yes Yes hsa-mir-194 chr1:
218358170-218358192 2541 TCCACATGGAGTTGCTGTTACA Yes Yes Yes Yes Yes
hsa-mir-197 chr1: 109943084-109943106 2542 TTCACCACCTTCTCCACCCAGC
Yes Yes Yes No No hsa-mir-191 chr3: 49033108-49033131 2543
CAGCTGCTTTTGGGATTCCGTTG Yes Yes Yes Yes Yes hsa-mir-190 chr15:
60903222-60903244 2544 TGATATGTTTGATATATTAGGT Yes Yes Yes Yes Yes
hsa-mir-192 chr11: 64415250-64415271 2545 GGCTGTCAATTCATAGGTCAG Yes
Yes Yes Yes Yes hsa-mir-449a chr5: 54502170-54502192 2546
ACCAGCTAACAATACACTGCCA No Yes Yes Yes Yes hsa-mir-339-3p chr7:
1029116-1029139 2547 CGGCTCTGTCGTCGAGGCGCTCA No Yes No No No
hsa-mir-508-5p chrX: 146126189-146126212 2548
CATGAGTGACGCCCTCTGGAGTA No No No No No hsa-mir-1284 chr3:
71673879-71673901 2549 GAAAAGCCAGGGTCTGTATAGA Yes No No No No
hsa-mir-362-5p chrX: 49660315-49660339 2550
AATCCTTGGAACCTAGGTGTGAGT Yes Yes Yes No No hsa-mir-125a-3p chr19:
56888370-56888392 2551 ACAGGTGAGGTTCTTGGGAGCC Yes Yes Yes Yes Yes
hsa-mir-34a* chr1: 9134338-9134360 2552 AGGGCAGTATACTTGCTGATTG Yes
Yes Yes Yes Yes hsa-mir-373 chr19: 58983813-58983836 2553
GAAGTGCTTCGATTTTGGGGTGT No Yes No No No hsa-mir-502-3p chrX:
49665996-49666018 2554 AATGCACCTGGGCAAGGATTCA Yes Yes Yes No No
hsa-mir-200b chr1: 1092402-1092424 2555 TAATACTGCCTGGTAATGATGA No
No Yes Yes Yes
hsa-mir-200c chr12: 6943165-6943188 2556 TAATACTGCCGGGTAATGATGGA
Yes Yes Yes Yes Yes hsa-mir-200a chr1: 1093158-1093180 2557
TAACACTGTCTGGTAACGATGT Yes Yes Yes Yes Yes hsa-mir-410 chr14:
100602050-100602071 2558 AATATAACACAGATGGCCTGT Yes Yes Yes Yes Yes
hsa-mir-411 chr14: 100559429-100559450 2559 TAGTAGACCGTATAGCGTACG
Yes Yes Yes Yes Yes hsa-mir-412 chr14: 100601589-100601612 2560
ACTTCACCTGGTCCACTAGCCGT Yes Yes No Yes Yes hsa-mir-555 chr1:
153582779-153582800 2561 ATCAGAGGTTCAGCTTACCCT Yes No No No No
hsa-mir-554 chr1: 149784910-149784931 2562 GCTAGTCCTGACTCAGCCAGT
Yes Yes No No No hsa-mir-493* chr14: 100405164-100405186 2563
TTGTACATGGTAGGCTTTCATT No Yes Yes Yes Yes hsa-mir-550 chr7:
30295955-30295978 2564 AGTGCCTGAGGGAGTAAGAGCCC Yes Yes No No No
hsa-mir-550 chr7: 32739138-32739161 2565 AGTGCCTGAGGGAGTAAGAGCCC
Yes Yes No No No hsa-mir-553 chr1: 100519399-100519420 2566
AAAACGGTGAGATTTTGTTTT Yes No No No No hsa-mir-193a-5p chr17:
26911147-26911169 2567 TGGGTCTTTGCGGGCGAGATGA Yes Yes Yes No No
hsa-mir-876-3p chr9: 28853633-28853655 2568 TGAATTACTTTGTAAACCACCA
Yes Yes Yes No No hsa-mir-139-3p chr11: 72003757-72003779 2569
ACTCCAACAGGGCCGCGTCTCC Yes Yes No Yes Yes hsa-mir-30a chr6:
72170018-72170040 2570 CTTCCAGTCGAGGATGTTTACA Yes Yes Yes Yes Yes
hsa-mir-30b chr8: 135881994-135882016 2571 AGCTGAGTGTAGGATGTTTACA
Yes Yes Yes Yes Yes hsa-mir-30c chr1: 40995558-40995581 2572
TGTAAACATCCTACACTCTCAGC Yes Yes Yes Yes Yes hsa-mir-30c chr6:
72143426-72143449 2573 GCTGAGAGTGTAGGATGTTTACA Yes Yes Yes Yes Yes
hsa-mir-30d chr8: 135886343-135886365 2574 CTTCCAGTCGGGGATGTTTACA
Yes Yes Yes Yes Yes hsa-mir-30e chr1: 40992629-40992651 2575
TGTAAACATCCTTGACTGGAAG Yes Yes Yes Yes Yes hsa-mir-374b* chrX:
73355116-73355138 2576 AATGATAATACAACCTGCTAAG Yes Yes No Yes No
hsa-mir-548b-3p chr6: 119431925-119431947 2577
ACAAAAGCAACTGAGGTTCTTG Yes No No No No hsa-mir-515-5p chr19:
58874081-58874105 2578 TTCTCCAAAAGAAAGCACTTTCTG Yes No No No No
hsa-mir-515-5p chr19: 58880087-58880111 2579
TTCTCCAAAAGAAAGCACTTTCTG Yes No No No No hsa-mir-429 chr1:
1094297-1094319 2580 TAATACTGTCTGGTAAAACCGT No Yes No No No
hsa-mir-486-5p chr8: 41637118-41637140 2581 TCCTGTACTGAGCTGCCCCGAG
Yes Yes Yes Yes No hsa-mir-486-5p chr8: 41637158-41637180 2582
CTCGGGGCAGCTCAGTACAGGA Yes Yes Yes Yes No hsa-mir-1206 chr8:
129090328-129090349 2583 TGTTCATGTAGATGTTTAAGC Yes No No No No
hsa-mir-99a chr21: 16833291-16833313 2584 AACCCGTAGATCCGATCTTGTG
Yes Yes Yes Yes Yes hsa-mir-188-3p chrX: 49654901-49654922 2585
CTCCCACATGCAGGGTTTGCA Yes Yes Yes Yes Yes hsa-mir-99b chr19:
56887682-56887704 2586 CACCCGTAGAACCGACCTTGCG Yes Yes Yes Yes Yes
hsa-mir-300 chr14: 100577503-100577525 2587 TATACAAGGGCAGACTCTCTCT
Yes No No No No hsa-mir-193b chr16: 14305374-14305396 2588
AACTGGCCCTCAAAGTCCCGCT Yes Yes No No No hsa-mir-1203 chr17:
43588846-43588867 2589 GAGCTGCATCCTGGCTCCGGG Yes No No No No
hsa-mir-30c-1* chr1: 40995597-40995619 2590 CTGGGAGAGGGTTGTTTACTCC
Yes Yes Yes Yes Yes hsa-mir-19b-2* chrX: 133131422-133131444 2591
TGAAATGCAAACCTGCAAAACT Yes Yes Yes No No hsa-mir-1286 chr22:
18616667-18616688 2592 AGGGCTCATCTTGGTCCTGCA Yes No No No No
hsa-let-7g* chr3: 52277335-52277356 2593 GCAAGGCAGTGGCCTGTACAG Yes
Yes Yes Yes No hsa-mir-361-3p chrX: 85045301-85045324 2594
AAATCAGAATCACACCTGGGGGA Yes Yes Yes Yes No hsa-mir-518a-5p chr19:
58926084-58926104 2595 CTGCAAAGGGAAGCCCTTTC Yes No No No No
hsa-mir-518a-5p chr19: 58934413-58934433 2596 CTGCAAAGGGAAGCCCTTTC
Yes No No No No hsa-mir-604 chr10: 29873953-29873972 2597
GTCCTGAATTCCGCAGCCT No No No No No hsa-mir-485-5p chr14:
100591516-100591538 2598 AGAGGCTGGCCGTGATGAATTC Yes Yes Yes Yes Yes
hsa-mir-452* chrX: 150878761-150878783 2599 CACTTACTTCTTTGCAGATGAG
Yes Yes Yes No No hsa-mir-450b-5p chrX: 133501926-133501948 2600
TATTCAGGAACATATTGCAAAA Yes Yes Yes No No hsa-mir-505 chrX:
138833984-138834006 2601 AGGAAACCAGCAAGTGTTGACG Yes Yes Yes No Yes
hsa-mir-299-5p chr14: 100559889-100559911 2602
TGGTTTACCGTCCCACATACAT Yes Yes Yes Yes Yes hsa-mir-181a-2* chr9:
126494617-126494639 2603 ACCACTGACCGTTGACTGTACC Yes Yes No No No
hsa-mir-29b-2* chr1: 206042459-206042481 2604
CTAAGCCACCATGTGAAACCAG Yes Yes Yes Yes Yes hsa-mir-323-3p chr14:
100561871-100561892 2605 CACATTACACGGTCGACCTCT Yes Yes Yes Yes Yes
hsa-mir-1256 chr1: 21187456-21187478 2606 AGCTAGTGAGAAGTCAATGCCT
Yes Yes No No No hsa-mir-144* chr17: 24212726-24212748 2607
CTTACAGTATATGATGATATCC Yes Yes Yes Yes Yes hsa-mir-1280 chr3:
129563701-129563718 2608 TCCCACCGCTGCCACCC Yes No No No No
hsa-mir-379* chr14: 100558198-100558220 2609 TATGTAACATGGTCCACTAACT
Yes Yes Yes Yes Yes hsa-mir-1252 chr12: 78337171-78337193 2610
AGAAGGAAATTGAATTCATTTA No No No No No hsa-mir-324-5p chr17:
7067384-7067407 2611 ACACCAATGCCCTAGGGGATGCG Yes Yes Yes Yes Yes
hsa-mir-516b* chr19: 58920562-58920580 2612 TGCTTCCTTTCAGAGGGT Yes
No No No No hsa-mir-516b* chr19: 58931970-58931988 2613
TGCTTCCTTTCAGAGGGT Yes Yes No No No hsa-mir-18b chrX:
133131779-133131802 2614 CTAACTGCACTAGATGCACCTTA Yes Yes Yes No No
hsa-mir-17 chr13: 90800872-90800895 2615 CAAAGTGCTTACAGTGCAGGTAG
Yes No Yes Yes Yes hsa-mir-16 chr3: 161605235-161605257 2616
TAGCAGCACGTAAATATTGGCG Yes Yes Yes Yes Yes hsa-mir-16 chr13:
49521163-49521185 2617 CGCCAATATTTACGTGCTGCTA Yes Yes Yes Yes No
hsa-mir-26b* chr2: 218975658-218975680 2618 CCTGTTCTCCATTACTTGGCTC
Yes Yes Yes Yes Yes hsa-mir-618 chr12: 79853705-79853728 2619
ACTCAGAAGGACAAGTAGAGTTT Yes Yes No No No hsa-mir-331-3p chr12:
94226386-94226407 2620 GCCCCTGGGCCTATCCTAGAA Yes Yes Yes Yes Yes
hsa-mir-605 chr10: 52729353-52729376 2621 TAAATCCCATGGTGCCTTCTCCT
Yes No No No No hsa-mir-376a chr14: 100576914-100576935 2622
ATCATAGAGGAAAATCCACGT Yes Yes Yes No No hsa-mir-376a chr14:
100576207-100576228 2623 ATCATAGAGGAAAATCCACGT Yes Yes Yes No No
hsa-mir-376b chr14: 100576586-100576608 2624 ATCATAGAGGAAAATCCATGTT
Yes Yes Yes No No hsa-mir-376c chr14: 100575821-100575842 2625
AACATAGAGGAAATTCCACGT Yes Yes Yes No No hsa-mir-601 chr9:
125204666-125204688 2626 CTCCTCCAACAATCCTAGACCA Yes Yes No No No
hsa-mir-600 chr9: 124913660-124913683 2627 GAGCAAGGCTCTTGTCTGTAAGT
Yes No No No No hsa-mir-603 chr10: 24604679-24604701 2628
CACACACTGCAATTACTTTTGC No No No No No hsa-mir-602 chr9:
139852706-139852729 2629 GACACGGGCGACAGCTGCGGCCC No No No No No
hsa-mir-609 chr10: 105968596-105968616 2630 AGAGATGAGAGAAACACCCT
Yes No No No No hsa-mir-608 chr10: 102724746-102724771 2631
AGGGGTGGTGTTGGGACAGCTCCGT No No No No No hsa-mir-551b* chr3:
169752356-169752378 2632 GAAATCAAGCGTGGGTGAGACC Yes Yes No No No
hsa-mir-544 chr14: 100584801-100584823 2633 ATTCTGCATTTTTAGCAAGTTC
Yes Yes Yes No No hsa-mir-664* chr1: 218440550-218440574 2634
ATCCAATCATTTTCCCTAGCCAGT Yes Yes No No No hsa-mir-409-5p chr14:
100601403-100601426 2635 AGGTTACCCGAGCAACTTTGCAT Yes Yes Yes Yes
Yes hsa-mir-136* chr14: 100420839-100420861 2636
CATCATCGTCTCAAATGAGTCT Yes Yes Yes Yes Yes hsa-mir-1282 chr15:
41873221-41873241 2637 AAGCAGAAAAAGGCAAACGA Yes Yes Yes Yes Yes
hsa-mir-519c-5p chr19: 58881549-58881571 2638
CTCTAGAGGGAAGCGCTTTCTG Yes No No No No hsa-mir-1208 chr8:
129231554-129231574 2639 TCACTGTTCAGACAGGCGGA Yes Yes No No No
hsa-mir-1205 chr8: 129042067-129042087 2640 TCTGCAGGGTTTGCTTTGAG
Yes No No No No hsa-mir-663b chr2: 132731012-132731034 2641
CCTCAGGCACGGCCGGGCCACC Yes No No No No hsa-mir-1201 chr14:
19864455-19864479 2642 TCAGAGCATGTGTTTAATCAGGCT Yes Yes No No No
hsa-mir-1200 chr7: 36925532-36925554 2643 GAGGCTCAGAATGGCTCAGGAG No
No No No No hsa-mir-338-5p chr17: 76714317-76714339 2644
CACTCAGCACCAGGATATTGTT Yes Yes Yes Yes Yes hsa-mir-1202 chr6:
156309634-156309655 2645 GTGCCAGCTGCAGTGGGGGAG Yes Yes No No No
hsa-mir-501-5p chrX: 49661082-49661104 2646 AATCCTTTGTCCCTGGGTGAGA
Yes Yes No No No hsa-mir-519b-5p chr19: 58890290-58890312 2647
CTCTAGAGGGAAGCGCTTTCTG Yes Yes No No No hsa-mir-101* chr1:
65296747-65296769 2648 AGCATCAGCACTGTGATAACTG Yes Yes Yes Yes Yes
hsa-mir-511 chr10: 17927127-17927148 2649 GTGTCTTTTGCTCTGCAGTCA Yes
No No No No hsa-mir-511 chr10: 18174056-18174077 2650
GTGTCTTTTGCTCTGCAGTCA Yes No No No No hsa-mir-510 chrX:
146161587-146161609 2651 GTGATTGCCACTCTCCTGAGTA No No No No No
hsa-let-7a* chr9: 95978115-95978136 2652 CTATACAATCTACTGTCTTTC Yes
Yes Yes Yes Yes hsa-let-7a* chr22: 44887343-44887364 2653
CTATACAATCTACTGTCTTTC Yes Yes Yes Yes Yes hsa-mir-514 chrX:
146173864-146173885 2654 TCTACTCACAGAAGTGTCAAT Yes Yes No No No
hsa-mir-514 chrX: 146171166-146171187 2655 TCTACTCACAGAAGTGTCAAT
Yes Yes No No No hsa-mir-514 chrX: 146168475-146168496 2656
TCTACTCACAGAAGTGTCAAT Yes No No No No hsa-mir-524-3p chr19:
58906119-58906140 2657 GAAGGCGCTTCCCTTTGGAGT Yes No No No No
hsa-mir-491-5p chr9: 20706118-20706140 2658 AGTGGGGAACCCTTCCATGAGG
Yes Yes Yes Yes No hsa-mir-18b* chrX: 133131737-133131759 2659
GCCAGAAGGGGCATTTAGGGCA No Yes No No No hsa-mir-411* chr14:
100559464-100559486 2660 TATGTAACACGGTCCACTAACC Yes Yes Yes Yes Yes
hsa-mir-548d-3p chr8: 124429469-124429491 2661
GCAAAAGAAACTGTGGTTTTTG No No No No No hsa-mir-548d-3p chr17:
62898081-62898103 2662 GCAAAAGAAACTGTGGTTTTTG No No No No No
hsa-mir-490-3p chr7: 136238528-136238550 2663
CAACCTGGAGGACTCCATGCTG Yes Yes Yes Yes Yes hsa-mir-576-3p chr4:
110629356-110629378 2664 AAGATGTGGAAAAATTGGAATC Yes Yes No No No
hsa-mir-34a chr1: 9134380-9134402 2665 ACAACCAGCTAAGACACTGCCA Yes
Yes Yes Yes Yes hsa-mir-34b chr11: 110888921-110888943 2666
CAATCACTAACTCCACTGCCAT Yes Yes Yes Yes Yes hsa-mir-654-5p chr14:
100576323-100576345 2667 TGGTGGGCCGCAGAACATGTGC Yes Yes No No No
hsa-mir-216a chr2: 56069658-56069680 2668 TCACAGTTGCCAGCTGAGATTA No
Yes Yes Yes Yes hsa-mir-216b chr2: 56081402-56081424 2669
TCACATTTGCCTGCAGAGATTT Yes Yes Yes Yes Yes hsa-mir-590-3p chr7:
73243518-73243539 2670 TAATTTTATGTATAAGCTAGT Yes No Yes No No
hsa-mir-939 chr8: 145590215-145590239 2671 CACCCCCAGAGCCTCAGCTCCCCA
Yes Yes No No No hsa-mir-938 chr10: 29931245-29931267 2672
ACTGGGTTCACCTTTAAGGGCA Yes No No No No hsa-mir-34c-5p chr11:
110889385-110889408 2673 AGGCAGTGTAGTTAGCTGATTGC Yes Yes Yes Yes
Yes hsa-mir-15a* chr13: 49521266-49521288 2674
TGAGGCAGCACAATATGGCCTG Yes Yes Yes No No hsa-mir-933 chr2:
175740615-175740637 2675 GGGAGAGGTCTCCCTGCGCACA Yes Yes No No No
hsa-mir-499-3p chr20: 33041908-33041930 2676 AACATCACAGCAAGTCTGTGCT
Yes Yes Yes Yes Yes hsa-mir-937 chr8: 144967128-144967150 2677
GGCAGAGAGTCAGAGCGCGGAT Yes No No No No hsa-mir-936 chr10:
105797898-105797920 2678 CTGCGATTCCTCCCTCTACTGT Yes No No No No
hsa-mir-935 chr19: 59177427-59177450 2679 CCAGTTACCGCTTCCGCTACCGC
Yes No No No Yes hsa-mir-654-3p chr14: 100576358-100576380 2680
TATGTCTGCTGACCATCACCTT Yes Yes No Yes No hsa-mir-93* chr7:
99529335-99529357 2681 CGGGAAGTGCTAGCTCAGCAGT Yes Yes Yes Yes Yes
hsa-mir-516b chr19: 58920522-58920544 2682 ATCTGGAGGTAAGAAGCACTTT
Yes No No No No hsa-mir-516b chr19: 58931925-58931947 2683
ATCTGGAGGTAAGAAGCACTTT Yes Yes No No No hsa-mir-551a chr1:
3467133-3467154 2684 TGGAAACCAAGAGTGGGTCGC Yes Yes Yes No No
hsa-mir-551b chr3: 169752395-169752416 2685 GCGACCCATACTTGGTTTCAG
Yes Yes Yes Yes Yes hsa-mir-345 chr14: 99843965-99843987 2686
GCTGACTCCTAGTCCAGGGCTC Yes No No No No hsa-mir-346 chr10:
88014483-88014506 2687 AGAGGCAGGCATGCGGGCAGACA Yes Yes Yes No No
hsa-mir-340 chr5: 179374966-179374988 2688 AATCAGTCTCATTGCTTTATAA
Yes Yes Yes Yes No hsa-mir-106a chrX: 133131939-133131962 2689
CTACCTGCACTGTAAGCACTTTT Yes Yes Yes No No hsa-mir-23b* chr9:
96887329-96887351 2690 TGGGTTCCTGGCATGCTGATTT Yes Yes Yes Yes Yes
hsa-mir-106b chr7: 99529601-99529622 2691 ATCTGCACTGTCAGCACTTTA Yes
Yes Yes Yes Yes hsa-mir-194* chr11: 64415415-64415437 2692
CAGATAACAGCAGCCCCACTGG Yes Yes No Yes Yes hsa-mir-519a* chr19:
58947476-58947498 2693 CTCTAGAGGGAAGCGCTTTCTG Yes No No No No
hsa-mir-519e chr19: 58875056-58875078 2694 AAGTGCCTCCTTTTAGAGTGTT
Yes No No No No hsa-mir-519d chr19: 58908465-58908487 2695
CAAAGTGCCTCCCTTTAGAGTG Yes No No No No hsa-mir-769-3p chr19:
51214097-51214120 2696 CTGGGATCTCCGGGGTCTTGGTT No No No No No
hsa-mir-519a chr19: 58947514-58947536 2697 AAAGTGCATCCTTTTAGAGTGT
Yes No No No No hsa-mir-519a chr19: 58957462-58957484 2698
AAAGTGCATCCTTTTAGAGTGT Yes Yes No No No hsa-mir-943 chr4:
1957927-1957948 2699 CTGGAGGACGGCAACAGTCAG Yes No No No No
hsa-mir-940 chr16: 2261807-2261828 2700 AAGGCAGGGCCCCCGCTCCCC Yes
Yes Yes No No hsa-mir-941 chr20: 62021710-62021733 2701
CACCCGGCTGTGTGCACATGTGC No No No No No hsa-mir-941 chr20:
62021598-62021621 2702 CACCCGGCTGTGTGCACATGTGC No No No No No
hsa-mir-941 chr20: 62021291-62021314 2703 CACCCGGCTGTGTGCACATGTGC
Yes No No No No hsa-mir-423-3p chr17: 25468274-25468297 2704
AGCTCGGTCTGAGGCCCCTCAGT Yes Yes Yes Yes Yes hsa-mir-203 chr14:
103653558-103653580 2705 GTGAAATGTTTAGGACCACTAG Yes Yes Yes Yes Yes
hsa-mir-202 chr10: 134911032-134911052 2706 TTCCCATGCCCTATACCTCT
Yes No No No No hsa-mir-205 chr1: 207672133-207672155 2707
TCCTTCATTCCACCGGAGTCTG Yes Yes Yes Yes Yes hsa-mir-204 chr9:
72614766-72614788 2708 AGGCATAGGATGACAAAGGGAA Yes Yes Yes Yes Yes
hsa-mir-526a chr19: 58921993-58922015 2709 CTCTAGAGGGAAGCACTTTCTG
Yes No No No No hsa-mir-526a chr19: 58901331-58901353 2710
CTCTAGAGGGAAGCACTTTCTG Yes No No No No hsa-mir-28-3p chr3:
189889315-189889337 2711 CACTAGATTGTGAGCTCCTGGA Yes Yes Yes No Yes
hsa-mir-302a* chr4: 113788828-113788851 2712
AGCAAGTACATCCACGTTTAAGT Yes Yes Yes No No hsa-mir-548c-3p chr12:
63302615-63302637 2713 CAAAAATCTCAATTACTTTTGC Yes No No No No
hsa-mir-424* chrX: 133508339-133508360 2714 ATAGCAGCGCCTCACGTTTTG
Yes Yes Yes No No hsa-mir-886-5p chr5: 135444163-135444186 2715
CCGCTTGAGCTAACTCCGACCCG Yes Yes No No No hsa-mir-877* chr6:
30660152-30660173 2716 TCCTCTTCTCCCTCCTCCCAG Yes Yes No Yes Yes
hsa-mir-29b chr7: 130212765-130212788 2717 AACACTGATTTCAAATGGTGCTA
Yes Yes Yes Yes Yes hsa-mir-29b chr1: 206042417-206042440 2718
AACACTGATTTCAAATGGTGCTA Yes Yes Yes Yes Yes hsa-mir-29c chr1:
206041832-206041854 2719 TAACCGATTTCAAATGGTGCTA Yes Yes Yes Yes Yes
hsa-mir-29a chr7: 130212046-130212068 2720 TAACCGATTTCAGATGGTGCTA
No Yes Yes Yes Yes hsa-mir-20a chr13: 90801326-90801349 2721
TAAAGTGCTTATAGTGCAGGTAG Yes No Yes Yes Yes hsa-mir-640 chr19:
19406931-19406952 2722 ATGATCCAGGAACCTGCCTCT Yes Yes No No No
hsa-mir-129-5p chr11: 43559533-43559554 2723 CTTTTTGCGGTCTGGGCTTGC
Yes Yes
Yes Yes Yes hsa-mir-129-5p chr7: 127635164-127635185 2724
CTTTTTGCGGTCTGGGCTTGC Yes Yes Yes Yes Yes hsa-mir-20b chrX:
133131545-133131568 2725 CTACCTGCACTATGAGCACTTTG Yes Yes No Yes Yes
hsa-mir-645 chr20: 48635789-48635808 2726 TCTAGGCTGGTACTGCTGA Yes
No No No No hsa-mir-644 chr20: 32517850-32517869 2727
AGTGTGGCTTTCTTAGAGC Yes No No No No hsa-mir-647 chr20:
62044487-62044508 2728 GAAGGAAGTGAGTGCAGCCAC No No No No No
hsa-mir-646 chr20: 58316986-58317005 2729 AAGCAGCTGCCTCTGAGGC Yes
No No No No hsa-mir-649 chr22: 19718479-19718501 2730
GACTCTTGAACAACACAGGTTT Yes Yes No No No hsa-mir-648 chr22:
16843693-16843712 2731 ACCAGTGCCCTGCACACTT No No No No No
hsa-mir-760 chr1: 94085023-94085043 2732 CGGCTCTGGGTCTGTGGGGA Yes
Yes No Yes Yes hsa-mir-766 chrX: 118664753-118664775 2733
GCTGAGGCTGTGGGGCTGGAGT Yes No No No No hsa-mir-765 chr1:
155172571-155172592 2734 CATCACCTTCCTTCTCCTCCA Yes No No No No
hsa-mir-628-3p chr15: 53452443-53452464 2735 TCGACTGCCACTCTTACTAGA
Yes Yes Yes No No hsa-mir-337-5p chr14: 100410604-100410625 2736
GAACGGCTTCATACAGGAGTT Yes Yes No No No hsa-mir-373* chr19:
58983775-58983797 2737 ACTCAAAATGGGGGCGCTTTCC Yes No No No No
hsa-mir-369-5p chr14: 100601695-100601717 2738
AGATCGACCGTGTTATATTCGC Yes Yes No Yes Yes hsa-mir-1285 chr7:
91671276-91671298 2739 AGGTCTCACTTTGTTGCCCAGA Yes No No No No
hsa-mir-1285 chr2: 70333568-70333590 2740 AGGTCTCACTTTGTTGCCCAGA No
No No No No hsa-mir-222* chrX: 45491422-45491444 2741
AGGATCTACACTGGCTACTGAG No Yes Yes Yes Yes hsa-mir-298 chr20:
56826729-56826753 2742 TGGGAGAACCTCCCTGCTTCTGCT Yes No No No No
hsa-mir-206 chr6: 52117157-52117179 2743 TGGAATGTAAGGAAGTGTGTGG Yes
Yes Yes Yes Yes hsa-mir-297 chr4: 112001228-112001249 2744
CATGCACATGCACACATACAT Yes No No No No hsa-mir-589* chr7:
5501990-5502014 2745 TCTGGGAACCGGCATTTGTTCTGA No No No No No
hsa-mir-124* chr20: 61280310-61280332 2746 CGTGTTCACAGCGGACCTTGAT
No Yes Yes Yes Yes hsa-mir-124* chr8: 9798357-9798379 2747
ATCAAGGTCCGCTGTGAACACG No Yes Yes Yes Yes hsa-mir-124* chr8:
65454283-65454305 2748 CGTGTTCACAGCGGACCTTGAT Yes Yes Yes Yes Yes
hsa-mir-185* chr22: 18400710-18400732 2749 AGGGGCTGGCTTTCCTCTGGTC
Yes Yes Yes Yes Yes hsa-mir-486-3p chr8: 41637160-41637181 2750
CGGGGCAGCTCAGTACAGGAT Yes Yes Yes Yes No hsa-mir-486-3p chr8:
41637117-41637138 2751 ATCCTGTACTGAGCTGCCCCG Yes Yes Yes Yes No
hsa-mir-1243 chr4: 114247471-114247493 2752 AACTGGATCAATTATAGGAGTG
Yes Yes No No No hsa-mir-616* chr12: 56199272-56199294 2753
AAGTCACTGAAGGGTTTTGAGT No No No No No hsa-mir-1245 chr2:
189551106-189551127 2754 AAGTGATCTAAAGGCCTACAT Yes No No No No
hsa-mir-1244 chr12: 12156206-12156232 2755
AAGTAGTTGGTTTGTATGAGATGGTT Yes Yes Yes Yes No hsa-mir-1244 chr12:
9283334-9283360 2756 AACCATCTCATACAAACCAACTACTT Yes Yes Yes Yes No
hsa-mir-1244 chr2: 232286321-232286347 2757
AAGTAGTTGGTTTGTATGAGATGGTT Yes Yes Yes Yes Yes hsa-mir-1244 chr5:
118338233-118338259 2758 AAGTAGTTGGTTTGTATGAGATGGTT Yes Yes Yes Yes
No hsa-mir-1247 chr14: 101096451-101096473 2759
TCCGGGGACGAACGGGACGGGT Yes Yes No Yes Yes hsa-mir-1246 chr2:
177173997-177174016 2760 CCTGCTCCAAAAATCCATT Yes Yes No No No
hsa-mir-1249 chr22: 43975502-43975524 2761 TGAAGAAGGGGGGGAAGGGCGT
Yes Yes Yes Yes No hsa-mir-491-3p chr9: 20706152-20706174 2762
CTTATGCAAGATTCCCTTCTAC Yes Yes Yes Yes No hsa-mir-148a* chr7:
25956104-25956126 2763 AGTCGGAGTGTCTCAGAACTTT Yes Yes Yes Yes No
hsa-mir-92b* chr1: 153431610-153431632 2764 AGGGACGGGACGCGGTGCAGTG
No Yes Yes No Yes hsa-mir-548o chr7: 101833199-101833221 2765
GCAAAAGTAACTGCAGTTTTGG Yes Yes No No No hsa-mir-891b chrX:
144890309-144860331 2766 TCAATGACTCAGGTAAGTTGCA Yes Yes No No No
hsa-mir-548m chrX: 94204846-94204867 2767 CAAAAACCACAAATACCTTTG No
No No No No hsa-mir-548l chr11: 93839358-93839380 2768
GACAAAACCCGCAAATACTTTT Yes Yes No No No hsa-mir-548k chr11:
69807739-69807761 2769 AAAAGTACTTGCGGATTTTGCT Yes No No No No
hsa-mir-1283 chr19: 58883559-58883581 2770 TCTACAAAGGAAAGCGCTTTCT
Yes No No No No hsa-mir-1283 chr19: 58953310-58953332 2771
TCTACAAAGGAAAGCGCTTTCT No No No No No hsa-mir-548i chrX:
83367460-83367482 2772 GGCAAAATCCGCAATTACTTTT No No No No No
hsa-mir-548i chr3: 126992025-126992047 2773 GGCAAAATCCGCAATTACTTTT
Yes No No No No hsa-mir-548i chr8: 7983961-7983983 2774
GGCAAAATCCGCAATTACTTTT Yes No No No No hsa-mir-548i chr4:
9166975-9166997 2775 GGCAAAATCCGCAATTACTTTT Yes No No No No
hsa-mir-548h chr17: 13387638-13387660 2776 GACAAAAACCGCGATTACTTTT
No No No No No hsa-mir-548h chr8: 26962359-26962381 2777
GACAAAAACCGCGATTACTTTT No No No No No hsa-mir-548h chr14:
63631554-63631576 2778 GACAAAAACCGCGATTACTTTT Yes No No No No
hsa-mir-548h chr16: 11307848-11307870 2779 GACAAAAACCGCGATTACTTTT
No No No No No hsa-mir-548g chr4: 148485244-148485266 2780
GTACAAAAGTAATTACAGTTTT No No No No No hsa-mir-548f chr5:
109877443-109877462 2781 AAAAGTAATTACAGTTTTT Yes No No No No
hsa-mir-548f chr7: 146706065-146706084 2782 AAAAGTAATTACAGTTTTT No
No No No No hsa-mir-548f chrX: 32569527-32569546 2783
AAAAGTAATTACAGTTTTT Yes No No No No hsa-mir-548f chr2:
212999252-212999271 2784 AAAAGTAATTACAGTTTTT No No No No No
hsa-mir-548f chr10: 56037654-56037673 2785 AAAAGTAATTACAGTTTTT No
No No No No hsa-mir-496 chr14: 100596717-100596739 2786
TGAGTATTACATGGCCAATCTC Yes Yes Yes Yes Yes hsa-mir-497 chr17:
6862021-6862042 2787 ACAAACCACAGTGTGCTGCTG Yes Yes Yes Yes Yes
hsa-mir-190b chr1: 152432812-152432833 2788 AACCCAATATCAAACATATCA
Yes Yes Yes Yes No hsa-mir-492 chr12: 93752333-93752356 2789
AGGACCTGCGGGACAAGATTCTT No No No No No hsa-mir-493 chr14:
100405205-100405227 2790 TGAAGGTCTACTGTGTGCCAGG No Yes Yes No Yes
hsa-mir-199b-5p chr9: 130046882-130046905 2791
GAACAGATAGTCTAAACACTGGG Yes No Yes No No hsa-mir-891a chrX:
144917050-144917072 2792 TCAGTGGCTCAGGTTCGTTGCA No No No No No
hsa-mir-500* chrX: 49659829-49659851 2793 ATGCACCTGGGCAAGGATTCTG
Yes Yes Yes No No hsa-mir-105* chrX: 151311355-151311377 2794
TAGCACATGCTCAAACATCCGT Yes Yes Yes No Yes hsa-mir-105* chrX:
151313548-151313570 2795 TAGCACATGCTCAAACATCCGT Yes Yes No No Yes
hsa-mir-513c chrX: 146078962-146078984 2796 ATAAACGACACCTCCTTGAGAA
No No No No No hsa-mir-513b chrX: 146088302-146088324 2797
ATAAATGACACCTCCTTGTGAA No Yes No No No hsa-mir-18a* chr13:
90801051-90801074 2798 ACTGCCCTAAGTGCTCCTTCTGG Yes No Yes Yes Yes
hsa-mir-548p chr5: 100180100-100180122 2799 AAAGTAACTGCAGTTTTTGCTA
Yes No No No No hsa-mir-24-1* chr9: 96888129-96888151 2800
TGCCTACTGAGCTGATATCAGT Yes Yes Yes Yes Yes hsa-mir-582-5p chr5:
59035248-59035271 2801 AGTAACTGGTTGAACAACTGTAA Yes Yes Yes No No
hsa-mir-668 chr14: 100591389-100591412 2802 TGTCACTCGGCTCGGCCCACTAC
Yes Yes No Yes Yes hsa-mir-516a-5p chr19: 58951821-58951844 2803
TTCTCGAGGAAAGAAGCACTTTC Yes No No No No hsa-mir-516a-5p chr19:
58956213-58956236 2804 TTCTCGAGGAAAGAAGCACTTTC Yes No No No No
hsa-mir-30a* chr6: 72169977-72169999 2805 GCTGCAAACATCCGACTGAAAG
Yes Yes Yes Yes Yes hsa-mir-183 chr7: 129202042-129202064 2806
AGTGAATTCTACCAGTGCCATA Yes Yes Yes Yes Yes
hsa-mir-186 chr1: 71305951-71305973 2807 AGCCCAAAAGGAGAATTCTTTG Yes
Yes Yes Yes Yes hsa-mir-187 chr18: 31738795-31738817 2808
CCGGCTGCAACACAAGACACGA No Yes Yes Yes Yes hsa-mir-184 chr15:
77289236-77289258 2809 TGGACGGAGAACTGATAAGGGT Yes Yes Yes Yes Yes
hsa-mir-185 chr22: 18400675-18400697 2810 TGGAGAGAAAGGCAGTTCCTGA
Yes Yes Yes Yes Yes hsa-mir-198 chr3: 121597239-121597261 2811
GAACCTATCTCCCCTCTGGACC Yes No No No No hsa-let-7b chr22:
44888234-44888256 2812 TGAGGTAGTAGGTTGTGTGGTT Yes Yes Yes Yes Yes
hsa-mir-455-5p chr9: 116011549-116011571 2813
TATGTGCCTTTGGACTACATCG Yes Yes Yes Yes Yes hsa-mir-518c chr19:
58903861-58903884 2814 CAAAGCGCTTCTCTTTAGAGTGT Yes No No No No
hsa-mir-770-5p chr14: 100388498-100388521 2815
TCCAGTACCACGTGTCAGGGCCA Yes Yes No No No hsa-mir-380 chr14:
100561145-100561167 2816 TATGTAATATGGTCCACATCTT Yes No No No No
hsa-mir-381 chr14: 100582057-100582079 2817 TATACAAGGGCAAGCTCTCTGT
Yes Yes Yes Yes Yes hsa-mir-382 chr14: 100590405-100590427 2818
GAAGTTGTTCGTGGTGGATTCG Yes Yes Yes Yes Yes hsa-mir-383 chr8:
14755362-14755384 2819 AGCCACAATCACCTTCTGATCT Yes Yes Yes No No
hsa-mir-384 chrX: 76056103-76056123 2820 TATGAACAATTTCTAGGAAT No
Yes No No No hsa-mir-661 chr8: 145091361-145091385 2821
ACGCGCAGGCCAGAGACCCAGGCA No No No No No hsa-mir-421 chrX:
73354951-73354974 2822 GCGCCCAATTAATGTCTGTTGAT Yes Yes Yes Yes Yes
hsa-mir-518f chr19: 58895132-58895153 2823 GAAAGCGCTTCTCTTTAGAGG
Yes No No No No hsa-mir-660 chrX: 49664603-49664625 2824
TACCCATTGCATATCGGAGTTG Yes Yes Yes No No hsa-mir-425 chr3:
49032635-49032658 2825 TCAACGGGAGTGATCGTGTCATT Yes Yes Yes Yes Yes
hsa-mir-424 chrX: 133508376-133508397 2826 TTCAAAACATGAATTGCTGCTG
Yes Yes Yes No No hsa-mir-518c* chr19: 58903823-58903646 2827
TCTCTGGAGGGAAGCACTTTCTG Yes No No No No hsa-mir-543 chr14:
100568122-100568144 2828 AAACATTCGCGGTGCACTTCTT Yes Yes Yes Yes Yes
hsa-mir-18a chr13: 90801010-90801033 2829 TAAGGTGCATCTAGTGCAGATAG
Yes No Yes Yes Yes hsa-mir-138-1* chr3: 44130769-44130791 2830
GCTACTTCACAACACCAGGGCC No No No Yes No hsa-let-7e* chr19:
56887902-56887924 2831 CTATACGGCCTCCTAGCTTTCC Yes Yes Yes Yes Yes
hsa-mir-545 chrX: 73423685-73423707 2832 GCACACAATAAATGTTTGCTGA Yes
Yes No No No hsa-mir-549 chr15: 78921388-78921409 2833
AGAGCTCATCCATAGTTGTCA Yes Yes No No No hsa-mir-549 chr15:
78921423-78921444 2834 TGACAACTATGGATGAGCTCT Yes Yes No No No
hsa-mir-133a chr20: 60572621-60572643 2835 TTTGGTCCCCTTCAACCAGCTG
Yes Yes Yes Yes Yes hsa-mir-133a chr18: 17659670-17659692 2836
CAGCTGGTTGAAGGGGACCAAA Yes Yes Yes Yes Yes hsa-mir-574-3p chr4:
38546107-38546129 2837 CACGCTCATGCACACACCCACA No No Yes Yes No
hsa-mir-133b chr6: 52121744-52121766 2838 TTTGGTCCCCTTCAACCAGCTA
Yes Yes Yes Yes Yes hsa-mir-1237 chr11: 63892730-63892751 2839
TCCTTCTGCTCCGTCCCCCAG Yes No No No No hsa-mir-220c chr19:
53755391-53755413 2840 AGTCTTCACAACAGCCCTGTGT No No No No No
hsa-mir-369-3p chr14: 100601730-100601751 2841
AATAATACATGGTTGATCTTT Yes Yes No Yes Yes hsa-mir-518e chr19:
58924956-58924977 2842 AAAGCGCTTCCCTTCAGAGTG Yes No No No No
hsa-mir-519e* chr19: 58875018-58875040 2843 TTCTCCAAAAGGGAGCACTTTC
Yes No No No No hsa-mir-15a chr13: 49521303-49521325 2844
CACAAACCATTATGTGCTGCTA Yes Yes Yes Yes No hsa-mir-769-5p chr19:
51214058-51214080 2845 TGAGACCTCTGGGTTCTGAGCT No No No No No
hsa-mir-15b chr3: 161605088-161605110 2846 TAGCAGCACATCATGGTTTACA
Yes Yes Yes Yes Yes hsa-mir-453 chr14: 100592322-100592345 2847
AGGTTGTCCGTGGTGAGTTCGCA Yes Yes Yes No No hsa-mir-876-5p chr9:
28853672-28853694 2848 TGGTGATTCACAAAGAAATCCA Yes Yes Yes No No
hsa-mir-1226 chr3: 47866101-47866123 2849 TCACCAGCCCTGTGTTCCCTAG
Yes Yes No No No hsa-mir-802 chr21: 36014899-36014922 2850
CAGTAACAAAGATTCATCCTTGT Yes Yes Yes Yes Yes hsa-mir-520a-5p chr19:
58885960-58885981 2851 CTCCAGAGGGAAGTACTTTCT Yes No No No No
hsa-mir-552 chr1: 34907801-34907822 2852 TTGTCTAACCAGTCACCTGTT Yes
No No No No hsa-mir-147b chr15: 43512587-43512609 2853
GTGTGCGGAAATGCTTCTGCTA Yes No Yes Yes Yes hsa-mir-432* chr14:
100420633-100420654 2854 CTGGATGGCTCCTCCATGTCT Yes Yes Yes No No
hsa-mir-650 chr22: 21495284-21495305 2855 AGGAGGCAGCGCTCTCAGGAC Yes
Yes No No No hsa-mir-146a* chr5: 159844992-159845014 2856
CCTCTGAAATTCAGTTCTTCAG No No No No No hsa-mir-335 chr7:
129923202-129923225 2857 TCAAGAGCAATAACGAAAAATGT Yes Yes Yes Yes No
hsa-mir-520d-3p chr19: 58915214-58915236 2858
AAAGTGCTTCTCTTTGGTGGGT Yes No No No No hsa-mir-19b-1* chr13:
90801461-90801484 2859 AGTTTTGCAGGTTTGCATCCAGC Yes No Yes Yes Yes
hsa-mir-1231 chr1: 200044365-200044386 2860 GTGTCTGGGCGGACAGCTGC No
No No No No hsa-mir-146b-3p chr10: 104186302-104186324 2861
TGCCCTGTGGACTCAGTTCTGG Yes No No No No hsa-mir-875-5p chr8:
100618233-100618255 2862 CACCTGATAAAACTGAGGTATA Yes Yes Yes Yes Yes
hsa-mir-874 chr5: 137011169-137011191 2863 TCGGTCCCTCGGGCCAGGGCAG
Yes Yes Yes Yes Yes hsa-mir-873 chr9: 28878922-28878943 2864
AGGAGACTCACAAGTTCCTGC Yes Yes Yes Yes Yes hsa-mir-15b* chr3:
161605126-161605148 2865 CGAATCATTATTTGCTGCTCTA Yes Yes Yes Yes Yes
hsa-mir-25* chr7: 99529168-99529189 2866 CAATTGCCCAAGTCTCCGCCT Yes
Yes Yes Yes No hsa-mir-1185 chr14: 100579080-100579101 2867
AGAGGATACCCTTTGTATGTT Yes Yes Yes No No hsa-mir-1185 chr14:
100580301-100580322 2868 AGAGGATACCCTTTGTATGTT Yes Yes Yes No No
hsa-mir-720 chr3: 165541848-165541865 2869 TCTCGCTGGGGCCTCCA Yes No
No No No hsa-mir-409-3p chr14: 100601435-100601457 2870
GAATGTTGCTCGGTGAACCCCT Yes Yes No Yes Yes hsa-mir-1182 chr1:
229222209-229222232 2871 GTCACATCCCTCCCAAGACCCTC Yes Yes No No No
hsa-mir-1179 chr15: 86952355-86952376 2872 AAGCATTCTTTCATTGGTTGG
Yes Yes No No No hsa-mir-1178 chr12: 118635836-118635857 2873
CTAGGGAAGAACAGTGAGCAA Yes Yes No No No hsa-mir-367* chr4:
113788519-113788541 2874 AGAGTTGCATATTAGCAACAGT Yes Yes Yes No No
hsa-mir-150 chr19: 54695900-54695922 2875 CACTGGTACAAGGGTTGGGAGA
Yes Yes Yes Yes Yes hsa-mir-153 chr7: 157059801-157059823 2876
GATCACTTTTGTGACTATGCAA Yes Yes Yes Yes Yes hsa-mir-153 chr2:
219867091-219867113 2877 GATCACTTTTGTGACTATGCAA No Yes No No No
hsa-mir-152 chr17: 43469538-43469559 2878 CCAAGTTCTGTCATGCACTGA Yes
Yes Yes Yes Yes hsa-mir-155 chr21: 25868165-25868188 2879
TTAATGCTAATCGTGATAGGGGT Yes Yes Yes No No hsa-mir-154 chr14:
100595858-100595880 2880 TAGGTTATCCGTGTTGCCTTCG Yes Yes No Yes Yes
hsa-mir-634 chr17: 62213711-62213733 2881 AACCAGCACCCCAACTTTGGAC
Yes No No No No hsa-mir-377* chr14: 100598145-100598167 2882
AGAGGTTGCCCTTGGTGAATTC Yes Yes Yes Yes Yes hsa-mir-1228 chr12:
55874604-55874624 2883 TCACACCTGCCTCGCCCCCC No Yes No No No
hsa-mir-199a-5p chr1: 170380354-170380377 2884
GAACAGGTAGTCTGAACACTGGG Yes Yes Yes Yes Yes hsa-mir-199a-5p chr19:
10789144-10789167 2885 GAACAGGTAGTCTGAACACTGGG Yes Yes Yes Yes No
hsa-mir-767-5p chrX: 151312608-151312631 2886
CATGCTCAGACAACCATGGTGCA No Yes No No No hsa-mir-151-3p chr8:
141811867-141811888 2887 CCTCAAGGAGCTTCAGTCTAG Yes Yes No No No
hsa-mir-154* chr14: 100595894-100595916 2888 AATCATACACGGTTGACCTATT
Yes Yes No Yes Yes hsa-mir-483-5p chr11: 2111986-2112008 2889
CTCCCTTCTTTCCTCCCGTCTT No No No No No hsa-mir-33a chr22:
40626898-40626919 2890 GTGCATTGTAGTTGCATTGCA Yes No Yes Yes Yes
hsa-mir-33b chr17: 17657935-17657955 2891 GCAATGCAACAGCAATGCAC Yes
Yes Yes No No hsa-mir-1304 chr11: 93106537-93106559 2892
CACATCTCACTGTAGCCTCAAA No Yes No No No hsa-mir-25 chr7:
99529129-99529151 2893 TCAGACCGAGACAAGTGCAATG No Yes Yes Yes Yes
hsa-mir-1306 chr22: 18453634-18453652 2894 ACGTTGGCTCTGGTGGTG Yes
Yes Yes Yes Yes hsa-mir-1307 chr10: 105144047-105144069 2895
CACGACCGACGCCACGCCGAGT Yes Yes Yes No No hsa-mir-1300 chr15:
51017866-51017884 2896 CAGCAGCCTCCTTCTCAA Yes No Yes Yes No
hsa-mir-21 chr17: 55273415-55273437 2897 TAGCTTATCAGACTGATGTTGA Yes
Yes Yes Yes Yes hsa-mir-22 chr17: 1563957-1563979 2898
ACAGTTCTTCAACTGGCAGCTT Yes No Yes Yes Yes hsa-mir-596 chr8:
1752818-1752839 2899 AAGCCTGCCCGGCTCCTCGGG No No No No No
hsa-mir-599 chr8: 100618054-100618074 2900 GTTTGATAAACTGACACAAC Yes
Yes Yes No No hsa-mir-598 chr8: 10930140-10930162 2901
TGACGATGACAACGATGACGTA Yes No No No No hsa-mir-610 chr11:
28034990-28035011 2902 TCCCAGCACACATTTAGCTCA Yes No No No No
hsa-mir-610 chr11: 28034952-28034973 2903 TGAGCTAAATGTGTGCTGGGA Yes
No No No No hsa-mir-611 chr11: 61316547-61316570 2904
GTCAGACCCCGAGGGGTCCTCGC No Yes No No No hsa-mir-616 chr12:
56199232-56199254 2905 CTGCTCAAACCCTCCAATGACT Yes No No No No
hsa-mir-617 chr12: 79750502-79750524 2906 GCCACCTTCAAATGGGAAGTCT
Yes No No No No hsa-mir-614 chr12: 12960082-12960105 2907
GAACGCCTGTTCTTGCCAGGTGG Yes No No No No hsa-mir-517c chr19:
58936434-58936456 2908 ATCGTGCATCCTTTTAGAGTGT No No No No No
hsa-mir-517b chr19: 58916184-58916206 2909 TCGTGCATCCCTTTAGAGTGTT
Yes No No No No hsa-mir-517a chr19: 58907386-58907408 2910
ATCGTGCATCCCTTTAGAGTGT Yes No No No No hsa-mir-495 chr14:
100569893-100569915 2911 AAACAAACATGGTGCACTTCTT Yes Yes Yes Yes Yes
hsa-mir-671-3p chr7: 150566506-150566527 2912 TCCGGTTCTCAGGGCTCCACC
Yes Yes Yes Yes Yes hsa-mir-135a* chr3: 52303287-52303309 2913
CGCCACGGCTCCAATCCCTATA Yes Yes Yes Yes No hsa-mir-513a-3p chrX:
146102707-146102730 2914 CCTTCTCAGAAAGGTGAAATTTA No No No No No
hsa-mir-513a-3p chrX: 146115069-146115092 2915
CCTTCTCAGAAAGGTGAAATTTA Yes No No No No hsa-mir-525-5p chr19:
58892612-58892633 2916 CTCCAGAGGGATGCACTTTCT Yes Yes No No No
hsa-mir-758 chr14: 100562160-100562182 2917 TTTGTGACCTGGTCCACTAACC
Yes No Yes Yes Yes hsa-mir-187* chr18: 31738831-31738853 2918
GCCCGGGTCCTGTGTTGTAGCC No No No Yes Yes hsa-mir-520d-5p chr19:
58915176-58915196 2919 CTACAAAGGGAAGCCCTTTC Yes Yes No No No
hsa-mir-522* chr19: 58946291-58946313 2920 CTCTAGAGGGAAGCGCTTTCTG
Yes No No No No hsa-mir-101 chr9: 4840344-4840365 2921
TACAGTACTGTGATAACTGAA Yes Yes Yes No No hsa-mir-101 chr1:
65296712-65296733 2922 TTCAGTTATCACAGTACTGTA Yes Yes Yes Yes Yes
hsa-mir-299-3p chr14: 100559921-100559943 2923
TATGTGGGATGGTAAACCGCTT No No No No No hsa-mir-107 chr10:
91342492-91342515 2924 TGATAGCCCTGTACAATGCTGCT Yes Yes Yes Yes Yes
hsa-mir-1278 chr1: 191372304-191372326 2925 TAGTACTGTGCATATCATCTAT
No No No No No hsa-mir-1279 chr12: 67953234-67953251 2926
AGAAAGAAGCAATATGA No No Yes Yes No hsa-mir-219-1-3p chr6:
33283650-33283672 2927 AGAGTTGAGTCTGGACGTCCCG Yes Yes Yes No No
hsa-mir-541 chr14: 100600637-100600659 2928 TGGTGGGCACAGAATCTGGACT
No No No No No hsa-mir-1270 chr19: 20371127-20371150 2929
ACACAGCTCTTCCATATCTCCAG No No No No No hsa-mir-1271 chr5:
175727568-175727590 2930 CTTGGCACCTAGCAAGCACTCA Yes Yes No No No
hsa-mir-1272 chr15: 62841722-62841748 2931
TTTCAGAATTTGCTGCCATCATCATC Yes No No No No hsa-mir-1273 chr8:
101105388-101105413 2932 AAGAAAGAGTCTTGCTTTGTCGCCC Yes No No No No
hsa-mir-1275 chr6: 34075772-34075789 2933 GACAGCCTCTCCCCCAC Yes No
No No No hsa-mir-1276 chr15: 84114782-84114802 2934
TGTCTCCACAGGGCTCTTTA Yes No No No No hsa-mir-1277 chrX:
117404430-117404452 2935 TACGTAGATATATATGTATTTT No Yes Yes No No
hsa-mir-488* chr1: 175265170-175265191 2936 TTGAGAGTGCCATTATCTGGG
Yes Yes Yes No Yes hsa-mir-219-2-3p chr9: 130194731-130194753 2937
ACAGATGTCCAGCCACAATTCT Yes Yes Yes Yes Yes hsa-mir-142-5p chr17:
53763642-53763663 2938 AGTAGTGCTTTCTACTTTATG Yes Yes Yes Yes Yes
hsa-mir-615-3p chr12: 52714060-52714082 2939 TCCGAGCCTGGGTCTCCCTCTT
Yes Yes No Yes Yes hsa-mir-130b chr22: 20337642-20337664 2940
CAGTGCAATGATGAAAGGGCAT Yes Yes Yes Yes Yes hsa-mir-506 chrX:
146119962-146119983 2941 TCTACTCAGAAGGGTGCCTTA Yes Yes No No No
hsa-mir-507 chrX: 146120211-146120232 2942 TTCACTCCAAAAGGTGCAAAA
Yes Yes No No No hsa-mir-504 chrX: 137577586-137577608 2943
GATAGAGTGCAGACCAGGGTCT Yes Yes Yes Yes No hsa-mir-885-5p chr3:
10411214-10411236 2944 AGAGGCAGGGTAGTGTAATGGA Yes Yes Yes No No
hsa-mir-944 chr3: 191030457-191030479 2945 AAATTATTGTACATCGGATGAG
Yes No No No No hsa-mir-500 chrX: 49659790-49659813 2946
TAATCCTTGCTACCTGGGTGAGA Yes Yes Yes No No hsa-let-7d* chr9:
95980997-95981019 2947 CTATACGACCTGCTGCCTTTCT Yes Yes Yes Yes Yes
hsa-mir-545* chrX: 73423723-73423745 2948 TCATCTAATAAACATTTACTGA
Yes Yes No No No hsa-mir-942 chr1: 117438799-117438821 2949
TCTTCTCTGTTTTGGCCATGTG Yes No No No No hsa-mir-200a* chr1:
1093120-1093142 2950 CATCTTACCGGACAGTGCTGGA Yes Yes Yes Yes Yes
hsa-mir-130a* chr11: 57165266-57165288 2951 TTCACATTGTGCTACTGTCTGC
Yes Yes Yes No No hsa-mir-1266 chr15: 50356654-50356677 2952
AGCCCTGTTCTACAGCCCTGAGG Yes No No No No hsa-mir-548a-3p chr6:
18680053-18680075 2953 CAAAACTGGCAATTACTTTTGC Yes No No No No
hsa-mir-548a-3p chr6: 135602050-135602072 2954
CAAAACTGGCAATTACTTTTGC Yes No No No No hsa-mir-548a-3p chr8:
105565787-105565809 2955 GCAAAAGTAATTGCCAGTTTTG No No No No No
hsa-mir-557 chr1: 166611445-166611468 2956 GTTTGCACGGGTGGGCCTTGTCT
Yes No No No No hsa-mir-1238 chr19: 10523858-10523878 2957
CTTCCTCGTCTGTCTGCCCC No No No No No hsa-mir-920 chr12:
24256671-24256691 2958 GGGGAGCTGTGGAAGCAGTA Yes No No No No
hsa-mir-921 chr1: 164390633-164390658 2959
GAATCCTGGTTCTGTCCCTCACTAG No No No No No hsa-mir-922 chr3:
198885765-198885788 2960 GACGTAGTCCTATTCTCTGCTGC No No No No No
hsa-mir-923 chr17: 30502320-30502341 2961 AGTTTCTTTTCCTCCGCTGAC Yes
No No No No hsa-mir-924 chr18: 35456114-35456134 2962
GCAAGACATCACAAGACTCT Yes No No No No hsa-mir-193b* chr16:
14305337-14305359 2963 CGGGGTTTTGAGGGCGAGATGA Yes Yes Yes Yes No
hsa-mir-378 chr5: 149092622-149092643 2964 ACTGGACTTGGAGTCAGAAGG
Yes Yes Yes No No hsa-mir-320c chr18: 20155677-20155697 2965
AAAAGCTGGGTTGAGAGGGT Yes No No No No hsa-mir-320c chr18:
17517517-17517537 2966 AAAAGCTGGGTTGAGAGGGT Yes Yes No No No
hsa-mir-320b chr1: 222511373-222511395 2967 TTGCCCTCTCAACCCAGCTTTT
Yes Yes No No No hsa-mir-320b chr1: 117015931-117015953 2968
AAAAGCTGGGTTGAGAGGGCAA Yes Yes No No No hsa-mir-320a chr8:
22158432-22158454 2969 TCGCCCTCTCAACCCAGCTTTT Yes Yes Yes Yes Yes
hsa-mir-324-3p chr17: 7067350-7067370 2970 CCAGCAGCACCTGGGGCAGT Yes
Yes Yes Yes Yes hsa-mir-370 chr14: 100447275-100447297 2971
GCCTGCTGGGGTGGAACCTGGT Yes Yes Yes Yes Yes hsa-mir-431* chr14:
100417158-100417180 2972 CAGGTCGTCTTGCAGGGCTTCT Yes Yes Yes Yes Yes
hsa-mir-372 chr19: 58982996-58983019 2973 AAAGTGCTGCGACATTTGAGCGT
Yes Yes No No No hsa-mir-375 chr2: 219574613-219574635 2974
TCACGCGAGCCGAACGAACAAA Yes Yes
Yes Yes Yes hsa-mir-422a chr15: 61950240-61950262 2975
GCCTTCTGACCCTAAGTCCAGT Yes No No No No hsa-mir-377 chr14:
100598183-100598205 2976 ATCACACAAAGGCAACTTTTGT Yes Yes Yes Yes No
hsa-mir-362-3p chrX: 49660352-49660374 2977 AACACACCTATTCAAGGATTCA
Yes Yes Yes No No hsa-mir-579 chr5: 32430254-32430277 2978
AATCGCGGTTTATACCAAATGAA Yes No No No No hsa-mir-578 chr4:
166526903-166526924 2979 CTTCTTGTGCTCTAGGATTGT Yes No No No No
hsa-mir-24-2* chr19: 13808139-13808161 2980 CTGTGTTTCAGCTCAGTAGGCA
Yes Yes Yes No No hsa-mir-573 chr4: 24130972-24130996 2981
CTGATCAGTTACACATCACTTCAG No No No No No hsa-mir-572 chr4:
10979608-10979628 2982 GTCCGCTCGGCGGTGGCCCA Yes Yes No No No
hsa-mir-571 chr4: 334005-334026 2983 TGAGTTGGCCATCTGAGTGAG No No No
No No hsa-mir-570 chr3: 196911510-196911532 2984
CGAAAACAGCAATTACCTTTGC No No No No No hsa-mir-577 chr4:
115797378-115797399 2985 TAGATAAAATATTGGTACCTG Yes Yes No No No
hsa-mir-520c-3p chr19: 58902571-58902593 2986
AAAGTGCTTCCTTTTAGAGGGT Yes No No No No hsa-mir-509-3-5p chrX:
146148905-146148927 2987 CATGATTGCCACGTCTGCAGTA Yes No No No No
hsa-mir-23a* chr19: 13808443-13808465 2988 AAATCCCATCCCCAGGAACCCC
Yes Yes Yes Yes Yes hsa-mir-518f* chr19: 58895095-58895117 2989
CTCTAGAGGGAAGCACTTTCTC Yes No No No No hsa-mir-195* chr17:
6861670-6861692 2990 GGAGCAGCACAGCCAATATTGG Yes Yes No Yes Yes
hsa-mir-576-5p chr4: 110629317-110629339 2991
ATTCTAATTTCTCCACGTCTTT No No No No No hsa-mir-575 chr4:
83893528-83893547 2992 GCTCCTGTCCAACTGGCTC Yes No No No No
hsa-mir-21* chr17: 55273453-55273474 2993 CAACACCAGTCGATGGGCTGT Yes
Yes No No No hsa-mir-27b* chr9: 96887565-96887587 2994
AGAGCTTAGCTGATTGGTGAAC Yes Yes Yes Yes Yes hsa-mir-217 chr2:
56063658-56063681 2995 TCCAATCAGTTCCTGATGCAGTA Yes Yes Yes No No
hsa-mir-214 chr1: 170374578-170374600 2996 ACTGCCTGTCTGTGCCTGCTGT
Yes Yes Yes Yes Yes hsa-mir-215 chr1: 218357880-218357901 2997
GTCTGTCAATTCATAGGTCAT Yes Yes No No No hsa-mir-212 chr17:
1900333-1900354 2998 GGCCGTGACTGGAGACTGTTA No No Yes Yes Yes
hsa-mir-210 chr11: 558111-558133 2999 TCAGCCGCTGTCACACGCACAG Yes
Yes Yes Yes Yes hsa-mir-211 chr15: 29144589-29144611 3000
AGGCGAAGGATGACAAAGGGAA Yes No No No No hsa-mir-92a chrX:
133131239-133131261 3001 ACAGGCCGGGACAAGTGCAATA Yes Yes Yes No No
hsa-mir-92a chr13: 90801615-90801637 3002 TATTGCACTTGTCCCGGCCTGT
Yes Yes Yes Yes Yes hsa-mir-92b chr1: 153431651-153431673 3003
TATTGCACTCGTCCCGGCCTCC No Yes Yes Yes Yes hsa-mir-218 chr4:
20139019-20139040 3004 TTGTGCTTGATCTAACCATGT Yes Yes Yes Yes Yes
hsa-mir-218 chr5: 168127793-168127814 3005 ACATGGTTAGATCAAGCACAA
Yes Yes Yes Yes Yes hsa-mir-515-3p chr19: 58874118-58874140 3006
GAGTGCCTTCTTTTGGAGCGTT Yes No No No No hsa-mir-515-3p chr19:
58880124-58880146 3007 GAGTGCCTTCTTTTGGAGCGTT Yes No No No No
hsa-mir-1 chr18: 17662973-17662995 3008 ATACATACTTCTTTACATTCCA Yes
Yes Yes Yes No hsa-mir-1 chr20: 60562002-60562024 3009
TGGAATGTAAAGAAGTATGTAT Yes Yes Yes Yes No hsa-mir-425* chr3:
49032595-49032617 3010 GGGCGGACACGACATTCCCGAT Yes Yes Yes Yes No
hsa-mir-522 chr19: 58946329-58946351 3011 AAAATGGTTCCCTTTAGAGTGT
Yes Yes No No No hsa-mir-7 chr9: 85774546-85774569 3012
ACAACAAAATCACTAGTCTTCCA Yes Yes Yes Yes Yes hsa-mir-7 chr15:
86956090-86956113 3013 TGGAAGACTAGTGATTTTGTTGT Yes Yes Yes Yes Yes
hsa-mir-7 chr19: 4721711-4721734 3014 TGGAAGACTAGTGATTTTGTTGT Yes
Yes Yes No No hsa-mir-9 chr15: 87712266-87712289 3015
TCTTTGGTTATCTAGCTGTATGA No Yes Yes Yes Yes hsa-mir-9 chr1:
154656807-154656830 3016 TCATACAGCTAGATAACCAAAGA Yes Yes Yes Yes
Yes hsa-mir-9 chr5: 87998475-87998498 3017 TCATACAGCTAGATAACCAAAGA
Yes Yes Yes Yes Yes hsa-mir-615-5p chr12: 52714017-52714039 3018
GGGGGTCCCCGGTGCTCGGATC Yes Yes No Yes Yes hsa-mir-512-3p chr19:
58861794-58861816 3019 AAGTGCTGTCATAGCTGAGGTC Yes No No No No
hsa-mir-512-3p chr19: 58864278-58864300 3020 AAGTGCTGTCATAGCTGAGGTC
No No No No No hsa-mir-202* chr10: 134911066-134911088 3021
CAAAGAAGTATATGCATAGGAA Yes No Yes Yes Yes hsa-mir-888* chrX:
144884003-144884025 3022 TTCACCCAAAGAGGTGTCAGTC No No No No No
hsa-mir-143* chr5: 148788699-148788721 3023 GGTGCAGTGCTGCATCTCTGGT
Yes Yes Yes Yes Yes hsa-mir-526b chr19: 58889471-58889494 3024
CTCTTGAGGGAAGCACTTTCTGT Yes Yes No No No hsa-mir-656 chr14:
100602855-100602876 3025 AATATTATACAGTCAACCTCT Yes Yes Yes No No
hsa-mir-657 chr17: 76713685-76713708 3026 CCTAGAGAGGGTGAGAACCTGCC
Yes No No No No hsa-mir-655 chr14: 100585699-100585721 3027
ATAATACATGGTTAACCTCTTT Yes No Yes No No hsa-mir-652 chrX:
109185272-109185293 3028 AATGGCGCCACTAGGGTTGTG Yes Yes No No No
hsa-mir-653 chr7: 92950070-92950091 3029 CAGTAGAGATTGTTTCAACAC Yes
Yes No Yes No hsa-mir-518a-3p chr19: 58926121-58926143 3030
GAAAGCGCTTCCCTTTGCTGGA No No No No No hsa-mir-518a-3p chr19:
58934450-58934472 3031 GAAAGCGCTTCCCTTTGCTGGA Yes No No No No
hsa-mir-651 chrX: 8055020-8055042 3032 TTTAGGATAAGCTTGACTTTTG No No
No No No hsa-mir-302f chr18: 26132899-26132916 3033
TAATTGCTTCCATGTTT Yes Yes No No No hsa-mir-1184 chrX:
154265958-154265981 3034 GGAAGCCATCAAGTCGCTGCAGG Yes Yes No No No
hsa-mir-1184 chrX: 154340431-154340454 3035 CCTGCAGCGACTTGATGGCTTCC
Yes Yes No No No hsa-mir-1184 chrX: 153768844-153768867 3036
GGAAGCCATCAAGTCGCTGCAGG Yes Yes No No No hsa-mir-302d chr4:
113788610-113788633 3037 ACACTCAAACATGGAAGCACTTA Yes Yes No Yes No
hsa-mir-302c chr4: 113788970-113788993 3038 CCACTGAAACATGGAAGCACTTA
Yes Yes Yes No No hsa-mir-302b chr4: 113789093-113789116 3039
CTACTAAAACATGGAAGCACTTA Yes Yes Yes Yes No hsa-mir-1180 chr17:
19188418-19188440 3040 ACACACCCACGCGAGCCGGAAA Yes Yes No No No
hsa-mir-1181 chr19: 10375180-10375201 3041 CGGCTCGGGTGGCGGCGACGG
Yes No No No No hsa-mir-629* chr15: 68158779-68158801 3042
GCTGGGCTTACGTTGGGAGAAC No No No No No hsa-mir-302e chr11:
7212577-7212594 3043 TAAGTGCTTCCATGCTT Yes Yes No No No hsa-mir-103
chr5: 167920486-167920509 3044 TCATAGCCCTGTACAATGCTGCT Yes Yes Yes
Yes Yes hsa-mir-103 chr20: 3846187-3846210 3045
AGCAGCATTGTACAGGGCTATGA Yes Yes Yes Yes Yes hsa-mir-100 chr11:
121528192-121528214 3046 CACAAGTTCGGATCTACGGGTT Yes Yes No Yes Yes
hsa-mir-138-2* chr16: 55449986-55450008 3047 GCTATTTCACGACACCAGGGTT
Yes Yes Yes Yes Yes hsa-mir-122* chr18: 54269335-54269357 3048
AACGCCATTATCACACTAAATA Yes Yes Yes Yes No hsa-mir-105 chrX:
151311392-151311415 3049 ACCACAGGAGTCTGAGCATTTGA Yes Yes Yes No No
hsa-mir-105 chrX: 151313585-151313608 3050 ACCACAGGAGTCTGAGCATTTGA
Yes Yes No No No hsa-mir-223* chrX: 65155461-65155483 3051
CGTGTATTTGACAAGCTGAGTT Yes Yes Yes Yes Yes hsa-mir-363* chrX:
133131120-133131142 3052 AAATTGCATCGTGATCCACCCG No Yes Yes No Yes
hsa-mir-28-5p chr3: 189889275-189889297 3053 AAGGAGCTCACAGTCTATTGAG
Yes Yes Yes Yes Yes hsa-mir-150* chr19: 54695865-54695887 3054
CTGTCCCCCAGGCCTGTACCAG Yes Yes No No Yes hsa-mir-99a* chr21:
16833328-16833350 3055 CAAGCTCGCTTCTATGGGTCTG Yes Yes Yes No No
hsa-mir-1825 chr20: 30289293-30289311 3056 TCCAGTGCCCTCCTCTCC Yes
Yes No No No hsa-mir-129* chr7: 127635208-127635230 3057
AAGCCCTTACCCCAAAAAGTAT Yes Yes Yes Yes Yes hsa-mir-556-3p chr1:
160579013-160579035 3058 ATATTACCATTAGCTCATCTTT Yes
No No No No hsa-mir-10b chr2: 176723302-176723325 3059
TACCCTGTAGAACCGAATTTGTG Yes Yes Yes Yes Yes hsa-mir-1827 chr12:
99107840-99107858 3060 TGAGGCAGTAGATTGAAT Yes Yes No No No
hsa-mir-10a chr17: 44012264-44012287 3061 CACAAATTCGGATCTACAGGGTA
Yes Yes Yes Yes Yes hsa-mir-623 chr13: 98806400-98806423 3062
ATCCCTTGCAGGGGCTGTTGGGT No No No No No hsa-mir-622 chr13:
89681496-89681517 3063 ACAGTCTGCTGAGGTTGGAGC Yes No No No No
hsa-mir-621 chr13: 40282961-40282982 3064 GGCTAGCAACAGCGCTTACCT Yes
No No No No hsa-mir-620 chr12: 115070762-115070782 3065
ATTTCTATATCTATCTCCAT No No No No No hsa-mir-127-5p chr14:
100419090-100419112 3066 CTGAAGCTCAGAGGGCTCTGAT Yes Yes Yes Yes Yes
hsa-mir-626 chr15: 39771134-39771153 3067 AGCTGTCTGAAAATGTCTT Yes
No No No No hsa-mir-625 chr14: 65007622-65007643 3068
GGACTATAGAACTTTCCCCCT Yes No No No No hsa-mir-625 chr14:
65007586-65007607 3069 AGGGGGAAAGTTCTATAGTCC Yes No No No No
hsa-mir-182* chr7: 129197481-129197502 3070 TAGTTGGCAAGTCTAGAACCA
Yes Yes Yes Yes No hsa-mir-1292 chr20: 2581424-2581449 3071
TGGGAACGGGTTCCGGCAGACGCTG Yes No No No No hsa-mir-342-3p chr14:
99645804-99645827 3072 TCTCACACAGAAATCGCACCCGT Yes Yes Yes Yes Yes
hsa-mir-1290 chr1: 19096158-19096177 3073 TCCCTGATCCAAAAATCCA Yes
No No No No hsa-mir-1291 chr12: 47334543-47334567 3074
ACTGCTGGTCTTCAGTCAGGGCCA Yes No No No No hsa-mir-1296 chr10:
64802777-64802799 3075 GGAGATGGAGCCAGGGCCCTAA Yes Yes Yes No No
hsa-mir-1297 chr13: 53784116-53784133 3076 CACCTGAATTACTTGAA Yes
Yes Yes No No hsa-mir-1294 chr5: 153706905-153706927 3077
TGTGAGGTTGGCATTGTTGTCT Yes No No No No hsa-mir-1225-5p chr16:
2080264-2080286 3078 CCCCCCACTGGGCCGTACCCAC Yes Yes Yes Yes Yes
hsa-mir-509-5p chrX: 146148020-146148041 3079 TGATTGCCACTGTCTGCAGTA
Yes No No No No hsa-mir-509-5p chrX: 146149795-146149816 3080
TGATTGCCACTGTCTGCAGTA Yes No No No No hsa-mir-1224-3p chr3:
185441950-185441971 3081 CCCCACCTCCTCTCTCCTCAG Yes Yes Yes No No
hsa-mir-140-3p chr16: 68524545-68524566 3082 TACCACAGGGTAGAACCACGG
Yes Yes Yes Yes Yes hsa-mir-532-3p chrX: 49654549-49654571 3083
CCTCCCACACCCAAGGCTTGCA Yes Yes Yes Yes Yes hsa-mir-1298 chrX:
113855922-113855944 3084 TTCATTCGGCTGTCCAGATGTA Yes Yes Yes Yes Yes
hsa-mir-26b chr2: 218975623-218975644 3085 TTCAAGTAATTCAGGATAGGT
Yes Yes Yes Yes Yes hsa-let-7f-2* chrX: 53600881-53600903 3086
GGAAAGACAGTAGACTGTATAG Yes Yes Yes Yes Yes hsa-mir-585 chr5:
168623197-168623216 3087 TAGCATACAGATACGCCCA No No No No No
hsa-mir-490-5p chr7: 136238491-136238511 3088 CCATGGATCTCCAGGTGGGT
Yes Yes Yes Yes Yes hsa-mir-519c-3p chr19: 58881587-58881609 3089
AAAGTGCATCTTTTTAGAGGAT Yes No No No No hsa-mir-513a-5p chrX:
146115109-146115127 3090 ATGACACCTCCCTGTGAA Yes Yes No No No
hsa-mir-513a-5p chrX: 146102747-146102765 3091 ATGACACCTCCCTGTGAA
Yes Yes No No No hsa-mir-591 chr7: 95686969-95686989 3092
ACAATGAGAACCCATGGTCT Yes No No No No hsa-mir-191* chr3:
49033067-49033089 3093 GGGGACGAAATCCAAGCGCAGC Yes Yes No No No
hsa-mir-1305 chr4: 183327489-183327511 3094 TTTTCAACTCTAATGGGAGAGA
No No No No No hsa-mir-624 chr14: 30553625-30553646 3095
AGGTAATACCAATACCTTGTG Yes No No No No hsa-mir-593 chr7:
127509226-127509245 3096 TGTCTCTGCTGGGGTTTCT Yes Yes No No No
hsa-mir-302a chr4: 113788790-113788813 3097 TCACCAAAACATGGAAGCACTTA
Yes Yes No Yes No hsa-mir-592 chr7: 126485437-126485459 3098
ACATCATCGCATATTGACACAA Yes Yes Yes Yes Yes hsa-mir-1293 chr12:
48914231-48914253 3099 GCACAAATCTCCAGACCACCCA Yes No No No No
hsa-mir-30e* chr1: 40992671-40992693 3100 CTTTCAGTCGGATGTTTACAGC
Yes Yes Yes Yes Yes hsa-mir-432 chr14: 100420585-100420608 3101
TCTTGGAGTAGGTCATTGGGTGG Yes Yes Yes No No hsa-mir-629 chr15:
68158819-68158840 3102 AGTTCTCCCAACGTAAACCCA No No No No No
hsa-mir-96* chr7: 129201772-129201794 3103 CATATTGGCACTGCACATGATT
Yes Yes Yes No Yes hsa-mir-1301 chr2: 25405023-25405047 3104
GAAGTCACTCCCAGGCAGCTGCAA No No Yes No No hsa-mir-200b* chr1:
1092366-1092388 3105 CATCTTACTGGGCAGCATTGGA No No Yes Yes Yes
hsa-mir-181c* chr19: 13846576-13846598 3106 AACCATCGACCGTTGAGTGGAC
Yes Yes Yes Yes Yes hsa-mir-508-3p chrX: 146126154-146126177 3107
TCTACTCCAAAAGGCTACAATCA No No No No No hsa-mir-1303 chr5:
154045579-154045601 3108 TTTAGAGACGGGGTCTTGCTCT Yes No No No No
hsa-mir-539 chr14: 100583418-100583440 3109 GGAGAAATTATCCTTGGTGTGT
Yes Yes Yes Yes Yes hsa-mir-10b* chr2: 176723341-176723363 3110
ACAGATTCGATTCTAGGGGAAT Yes Yes Yes Yes Yes hsa-mir-612 chr11:
64968519-64968544 3111 GCTGGGCAGGGCTTCTGAGCTCCTT Yes No No No No
hsa-mir-613 chr12: 12808909-12808929 3112 AGGAATGTTCCTTCTTTGCC Yes
No No No No hsa-mir-1295 chr1: 169337502-169337523 3113
TCACCCAGATCTGCGGCCTAA Yes No No No No hsa-mir-196a chr17:
44064892-44064914 3114 CCCAACAACATGAAACTACCTA Yes Yes Yes Yes No
hsa-mir-196a chr12: 52671812-52671834 3115 TAGGTAGTTTCATGTTGTTGGG
Yes Yes Yes Yes Yes hsa-mir-196b chr7: 27175671-27175693 3116
CCCAACAACAGGAAACTACCTA Yes Yes Yes Yes Yes hsa-mir-296-3p chr20:
56826075-56826097 3117 GGAGAGCCTCCACCCAACCCTC Yes Yes No Yes Yes
hsa-mir-518d-3p chr19: 58929994-58930015 3118 CAAAGCGCTTCCCTTTGGAGC
Yes No No No No hsa-mir-1308 chrX: 21990211-21990229 3119
CCACTGAACCACCCATGC No No No No No hsa-mir-92a-2* chrX:
133131278-133131300 3120 GTAATGCAACAAATCCCCACCC Yes Yes No No No
hsa-mir-658 chr22: 36570239-36570264 3121 ACCAACGGACCTACTTCCCTCCGCC
No No No No No hsa-mir-106b* chr7: 99529560-99529582 3122
GCAGCAAGTACCCACAGTGCGG Yes Yes Yes Yes Yes hsa-mir-374a* chrX:
73423854-73423876 3123 AATTACAATACAATCTGATAAG Yes Yes No No No
hsa-mir-595 chr7: 158018185-158018206 3124 AGACACACCACGGCACACTTC
Yes No No No No hsa-mir-518d-5p chr19: 58929957-58929979 3125
CTCTAGAGGGAAGCACTTTCTG Yes No No No No hsa-mir-590-5p chr7:
73243478-73243500 3126 GAGCTTATTCATAAAAGTGCAG Yes Yes No No No
hsa-mir-448 chrX: 113964342-113964364 3127 TTGCATATGTAGGATGTCCCAT
Yes Yes Yes Yes Yes hsa-mir-326 chr11: 74723799-74723819 3128
CTGGAGGAAGGGCCCAGAGG Yes No Yes Yes Yes hsa-mir-325 chrX:
76142279-76142302 3129 ACACTTACTGGACACCTACTAGG No Yes No No No
hsa-mir-632 chr17: 27701300-27701319 3130 GTGTCTGCTTCCTGTGGGA Yes
Yes No No No hsa-mir-328 chr16: 65793730-65793752 3131
ACGGAAGGGCAGAGAGGGCCAG Yes No Yes Yes Yes hsa-mir-329 chr14:
100563240-100563262 3132 AACACACCTGGTTAACCTCTTT Yes Yes No No No
hsa-mir-329 chr14: 100562923-100562945 3133 AACACACCTGGTTAACCTCTTT
Yes Yes Yes No No hsa-mir-659 chr22: 36573645-36573667 3134
TGGGGACCCTCCCTGAACCAAG No No No No No hsa-mir-214* chr1:
170374619-170374641 3135 GCACAGCAAGTGTAGACAGGCA Yes Yes Yes Yes Yes
hsa-mir-483-3p chr11: 2111947-2111968 3136 AAGACGGGAGGAGAGGAGTGA No
No No No No hsa-mir-376a* chr14: 100576877-100576899 3137
GTAGATTCTCCTTCTATGAGTA Yes Yes Yes Yes Yes hsa-mir-218-1* chr4:
20139062-20139084 3138 ATGGTTCCGTCAAGCACCATGG Yes Yes Yes Yes Yes
hsa-mir-302d* chr4: 113788649-113788671 3139 GCAAGTGCCTCCATGTTAAAGT
Yes Yes Yes Yes No hsa-mir-887 chr5: 15988337-15988359 3140
GTGAACGGGCGCCATCCCGAGG No Yes No No No hsa-mir-380* chr14:
100561110-100561132 3141 TGGTTGACCATAGAACATGCGC Yes Yes Yes Yes
Yes
hsa-mir-32* chr9: 110848331-110848353 3142 AAATATCACACACACTAAATTG
Yes Yes Yes Yes No hsa-mir-889 chr14: 100584038-100584059 3143
TTAATATCGGACAACCATTGT Yes Yes Yes No No hsa-mir-768-5p chr16:
70349860-70349886 3144 ATCACTCCGTACTTTCATCCTCCAAC Yes Yes No No No
hsa-mir-501-3p chrX: 49661119-49661141 3145 AATGCACCCGGGCAAGGATTCT
Yes No No No No hsa-mir-485-3p chr14: 100591553-100591575 3146
GTCATACACGGCTCTCCTCTCT Yes Yes Yes Yes Yes hsa-mir-1234 chr8:
145596285-145596307 3147 GTGGGGTGGGTGGTCAGGCCGA Yes Yes No No No
hsa-mir-22* chr17: 1563995-1564017 3148 TAAAGCTTGCCACTGAAGAACT Yes
No Yes Yes Yes hsa-mir-125a-5p chr19: 56888332-56888356 3149
TCCCTGAGACCCTTTAACCTGTGA Yes Yes Yes Yes Yes hsa-mir-643 chr19:
57476921-57476943 3150 ACTTGTATGCTAGCTCAGGTAG Yes No No No No
hsa-mir-147 chr9: 122047083-122047103 3151 GCAGAAGCATTTCCACACAC Yes
Yes No No No hsa-mir-144 chr17: 24212691-24212711 3152
AGTACATCATCTATACTGTA Yes Yes Yes Yes Yes hsa-mir-145 chr5:
148790416-148790439 3153 GTCCAGTTTTCCCAGGAATCCCT Yes Yes Yes Yes
Yes hsa-mir-143 chr5: 148788733-148788754 3154
TGAGATGAAGCACTGTAGCTC Yes Yes Yes Yes Yes hsa-mir-597 chr8:
9636606-9636628 3155 TGTGTCACTCGATGACCACTGT Yes No No No No
hsa-mir-141 chr12: 6943578-6943600 3156 TAACACTGTCTGGTAAAGATGG Yes
Yes Yes Yes Yes hsa-mir-512-5p chr19: 58864241-58864264 3157
CACTCAGCCTTGAGGGCACTTTC Yes No No No No hsa-mir-512-5p chr19:
58861757-58861780 3158 CACTCAGCCTTGAGGGCACTTTC Yes No No No No
hsa-mir-323-5p chr14: 100561836-100561858 3159
AGGTGGTCCGTGGCGCGTTCGC Yes Yes Yes Yes Yes hsa-mir-224 chrX:
150877758-150877779 3160 AACGGAACCACTAGTGACTTG Yes Yes Yes No Yes
hsa-mir-223 chrX: 65155503-65155525 3161 TGTCAGTTTGTCAAATACCCCA Yes
Yes Yes Yes Yes hsa-mir-222 chrX: 45491385-45491406 3162
ACCCAGTAGCCAGATGTAGCT No Yes Yes Yes Yes hsa-mir-221 chrX:
45490551-45490574 3163 GAAACCCAGCAGACAATGTAGCT Yes Yes Yes Yes Yes
hsa-mir-149 chr2: 241044104-241044127 3164 TCTGGCTCCGTGTCTTCACTCCC
Yes Yes Yes Yes No hsa-mir-520a-3p chr19: 58885998-58886020 3165
AAAGTGCTTCCCTTTGGACTGT Yes Yes No No No hsa-mir-548c-5p chr12:
63302579-63302601 3166 AAAAGTAATTGCGGTTTTTGCC Yes No No No No
hsa-mir-374b chrX: 73355146-73355168 3167 CACTTAGCAGGTTGTATTATAT
Yes Yes Yes Yes Yes hsa-mir-26a chr12: 56504707-56504729 3168
AGCCTATCCTGGATTACTTGAA Yes Yes Yes Yes No hsa-mir-26a chr3:
37985907-37985929 3169 TTCAAGTAATCCAGGATAGGCT Yes Yes Yes Yes Yes
hsa-mir-374a chrX: 73423884-73423906 3170 CACTTATCAGGTTGTATTATAA
Yes Yes Yes No No hsa-mir-1302 chr9: 99165698-99165719 3171
TTTAGCATAAGTATGTCCCAA Yes Yes No No No hsa-mir-1302 chr15:
100318229-100318250 3172 TTTAGCATAAGTATGTCCCAA Yes Yes No No No
hsa-mir-1302 chr12: 111617269-111617290 3173 TTTAGCATAAGTATGTCCCAA
Yes No No No No hsa-mir-1302 chr8: 142665522-142865543 3174
TTTAGCATAAGTATGTCCCAA Yes Yes No No No hsa-mir-1302 chr2:
114057050-114057071 3175 TTTAGCATAAGTATGTCCCAA Yes Yes No No No
hsa-mir-1302 chr1: 20300-20321 3176 TTGGGACATACTTATGCTAAA Yes Yes
No No No hsa-mir-1302 chr7: 18133381-18133402 3177
TTTAGCATAAGTATGTCCCAA Yes No No No No hsa-mir-1302 chr19:
23044-23065 3178 TTGGGACATACTTATGCTAAA Yes Yes No No No
hsa-mir-1302 chr2: 207842296-207842317 3179 TTTAGCATAAGTATGTCCCAA
No Yes No No No hsa-mir-1302 chr9: 20215-20236 3180
TTGGGACATACTTATGCTAAA Yes Yes No No No hsa-mir-1302 chr20:
48664632-48664653 3181 TTTAGCATAAGTATGTCCCAA No No No No No
hsa-mir-624* chr14: 30553662-30553684 3182 TGAACACAAGGTACTGGTACTA
Yes No No No No hsa-mir-619 chr12: 107754827-107754851 3183
ACTGGGCACAAACATGTCCAGGTC Yes No No No No hsa-mir-586 chr6:
45273448-45273470 3184 GGACCTAAAAATACAATGCATA Yes No No No No
hsa-mir-587 chr6: 107338707-107338728 3185 TTTCCATAGGTGATGAGTCAC
Yes No No No No hsa-mir-584 chr5: 148422128-148422150 3186
CTCAGTCCCAGGCAAACCATAA Yes Yes No No No hsa-mir-30d* chr8:
135886303-135886325 3187 GCAGCAAACATCTGACTGAAAG Yes Yes Yes Yes Yes
hsa-mir-450a chrX: 133502088-133502110 3188 ATATTAGGAACACATCGCAAAA
Yes Yes Yes Yes No hsa-mir-450a chrX: 133502259-133502281 3189
ATATTAGGAACACATCGCAAAA Yes Yes Yes Yes Yes hsa-mir-583 chr5:
95440612-95440633 3190 CAAAGAGGAAGGTCCCATTAC Yes No No No No
hsa-mir-580 chr5: 36183765-36183787 3191 CCTAATGATTCATCATTCTCAA Yes
No No No No hsa-mir-581 chr5: 53283150-53283171 3192
ACTGATCTAGAGAACACAAGA Yes No No No No hsa-mir-129-3p chr11:
43559575-43559597 3193 AAGCCCTTACCCCAAAAAGCAT Yes Yes Yes Yes Yes
hsa-mir-331-5p chr12: 94226351-94226373 3194 CTAGGTATGGTCCCAGGGATCC
Yes Yes Yes Yes Yes hsa-mir-665 chr14: 100411164-100411184 3195
ACCAGGAGGCTGAGGCCCCT Yes Yes No No No hsa-mir-664 chr1:
218440513-218440536 3196 TGTAGGCTGGGGATAAATGAATA Yes Yes No No No
hsa-mir-663 chr20: 26136878-26136900 3197 GCGGTCCCGCGGCGCCCCGCCT
Yes No No No No hsa-mir-662 chr16: 760243-760264 3198
TCCCACGTTGTGGCCCAGCAG No Yes No No No hsa-mir-588 chr6:
126847484-126847505 3199 TTGGCCACAATGGGTTAGAAC Yes No No No No
hsa-mir-589 chr7: 5502029-5502051 3200 CTCAGAGCAGACGTGGTTCTCA No
Yes No No No hsa-mir-220a chrX: 122523693-122523714 3201
AAAGTGTCAGATACGGTGTGG Yes No No No No hsa-mir-220b chr19:
6446968-6446989 3202 CCACCACCGTGTCTGACACTT Yes No No No No
hsa-mir-371-3p chr19: 58982781-58982804 3203
AAGTGCCGCCATCTTTTGAGTGT Yes No No No No hsa-mir-744 chr17:
11925950-11925972 3204 TGCGGGGCTAGGGCTAACAGCA Yes Yes Yes Yes No
hsa-mir-934 chrX: 135460716-135460738 3205 TGTCTACTACTGGAGACACTGG
Yes No No No No hsa-mir-628-5p chr15: 53452480-53452502 3206
CCTCTAGTAAATATGTCAGCAT Yes Yes Yes No No hsa-mir-888 chrX:
144884039-144884060 3207 TGACTGACAGCTTTTTGAGTA No Yes No No No
hsa-mir-126* chr9: 138684888-138684909 3208 CATTATTACTTTTGGTACGCG
Yes Yes Yes Yes Yes hsa-mir-99b* chr19: 56887720-56887742 3209
CAAGCTCGTGTCTGTGGGTCCG Yes Yes No Yes Yes hsa-mir-137 chr1:
98284234-98284257 3210 CTACGCGTATTCTTAAGCAATAA Yes Yes Yes Yes Yes
hsa-mir-138 chr14: 100420805-100420828 3211 ACTCCATTTGTTTTGATGATGGA
Yes Yes Yes Yes Yes hsa-mir-149* chr2: 241044145-241044166 3212
AGGGAGGGACGGGGGCTGTGC Yes Yes Yes No No hsa-mir-134 chr14:
100590783-100590805 3213 TGTGACTGGTTGACCAGAGGGG Yes Yes Yes Yes Yes
hsa-mir-138 chr16: 55449939-55449962 3214 AGCTGGTGTTGTGAATCAGGCCG
Yes Yes No Yes Yes hsa-mir-138 chr3: 44130729-44130752 3215
AGCTGGTGTTGTGAATCAGGCCG No No Yes Yes Yes hsa-mir-1269 chr4:
66825202-66825224 3216 CTGGACTGAGCCGTGCTACTGG No No No No No
hsa-mir-1268 chr15: 20014622-20014640 3217 CCCCCACCACCACGCCCG No No
No No No hsa-mir-196a* chr12: 52671849-52671871 3218
CGGCAACAAGAAACTGCCTGAG Yes Yes Yes Yes Yes hsa-mir-20b* chrX:
133131508-133131530 3219 CTGGAAGTGCCCATACTACAGT Yes No No No No
hsa-mir-199a-3p chr19: 10789104-10789126 3220
TAACCAATGTGCAGACTACTGT Yes Yes Yes Yes No hsa-mir-199a-3p chr1:
170380316-170380338 3221 TAACCAATGTGCAGACTACTGT Yes Yes Yes Yes Yes
hsa-mir-1263 chr3: 165372004-165372026 3222 ACTCAGTATGCCAGGGTACCAT
Yes No No No No hsa-mir-1262 chr1: 68421846-68421868 3223
ATCCTTCTACAAATTCACCCAT Yes Yes No No No hsa-mir-1261 chr11:
90241995-90242014 3224 AAGCCAAAGCCTTATCCAT Yes No No No No
hsa-mir-1260 chr14: 76802326-76802344 3225 ATCCCACCTCTGCCACCA No
Yes No No No
hsa-mir-1267 chr13: 106981565-106981586 3226 TGGGGATTACACTTCAACAGG
Yes No No No No hsa-mir-151-5p chr8: 141811903-141811924 3227
ACTAGACTGTGAGCTCCTCGA Yes Yes Yes No No hsa-mir-1265 chr10:
14518593-14518615 3228 CAGGATGTGGTCAAGTGTTGTT Yes No No No No
hsa-mir-1264 chrX: 113793426-113793449 3229 CAAGTCTTATTTGAGCACCTGTT
Yes Yes Yes No No hsa-mir-125b-2* chr21: 16884480-16884502 3230
TCACAAGTCAGGCTCTTGGGAC Yes Yes Yes No Yes hsa-mir-33a* chr22:
40626938-40626960 3231 CAATGTTTCCACAGTGCATCAC Yes No No Yes Yes
hsa-mir-339-5p chr7: 1029151-1029174 3232 CGTGAGCTCCTGGAGGACAGGGA
Yes Yes No Yes No hsa-mir-708* chr11: 78790723-78790745 3233
CTAGAAGCTCACAGTCTAGTTG Yes Yes Yes Yes Yes hsa-mir-1255a chr4:
102470544-102470567 3234 AATCTACTTTCTTTGCTCATCCT No No No No No
hsa-mir-1255b chr4: 36104421-36104443 3235 AACCACTTTCTTTGCTCATCCG
No No No No No hsa-mir-1255b chr1: 166234526-166234548 3236
CGGATGAGCAAAGAAAGTGGTT Yes No No No No hsa-mir-7-1* chr9:
85774505-85774527 3237 TATGGCAGACTGTGATTTGTTG Yes Yes Yes Yes Yes
hsa-mir-199b-3p chr9: 130046844-130046866 3238
TAACCAATGTGCAGACTACTGT Yes Yes Yes Yes No hsa-mir-641 chr19:
45480349-45480373 3239 GAGGTGACTCTATCCTATGTCTTT No No No No No
hsa-mir-193a-3p chr17: 26911181-26911203 3240
AACTGGCCTACAAAGTCCCAGT Yes Yes Yes Yes Yes hsa-mir-186* chr1:
71305912-71305934 3241 CCCAAAAAATTCACCTTTGGGC Yes No Yes No Yes
hsa-mir-139-5p chr11: 72003794-72003816 3242 CTGGAGACACGTGCACTGTAGA
Yes Yes Yes Yes Yes hsa-mir-671-5p chr7: 150566467-150566490 3243
AGGAAGCCCTGGAGGGGCTGGAG Yes Yes Yes Yes Yes hsa-mir-582-3p chr5:
59035212-59035234 3244 GGTTCAGTTGTTCAACCAGTTA Yes Yes No No No
hsa-mir-548d-5p chr17: 62898117-62898139 3245
GGCAAAAACCACAATTACTTTT Yes No No No No hsa-mir-548d-5p chr8:
124429505-124429527 3246 GGCAAAAACCACAATTACTTTT No No No No No
hsa-mir-130b* chr22: 20337604-20337625 3247 ACTCTTTCCCTGTTGCACTAC
Yes Yes Yes Yes Yes hsa-let-7f-1* chr9: 95978511-95978533 3248
CTATACAATCTATTGCCTTCCC Yes Yes Yes Yes Yes hsa-mir-767-3p chrX:
151312574-151312597 3249 AGAAACCATGGGGTATGAGCAGA No Yes No No No
hsa-mir-363 chrX: 133131077-133131099 3250 TACAGATGGATACCGTGCAATT
No Yes Yes Yes Yes hsa-mir-32 chr9: 110848372-110848394 3251
TGCAACTTAGTAATGTGCAATA Yes Yes Yes Yes Yes hsa-mir-31 chr9:
21502156-21502177 3252 AGCTATGCCAGCATCTTGCCT Yes Yes Yes Yes Yes
hsa-mir-525-3p chr19: 58892649-58892671 3253 GAAGGCGCTTCCCTTTAGAGCG
Yes No No No No hsa-mir-181d chr19: 13846723-13846746 3254
AACATTCATTGTTGTCGGTGGGT Yes Yes Yes Yes Yes hsa-mir-568 chr3:
115518071-115518091 3255 GTGTGTATACATTTATACAT Yes Yes Yes Yes Yes
hsa-mir-548b-5p chr6: 119431961-119431983 3256
GGCCAAAACCACAATTACTTTT No No No No No hsa-mir-559 chr2:
47458332-47458353 3257 TAAAGTAAATATGCACCAAAA Yes No No No No
hsa-mir-559 chr2: 47458372-47458393 3258 TTTTGGTGCATATTTACTTTA Yes
No No No No hsa-mir-181a chr9: 126494579-126494602 3259
AACATTCAACGCTGTCGGTGAGT Yes Yes Yes Yes Yes hsa-mir-181a chr1:
197094859-197094882 3260 ACTCACCGACAGCGTTGAATGTT Yes Yes Yes Yes
Yes hsa-mir-181b chr9: 126495824-126495847 3261
AACATTCATTGCTGTCGGTGGGT Yes Yes Yes Yes Yes hsa-mir-181b chr1:
197094676-197094699 3262 ACCCACCGACAGCAATGAATGTT Yes Yes Yes Yes
Yes hsa-mir-181c chr19: 13846538-13846560 3263
AACATTCAACCTGTCGGTGAGT Yes Yes Yes Yes Yes hsa-mir-34b* chr11:
110888884-110888907 3264 TAGGCAGTGTCATTAGCTGATTG Yes Yes No No No
hsa-mir-188-5p chrX: 49654862-49654883 3265 CATCCCTTGCATGGTGGAGGG
Yes Yes Yes Yes Yes hsa-mir-367 chr4: 113788481-113788503 3266
TCACCATTGCTAAAGTGCAATT Yes Yes Yes Yes No hsa-mir-365 chr17:
26926609-26926631 3267 TAATGCCCCTAAAAATCCTTAT Yes Yes Yes Yes Yes
hsa-mir-365 chr16: 14310697-14310719 3268 TAATGCCCCTAAAAATCCTTAT
Yes Yes Yes Yes Yes hsa-mir-449b chr5: 54502290-54502312 3269
GCCAGCTAACAATACACTGCCT Yes Yes Yes No No hsa-mir-29a* chr7:
130212084-130212106 3270 CTGAACACCAAAAGAAATCAGT No Yes Yes Yes Yes
hsa-let-7c* chr21: 16834050-16834072 3271 TAGAGTTACACCCTGGGAGTTA
Yes Yes Yes Yes Yes hsa-mir-558 chr2: 32610783-32610802 3272
TGAGCTGCTGTACCAAAAT Yes Yes No No No hsa-mir-10a* chr17:
44012224-44012246 3273 TATTCCCCTAGATACGAATTTG Yes Yes Yes Yes Yes
hsa-mir-518e* chr19: 58924918-58924940 3274 CTCTAGAGGGAAGCGCTTTCTG
Yes No No No No hsa-mir-561 chr2: 188870523-188870545 3275
CAAAGTTTAAGATCCTTGAAGT Yes No No No No hsa-mir-562 chr2:
232745666-232745686 3276 AAAGTAGCTGTACCATTTGC Yes Yes No No No
hsa-mir-563 chr3: 15890332-15890351 3277 AGGTTGACATACGTTTCCC No No
No No No hsa-mir-361-5p chrX: 85045341-85045363 3278
GTACCCCTGGAGATTCTGATAA Yes Yes Yes Yes Yes hsa-mir-566 chr3:
50185777-50185796 3279 GGGCGCCTGTGATCCCAAC Yes No No No No
hsa-mir-567 chr3: 113314352-113314375 3280 AGTATGTTCTTCCAGGACAGAAC
Yes No No No No hsa-mir-642 chr19: 50870040-50870062 3281
GTCCCTCTCCAAATGTGTCTTG Yes Yes No No No hsa-mir-192* chr11:
64415206-64415228 3282 CTGTGACCTATGGAATTGGCAG Yes Yes Yes Yes No
hsa-mir-92a-1* chr13: 90801578-90801601 3283
AGGTTGGGATCGGTTGCAATGCT Yes No Yes No No hsa-mir-27a* chr19:
13808300-13808322 3284 TGCTCACAAGCAGCTAAGCCCT Yes Yes Yes Yes Yes
hsa-mir-564 chr3: 44878398-44878417 3285 AGGCACGGTGTCAGCAGGC Yes No
No No No hsa-mir-106a* chrX: 133131903-133131925 3286
GTAAGAAGTGCTTACATTGCAG No No No No No hsa-mir-26a-1* chr3:
37985946-37985968 3287 CCTATTCTTGGTTACTTGCACG Yes Yes Yes Yes Yes
hsa-mir-498 chr19: 58869295-58869318 3288 TTTCAAGCCAGGGGGCGTTTTTC
Yes Yes No No No hsa-mir-454* chr17: 54569970-54569992 3289
GCAGAGACAATATTGATAGGGT Yes Yes No No No hsa-mir-502-5p chrX:
49665960-49665981 3290 ATCCTTGCTATCTGGGTGCTA Yes Yes Yes No No
hsa-mir-218-2* chr5: 168127750-168127772 3291
CGCGGTGCTTGACAGAACCATG Yes Yes Yes Yes Yes hsa-mir-30c-2* chr6:
72143387-72143409 3292 AGAGTAAACAGCCTTCTCCCAG Yes Yes Yes Yes Yes
hsa-mir-526b* chr19: 58889508-58889530 3293 GAAAGTGCTTCCTTTTAGAGGC
Yes Yes No No No hsa-mir-542-5p chrX: 133503095-133503118 3294
TCTCGTGACATGATGATCCCCGA No Yes Yes Yes Yes hsa-mir-433 chr14:
100418038-100418060 3295 ATCATGATGGGCTCCTCGGTGT Yes Yes Yes Yes Yes
hsa-mir-27a chr19: 13808260-13808281 3296 GCGGAACTTAGCCACTGTGAA Yes
Yes Yes Yes Yes hsa-mir-27b chr9: 96887607-96887628 3297
TTCACAGTGGCTAAGTTCTGC Yes Yes Yes Yes Yes hsa-mir-330-3p chr19:
50834106-50834129 3298 TCTCTGCAGGCCGTGTGCTTTGC Yes Yes Yes No No
hsa-mir-431 chr14: 100417115-100417136 3299 TGTCTTGCAGGCCGTCATGCA
Yes Yes Yes Yes Yes hsa-mir-520c-5p chr19: 58902533-58902555 3300
CTCTAGAGGGAAGCACTTTCTG Yes No No No No hsa-mir-708 chr11:
78790768-78790791 3301 CCCAGCTAGATTGTAAGCTCCTT Yes Yes Yes Yes Yes
hsa-mir-17* chr13: 90800909-90800931 3302 ACTGCAGTGAAGGCACTTGTAG
Yes No Yes No No hsa-mir-1197 chr14: 100561709-100561730 3303
TAGGACACATGGTCTACTTCT Yes Yes Yes Yes Yes hsa-mir-548a-5p chr8:
105565823-105565845 3304 GGTAAAACTCGCAATTACTTTT No Yes No No No
hsa-mir-1248 chr3: 187987157-187987184 3305
ACCTTCTTGTATAAGCACTGTGCTAAA Yes Yes Yes Yes Yes hsa-mir-208b chr14:
22957045-22957067 3306 ACAAACCTTTTGTTCGTCTTAT Yes Yes Yes Yes Yes
hsa-mir-208a chr14: 22927650-22927672 3307 ACAAGCTTTTTGCTCGTCTTAT
Yes Yes Yes Yes Yes hsa-mir-499-5p chr20: 33041871-33041892 3308
TTAAGACTTGCAGTGATGTTT Yes Yes Yes Yes Yes hsa-mir-29b-1* chr7:
130212805-130212829 3309 TCTAAACCACCATATGAAACCAGC Yes
Yes Yes Yes Yes hsa-mir-378* chr5: 149092584-149092606 3310
CTCCTGACTCCAGGTCCTGTGT Yes Yes Yes No Yes hsa-mir-16-1* chr13:
49521121-49521143 3311 TCAGCAGCACAGTTAATACTGG Yes Yes Yes No No
hsa-mir-338-3p chr17: 76714281-76714303 3312 CAACAAAATCACTGATGCTGGA
Yes Yes Yes Yes Yes hsa-mir-145* chr5: 148790454-148790476 3313
GGATTCCTGGAAATACTGTTCT Yes Yes Yes Yes Yes hsa-mir-337-3p chr14:
100410642-100410664 3314 CTCCTATATGATGCCTTTCTTC Yes Yes No Yes Yes
hsa-mir-593* chr7: 127509163-127509188 3315
AGGCACCAGCCAGGCATTGCTCAGC Yes No No No No hsa-mir-130a chr11:
57165300-57165322 3316 CAGTGCAATGTTAAAAGGGCAT Yes Yes Yes Yes Yes
hsa-mir-627 chr15: 40279119-40279141 3317 TCCTCTTTTCTTAGAGACTCAC
Yes Yes No No No hsa-mir-892b chrX: 144886417-144886439 3318
TCTACCCAGAAAGGAGCCAGTG Yes Yes No No No hsa-mir-892a chrX:
144885888-144885909 3319 CTACGCAGAAAGGACACAGTG Yes Yes No No No
hsa-mir-548n chr7: 34946940-34946962 3320 ACAAAATCCACAATTACTTTTG
Yes No No No No hsa-mir-768-3p chr16: 70349813-70349841 3321
GTCAGCAGTTTGAGTGTCAGCATTGTGA No Yes No No No hsa-mir-630 chr15:
70666671-70666693 3322 AGTATTCTGTACCAGGGAAGGT Yes No No No No
hsa-mir-631 chr15: 73433043-73433064 3323 GCTGAGGTCTGGGCCAGGTCT No
Yes No No No hsa-mir-1287 chr10: 100145017-100145039 3324
GACTCGAACCACTGATCCAGCA No No No No No hsa-mir-633 chr17:
58375367-58375390 3325 CTAATAGTATCTACCACAATAAA Yes Yes No No No
hsa-mir-1281 chr22: 39818494-39818511 3326 TCGCCTCCTCCTCTCCC Yes
Yes Yes Yes Yes hsa-mir-635 chr17: 63932246-63932269 3327
GGACATTGTTTCAGTGCCCAAGT Yes No No No No hsa-mir-636 chr17:
72244142-72244165 3328 TGCGGGCGGGACGAGCAAGCACA No No No No No
hsa-mir-637 chr19: 3912426-3912450 3329 ACGCAGAGCCCGAAAGCCCCCAGT
Yes No No No No hsa-mir-638 chr19: 10690094-10690119 3330
AGGGATCGCGGGCGGGTGGCGGCCT No No No No No hsa-mir-639 chr19:
14501414-14501437 3331 ATCGCTGCGGTTGCGAGCGCTGT No No No No No
hsa-mir-1289 chr5: 132791205-132791228 3332 AAAATGCAGATTCCTGGACTCCA
Yes Yes No No No hsa-mir-1289 chr20: 33505225-33505248 3333
AAAATGCAGATTCCTGGACTCCA Yes Yes No No No hsa-mir-1288 chr17:
16126096-16126117 3334 TGGACTGCCCTGATCTGGAGA Yes Yes No No No
hsa-mir-548j chr22: 25281239-25281261 3335 ACCAAAGACCGCAATTACTTTT
No No No No No hsa-mir-518b chr19: 58897852-58897874 3336
CAAAGCGCTCCCCTTTAGAGGT Yes No No No No hsa-let-7c chr21:
16834028-16834050 3337 TGAGGTAGTAGGTTGTATGGTT Yes Yes Yes Yes Yes
hsa-let-7a chr22: 44887295-44887317 3338 TGAGGTAGTAGGTTGTATAGTT Yes
Yes Yes No No hsa-let-7a chr11: 121522485-121522507 3339
AACTATACAACCTACTACCTCA Yes Yes Yes Yes Yes hsa-let-7a chr9:
95978064-95978086 3340 TGAGGTAGTAGGTTGTATAGTT Yes Yes Yes Yes Yes
hsa-let-7f chrX: 53600931-53600953 3341 AACTATACAATCTACTACCTCA Yes
Yes Yes Yes Yes hsa-let-7f chr9: 95978455-95978477 3342
TGAGGTAGTAGATTGTATAGTT Yes Yes Yes Yes Yes hsa-let-7g chr3:
52277391-52277413 3343 AACTGTACAAACTACTACCTCA Yes Yes Yes Yes No
hsa-let-7d chr9: 95980943-95980965 3344 AGAGGTAGTAGGTTGCATAGTT Yes
Yes Yes Yes Yes hsa-let-7e chr19: 56887857-56887879 3345
TGAGGTAGGAGGTTGTATAGTT Yes Yes Yes Yes Yes hsa-mir-516a-3p chr19:
58956258-58956276 3346 TGCTTCCTTTCAGAGGGT Yes No No No No
hsa-mir-516a-3p chr19: 58951866-58951884 3347 TGCTTCCTTTCAGAGGGT
Yes No No No No hsa-let-7i chr12: 61283737-61283759 3348
TGAGGTAGTAGTTTGTGCTGTT Yes Yes Yes Yes Yes hsa-mir-503 chrX:
133508066-133508089 3349 CTGCAGAACTGTTCCCGCTGCTA Yes Yes No No No
hsa-mir-494 chr14: 100565770-100565792 3350 TGAAACATACACGGGAAACCTC
Yes Yes Yes Yes Yes hsa-mir-519b-3p chr19: 58890328-58890350 3351
AAAGTGCATCCTTTTAGAGGTT Yes No No No No hsa-mir-1207-5p chr8:
129130586-129130607 3352 TGGCAGGGAGGCTGGGAGGGG Yes No No No No
hsa-let-7b* chr22: 44888288-44888310 3353 CTATACAACCTACTGCCTTCCC
Yes Yes Yes Yes Yes hsa-mir-181a* chr1: 197094820-197094842 3354
GGTACAATCAACGGTCGATGGT Yes Yes Yes Yes Yes hsa-mir-548e chr10:
112738725-112738747 3355 AAAAACTGAGACTACTTTTGCA No No No No No
hsa-mir-125b chr21: 16884443-16884465 3356 TCCCTGAGACCCTAACTTGTGA
Yes Yes Yes Yes Yes hsa-mir-125b chr11: 121475726-121475748 3357
TCACAAGTTAGGGTCTCAGGGA Yes Yes Yes Yes Yes hsa-mir-9* chr1:
154656769-154656791 3358 ACTTTCGGTTATCTAGCTTTAT Yes Yes Yes Yes Yes
hsa-mir-9* chr5: 87998439-87998461 3359 ACTTTCGGTTATCTAGCTTTAT Yes
Yes Yes Yes Yes hsa-mir-9* chr15: 87712305-87712327 3360
ATAAAGCTAGATAACCGAAAGT Yes No Yes Yes Yes hsa-mir-301b chr22:
20337313-20337336 3361 CAGTGCAATGATATTGTCAAAGC Yes Yes Yes No No
hsa-mir-301a chr17: 54583291-54583314 3362 GCTTTGACAATACTATTGCACTG
Yes Yes Yes Yes Yes hsa-mir-98 chrX: 53599984-53600006 3363
AACAATACAACTTACTACCTCA Yes Yes Yes Yes Yes hsa-mir-550* chr7:
30295994-30296016 3364 TGTCTTACTCCCTCAGGCACAT Yes No No No No
hsa-mir-550* chr7: 32739177-32739199 3365 TGTCTTACTCCCTCAGGCACAT
Yes No No No No hsa-mir-505* chrX: 138834020-138834042 3366
ACATCAATACTTCCTGGCTCCC Yes Yes Yes Yes Yes hsa-mir-142-3p chr17:
53763604-53763627 3367 TCCATAAAGTAGGAAACACTACA Yes Yes Yes Yes Yes
hsa-mir-487a chr14: 100588583-100588605 3368 AATCATACAGGGACATCCAGTT
Yes Yes Yes No No hsa-mir-93 chr7: 99529373-99529396 3369
CTACCTGCACGAACAGCACTTTG Yes Yes Yes Yes Yes hsa-mir-95 chr4:
8057938-8057960 3370 TGCTCAATAAATACCCGTTGAA Yes Yes Yes No No
hsa-mir-96 chr7: 129201814-129201837 3371 AGCAAAAATGTGCTAGTGCCAAA
Yes Yes Yes Yes Yes hsa-mir-200c* chr12: 6943126-6943148 3372
CGTCTTACCCAGCAGTGTTTGG No Yes Yes Yes Yes hsa-mir-527 chr19:
58949096-58949116 3373 CTGCAAAGGGAAGCCCTTTC Yes No No No No
hsa-mir-521 chr19: 58943754-58943776 3374 AACGCACTTCCCTTTAGAGTGT
Yes No No No No hsa-mir-521 chr19: 58911712-58911734 3375
AACGCACTTCCCTTTAGAGTGT Yes No No No No hsa-mir-127-3p chr14:
100419124-100419146 3376 TCGGATCCGTCTGAGCTTGGCT Yes Yes Yes Yes Yes
hsa-mir-523 chr19: 58893502-58893525 3377 GAACGCGCTTCCCTATAGAGGGT
Yes No No No No hsa-mir-135b chr1: 203684111-203684134 3378
TCACATAGGAATGAAAAGCCATA Yes Yes Yes Yes Yes hsa-mir-135a chr3:
52303325-52303348 3379 TCACATAGGAATAAAAAGCCATA Yes Yes Yes Yes Yes
hsa-mir-135a chr12: 96481742-96481765 3380 TATGGCTTTTTATTCCTATGTGA
Yes Yes Yes Yes Yes hsa-mir-146b-5p chr10: 104186266-104186288 3381
TGAGAACTGAATTCCATAGGCT Yes No Yes Yes Yes hsa-mir-509-3p chrX:
146148871-146148893 3382 CTACCCACAGACGTACCAATCA No No No No No
hsa-mir-509-3p chrX: 146147984-146148006 3383
CTACCCACAGACGTACCAATCA No No No No No hsa-mir-509-3p chrX:
146149759-146149781 3384 CTACCCACAGACGTACCAATCA No No No No No
hsa-mir-33b* chr17: 17657895-17657917 3385 GGGCTGCACTGCCGAGGCACTG
Yes Yes Yes No No hsa-mir-744* chr17: 11926007-11926029 3386
CTGTTGCCACTAACCTCAACCT Yes Yes Yes Yes No hsa-mir-1274a chr5:
41511503-41511521 3387 GTCCCTGTTCAGGCGCCA Yes No No No No
hsa-mir-532-5p chrX: 49654512-49654534 3388 CATGCCTTGAGTGTAGGACCGT
Yes Yes Yes Yes No hsa-mir-1274b chr19: 62716222-62716239 3389
TGGCGCCCGAACAGGGA Yes No No No No hsa-let-7i* chr12:
61283793-61283815 3390 CTGCGCAAGCTACTGCCTTGCT Yes Yes No Yes Yes
hsa-mir-132 chr17: 1899972-1899994 3391 CGACCATGGCTGTAGACTGTTA No
Yes Yes Yes Yes hsa-mir-20a* chr13: 90801362-90801384 3392
ACTGCATTATGAGCACTTAAAG Yes No Yes No No
hsa-mir-23a chr19: 13808408-13808429 3393 GGAAATCCCTGGCAATGTGAT Yes
Yes Yes Yes Yes hsa-mir-23b chr9: 96887367-96887388 3394
ATCACATTGCCAGGGATTACC Yes Yes Yes Yes Yes hsa-mir-542-3p chrX:
133503059-133503081 3395 TTTCAGTTATCAATCTGTCACA No Yes Yes Yes Yes
hsa-mir-148b chr12: 53017328-53017350 3396 TCAGTGCATCACAGAACTTTGT
Yes Yes Yes Yes Yes hsa-mir-148a chr7: 25956066-25956088 3397
ACAAAGTTCTGTAGTGCACTGA Yes Yes Yes Yes No hsa-mir-886-3p chr5:
135444086-135444107 3398 AAGGGTCAGTAAGCACCCGCG Yes Yes No No No
hsa-mir-24 chr19: 13808102-13808124 3399 CTGTTCCTGCTGAACTGAGCCA Yes
Yes Yes Yes Yes hsa-mir-24 chr9: 96888166-96888188 3400
TGGCTCAGTTCAGCAGGAACAG Yes Yes Yes Yes Yes hsa-mir-330-5p chr19:
50834146-50834168 3401 GCCTAAGACACAGGCCCAGAGA Yes Yes Yes Yes Yes
hsa-mir-497* chr17: 6861980-6862002 3402 TCTAACACCACAGTGTGGTTTG Yes
Yes No Yes Yes hsa-mir-451 chr17: 24212546-24212568 3403
AACTCAGTAATGGTAACGGTTT Yes Yes Yes Yes Yes hsa-mir-452 chrX:
150878805-150878827 3404 TCAGTTTCCTCTGCAAACAGTT Yes Yes Yes Yes No
hsa-mir-340* chr5: 179374924-179374946 3405 GCTATAAAGTAACTGAGACGGA
Yes Yes Yes Yes No hsa-mir-454 chr17: 54569929-54569952 3406
ACCCTATAAGCAATATTGCACTA Yes Yes Yes No No hsa-mir-890 chrX:
144883530-144883551 3407 CAACTGATGCCTTTCCAAGTA Yes No No No No
hsa-mir-135b* chr1: 203684073-203684095 3408 CCCATGGCTTTTAGCCCTACAT
Yes Yes Yes Yes Yes hsa-mir-875-3p chr8: 100618200-100618221 3409
CACAACCTCAGTGTTTCCAGG No No No No No hsa-mir-541* chr14:
100600593-100600618 3410 AAAGGATTCTGCTGTCGGTCCCACT No Yes No No No
hsa-mir-26a-2* chr12: 56504669-56504691 3411 GAAACAAGTAATCAAGAATAGG
Yes Yes Yes No No hsa-mir-302c* chr4: 113789006-113789028 3412
CAGCAGGTACCCCCATGTTAAA Yes Yes Yes No No hsa-mir-885-3p chr3:
10411182-10411204 3413 TATCCACTACACCCCGCTGCCT Yes Yes Yes No No
hsa-mir-450b-3p chrX: 133501889-133501911 3414
TATGGATGCAAAATGATCCCAA Yes Yes No No No hsa-mir-296-5p chr20:
56826110-56826131 3415 ACAGGATTGAGGGGGGGCCCT Yes Yes No Yes Yes
hsa-mir-221* chrX: 45490592-45490614 3416 AAATCTACATTGTATGCCAGGT
Yes Yes Yes Yes Yes hsa-mir-100* chr11: 121528157-121528179 3417
CATACCTATAGATACAAGCTTG Yes No No No No hsa-mir-302b* chr4:
113789130-113789152 3418 GAAAGCACTTCCATGTTAAAGT Yes Yes No No No
hsa-mir-487b chr14: 100582594-100582616 3419 AATCGTACAGGGTCATCCACTT
Yes Yes Yes Yes Yes hsa-mir-607 chr10: 98578430-98578451 3420
GTTATAGATCTGGATTTGAAC No No No No No hsa-mir-625* chr14:
65007623-65007645 3421 GACTATAGAACTTTCCCCCTCA Yes No No No No
hsa-mir-625* chr14: 65007584-65007606 3422 TGAGGGGGAAAGTTCTATAGTC
Yes No No No No hsa-mir-141* chr12: 6943536-6943558 3423
CATCTTCCAGTACAGTGTTGGA Yes Yes Yes No No hsa-mir-606 chr10:
76982281-76982302 3424 AAACTACTGAAAATCAAAGAT No No No No No
hsa-mir-155* chr21: 25868204-25868226 3425 CTCCTACATATTAGCATTAACA
Yes No No No No hsa-mir-146a chr5: 159844956-159844978 3426
TGAGAACTGAATTCCATGGGTT Yes Yes Yes Yes Yes hsa-mir-1183 chr7:
21477247-21477274 3427 CACTGTAGGTGATGGTGAGAGTGGGCA Yes Yes No No No
(2) Conservation of seed sequence miRNA identified in B cell
libraries and deposited in miRBase database Seq ID Conservation ID
Genomic Coordinates No. Sequence Chimp Monkey Dog Mouse Rat CU-1001
chr11: 121522485-121522507 3428 TGAGGTAGTAGGTTGTATAGTT Yes Yes Yes
Yes Yes CU-1001 chr9: 95978064-95978086 3429 TGAGGTAGTAGGTTGTATAGTT
Yes Yes Yes Yes Yes CU-1003 chr22: 44888234-44888256 3430
TGAGGTAGTAGGTTGTGTGGTT Yes Yes Yes Yes Yes CU-1004 chr9:
95980943-95980965 3431 AGAGGTAGTAGGTTGCATAGTT Yes Yes Yes Yes Yes
CU-1005 chr19: 56887857-56887879 3432 TGAGGTAGGAGGTTGTATAGTT Yes
Yes Yes Yes Yes CU-1006 chrX: 53600931-53600953 3433
TGAGGTAGTAGATTGTATAGTT Yes Yes Yes Yes Yes CU-1007 chr3:
52277391-52277413 3434 TGAGGTAGTAGTTTGTACAGTT Yes Yes Yes Yes No
CU-1008 chr12: 61283737-61283759 3435 TGAGGTAGTAGTTTGTGCTGTT Yes
Yes Yes Yes Yes CU-1009 chr1: 65296711-65296733 3436
TACAGTACTGTGATAACTGAAG Yes Yes Yes Yes Yes CU-1009 chr9:
4840344-4840366 3437 TACAGTACTGTGATAACTGAAG Yes Yes Yes Yes Yes
CU-1010 chr20: 3846187-3846210 3438 AGCAGCATTGTACAGGGCTATGA Yes Yes
Yes Yes Yes CU-1011 chr7: 99529562-99529582 3439
CCGCACTGTGGGTACTTGCT Yes Yes Yes Yes Yes CU-1012 chr7:
99529601-99529622 3440 TAAAGTGCTGACAGTGCAGAT Yes Yes Yes Yes Yes
CU-1014 chr19: 56888332-56888356 3441 TCCCTGAGACCCTTTAACCTGTGA Yes
Yes Yes Yes Yes CU-1015 chr21: 16884443-16884465 3442
TCCCTGAGACCCTAACTTGTGA Yes Yes Yes Yes Yes CU-1016 chr6:
131417431-131417449 3443 GTCCCTGTTCGGGCGCCA Yes Yes No No No
CU-1016 chr19: 62716222-62716240 3444 GTCCCTGTTCGGGCGCCA Yes No No
No No CU-1017 chr1: 150066843-150066860 3445 GTGGGGGAGAGGCTGTA Yes
No No No No CU-1018 chr7: 35602718-35602735 3446 TCCCACCGCTGCCACCA
No No No No No CU-1018 chr2: 72555764-72555781 3447
TCCCACCGCTGCCACCA No No No No No CU-1018 chrX: 55565708-55565725
3448 TCCCACCGCTGCCACCA No No No No No CU-1018 chr1:
225154598-225154615 3449 TCCCACCGCTGCCACCA Yes No No No No CU-1018
chr11: 95714259-95714276 3450 TCCCACCGCTGCCACCA Yes Yes Yes No No
CU-1018 chr7: 5368308-5368325 3451 TCCCACCGCTGCCACCA Yes Yes No No
No CU-1018 chr6: 140362954-140362971 3452 TCCCACCGCTGCCACCA Yes No
No No No CU-1019 chr2: 136139485-136139506 3453
TCACAGTGAACCGGTCTCTTT Yes Yes Yes Yes Yes CU-1021 chr1:
159701881-159701904 3454 GCATGGGTGGTTCAGTGGTAGAA Yes Yes No No No
CU-1021 chr1: 159694521-159694544 3455 GCATGGGTGGTTCAGTGGTAGAA Yes
Yes No No No CU-1021 chr1: 159687090-159687113 3456
GCATGGGTGGTTCAGTGGTAGAA Yes Yes No No No CU-1021 chr21:
17749025-17749048 3457 GCATGGGTGGTTCAGTGGTAGAA Yes Yes No No No
CU-1021 chr1: 159679717-159679740 3458 GCATGGGTGGTTCAGTGGTAGAA No
Yes Yes No No CU-1022 chr22: 20337642-20337664 3459
CAGTGCAATGATGAAAGGGCAT Yes Yes Yes Yes Yes CU-1023 chr3:
44130729-44130753 3460 AGCTGGTGTTGTGAATCAGGCCGT No No Yes Yes Yes
CU-1024 chr16: 68524545-68524567 3461 TACCACAGGGTAGAACCACGGA Yes
Yes Yes Yes Yes CU-1025 chr16: 68524506-68524527 3462
CAGTGGTTTTACCCTATGGTA Yes Yes Yes Yes Yes CU-1026 chr17:
53763604-53763627 3463 TGTAGTGTTTCCTACTTTATGGA Yes Yes Yes Yes Yes
CU-1027 chr5: 159844956-159844978 3464 TGAGAACTGAATTCCATGGGTT Yes
Yes Yes Yes Yes CU-1028 chr10: 104186266-104186290 3465
TGAGAACTGAATTCCATAGGCTGT Yes No Yes Yes Yes CU-1029 chr19:
54695901-54695922 3466 TCTCCCAACCCTTGTACCAGT Yes Yes Yes Yes Yes
CU-1030 chr17: 17715007-17715028 3467 CTAGACTGAAGCTCCTTGAGG Yes Yes
No No No CU-1030 chr7: 150838585-150838606 3468
CTAGACTGAAGCTCCTTGAGG Yes No No No No CU-1031 chrX:
53425327-53425349 3469 TCGAGGAGCTCACAGTCTAGTA Yes Yes No No No
CU-1031 chr8: 141811902-141811924 3470 TCGAGGAGCTCACAGTCTAGTA Yes
Yes Yes No No CU-1032 chr21: 25868165-25868188 3471
TTAATGCTAATCGTGATAGGGGT Yes Yes Yes Yes No CU-1033 chr13:
49521304-49521325 3472 TAGCAGCACATAATGGTTTGT Yes Yes Yes Yes No
CU-1033 chr7: 3516339-3516360 3473 TAGCAGCACATAATGGTTTGT Yes Yes No
No No CU-1034 chr3: 161605126-161605147 3474 CGAATCATTATTTGCTGCTCT
Yes Yes Yes Yes Yes CU-1035 chr3: 161605088-161605110 3475
TAGCAGCACATCATGGTTTACA Yes Yes Yes Yes Yes CU-1037 chr3:
161605235-161605257 3476 TAGCAGCACGTAAATATTGGCG Yes Yes Yes Yes Yes
CU-1037 chr13: 49521163-49521185 3477 TAGCAGCACGTAAATATTGGCG Yes
Yes Yes Yes No
CU-1038 chr13: 90800909-90800931 3478 ACTGCAGTGAAGGCACTTGTAG Yes No
Yes Yes Yes CU-1039 chr13: 90800872-90800895 3479
CAAAGTGCTTACAGTGCAGGTAG Yes Yes Yes Yes Yes CU-1040 chr1:
197094822-197094842 3480 ACCATCGACCGTTGATTGTA Yes Yes Yes Yes Yes
CU-1042 chr9: 126494579-126494603 3481 AACATTCAACGCTGTCGGTGAGTT Yes
Yes Yes Yes Yes CU-1042 chr1: 197094858-197094882 3482
AACATTCAACGCTGTCGGTGAGTT Yes Yes Yes Yes Yes CU-1044 chr13:
90801051-90801073 3483 ACTGCCCTAAGTGCTCCTTCTG Yes No Yes Yes Yes
CU-1045 chr13: 90801010-90801032 3484 TAAGGTGCATCTAGTGCAGATA Yes
Yes Yes Yes Yes CU-1046 chr3: 49033108-49033131 3485
CAACGGAATCCCAAAAGCAGCTG Yes Yes Yes Yes Yes CU-1047 chr11:
64415251-64415271 3486 CTGACCTATGAATTGACAGC Yes Yes Yes Yes Yes
CU-1050 chr16: 14305374-14305396 3487 AACTGGCCCTCAAAGTCCCGCT Yes
Yes Yes Yes No CU-1052 chr17: 6861708-6861730 3488
TAGCAGCACAGAAATATTGGCA Yes Yes Yes Yes Yes CU-1053 chr1:
109943084-109943105 3489 TTCACCACCTTCTCCACCCAG Yes Yes Yes No No
CU-1054 chr1: 170380354-170380377 3490 CCCAGTGTTCAGACTACCTGTTC Yes
Yes Yes Yes Yes CU-1054 chr19: 10789144-10789167 3491
CCCAGTGTTCAGACTACCTGTTC Yes Yes Yes Yes No CU-1055 chr19:
10789105-10789126 3492 ACAGTAGTCTGCACATTGGTT Yes Yes Yes Yes Yes
CU-1055 chr1: 170380317-170380338 3493 ACAGTAGTCTGCACATTGGTT Yes
Yes Yes Yes Yes CU-1055 chr9: 130046845-130046866 3494
ACAGTAGTCTGCACATTGGTT Yes Yes Yes Yes No CU-1056 chr13:
90801193-90801216 3495 TGTGCAAATCTATGCAAAACTGA Yes No Yes Yes Yes
CU-1057 chrX: 133131378-133131401 3496 TGTGCAAATCCATGCAAAACTGA Yes
Yes Yes Yes Yes CU-1057 chr13: 90801499-90801522 3497
TGTGCAAATCCATGCAAAACTGA Yes Yes Yes Yes Yes CU-1061 chr13:
90801326-90801349 3498 TAAAGTGCTTATAGTGCAGGTAG Yes Yes Yes Yes Yes
CU-1062 chrX: 133131545-133131568 3499 CAAAGTGCTTATAGTGCAGGTAG Yes
Yes Yes Yes Yes CU-1064 chr17: 55273415-55273437 3500
TAGCTTATCAGACTGATGTTGA Yes Yes Yes Yes Yes CU-5016 chr3:
49032634-49032658 3501 AATGACACGATCACTCCCGTTGAG Yes Yes Yes Yes Yes
CU-1065 chrX: 45490553-45490574 3502 AGCTACATTGTCTGCTGGGTT Yes Yes
Yes Yes Yes CU-1066 chrX: 45491383-45491406 3503
AGCTACATCTGGCTACTGGGTCT No Yes Yes Yes Yes CU-1067 chrX:
65155503-65155525 3504 TGTCAGTTTGTCAAATACCCCA Yes Yes Yes Yes Yes
CU-1068 chr19: 13808407-13808429 3505 ATCACATTGCCAGGGATTTCCA Yes
Yes Yes Yes Yes CU-1069 chr9: 96887367-96887389 3506
ATCACATTGCCAGGGATTACCA Yes Yes Yes Yes Yes CU-1071 chr7:
99529129-99529151 3507 CATTGCACTTGTCTCGGTCTGA Yes Yes Yes Yes Yes
CU-1072 chr12: 56504707-56504729 3508 TTCAAGTAATCCAGGATAGGCT Yes
Yes Yes Yes Yes CU-1072 chr3: 37985907-37985929 3509
TTCAAGTAATCCAGGATAGGCT Yes Yes Yes Yes Yes CU-1073 chr2:
218975623-218975645 3510 TTCAAGTAATTCAGGATAGGTT Yes Yes Yes Yes Yes
CU-1075 chr9: 96887607-96887627 3511 TTCACAGTGGCTAAGTTCTG Yes Yes
Yes Yes Yes CU-1076 chr3: 189889315-189889337 3512
CACTAGATTGTGAGCTCCTGGA Yes Yes Yes Yes Yes CU-1077 chr3:
189889275-189889297 3513 AAGGAGCTCACAGTCTATTGAG Yes Yes Yes Yes Yes
CU-1079 chr7: 130212046-130212068 3514 TAGCACCATCTGAAATCGGTTA Yes
Yes Yes Yes Yes CU-1080 chr1: 206042417-206042440 3515
TAGCACCATTTGAAATCAGTGTT Yes Yes Yes Yes Yes CU-1081 chr1:
206041871-206041892 3516 TGACCGATTTCTCCTGGTGTT Yes Yes Yes Yes Yes
CU-1082 chr1: 206041832-206041854 3517 TAGCACCATTTGAAATCGGTTA Yes
Yes Yes Yes Yes CU-1083 chr6: 72170020-72170040 3518
TGTAAACATCCTCGACTGGA Yes Yes Yes Yes Yes CU-1084 chr8:
135881994-135882016 3519 TGTAAACATCCTACACTCAGCT Yes Yes Yes Yes Yes
CU-1085 chr1: 40995558-40995581 3520 TGTAAACATCCTACACTCTCAGC Yes
Yes Yes Yes Yes CU-1086 chr8: 135886343-135886365 3521
TGTAAACATCCCCGACTGGAAG Yes Yes Yes Yes Yes CU-1087 chr1:
40992629-40992653 3522 TGTAAACATCCTTGACTGGAAGCT Yes Yes Yes Yes Yes
CU-1088 chr8: 22158432-22158448 3523 TGGGTTGAGAGGGCGA Yes Yes Yes
Yes Yes CU-1089 chr16: 65793734-65793752 3524 CTGGCCCTCTCTGCCCTT
Yes No Yes Yes Yes CU-1091 chr12: 94226386-94226407 3525
GCCCCTGGGCCTATCCTAGAA Yes Yes Yes Yes Yes CU-1092 chr7:
1029154-1029174 3526 TCCCTGTCCTCCAGGAGCTC Yes Yes Yes Yes No
CU-1092 chr10: 22978473-22978493 3527 TCCCTGTCCTCCAGGAGCTC Yes Yes
No No No CU-1093 chr14: 99645804-99645828 3528
TCTCACACAGAAATCGCACCCGTC Yes Yes Yes Yes Yes CU-1094 chr14:
99645763-99645783 3529 GGGGTGCTATCTGTGATTGA Yes Yes Yes Yes Yes
CU-1095 chr1: 9134379-9134402 3530 TGGCAGTGTCTTAGCTGGTTGTT Yes Yes
Yes Yes Yes CU-1096 chrX: 85045302-85045324 3531
TCCCCCAGGTGTGATTCTGATT Yes Yes Yes Yes Yes CU-1098 chr17:
26926609-26926631 3532 TAATGCCCCTAAAAATCCTTAT Yes Yes Yes Yes Yes
CU-1098 chr16: 14310697-14310719 3533 TAATGCCCCTAAAAATCCTTAT Yes
Yes Yes Yes Yes CU-1099 chr5: 149092584-149092605 3534
CTCCTGACTCCAGGTCCTGTG Yes Yes Yes No Yes CU-1100 chr17:
25468274-25468296 3535 AGCTCGGTCTGAGGCCCCTCAG Yes Yes Yes Yes Yes
CU-1101 chr17: 25468238-25468260 3536 TGAGGGGCAGAGAGCGAGACTT Yes
Yes Yes Yes Yes CU-1103 chr8: 41637118-41637140 3537
TCCTGTACTGAGCTGCCCCGAG Yes Yes Yes Yes Yes CU-1104 chr17:
6862021-6862042 3538 CAGCAGCACACTGTGGTTTGT Yes Yes Yes Yes Yes
CU-1105 chrX: 138833988-138834006 3539 CGTCAACACTTGCTGGTT Yes Yes
Yes Yes Yes CU-1106 chr4: 38546107-38546128 3540
CACGCTCATGCACACACCCAC No No Yes Yes No CU-1108 chr14:
65007623-65007643 3541 AGGGGGAAAGTTCTATAGTC Yes No No No No CU-1108
chr14: 65007586-65007606 3542 AGGGGGAAAGTTCTATAGTC Yes No No No No
CU-1110 chr15: 68158819-68158840 3543 TGGGTTTACGTTGGGAGAACT No No
No No No CU-1111 chr9: 85774506-85774527 3544 CAACAAATCACAGTCTGCCAT
Yes Yes Yes Yes Yes CU-1113 chr9: 85774546-85774569 3545
TGGAAGACTAGTGATTTTGTTGT Yes Yes Yes Yes Yes CU-1113 chr15:
86956090-86956113 3546 TGGAAGACTAGTGATTTTGTTGT Yes Yes Yes Yes Yes
CU-1113 chr19: 4721711-4721734 3547 TGGAAGACTAGTGATTTTGTTGT Yes Yes
Yes Yes Yes CU-1115 chr13: 90801578-90801601 3548
AGGTTGGGATCGGTTGCAATGCT Yes No Yes No No CU-1116 chrX:
133131239-133131261 3549 TATTGCACTTGTCCCGGCCTGT Yes Yes Yes Yes Yes
CU-1116 chr13: 90801615-90801637 3550 TATTGCACTTGTCCCGGCCTGT Yes
Yes Yes Yes Yes CU-1117 chr1: 153431651-153431670 3551
TATTGCACTCGTCCCGGCC No Yes Yes Yes Yes CU-1118 chr7:
99529373-99529396 3552 CAAAGTGCTGTTCGTGCAGGTAG Yes Yes Yes Yes Yes
CU-1119 chrX: 53599984-53600006 3553 TGAGGTAGTAAGTTGTATTGTT Yes Yes
Yes Yes Yes CU-1124 chr17: 53763644-53763665 3554
CCCATAAAGTAGAAAGCACTA Yes Yes Yes Yes Yes CU-1125 chr3:
161605277-161605298 3555 ACCAATATTACTGTGCTGCTT Yes Yes Yes Yes Yes
CU-1126 chr9: 126495825-126495848 3556 ACATTCATTGCTGTCGGTGGGTT Yes
Yes Yes Yes Yes CU-1126 chr1: 197094675-197094698 3557
ACATTCATTGCTGTCGGTGGGTT Yes Yes Yes Yes Yes CU-1568 chr21:
16834028-16834046 3558 TGAGGTAGTAGGTTGTAT Yes Yes Yes Yes Yes
CU-5001 chr9: 95980997-95981018 3559 CTATACGACCTGCTGCCTTTC Yes Yes
Yes Yes Yes CU-5002 chr3: 49032596-49032618 3560
CATCGGGAATGTCGTGTCCGCC Yes Yes Yes Yes Yes new miRNA identified in
B cell libraries Seq ID Conservation
ID Genomic Coordinates No. Sequence Chimp Monkey Dog Mouse Rat
CU-1130 chr4: 84650562-84650579 3561 CCCGGGTTTCGGCACCA Yes No No No
No CU-1130 chr7: 152741807-152741824 3562 CCCGGGTTTCGGCACCA No No
No No No CU-1132 chr12: 123990125-123990145 3563
GCCGGGTACTTTCGTATTTT No No No No No CU-1137 chr17: 8030990-8031016
3564 GCTAAGGAAGTCCTGTGCTCAGTTTT Yes No No No No CU-1142 chr5:
180625271-180625293 3565 TCGATTCCCGGCCCATGCACCA No No No No No
CU-1142 chr21: 17748974-17748996 3566 TCGATTCCCGGCCCATGCACCA Yes No
No No No CU-1142 chr1: 159687142-159687164 3567
TCGATTCCCGGCCCATGCACCA Yes Yes No No No CU-1142 chr1:
159701933-159701955 3568 TCGATTCCCGGCCCATGCACCA Yes Yes No No No
CU-1142 chr1: 159679769-159679791 3569 TCGATTCCCGGCCCATGCACCA No
Yes Yes No No CU-1142 chr1: 159694573-159694595 3570
TCGATTCCCGGCCCATGCACCA Yes Yes No No No CU-1146 chr16:
3142975-3142992 3571 AGAAAGGCCGAATTTTA Yes No No No No CU-1148
chr10: 5935660-5935679 3572 TGGTGTGGTCTGTTGTTTT Yes No No No No
CU-1153 chr14: 22388241-22388268 3573 CCCCCCACTGCTAAATTTGACTGGCTT
Yes Yes No No No CU-1153 chr17: 35653067-35653094 3574
CCCCCCACTGCTAAATTTGACTGGCTT Yes No No No No CU-1155 chr20:
58490320-58490337 3575 TCCCCGCACCTCCACCA Yes Yes No No No CU-1164
chr6: 29057409-29057426 3576 GAGAGCGCTCGGTTTTT Yes No No No No
CU-1173 chr18: 1681856-1681874 3577 ATCCCACTCCTGACACCA Yes No No No
No CU-1175 chr11: 59075015-59075034 3578 GGCGTGATTCATACCTTTT Yes No
No No No CU-1178 chr6: 28723944-28723961 3579 AGGGTGTGCGTGTTTTT Yes
No No No No CU-1180 chr19: 38359877-38359905 3580
AACCGAGCGTCCAAGCTCTTTCCATTTT Yes Yes No No No CU-1186 chr18:
73990174-73990192 3581 TCCCCGACACCTCCACCA No No No No No CU-1191
chr12: 46439968-46439985 3582 GCCCGCATCCTCCACCA Yes No No No No
CU-1197 chr15: 38673296-38673314 3583 ATGTGGTGGCTTACTTTT Yes No No
No No CU-1212 chr20: 60596937-60596955 3584 TCCCCGGCACTTCCACCA No
No No No No CU-1213 chr3: 73875819-73875836 3585 TCACCCCATAAACACCA
Yes Yes Yes No No CU-1220 chr1: 159706825-159706843 3586
TTCCCCGACGGGGAGCCA Yes Yes No No No CU-1220 chr1:
159692034-159692052 3587 TTCCCCGACGGGGAGCCA Yes Yes No No No
CU-1220 chr1: 159677235-159677253 3588 TTCCCCGACGGGGAGCCA Yes Yes
Yes No No CU-1220 chr1: 159699444-159699462 3589 TTCCCCGACGGGGAGCCA
Yes Yes No No No CU-1220 chr1: 159684653-159684671 3590
TTCCCCGACGGGGAGCCA Yes Yes No No No CU-1221 chr17:
34564245-34564268 3591 TGTGCTCCGGAGTTACCTCGTTT No No No No No
CU-1222 chrX: 70920902-70920919 3592 TCACGTCGGGGTCACCA Yes No No No
No CU-1241 chr2: 167308360-167308379 3593 AGTCCCATCTGGGTCGCCA Yes
No No No No CU-1241 chr1: 29814092-29814111 3594
AGTCCCATCTGGGTCGCCA Yes Yes No No No CU-1241 chrX:
51239676-51239695 3595 AGTCCCATCTGGGTCGCCA Yes Yes No No No CU-1241
chr13: 22997399-22997418 3596 AGTCCCATCTGGGTCGCCA Yes No No No No
CU-1241 chr6: 70235237-70235256 3597 AGTCCCATCTGGGTCGCCA Yes No No
No No CU-1241 chr6: 141377023-141377042 3598 AGTCCCATCTGGGTCGCCA
Yes Yes No No No CU-1241 chr16: 21555749-21555768 3599
AGTCCCATCTGGGTCGCCA Yes No No No No CU-1241 chr3: 97152533-97152552
3600 AGTCCCATCTGGGTCGCCA Yes No No No No CU-1241 chrX:
70638471-70638490 3601 AGTCCCATCTGGGTCGCCA Yes No No No No CU-1241
chr2: 47181625-47181644 3602 AGTCCCATCTGGGTCGCCA No No No No No
CU-1241 chr3: 114548556-114548575 3603 AGTCCCATCTGGGTCGCCA Yes No
No No No CU-1241 chr8: 107870541-107870560 3604 AGTCCCATCTGGGTCGCCA
No Yes No No No CU-1241 chr10: 118251348-118251367 3605
AGTCCCATCTGGGTCGCCA Yes No No No No CU-1241 chr13:
110648656-110648675 3606 AGTCCCATCTGGGTCGCCA Yes No No No No
CU-1241 chr1: 74982888-74982907 3607 AGTCCCATCTGGGTCGCCA No Yes No
No No CU-1241 chr1: 74982864-74982883 3608 AGTCCCATCTGGGTCGCCA No
Yes No No No CU-1241 chrX: 120113204-120113223 3609
AGTCCCATCTGGGTCGCCA Yes No No No No CU-1242 chr7:
148897373-148897391 3610 TCCCCGTACGGGCCACCA Yes No No No No CU-1242
chr6: 159071498-159071516 3611 TCCCCGTACGGGCCACCA Yes No No No No
CU-1243 chr1: 173342843-173342861 3612 GTCCCTTCGTGGTCGCCA No No No
No No CU-1243 chr19: 55148120-55148138 3613 GTCCCTTCGTGGTCGCCA Yes
No No No No CU-1243 chrX: 117299486-117299504 3614
GTCCCTTCGTGGTCGCCA No No No No No CU-1243 chr8: 4429174-4429192
3615 GTCCCTTCGTGGTCGCCA Yes No No No No CU-1243 chr11:
84485385-84485403 3616 GTCCCTTCGTGGTCGCCA Yes Yes No No No CU-1243
chr21: 26073725-26073743 3617 GTCCCTTCGTGGTCGCCA Yes No No No No
CU-1243 chr5: 77142069-77142087 3618 GTCCCTTCGTGGTCGCCA Yes No No
No No CU-1243 chr19: 8350798-8350816 3619 GTCCCTTCGTGGTCGCCA Yes No
No No No CU-1243 chr12: 20827096-20827114 3620 GTCCCTTCGTGGTCGCCA
No No No No No CU-1244 chr1: 159766817-159766838 3621
GTCAGGATGGCCGAGCGGTCT Yes Yes No No No CU-1244 chr1:
159700155-159700176 3622 GTCAGGATGGCCGAGCGGTCT Yes Yes No No No
CU-1244 chr1: 159677946-159677967 3623 GTCAGGATGGCCGAGCGGTCT Yes
Yes Yes No No CU-1244 chr1: 159685364-159685385 3624
GTCAGGATGGCCGAGCGGTCT Yes Yes No No No CU-1244 chr16:
55891954-55891975 3625 GTCAGGATGGCCGAGCGGTCT Yes Yes No No No
CU-1244 chr1: 159692745-159692766 3626 GTCAGGATGGCCGAGCGGTCT Yes
Yes No No No CU-1244 chr1: 159707536-159707557 3627
GTCAGGATGGCCGAGCGGTCT Yes Yes No No No CU-1244 chr1:
240532967-240532988 3628 GTCAGGATGGCCGAGCGGTCT Yes No No No No
CU-1246 chr14: 65014334-65014351 3629 AGGGGGGTAAAAAAAAA Yes No No
No No CU-1246 chr14: 93614119-93614136 3630 AGGGGGGTAAAAAAAAA Yes
No No No No CU-1251 chr12: 31408926-31408943 3631 CCCACCCAGGGACGCCA
No No No No No CU-1251 chr17: 34161556-34161573 3632
CCCACCCAGGGACGCCA Yes Yes Yes No No CU-1251 chr1:
146614798-146614815 3633 CCCACCCAGGGACGCCA Yes No No No No CU-1251
chr19: 33728787-33728804 3634 CCCACCCAGGGACGCCA Yes No No No No
CU-1251 chr9: 136463072-136463089 3635 CCCACCCAGGGACGCCA Yes No No
No No CU-1254 chr4: 2032401-2032419 3636 TCCCCGGCACCTCCACCA No Yes
No No No CU-1264 chr3: 37897506-37897524 3637 GAGGGGGACCAAAAAAAA
Yes Yes No No No CU-1269 chr17: 21946878-21946897 3638
TACCGAGCCTGGTGATAGC No No No No No CU-1269 chr11:
102785624-102785643 3639 TACCGAGCCTGGTGATAGC Yes No No No No
CU-1276 chr17: 7969840-7969862 3640 TCGATTCCCGGCCAATGCACCA No Yes
Yes No Yes CU-1276 chr19: 39807750-39807772 3641
TCGATTCCCGGCCAATGCACCA No No No No No CU-1277 chr1:
153990335-153990358 3642 GAGCCATGATGATACCACTGAGC Yes No No No No
CU-1278 chr5: 79981714-79981731 3643 TAACGGCCGCGGTACCC Yes Yes No
No No CU-1278 chr3: 97818860-97818877 3644 TAACGGCCGCGGTACCC Yes
Yes No No No CU-1281 chr1: 173235999-173236022 3645
GCAGCGCCAGCCTCCCGCCCTAC Yes No No No No CU-1288 chr19:
54685975-54685994 3646 CGTCCATGATGTTCCGCAA No No No No No CU-1293
chr2: 38390703-38390730 3647 AGCAGTGATGTCCTGAAAATTCTGAAG No No No
No No CU-1294 chr5: 79983107-79983127 3648 AAAGGACCTGGCGGTGCTTC Yes
No No No No CU-1294 chr11: 10487796-10487816 3649
AAAGGACCTGGCGGTGCTTC Yes No No No No CU-1294 chr13:
108874524-108874544 3650 AAAGGACCTGGCGGTGCTTC Yes No No No No
CU-1298 chr16: 3178151-3178169 3651 ATCCCGGACGAGCCCCCA Yes No No No
No CU-1298 chr22: 44955360-44955378 3652 ATCCCGGACGAGCCCCCA Yes No
No No No CU-1298 chr11: 49720969-49720987 3653 ATCCCGGACGAGCCCCCA
Yes Yes No No No CU-1298 chr16: 3174130-3174148 3654
ATCCCGGACGAGCCCCCA Yes No No No No CU-1298 chr11: 75624513-75624531
3655 ATCCCGGACGAGCCCCCA Yes No Yes No No CU-1300 chr6:
101499628-101499646 3656 TCCTCACACGGGGCACCA Yes Yes No No No
CU-1300 chr7: 106814117-106814135 3657 TCCTCACACGGGGCACCA Yes Yes
No No No CU-1303 chr4: 151694303-151694321 3658 ATCCCACTTCTGACACCA
Yes Yes No No No CU-1303 chr1: 212585032-212585050 3659
ATCCCACTTCTGACACCA Yes No No No No CU-1303 chr3:
194813519-194813537 3660 ATCCCACTTCTGACACCA Yes No No No No CU-1303
chr2: 55018611-55018629 3661 ATCCCACTTCTGACACCA Yes Yes No No No
CU-1303 chr5: 143373194-143373212 3662 ATCCCACTTCTGACACCA No Yes No
No No CU-1303 chr1: 36261536-36261554 3663 ATCCCACTTCTGACACCA Yes
No No No No
CU-1303 chr12: 67663402-67663420 3664 ATCCCACTTCTGACACCA Yes Yes No
No No CU-1303 chr4: 119344866-119344884 3665 ATCCCACTTCTGACACCA No
Yes No No No CU-1303 chr12: 70175143-70175161 3666
ATCCCACTTCTGACACCA Yes Yes No No No CU-1307 chr1: 9557438-9557458
3667 ACCCCACTATGCTTAGCCCT Yes Yes No Yes Yes CU-1323 chr2:
232028754-232028771 3668 TGTATTGTGAGACATTC Yes No No No No CU-1324
chr4: 3167100-3167117 3669 TCTCGGTGGAACCTCCA Yes No No No No
CU-1324 chr15: 63948450-63948467 3670 TCTCGGTGGAACCTCCA No No No No
No CU-1339 chr8: 141129909-141129928 3671 ATCCCCAGCACCTCCACCA Yes
Yes No No No CU-1345 chr11: 10487827-10487845 3672
AGAACACTACGAGCCACA Yes No No No No CU-1345 chr5: 79983138-79983156
3673 AGAACACTACGAGCCACA Yes No No No No CU-1345 chr13:
108874555-108874573 3674 AGAACACTACGAGCCACA Yes No No No No CU-1352
chr12: 12693348-12693366 3675 ACCCCACTTCTGGTACCA Yes Yes No No No
CU-1352 chr5: 119090314-119090332 3676 ACCCCACTTCTGGTACCA No No No
No No CU-1352 chr14: 56457992-56458010 3677 ACCCCACTTCTGGTACCA Yes
Yes No No No CU-1352 chr7: 7637279-7637297 3678 ACCCCACTTCTGGTACCA
Yes No No No No CU-1352 chr1: 34288353-34288371 3679
ACCCCACTTCTGGTACCA No No No No No CU-1352 chr1: 107581087-107581105
3680 ACCCCACTTCTGGTACCA Yes Yes No No No CU-1352 chr7:
66011743-66011761 3681 ACCCCACTTCTGGTACCA Yes Yes No No No CU-1352
chr7: 119683539-119683557 3682 ACCCCACTTCTGGTACCA Yes No No No No
CU-1352 chr18: 16775205-16775223 3683 ACCCCACTTCTGGTACCA Yes Yes No
No No CU-1352 chr2: 6916389-6916407 3684 ACCCCACTTCTGGTACCA Yes Yes
No No No CU-1352 chr6: 98788231-98788249 3685 ACCCCACTTCTGGTACCA
Yes Yes No No No CU-1352 chr1: 201394394-201394412 3686
ACCCCACTTCTGGTACCA Yes Yes No No No CU-1352 chrX: 85448496-85448514
3687 ACCCCACTTCTGGTACCA No Yes No No No CU-1352 chr8:
140073141-140073159 3688 ACCCCACTTCTGGTACCA Yes Yes No No No
CU-1352 chr12: 8391052-8391070 3689 ACCCCACTTCTGGTACCA Yes No No No
No CU-1352 chrX: 77289492-77289510 3690 ACCCCACTTCTGGTACCA No No No
No No CU-1352 chr2: 116637798-116637816 3691 ACCCCACTTCTGGTACCA Yes
No No No No CU-1352 chr4: 72493755-72493773 3692 ACCCCACTTCTGGTACCA
Yes No No No No CU-1352 chr15: 94045767-94045785 3693
ACCCCACTTCTGGTACCA Yes Yes No No No CU-1352 chrX: 85947724-85947742
3694 ACCCCACTTCTGGTACCA No Yes No No No CU-1352 chr20:
60081974-60081992 3695 ACCCCACTTCTGGTACCA Yes No No No No CU-1352
chr18: 31113119-31113137 3696 ACCCCACTTCTGGTACCA Yes Yes No No No
CU-1352 chr11: 8446114-8446132 3697 ACCCCACTTCTGGTACCA Yes Yes No
No No CU-1352 chr6: 140796063-140796081 3698 ACCCCACTTCTGGTACCA Yes
Yes No No No CU-1352 chr22: 19662967-19662985 3699
ACCCCACTTCTGGTACCA Yes No No No No CU-1352 chrX:
116622706-116622724 3700 ACCCCACTTCTGGTACCA Yes No No No No CU-1352
chr22: 43646515-43646533 3701 ACCCCACTTCTGGTACCA Yes No No No No
CU-1352 chr11: 3516223-3516241 3702 ACCCCACTTCTGGTACCA No No No No
No CU-1352 chr10: 123734159-123734177 3703 ACCCCACTTCTGGTACCA No No
No No No CU-1352 chr18: 120806-120824 3704 ACCCCACTTCTGGTACCA Yes
Yes No No No CU-1352 chr1: 174219317-174219335 3705
ACCCCACTTCTGGTACCA Yes Yes No No No CU-1352 chr7:
156114211-156114229 3706 ACCCCACTTCTGGTACCA Yes No No No No CU-1352
chr3: 107173811-107173829 3707 ACCCCACTTCTGGTACCA Yes Yes No No No
CU-1363 chr1: 17095207-17095225 3708 CGTTCGCGCTTTCCCCTG Yes Yes No
No No CU-1363 chr1: 147460729-147460747 3709 CGTTCGCGCTTTCCCCTG No
Yes No No No CU-1363 chr14: 34085816-34085834 3710
CGTTCGCGCTTTCCCCTG Yes Yes No No No CU-1363 chr14:
34095182-34095200 3711 CGTTCGCGCTTTCCCCTG Yes Yes No No No CU-1368
chr6: 27173063-27173081 3712 GACGAGGTGGCCGAGTGG Yes Yes Yes No No
CU-1368 chr6: 28288793-28288811 3713 GACGAGGTGGCCGAGTGG Yes Yes No
No No CU-1368 chr11: 65872166-65872184 3714 GACGAGGTGGCCGAGTGG Yes
Yes Yes Yes Yes CU-1368 chr15: 38673378-38673396 3715
GACGAGGTGGCCGAGTGG Yes Yes Yes No Yes CU-1368 chr6:
27373753-27373771 3716 GACGAGGTGGCCGAGTGG Yes Yes No No No CU-1368
chr2: 228333400-228333418 3717 GACGAGGTGGCCGAGTGG Yes No No No No
CU-1368 chr6: 28673159-28673177 3718 GACGAGGTGGCCGAGTGG Yes Yes No
No No CU-1368 chr17: 8030908-8030926 3719 GACGAGGTGGCCGAGTGG Yes
Yes No No Yes CU-1369 chr15: 94627153-94627171 3720
TCCCCGGCATCTCCACCA No No No No No CU-1370 chr1: 232795752-232795772
3721 CTGATTGCTCCTGTCTGATT No Yes No No No CU-1371 chr13:
108874496-108874517 3722 TCTAGAGGAGCCTGTTCTGTA Yes No Yes Yes No
CU-1379 chr1: 165950616-165950638 3723 TCGGGTGCGAGAGGTCCCGGGT Yes
Yes Yes Yes Yes CU-1380 chr11: 10488308-10488331 3724
ATAGGTTTGGTCCTAGCCTTTCT Yes No No No No CU-1381 chr1:
169836691-169836713 3725 TCGATTCCCGGTCAGGGAACCA No No No No No
CU-1382 chr6: 27555431-27555459 3726 TCCTCGTTAGTATAGTGGTGAGTATCCC
Yes Yes No No No CU-1382 chr1: 159677282-159677310 3727
TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes Yes No No CU-1382 chr17:
8066324-8066352 3728 TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No No
CU-1382 chr1: 159699491-159699519 3729 TCCTCGTTAGTATAGTGGTGAGTATCCC
Yes Yes No No No CU-1382 chr1: 159692081-159692109 3730
TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No No CU-1382 chr6:
27579501-27579529 3731 TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No
No CU-1382 chr1: 159684700-159684728 3732
TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No No CU-1382 chr12:
123990189-123990217 3733 TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No
No CU-1382 chr12: 94953929-94953957 3734
TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes Yes Yes No CU-1382 chr12:
123977887-123977915 3735 TCCTCGTTAGTATAGTGGTGAGTATCCC Yes No No No
No CU-1382 chr1: 159706872-159706900 3736
TCCTCGTTAGTATAGTGGTGAGTATCCC Yes Yes No No No CU-1388 chr1:
144110633-144110661 3737 TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No
No CU-1388 chr1: 159698476-159698504 3738
TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No No CU-1388 chr1:
159705856-159705884 3739 TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No
No CU-1388 chr1: 159683685-159683713 3740
TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No No CU-1388 chr1:
247135069-247135097 3741 TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No
No CU-1388 chr1: 159691065-159691093 3742
TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No No No CU-1388 chr6:
126143129-126143157 3743 TCCCTGGTGGTCTAGTGGTTAGGATTCG Yes Yes No
Yes Yes CU-1396 chr1: 556086-556103 3744 TAAGTGTTTGTGGGTTA No No No
No No CU-1403 chr17: 7969788-7969810 3745 GCATTGGTGGTTCAGTGGTAGA No
Yes Yes No Yes CU-1403 chr16: 69370491-69370513 3746
GCATTGGTGGTTCAGTGGTAGA Yes Yes Yes No No CU-1403 chr1:
17061002-17061024 3747 GCATTGGTGGTTCAGTGGTAGA No No Yes No No
CU-1403 chr3: 15524502-15524524 3748 GCATTGGTGGTTCAGTGGTAGA Yes No
No No No CU-1403 chr16: 69380097-69380119 3749
GCATTGGTGGTTCAGTGGTAGA Yes Yes Yes Yes Yes CU-1403 chr1:
227740226-227740248 3750 GCATTGGTGGTTCAGTGGTAGA Yes Yes No No No
CU-1403 chr1: 16745069-16745091 3751 GCATTGGTGGTTCAGTGGTAGA Yes No
Yes No No CU-1403 chr1: 159760309-159760331 3752
GCATTGGTGGTTCAGTGGTAGA Yes Yes No No No CU-1403 chr2:
156965953-156965975 3753 GCATTGGTGGTTCAGTGGTAGA Yes Yes No No No
CU-1403 chrX: 64154569-64154591 3754 GCATTGGTGGTTCAGTGGTAGA Yes Yes
No No No CU-1403 chr6: 27978713-27978735 3755
GCATTGGTGGTTCAGTGGTAGA Yes Yes No No No CU-1440 chr5:
180533270-180533287 3756 TGGTTATCACGTTCGCC Yes Yes No No No CU-1440
chr5: 180456690-180456707 3757 TGGTTATCACGTTCGCC Yes Yes No No No
CU-1440 chr6: 27281886-27281903 3758 TGGTTATCACGTTCGCC Yes Yes No
No No CU-1440 chr1: 147565219-147565236 3759 TGGTTATCACGTTCGCC Yes
Yes No No No CU-1440 chr5: 180461899-180461916 3760
TGGTTATCACGTTCGCC Yes Yes No No No CU-1453 chr3:
191522810-191522827 3761 CCCTGCTCGCTGCGCCA Yes Yes No No No CU-1457
chr7: 43102939-43102961 3762 TTCTCACTACTGCACTTGACTA Yes No No No No
CU-1457 chr14: 67153778-67153800 3763 TTCTCACTACTGCACTTGACTA Yes No
No No No CU-1457 chr1: 238571371-238571393 3764
TTCTCACTACTGCACTTGACTA Yes Yes No No No CU-1457 chr2:
147946177-147946199 3765 TTCTCACTACTGCACTTGACTA Yes Yes No
No No CU-1470 chr16: 30675216-30675234 3766 CTCCTGGCTGGCTCGCCA Yes
Yes No No No CU-1470 chr14: 43074235-43074253 3767
CTCCTGGCTGGCTCGCCA Yes No No No No CU-1477 chr17: 26124435-26124459
3768 CTCCCACTGCTTCACTTGACTAGC No Yes No No No CU-1477 chr17:
27331095-27331119 3769 CTCCCACTGCTTCACTTGACTAGC Yes Yes No No No
CU-1477 chr10: 21810723-21810747 3770 CTCCCACTGCTTCACTTGACTAGC Yes
No No No No CU-1477 chr14: 99119179-99119203 3771
CTCCCACTGCTTCACTTGACTAGC Yes Yes No No No CU-1477 chr11:
107460922-107460946 3772 CTCCCACTGCTTCACTTGACTAGC Yes Yes No No No
CU-1477 chr4: 154407515-154407539 3773 CTCCCACTGCTTCACTTGACTAGC Yes
Yes No No No CU-1486 chr17: 59577172-59577189 3774
CTGCTGTGATGACATTC Yes Yes No No No CU-1488 chr1: 4671944-4671961
3775 TCCTGCCGCGGTCGCCA Yes Yes No No No CU-1513 chr17:
59577217-59577244 3776 GCGGGTGATGCGAACTGGAGTCTGAGC Yes No Yes No No
CU-1524 chr7: 148269562-148269586 3777 CCCCCACAACCGCGCTTGACTAGC Yes
Yes Yes No No CU-1528 chr17: 8066916-8066935 3778
TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528 chr6:
27167511-27167530 3779 TAGGGGTATGATTCTCGCT Yes Yes Yes No No
CU-1528 chr14: 20222026-20222045 3780 TAGGGGTATGATTCTCGCT Yes Yes
No Yes Yes CU-1528 chr14: 20151440-20151459 3781
TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528 chr6:
26663488-26663507 3782 TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528
chr16: 3172676-3172695 3783 TAGGGGTATGATTCTCGCT Yes Yes No No No
CU-1528 chr14: 20147375-20147394 3784 TAGGGGTATGATTCTCGCT Yes Yes
No No No CU-1528 chr5: 180548500-180548519 3785 TAGGGGTATGATTCTCGCT
Yes Yes No No No CU-1528 chr16: 3148935-3148954 3786
TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528 chr16: 3179646-3179665
3787 TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528 chr4:
18668214-18668233 3788 TAGGGGTATGATTCTCGCT Yes No No No No CU-1528
chr1: 165950597-165950616 3789 TAGGGGTATGATTCTCGCT Yes Yes Yes No
Yes CU-1528 chr16: 3182001-3182020 3790 TAGGGGTATGATTCTCGCT Yes No
No No No CU-1528 chr11: 75624216-75624235 3791 TAGGGGTATGATTCTCGCT
Yes Yes Yes No No CU-1528 chr16: 3162061-3162080 3792
TAGGGGTATGATTCTCGCT Yes Yes No No No CU-1528 chr7:
128210751-128210770 3793 TAGGGGTATGATTCTCGCT Yes Yes Yes Yes Yes
CU-1538 chrX: 16840335-16840361 3794 GGCTGGTCCGAGTGCAGTGGTGTTTA Yes
No No No No CU-1538 chr13: 98986625-98986651 3795
GGCTGGTCCGAGTGCAGTGGTGTTTA Yes Yes No No No CU-1538 chr10:
128599365-128599391 3796 GGCTGGTCCGAGTGCAGTGGTGTTTA Yes Yes No No
No CU-1538 chr7: 148311779-148311805 3797
GGCTGGTCCGAGTGCAGTGGTGTTTA Yes No Yes No No CU-1538 chr15:
73062744-73062770 3798 GGCTGGTCCGAGTGCAGTGGTGTTTA No No No No No
CU-1538 chrX: 116932310-116932336 3799 GGCTGGTCCGAGTGCAGTGGTGTTTA
Yes Yes No No No CU-1538 chr11: 47705094-47705120 3800
GGCTGGTCCGAGTGCAGTGGTGTTTA Yes No No No No CU-1542 chr7:
148291339-148291362 3801 GGCTGGTCCGATGGTAGTGGGTT Yes Yes Yes No No
CU-1542 chr6: 33275355-33275378 3802 GGCTGGTCCGATGGTAGTGGGTT Yes
Yes No No No CU-1545 chr17: 19031996-19032016 3803
CCACGAGGAAGAGAGGTAGC No No No No No CU-1550 chr6: 26438546-26438564
3804 CGGAAGCGTGCTGGGCCC Yes Yes No No No CU-1550 chr6:
27853657-27853675 3805 CGGAAGCGTGCTGGGCCC Yes Yes No No No CU-1550
chr6: 26421369-26421387 3806 CGGAAGCGTGCTGGGCCC Yes Yes No No No
CU-1550 chr6: 27408781-27408799 3807 CGGAAGCGTGCTGGGCCC Yes Yes No
No No CU-1550 chr6: 27668617-27668635 3808 CGGAAGCGTGCTGGGCCC Yes
Yes No No No CU-1557 chr17: 19033934-19033957 3809
GGAGAGAACGCGGTCTGAGTGGT Yes No No No No CU-1557 chr17:
18907957-18907980 3810 GGAGAGAACGCGGTCTGAGTGGT Yes No No No No
CU-1557 chr17: 19032115-19032138 3811 GGAGAGAACGCGGTCTGAGTGGT Yes
No No No No CU-1557 chr17: 18956457-18956480 3812
GGAGAGAACGCGGTCTGAGTGGT Yes No No No No CU-1557 chr17:
18906143-18906166 3813 GGAGAGAACGCGGTCTGAGTGGT Yes No No No No
CU-1570 chr17: 36922634-36922653 3814 ATCCCCAGCATCTCCACCA Yes No No
No No CU-1575 chr7: 148291405-148291430 3815
CCCCCCACTGCTAAATTTGACTGGA Yes Yes Yes No No miRNA deposited in
miRBase database Seq ID Conservation ID Genomic Coordinates No.
Sequence Chimp Monkey Dog Mouse Rat hsa-mir-1322 chr8:
10720294-10720313 3816 CAGCATCAGCAGCATCATC Yes No No No No
hsa-mir-1323 chr19: 58867043-58867065 3817 TCAAAACTGAGGGGCATTTTCT
Yes Yes No No No hsa-mir-1321 chrX: 84977492-84977510 3818
CAGGGAGGTGAATGTGAT Yes No No No No hsa-mir-29c* chr1:
206041870-206041892 3819 GAACACCAGGAGAAATCGGTCA Yes Yes Yes Yes Yes
hsa-mir-1324 chr3: 75762663-75762687 3820 CCAGACAGAATTCTATGCACTTTC
No No No No No hsa-mir-675 chr11: 1974605-1974628 3821
CACTGTGGGCCCTCTCCGCACCA No Yes Yes Yes Yes hsa-mir-183* chr7:
129202003-129202025 3822 TTATGGCCCTTCGGTAATTCAC Yes Yes Yes Yes Yes
hsa-mir-335* chr7: 129923238-129923260 3823 TTTTTCATTATTGCTCCTGACC
Yes Yes Yes Yes No hsa-mir-19a* chr13: 90801158-90801180 3824
AGTTTTGCATAGTTGCACTACA Yes No Yes Yes Yes hsa-mir-132* chr17:
1900008-1900030 3825 AGTAACAATCGAAAGCCACGGT No Yes Yes Yes Yes
hsa-mir-182 chr7: 129197522-129197546 3826 AGTGTGAGTTCTACCATTGCCAAA
Yes Yes Yes Yes Yes hsa-mir-122 chr18: 54269299-54269321 3827
TGGAGTGTGACAATGGTGTTTG Yes Yes Yes Yes Yes hsa-mir-16-2* chr3:
161605278-161605300 3828 CCAATATTACTGTGCTGCTTTA Yes Yes Yes Yes Yes
hsa-mir-124 chr8: 65454320-65454340 3829 TAAGGCACGCGGTGAATGCC Yes
Yes Yes Yes Yes hsa-mir-124 chr8: 9798320-9798340 3830
GGCATTCACCGCGTGCCTTA No Yes Yes Yes Yes hsa-mir-124 chr20:
61280348-61280368 3831 TAAGGCACGCGGTGAATGCC No Yes Yes Yes Yes
hsa-mir-126 chr9: 138684925-138684947 3832 TCGTACCGTGAGTAATAATGCG
Yes Yes Yes Yes Yes hsa-mir-31* chr9: 21502119-21502141 3833
ATGGCAATATGTTGGCATAGCA Yes Yes Yes Yes Yes hsa-mir-128 chr2:
136139485-136139506 3834 TCACAGTGAACCGGTCTCTTT Yes Yes Yes Yes Yes
hsa-mir-128 chr3: 35761022-35761043 3835 TCACAGTGAACCGGTCTCTTT Yes
Yes Yes Yes Yes hsa-mir-19a chr13: 90801193-90801216 3836
TGTGCAAATCTATGCAAAACTGA Yes No Yes Yes Yes hsa-mir-524-5p chr19:
58906082-58906104 3837 CTACAAAGGGAAGCACTTTCTC Yes Yes No No No
hsa-mir-19b chrX: 133131378-133131401 3838 TCAGTTTTGCATGGATTTGCACA
Yes Yes Yes Yes Yes hsa-mir-19b chr13: 90801499-90801522 3839
TGTGCAAATCCATGCAAAACTGA Yes Yes Yes Yes Yes hsa-mir-148b* chr12:
53017290-53017312 3840 AAGTTCTGTTATACACTCAGGC Yes Yes Yes Yes Yes
hsa-mir-1257 chr20: 59962071-59962092 3841 GGTCAGAACCCATCATTCACT No
No No No No hsa-mir-1254 chr10: 70189097-70189121 3842
AGCCTGGAAGCTGGAGCCTGCAGT Yes Yes No No No hsa-mir-455-3p chr9:
116011587-116011608 3843 GCAGTCCATGGGCATATACAC Yes Yes Yes Yes Yes
hsa-mir-1253 chr17: 2598182-2598203 3844 TGCAGGCTGATCTTCTTCTCT Yes
No No No No hsa-mir-1250 chr17: 76721659-76721680 3845
AAAGGCCACATCCAGCACCGT Yes Yes No No No hsa-mir-1251 chr12:
96409821-96409842 3846 ACTCTAGCTGCCAAAGGCGCT Yes Yes Yes Yes Yes
hsa-mir-1258 chr2: 180433852-180433873 3847 AGTTAGGATTAGGTCGTGGAA
Yes Yes No No No hsa-mir-1258 chr2: 180433816-180433837 3848
TTCCACGACCTAATCCTAACT Yes Yes No No No hsa-mir-1259 chr20:
47330268-47330289 3849 ATATATGATGACTTAGCTTTT Yes Yes No No No
hsa-mir-1207-3p chr8: 129130630-129130648 3850 TCAGCTGGCCCTCATTTC
Yes Yes No Yes No hsa-mir-34c-3p chr11: 110889418-110889440 3851
AATCACTAACCACACGGCCAGG Yes Yes Yes Yes Yes hsa-mir-489 chr7:
92951194-92951216 3852 GCTGCCGTATATGTGATGTCAC Yes Yes Yes No Yes
hsa-mir-488 chr1: 175265132-175265153 3853 GACCAAGAAATAGCCTTTCAA
Yes Yes Yes Yes Yes
hsa-mir-556-5p chr1: 160578974-160578996 3854
GATGAGCTCATTGTAATATGAG Yes No No No No hsa-mir-484 chr16:
15644658-15644680 3855 TCAGGCTCAGTCCCCTCCCGAT Yes Yes No Yes Yes
hsa-mir-523* chr19: 58893465-58893487 3856 CTCTAGAGGGAAGCGCTTTCTG
Yes No No No No hsa-mir-125b-1* chr11: 121475686-121475708 3857
AGCTCCCAAGAGCCTAACCCGT Yes Yes Yes Yes Yes hsa-mir-7-2* chr15:
86956130-86956152 3858 CAACAAATCCCAGTCTACCTAA Yes Yes No No No
hsa-mir-569 chr3: 172307161-172307182 3859 ACTTTCCAGGATTCATTAACT
Yes Yes Yes No No hsa-mir-574-5p chr4: 38546071-38546094 3860
TGAGTGTGTGTGTGTGAGTGTGT No No Yes Yes No hsa-mir-342-5p chr14:
99645762-99645783 3861 AGGGGTGCTATCTGTGATTGA Yes Yes Yes Yes Yes
hsa-mir-379 chr14: 100558160-100558181 3862 TGGTAGACTATGGAACGTAGG
Yes Yes Yes Yes Yes hsa-mir-520b chr19: 58896332-58896353 3863
AAAGTGCTTCCTTTTAGAGGG Yes Yes No No No hsa-mir-520e chr19:
58870829-58870850 3864 AAAGTGCTTCCTTTTTGAGGG Yes No No No No
hsa-mir-371-5p chr19: 58985745-58982765 3865 ACTCAAACTGTGGGGGCACT
Yes Yes Yes No Yes hsa-mir-520g chr19: 58917285-58917309 3866
ACAAAGTGCTTCCCTTTAGAGTGT Yes Yes No No No hsa-mir-520f chr19:
58877278-58877300 3867 AAGTGCTTCCTTTTAGAGGGTT Yes No No No No
hsa-mir-520h chr19: 58937631-58937653 3868 ACAAAGTGCTTCCCTTTAGAGT
Yes No No No No hsa-mir-219-5p chr9: 130194775-130194796 3869
AGAATTGCGTTTGGACAATCA Yes Yes Yes Yes Yes hsa-mir-219-5p chr6:
33283609-33283630 3870 TGATTGTCCAAACGCAATTCT Yes Yes Yes Yes Yes
hsa-mir-140-5p chr16: 68524506-68524528 3871 CAGTGGTTTTACCCTATGGTAG
Yes Yes Yes Yes Yes hsa-mir-423-5p chr17: 25468238-25468261 3872
TGAGGGGCAGAGAGCGAGACTTT Yes Yes Yes Yes Yes hsa-mir-30b* chr8:
135881956-135881978 3873 GAAGTAAACATCCACCTCCCAG Yes Yes Yes No No
hsa-mir-195 chr17: 6861709-6861730 3874 GCCAATATTTCTGTGCTGCTA Yes
Yes Yes Yes Yes hsa-mir-194 chr11: 64415451-64415473 3875
TCCACATGGAGTTGCTGTTACA Yes Yes Yes Yes Yes hsa-mir-194 chr1:
218358170-218358192 3876 TCCACATGGAGTTGCTGTTACA Yes Yes Yes Yes Yes
hsa-mir-197 chr1: 109943084-109943106 3877 TTCACCACCTTCTCCACCCAGC
Yes Yes Yes No No hsa-mir-191 chr3: 49033108-49033131 3878
CAGCTGCTTTTGGGATTCCGTTG Yes Yes Yes Yes Yes hsa-mir-190 chr15:
60903222-60903244 3879 TGATATGTTTGATATATTAGGT Yes Yes Yes Yes Yes
hsa-mir-192 chr11: 64415250-64415271 3880 GGCTGTCAATTCATAGGTCAG Yes
Yes Yes Yes Yes hsa-mir-449a chr5: 54502170-54502192 3881
ACCAGCTAACAATACACTGCCA Yes Yes Yes Yes Yes hsa-mir-339-3p chr7:
1029116-1029139 3882 CGGCTCTGTCGTCGAGGCGCTCA Yes Yes No Yes Yes
hsa-mir-508-5p chrX: 146126189-146126212 3883
CATGAGTGACGCCCTCTGGAGTA Yes Yes No No No hsa-mir-1284 chr3:
71673879-71673901 3884 GAAAAGCCAGGGTCTGTATAGA Yes No No Yes Yes
hsa-mir-362-5p chrX: 49660315-49660339 3885
AATCCTTGGAACCTAGGTGTGAGT Yes Yes Yes Yes Yes hsa-mir-125a-3p chr19:
56888370-56888392 3886 ACAGGTGAGGTTCTTGGGAGCC Yes Yes Yes Yes Yes
hsa-mir-34a* chr1: 9134338-9134360 3887 AGGGCAGTATACTTGCTGATTG Yes
Yes Yes Yes Yes hsa-mir-373 chr19: 58983813-58983836 3888
GAAGTGCTTCGATTTTGGGGTGT Yes Yes Yes No No hsa-mir-502-3p chrX:
49665996-49666018 3889 AATGCACCTGGGCAAGGATTCA Yes Yes Yes Yes Yes
hsa-mir-200b chr1: 1092402-1092424 3890 TAATACTGCCTGGTAATGATGA No
No Yes Yes Yes hsa-mir-200c chr12: 6943165-6943188 3891
TAATACTGCCGGGTAATGATGGA Yes Yes Yes Yes Yes hsa-mir-200a chr1:
1093158-1093180 3892 TAACACTGTCTGGTAACGATGT Yes Yes Yes Yes Yes
hsa-mir-410 chr14: 100602050-100602071 3893 AATATAACACAGATGGCCTGT
Yes Yes Yes Yes Yes hsa-mir-411 chr14: 100559429-100559450 3894
TAGTAGACCGTATAGCGTACG Yes Yes Yes Yes Yes hsa-mir-412 chr14:
100601589-100601612 3895 ACTTCACCTGGTCCACTAGCCGT Yes Yes No Yes Yes
hsa-mir-555 chr1: 153582779-153582800 3896 ATCAGAGGTTCAGCTTACCCT
Yes Yes No Yes No hsa-mir-554 chr1: 149784910-149784931 3897
GCTAGTCCTGACTCAGCCAGT Yes Yes No No No hsa-mir-493* chr14:
100405164-100405186 3898 TTGTACATGGTAGGCTTTCATT No Yes Yes Yes Yes
hsa-mir-550 chr7: 30295955-30295978 3899 AGTGCCTGAGGGAGTAAGAGCCC
Yes Yes No No No hsa-mir-550 chr7: 32739138-32739161 3900
AGTGCCTGAGGGAGTAAGAGCCC Yes Yes No No No hsa-mir-553 chr1:
100519399-100519420 3901 AAAACGGTGAGATTTTGTTTT Yes No No No No
hsa-mir-193a-5p chr17: 26911147-26911169 3902
TGGGTCTTTGCGGGCGAGATGA Yes Yes Yes Yes Yes hsa-mir-876-3p chr9:
28853633-28853655 3903 TGAATTACTTTGTAAACCACCA Yes Yes Yes Yes Yes
hsa-mir-139-3p chr11: 72003757-72003779 3904 ACTCCAACAGGGCCGCGTCTCC
Yes Yes Yes Yes Yes hsa-mir-30a chr6: 72170018-72170040 3905
CTTCCAGTCGAGGATGTTTACA Yes Yes Yes Yes Yes hsa-mir-30b chr8:
135881994-135882016 3906 AGCTGAGTGTAGGATGTTTACA Yes Yes Yes Yes Yes
hsa-mir-30c chr1: 40995558-40995581 3907 TGTAAACATCCTACACTCTCAGC
Yes Yes Yes Yes Yes hsa-mir-30c chr6: 72143426-72143449 3908
GCTGAGAGTGTAGGATGTTTACA Yes Yes Yes Yes Yes hsa-mir-30d chr8:
135886343-135886365 3909 CTTCCAGTCGGGGATGTTTACA Yes Yes Yes Yes Yes
hsa-mir-30e chr1: 40992629-40992651 3910 TGTAAACATCCTTGACTGGAAG Yes
Yes Yes Yes Yes hsa-mir-374b* chrX: 73355116-73355138 3911
AATGATAATACAACCTGCTAAG Yes Yes Yes Yes Yes hsa-mir-548b-3p chr6:
119431925-119431947 3912 ACAAAAGCAACTGAGGTTCTTG Yes No No No No
hsa-mir-515-5p chr19: 58874081-58874105 3913
TTCTCCAAAAGAAAGCACTTTCTG Yes Yes No No No hsa-mir-515-5p chr19:
58880087-58880111 3914 TTCTCCAAAAGAAAGCACTTTCTG Yes Yes No No No
hsa-mir-429 chr1: 1094297-1094319 3915 TAATACTGTCTGGTAAAACCGT No
Yes Yes Yes Yes hsa-mir-486-5p chr8: 41637118-41637140 3916
TCCTGTACTGAGCTGCCCCGAG Yes Yes Yes Yes Yes hsa-mir-486-5p chr8:
41637158-41637180 3917 CTCGGGGCAGCTCAGTACAGGA Yes Yes Yes Yes Yes
hsa-mir-1206 chr8: 129090328-129090349 3918 TGTTCATGTAGATGTTTAAGC
Yes Yes No No No hsa-mir-99a chr21: 16833291-16833313 3919
AACCCGTAGATCCGATCTTGTG Yes Yes Yes Yes Yes hsa-mir-188-3p chrX:
49654901-49654922 3920 CTCCCACATGCAGGGTTTGCA Yes Yes Yes Yes Yes
hsa-mir-99b chr19: 56887682-56887704 3921 CACCCGTAGAACCGACCTTGCG
Yes Yes Yes Yes Yes hsa-mir-300 chr14: 100577503-100577525 3922
TATACAAGGGCAGACTCTCTCT Yes No No No No hsa-mir-193b chr16:
14305374-14305396 3923 AACTGGCCCTCAAAGTCCCGCT Yes Yes Yes Yes No
hsa-mir-1203 chr17: 43588846-43588867 3924 GAGCTGCATCCTGGCTCCGGG
Yes Yes No No No hsa-mir-30c-1* chr1: 40995597-40995619 3925
CTGGGAGAGGGTTGTTTACTCC Yes Yes Yes Yes Yes hsa-mir-19b-2* chrX:
133131422-133131444 3926 TGAAATGCAAACCTGCAAAACT Yes Yes Yes Yes Yes
hsa-mir-1286 chr22: 18616667-18616688 3927 AGGGCTCATCTTGGTCCTGCA
Yes No No No No hsa-let-7g* chr3: 52277335-52277356 3928
GCAAGGCAGTGGCCTGTACAG Yes Yes Yes Yes No hsa-mir-361-3p chrX:
85045301-85045324 3929 AAATCAGAATCACACCTGGGGGA Yes Yes Yes Yes Yes
hsa-mir-518a-5p chr19: 58926084-58926104 3930 CTGCAAAGGGAAGCCCTTTC
Yes No No No No hsa-mir-518a-5p chr19: 58934413-58934433 3931
CTGCAAAGGGAAGCCCTTTC Yes No No No No hsa-mir-604 chr10:
29873953-29873972 3932 GTCCTGAATTCCGCAGCCT Yes Yes No No No
hsa-mir-485-5p chr14: 100591516-100591538 3933
AGAGGCTGGCCGTGATGAATTC Yes Yes Yes Yes Yes hsa-mir-452* chrX:
150878761-150878783 3934 CACTTACTTCTTTGCAGATGAG Yes Yes Yes No No
hsa-mir-450b-5p chrX: 133501926-133501948 3935
TATTCAGGAACATATTGCAAAA Yes Yes Yes No No hsa-mir-505 chrX:
138833984-138834006 3936 AGGAAACCAGCAAGTGTTGACG Yes Yes Yes Yes Yes
hsa-mir-299-5p chr14: 100559889-100559911 3937
TGGTTTACCGTCCCACATACAT Yes
Yes Yes Yes Yes hsa-mir-181a-2* chr9: 126494617-126494639 3938
ACCACTGACCGTTGACTGTACC Yes Yes Yes No No hsa-mir-29b-2* chr1:
206042459-206042481 3939 CTAAGCCACCATGTGAAACCAG Yes Yes Yes Yes Yes
hsa-mir-323-3p chr14: 100561871-100561892 3940
CACATTACACGGTCGACCTCT Yes Yes Yes Yes Yes hsa-mir-1256 chr1:
21187456-21187478 3941 AGCTAGTGAGAAGTCAATGCCT Yes Yes No No No
hsa-mir-144* chr17: 24212726-24212748 3942 CTTACAGTATATGATGATATCC
Yes Yes Yes Yes Yes hsa-mir-1280 chr3: 129563701-129563718 3943
TCCCACCGCTGCCACCC Yes Yes No No No hsa-mir-379* chr14:
100558198-100558220 3944 TATGTAACATGGTCCACTAACT Yes Yes Yes Yes Yes
hsa-mir-1252 chr12: 78337171-78337193 3945 AGAAGGAAATTGAATTCATTTA
Yes Yes No No No hsa-mir-324-5p chr17: 7067384-7067407 3946
ACACCAATGCCCTAGGGGATGCG Yes Yes Yes Yes Yes hsa-mir-516b* chr19:
58920562-58920580 3947 TGCTTCCTTTCAGAGGGT Yes No No No No
hsa-mir-516b* chr19: 58931970-58931988 3948 TGCTTCCTTTCAGAGGGT Yes
Yes No No No hsa-mir-18b chrX: 133131779-133131802 3949
CTAACTGCACTAGATGCACCTTA Yes Yes Yes Yes Yes hsa-mir-17 chr13:
90800872-90800895 3950 CAAAGTGCTTACAGTGCAGGTAG Yes Yes Yes Yes Yes
hsa-mir-16 chr3: 161605235-161605257 3951 TAGCAGCACGTAAATATTGGCG
Yes Yes Yes Yes Yes hsa-mir-16 chr13: 49521163-49521185 3952
CGCCAATATTTACGTGCTGCTA Yes Yes Yes Yes No hsa-mir-26b* chr2:
218975658-218975680 3953 CCTGTTCTCCATTACTTGGCTC Yes Yes Yes Yes Yes
hsa-mir-618 chr12: 79853705-79853728 3954 ACTCAGAAGGACAAGTAGAGTTT
Yes Yes No No No hsa-mir-331-3p chr12: 94226386-94226407 3955
GCCCCTGGGCCTATCCTAGAA Yes Yes Yes Yes Yes hsa-mir-605 chr10:
52729353-52729376 3956 TAAATCCCATGGTGCCTTCTCCT Yes No No No No
hsa-mir-376a chr14: 100576914-100576935 3957 ATCATAGAGGAAAATCCACGT
Yes Yes Yes No No hsa-mir-376a chr14: 100576207-100576228 3858
ATCATAGAGGAAAATCCACGT Yes Yes Yes No Yes hsa-mir-376b chr14:
100576586-100576608 3959 ATCATAGAGGAAAATCCATGTT Yes Yes Yes Yes Yes
hsa-mir-376c chr14: 100575821-100575842 3960 ATCATAGAGGAAATTCCACGT
Yes Yes Yes Yes Yes hsa-mir-601 chr9: 125204666-125204688 3961
CTCCTCCAACAATCCTAGACCA Yes Yes No No No hsa-mir-600 chr9:
124913660-124913683 3962 GAGCAAGGCTCTTGTCTGTAAGT Yes Yes No No No
hsa-mir-603 chr10: 24604679-24604701 3963 CACACACTGCAATTACTTTTGC No
Yes No No No hsa-mir-602 chr9: 139852706-139852729 3964
GACACGGGCGACAGCTGCGGCCC Yes No No No No hsa-mir-609 chr10:
105968596-105968616 3965 AGAGATGAGAGAAACACCCT Yes Yes No No No
hsa-mir-608 chr10: 102724746-102724771 3966
AGGGGTGGTGTTGGGACAGCTCCGT Yes No No No No hsa-mir-551b* chr3:
169752356-169752378 3967 GAAATCAAGCGTGGGTGAGACC Yes Yes Yes Yes Yes
hsa-mir-544 chr14: 100584801-100584823 3968 ATTCTGCATTTTTAGCAAGTTC
Yes Yes Yes Yes No hsa-mir-664* chr1: 218440550-218440574 3969
ATCCAATCATTTTCCCTAGCCAGT Yes Yes Yes No No hsa-mir-409-5p chr14:
100601403-100601426 3970 AGGTTACCCGAGCAACTTTGCAT Yes Yes Yes Yes
Yes hsa-mir-136* chr14: 100420839-100420861 3971
CATCATCGTCTCAAATGAGTCT Yes Yes Yes Yes Yes hsa-mir-1282 chr15:
41873221-41873241 3972 AAGCAGAAAAAGGCAAACGA Yes Yes Yes Yes Yes
hsa-mir-519c-5p chr19: 58881549-58881571 3973
CTCTAGAGGGAAGCGCTTTCTG Yes No No No No hsa-mir-1208 chr8:
129231554-129231574 3974 TCACTGTTCAGACAGGCGGA Yes Yes No Yes Yes
hsa-mir-1205 chr8: 129042067-129042087 3975 TCTGCAGGGTTTGCTTTGAG
Yes No No Yes Yes hsa-mir-663b chr2: 132731012-132731034 3976
CCTCAGGCACGGCCGGGCCACC Yes No No No No hsa-mir-1201 chr14:
19864455-19864479 3977 TCAGAGCATGTGTTTAATCAGGCT Yes Yes Yes No No
hsa-mir-1200 chr7: 36925532-36925554 3978 GAGGCTCAGAATGGCTCAGGAG
Yes No No No No hsa-mir-338-5p chr17: 76714317-76714339 3979
CACTCAGCACCAGGATATTGTT Yes Yes Yes Yes Yes hsa-mir-1202 chr6:
156309634-156309655 3980 GTGCCAGCTGCAGTGGGGGAG Yes Yes No No No
hsa-mir-501-5p chrX: 49661082-49661104 3981 AATCCTTTGTCCCTGGGTGAGA
Yes Yes No Yes Yes hsa-mir-519b-5p chr19: 58890290-58890312 3982
CTCTAGAGGGAAGCGCTTTCTG Yes Yes No No No hsa-mir-101* chr1:
65296747-65296769 3983 AGCATCAGCACTGTGATAACTG Yes Yes Yes Yes Yes
hsa-mir-511 chr10: 17927127-17927148 3984 GTGTCTTTTGCTCTGCAGTCA Yes
Yes Yes No No hsa-mir-511 chr10: 18174056-18174077 3985
GTGTCTTTTGCTCTGCAGTCA Yes Yes Yes No No hsa-mir-510 chrX:
146161587-146161609 3986 GTGATTGCCACTCTCCTGAGTA Yes Yes Yes No No
hsa-let-7a* chr9: 95978115-95978136 3987 CTATACAATCTACTGTCTTTC Yes
Yes Yes Yes Yes hsa-let-7a* chr22: 44887343-44887364 3988
CTATACAATCTACTGTCTTTC Yes Yes Yes Yes Yes hsa-mir-514 chrX:
146173864-146173885 3989 TCTACTCACAGAAGTGTCAAT Yes Yes No No No
hsa-mir-514 chrX: 146171166-146171187 3990 TCTACTCACAGAAGTGTCAAT
Yes Yes Yes No No hsa-mir-514 chrX: 146168475-146168496 3991
TCTACTCACAGAAGTGTCAAT Yes No Yes No No hsa-mir-524-3p chr19:
58906119-58906140 3992 GAAGGCGCTTCCCTTTGGAGT Yes No No No No
hsa-mir-491-5p chr9: 20706118-20706140 3993 AGTGGGGAACCCTTCCATGAGG
Yes Yes Yes Yes No hsa-mir-18b* chrX: 133131737-133131759 3994
GCCAGAAGGGGCATTTAGGGCA Yes Yes Yes Yes Yes hsa-mir-411* chr14:
100559464-100559486 3995 TATGTAACACGGTCCACTAACC Yes Yes Yes Yes Yes
hsa-mir-548d-3p chr8: 124429469-124429491 3996
GCAAAAGAAACTGTGGTTTTTG No Yes No No No hsa-mir-548d-3p chr17:
62898081-62898103 3997 GCAAAAGAAACTGTGGTTTTTG No No No No No
hsa-mir-490-3p chr7: 136238528-136238550 3998
CAACCTGGAGGACTCCATGGCTG Yes Yes Yes Yes Yes hsa-mir-576-3p chr4:
110629356-110629378 3999 AAGATGTGGAAAAATTGGAATC Yes Yes No No No
hsa-mir-34a chr1: 9134380-9134402 4000 ACAACCAGCTAAGACACTGCCA Yes
Yes Yes Yes Yes hsa-mir-34b chr11: 110888921-110888943 4001
CAATCACTAACTCCACTGCCAT Yes Yes Yes Yes Yes hsa-mir-654-5p chr14:
100576323-100576345 4002 TGGTGGGCCGCAGAACATGTGC Yes Yes No No No
hsa-mir-216a chr2: 56069658-56069680 4003 TCACAGTTGCCAGCTGAGATTA
Yes Yes Yes Yes Yes hsa-mir-216b chr2: 56081402-56081424 4004
TCACATTTGCCTGCAGAGATTT Yes Yes Yes Yes Yes hsa-mir-590-3p chr7:
73243518-73243539 4005 TAATTTTATGTATAAGCTAGT Yes Yes Yes No Yes
hsa-mir-939 chr8: 145590215-145590239 4006 CACCCCCAGAGCCTCAGCTCCCCA
Yes Yes No No No hsa-mir-938 chr10: 29931245-29931267 4007
ACTGGGTTCACCTTTAAGGGCA Yes No No No No hsa-mir-34c-5p chr11:
110889385-110889408 4008 AGGCAGTGTAGTTAGCTGATTGC Yes Yes Yes Yes
Yes hsa-mir-15a* chr13: 49521266-49521288 4009
TGAGGCAGCCACAATATGGCCTG Yes Yes Yes Yes No hsa-mir-933 chr2:
175740615-175740637 4010 GGGAGAGGTCTCCCTGCGCACA Yes Yes No No No
hsa-mir-499-3p chr20: 33041908-33041930 4011 AACATCACAGCAAGTCTGTGCT
Yes Yes Yes Yes Yes hsa-mir-937 chr8: 144967128-144967150 4012
GGCAGAGAGTCAGAGCGCGGAT Yes No No No No hsa-mir-936 chr10:
105797898-105797920 4013 CTGCGATTCCTCCCTCTACTGT Yes Yes No No No
hsa-mir-935 chr19: 59177427-59177450 4014 CCAGTTACCGCTTCCGCTACCGC
Yes No No No Yes hsa-mir-654-3p chr14: 100576358-100576380 4015
TATGTCTGCTGACCATCACCTT Yes Yes Yes Yes No hsa-mir-93* chr7:
99529335-99529357 4016 CGGGAAGTGCTAGCTCAGCAGT Yes Yes Yes Yes Yes
hsa-mir-516b chr19: 58920522-58920544 4017 ATCTGGAGGTAAGAAGCACTTT
Yes No No No No hsa-mir-516b chr19: 58931925-58931947 4018
ATCTGGAGGTAAGAAGCACTTT Yes Yes No No No hsa-mir-551a chr1:
3467133-3467154 4019 TGGAAACCAAGAGTGGGTCGC Yes Yes Yes No No
hsa-mir-551b chr3: 169752395-169752416 4020 GCGACCCATACTTGGTTTCAG
Yes Yes Yes Yes Yes
hsa-mir-345 chr14: 99843965-99843987 4021 GCTGACTCCTAGTCCAGGGCTC
Yes No Yes No No hsa-mir-346 chr10: 88014483-88014506 4022
AGAGGCAGGCATGCGGGCAGACA Yes Yes Yes Yes Yes hsa-mir-340 chr5:
179374966-179374988 4023 AATCAGTCTCATTGCTTTATAA Yes Yes Yes Yes No
hsa-mir-106a chrX: 133131939-133131962 4024 CTACCTGCACTGTAAGCACTTTT
Yes Yes Yes Yes Yes hsa-mir-23b* chr9: 96887329-96887351 4025
TGGGTTCCTGGCATGCTGATTT Yes Yes Yes Yes Yes hsa-mir-106b chr7:
99529601-99529622 4026 ATCTGCACTGTCAGCACTTTA Yes Yes Yes Yes Yes
hsa-mir-194* chr11: 64415415-64415437 4027 CAGATAACAGCAGCCCCACTGG
Yes Yes Yes Yes Yes hsa-mir-519a* chr19: 58947476-58947498 4028
CTCTAGAGGGAAGCGCTTTCTG Yes No No No No hsa-mir-519e chr19:
58875056-58875078 4029 AAGTGCCTCCTTTTAGAGTGTT Yes No No No No
hsa-mir-519d chr19: 58908465-58908487 4030 CAAAGTGCCTCCCTTTAGAGTG
Yes Yes No No No hsa-mir-769-3p chr19: 51214097-51214120 4031
CTGGGATCTCCGGGGTCTTGGTT No No Yes No No hsa-mir-519a chr19:
58947514-58947536 4032 AAAGTGCATCCTTTTAGAGTGT Yes Yes No No No
hsa-mir-519a chr19: 58957465-58957484 4033 AAAGTGCATCCTTTTAGAGTGT
Yes Yes No No No hsa-mir-943 chr4: 1957927-1957948 4034
CTGGAGGACGGCAACAGTCAG Yes No No No No hsa-mir-940 chr16:
2261807-2261828 4035 AAGGCAGGGCCCCCGCTCCCC Yes Yes Yes No No
hsa-mir-941 chr20: 62021710-62021733 4036 CACCCGGCTGTGTGCACATGTGC
Yes No No No No hsa-mir-941 chr20: 62021598-62021621 4037
CACCCGGCTGTGTGCACATGTGC Yes No No No No hsa-mir-941 chr20:
62021291-62021314 4038 CACCCGGCTGTGTGCACATGTGC Yes No No No No
hsa-mir-423-3p chr17: 25468274-25468297 4039
AGCTCGGTCTGAGGCCCCTCAGT Yes Yes Yes Yes Yes hsa-mir-203 chr14:
103653558-103653580 4040 GTGAAATGTTTAGGACCACTAG Yes Yes Yes Yes Yes
hsa-mir-202 chr10: 134911032-134911052 4041 TTCCCATGCCCTATACCTCT
Yes No Yes Yes Yes hsa-mir-205 chr1: 207672133-207672155 4042
TCCTTCATTCCACCGGAGTCTG Yes Yes Yes Yes Yes hsa-mir-204 chr9:
72614766-72614788 4043 AGGCATAGGATGACAAAGGGAA Yes Yes Yes Yes Yes
hsa-mir-526a chr19: 58921993-58922015 4044 CTCTAGAGGGAAGCACTTTCTG
Yes No No No No hsa-mir-526a chr19: 58901331-58901353 4045
CTCTAGAGGGAAGCACTTTCTG Yes No No No No hsa-mir-28-3p chr3:
189889315-189889337 4046 CACTAGATTGTGAGCTCCTGGA Yes Yes Yes Yes Yes
hsa-mir-302a* chr4: 113788828-113788851 4047
AGCAAGTACATCCACGTTTAAGT Yes Yes Yes Yes No hsa-mir-548c-3p chr12:
63302615-63302637 4048 CAAAAATCTCAATTACTTTTGC Yes Yes No No No
hsa-mir-424* chrX: 133508339-133508360 4049 ATAGCAGCGCCTCACGTTTTG
Yes Yes Yes No No hsa-mir-886-5p chr5: 135444163-135444186 4050
CCGCTTGAGCTAACTCCGACCCG Yes Yes No No No hsa-mir-877* chr6:
30660152-30660173 4051 TCCTCTTCTCCCTCCTCCCAG Yes Yes Yes Yes Yes
hsa-mir-29b chr7: 130212765-130212788 4052 AACACTGATTTCAAATGGTGCTA
Yes Yes Yes Yes Yes hsa-mir-29b chr1: 206042417-206042440 4053
AACACTGATTTCAAATGGTGCTA Yes Yes Yes Yes Yes hsa-mir-29c chr1:
206041832-206041854 4054 TAACCGATTTCAAATGGTGCTA Yes Yes Yes Yes Yes
hsa-mir-29a chr7: 130212046-130212068 4055 TAACCGATTTCAGATGGTGCTA
Yes Yes Yes Yes Yes hsa-mir-20a chr13: 90801326-90801349 4056
TAAAGTGCTTATAGTGCAGGTAG Yes Yes Yes Yes Yes hsa-mir-640 chr19:
19406931-19406952 4057 ATGATCCAGGAACCTGCCTCT Yes Yes No No No
hsa-mir-129-5p chr11: 43559533-43559554 4058 CTTTTTGCGGTCTGGGCTTGC
Yes Yes Yes Yes Yes hsa-mir-129-5p chr7: 127635164-127635185 4059
CTTTTTGCGGTCTGGGCTTGC Yes Yes Yes Yes Yes hsa-mir-20b chrX:
133131545-133131568 4060 CTACCTGCACTATGAGCACTTTG Yes Yes Yes Yes
Yes hsa-mir-645 chr20: 48635789-48635808 4061 TCTAGGCTGGTACTGCTGA
Yes No No No No hsa-mir-644 chr20: 32517850-32517869 4062
AGTGTGGCTTTCTTAGAGC Yes Yes No No No hsa-mir-647 chr20:
62044487-62044508 4063 GAAGGAAGTGAGTGCAGCCAC No No No No No
hsa-mir-646 chr20: 58316986-58317005 4064 AAGCAGCTGCCTCTGAGGC Yes
No No No No hsa-mir-649 chr22: 19718479-19718501 4065
GACTCTTGAACAACACAGGTTT Yes Yes No No No hsa-mir-648 chr22:
16843693-16843712 4066 ACCAGTGCCCTGCACACTT Yes Yes No No No
hsa-mir-760 chr1: 94085023-94085043 4067 CGGCTCTGGGTCTGTGGGGA Yes
Yes Yes Yes Yes hsa-mir-766 chrX: 118664753-118664775 4068
GCTGAGGCTGTGGGGCTGGAGT Yes Yes No No No hsa-mir-765 chr1:
155172571-155172592 4069 CATCACCTTCCTTCTCCTCCA Yes Yes No No No
hsa-mir-628-3p chr15: 53452443-53452464 4070 TCGACTGCCACTCTTACTAGA
Yes Yes Yes No No hsa-mir-337-5p chr14: 100410604-100410625 4071
GAACGGCTTCATACAGGAGTT Yes Yes No No No hsa-mir-373* chr19:
58983775-58983797 4072 ACTCAAAATGGGGGCGCTTTCC Yes No No No No
hsa-mir-369-5p chr14: 100601695-100601717 4073
AGATCGACCGTGTTATATTCGC Yes Yes No Yes Yes hsa-mir-1285 chr7:
91671276-91671298 4074 AGGTCTCACTTTGTTGCCCAGA Yes No No No No
hsa-mir-1285 chr2: 70333568-70333590 4075 AGGTCTCACTTTGTTGCCCAGA
Yes No No No No hsa-mir-222* chrX: 45491422-45491444 4076
AGGATCTACACTGGCTACTGAG No Yes Yes Yes Yes hsa-mir-298 chr20:
56826729-56826753 4077 TGGGAGAACCTCCCTGCTTCTGCT Yes Yes No No No
hsa-mir-206 chr6: 52117157-52117179 4078 TGGAATGTAAGGAAGTGTGTGG Yes
Yes Yes Yes Yes hsa-mir-297 chr4: 112001228-112001249 4079
CATGCACATGCACACATACAT Yes Yes Yes No No hsa-mir-589* chr7:
5501990-5502014 4080 TCTGGGAACCGGCATTTGTTCTGA Yes No Yes No No
hsa-mir-124* chr20: 61280310-61280332 4081 CGTGTTCACAGCGGACCTTGAT
No Yes Yes Yes Yes hsa-mir-124* chr8: 9798357-9798379 4082
ATCAAGGTCCGCTGTGAACACG No Yes Yes Yes Yes hsa-mir-124* chr8:
65454283-65454305 4083 CGTGTTCACAGCGGACCTTGAT Yes Yes Yes Yes Yes
hsa-mir-185* chr22: 18400710-18400732 4084 AGGGGCTGGCTTTCCTCTGGTC
Yes Yes Yes Yes Yes hsa-mir-486-3p chr8: 41637160-41637181 4085
CGGGGCAGCTCAGTACAGGAT Yes Yes Yes Yes Yes hsa-mir-486-3p chr8:
41637117-41637138 4086 ATCCTGTACTGAGCTGCCCCG Yes Yes Yes Yes No
hsa-mir-1243 chr4: 114247471-114247493 4087 AACTGGATCAATTATAGGAGTG
Yes Yes No No No hsa-mir-616* chr12: 56199272-56199294 4088
AAGTCACTGAAGGGTTTTGAGT Yes Yes No No No hsa-mir-1245 chr2:
189551106-189551127 4089 AAGTGATCTAAAGGCCTACAT Yes No No No No
hsa-mir-1244 chr12: 12156206-12156232 4090
AAGTAGTTGGTTTGTATGAGATGGTT Yes Yes Yes Yes Yes hsa-mir-1244 chr12:
9283334-9283360 4091 AACCATCTCATACAAACCAACTACTT Yes Yes Yes Yes Yes
hsa-mir-1244 chr2: 232286321-232286347 4092
AAGTAGTTGGTTTGTATGAGATGGTT Yes Yes Yes Yes Yes hsa-mir-1244 chr5:
118338233-118338259 4093 AAGTAGTTGGTTTGTATGAGATGGTT Yes Yes Yes Yes
Yes hsa-mir-1247 chr14: 101096451-101096473 4094
TCCGGGGACGAACGGGACGGGT Yes Yes No Yes Yes hsa-mir-1246 chr2:
177173997-177174016 4095 CCTGCTCCAAAAATCCATT Yes Yes Yes No No
hsa-mir-1249 chr22: 43975502-43975524 4096 TGAAGAAGGGGGGGAAGGGCGT
Yes Yes Yes Yes No hsa-mir-491-3p chr9: 20706152-20706174 4097
CTTATGCAAGATTCCCTTCTAC Yes Yes Yes Yes No hsa-mir-148a* chr7:
25956104-25956126 4098 AGTCGGAGTGTCTCAGAACTTT Yes Yes Yes Yes No
hsa-mir-92b* chr1: 153431610-153431632 4099 AGGGACGGGACGCGGTGCAGTG
No Yes Yes Yes Yes hsa-mir-548o chr7: 101833199-101833221 4100
GCAAAAGTAACTGCAGTTTTGG Yes Yes No No No hsa-mir-891b chrX:
144890309-144890331 4101 TCAATGACTCAGGTAAGTTGCA Yes Yes No No No
hsa-mir-548m chrX: 94204846-94204867 4102 CAAAAACCACAAATACCTTTG No
No No No No hsa-mir-548l chr11: 93839358-93839380 4103
GACAAAACCCGCAAATACTTTT Yes Yes No No No hsa-mir-548k chr11:
69807739-69807761 4104 AAAAGTACTTGCGGATTTTGCT Yes No No No No
hsa-mir-1283 chr19: 58883559-58883581 4105 TCTACAAAGGAAAGCGCTTTCT
Yes Yes No No No hsa-mir-1283 chr19: 58953310-58953332 4106
TCTACAAAGGAAAGCGCTTTCT No No No No No hsa-mir-548i chrX:
83367460-83367482 4107 GGCAAAATCCGCAATTACTTTT No No No No No
hsa-mir-548i chr3: 126992025-126992047 4108 GGCAAAATCCGCAATTACTTTT
Yes No No No No hsa-mir-548i chr8: 7983961-7983983 4109
GGCAAAATCCGCAATTACTTTT Yes No No No No hsa-mir-548i chr4:
9166975-9166997 4110 GGCAAAATCCGCAATTACTTTT Yes No No No No
hsa-mir-548h chr17: 13387638-13387660 4111 GACAAAAACCGCGATTACTTTT
No Yes No No No hsa-mir-548h chr8: 26962359-26962381 4112
GACAAAAACCGCGATTACTTTT No No No No No hsa-mir-548h chr14:
63631554-63631576 4113 GACAAAAACCGCGATTACTTTT Yes Yes No No No
hsa-mir-548h chr16: 11307848-11307870 4114 GACAAAAACCGCGATTACTTTT
Yes Yes No No No hsa-mir-548g chr4: 148485244-148485266 4115
GTACAAAAGTAATTACAGTTTT Yes No No No No hsa-mir-548f chr5:
109877443-109877462 4116 AAAAGTAATTACAGTTTTT Yes Yes No No No
hsa-mir-548f chr7: 146706065-146706084 4117 AAAAGTAATTACAGTTTTT Yes
Yes No No No hsa-mir-548f chrX: 32569527-32569546 4118
AAAAGTAATTACAGTTTTT Yes Yes No No No hsa-mir-548f chr2:
212999252-212999271 4119 AAAAGTAATTACAGTTTTT Yes Yes No No No
hsa-mir-548f chr10: 56037654-56037673 4120 AAAAGTAATTACAGTTTTT No
No No No No hsa-mir-496 chr14: 100596717-100596739 4121
TGAGTATTACATGGCCAATCTC Yes Yes Yes Yes Yes hsa-mir-497 chr17:
6862021-6862042 4122 ACAAACCACAGTGTGCTGCTG Yes Yes Yes Yes Yes
hsa-mir-190b chr1: 152432812-152432833 4123 AACCCAATATCAAACATATCA
Yes Yes Yes Yes Yes hsa-mir-492 chr12: 93752333-93752356 4124
AGGACCTGCGGGACAAGATTCTT Yes Yes Yes No No hsa-mir-493 chr14:
100405205-100405227 4125 TGAAGGTCTACTGTGTGCCAGG No Yes Yes No Yes
hsa-mir-199b-5p chr9: 130046882-130046905 4126
GAACAGATAGTCTAAACACTGGG Yes No Yes Yes No hsa-mir-891a chrX:
144917050-144917072 4127 TCAGTGGCTCAGGTTCGTTGCA Yes Yes No No No
hsa-mir-500* chrX: 49659829-49659851 4128 ATGCACCTGGGCAAGGATTCTG
Yes Yes Yes No No hsa-mir-105* chrX: 151311355-151311377 4129
TAGCACATGCTCAAACATCCGT Yes Yes Yes No Yes hsa-mir-105* chrX:
151313548-151313570 4130 TAGCACATGCTCAAACATCCGT Yes Yes Yes No Yes
hsa-mir-513c chrX: 146078962-146078984 4131 ATAAACGACACCTCCTTGAGAA
No No No No No hsa-mir-513b chrX: 146088302-146088324 4132
ATAAATGACACCTCCTTGTGAA Yes Yes No No No hsa-mir-18a* chr13:
90801051-90801074 4133 ACTGCCCTAAGTGCTCCTTCTGG Yes Yes Yes Yes Yes
hsa-mir-548p chr5: 100180100-100180122 4134 AAAGTAACTGCAGTTTTTGCTA
Yes No No No No hsa-mir-24-1* chr9: 96888129-96888151 4135
TGCCTACTGAGCTGATATCAGT Yes Yes Yes Yes Yes hsa-mir-582-5p chr5:
59035248-59035271 4136 AGTAACTGGTTGAACAACTGTAA Yes Yes Yes Yes Yes
hsa-mir-668 chr14: 100591389-100591412 4137 TGTCACTCGGCTCGGCCCACTAC
Yes Yes No Yes Yes hsa-mir-516a-5p chr19: 58951821-58951844 4138
TTCTCGAGGAAAGAAGCACTTTC Yes Yes No No No hsa-mir-516a-5p chr19:
58956213-58956236 4139 TTCTCGAGGAAAGAAGCACTTTC Yes Yes No No No
hsa-mir-30a* chr6: 72169977-72169999 4140 GCTGCAAACATCCGACTGAAAG
Yes Yes Yes Yes Yes hsa-mir-183 chr7: 129202042-129202064 4141
AGTGAATTCTACCAGTGCCATA Yes Yes Yes Yes Yes hsa-mir-186 chr1:
71305951-71305973 4142 AGCCCAAAAGGAGAATTCTTTG Yes Yes Yes Yes Yes
hsa-mir-187 chr18: 31738795-31738817 4143 CCGGCTGCAACACAAGACACGA No
Yes Yes Yes Yes hsa-mir-184 chr15: 77289236-77289258 4144
TGGACGGAGAACTGATAAGGGT Yes Yes Yes Yes Yes hsa-mir-185 chr22:
18400675-18400697 4145 TGGAGAGAAAGGCAGTTCCTGA Yes Yes Yes Yes Yes
hsa-mir-198 chr3: 121597239-121597261 4146 GAACCTATCTCCCCTCTGGACC
Yes Yes No No No hsa-let-7b chr22: 44888234-44888256 4147
TGAGGTAGTAGGTTGTGTGGTT Yes Yes Yes Yes Yes hsa-mir-455-5p chr9:
116011549-116011571 4148 TATGTGCCTTTGGACTACATCG Yes Yes Yes Yes Yes
hsa-mir-518c chr19: 58903861-58903884 4149 CAAAGCGCTTCTCTTTAGAGTGT
Yes Yes No No No hsa-mir-770-5p chr14: 100388498-100388521 4150
TCCAGTACCACGTGTCAGGGCCA Yes Yes No No No hsa-mir-380 chr14:
100561145-100561167 4151 TATGTAATATGGTCCACATCTT Yes Yes Yes No No
hsa-mir-381 chr14: 100582057-100582079 4152 TATACAAGGGCAAGCTCTCTGT
Yes Yes Yes Yes Yes hsa-mir-382 chr14: 100590405-100590427 4153
GAAGTTGTTCGTGGTGGATTCG Yes Yes Yes Yes Yes hsa-mir-383 chr8:
14755362-14755384 4154 AGCCACAATCACCTTCTGATCT Yes Yes Yes No No
hsa-mir-384 chrX: 76056103-76056123 4155 TATGAACAATTTCTAGGAAT Yes
Yes Yes Yes Yes hsa-mir-661 chr8: 145091361-145091385 4156
ACGCGCAGGCCAGAGACCCAGGCA Yes Yes No No No hsa-mir-421 chrX:
73354951-73354974 4157 GCGCCCAATTAATGTCTGTTGAT Yes Yes Yes Yes Yes
hsa-mir-518f chr19: 58895132-58895153 4158 GAAAGCGCTTCTCTTTAGAGG
Yes Yes No No No hsa-mir-660 chrX: 49664603-49664625 4159
TACCCATTGCATATCGGAGTTG Yes Yes Yes No No hsa-mir-425 chr3:
49032635-49032658 4160 TCAACGGGAGTGATCGTGTCATT Yes Yes Yes Yes Yes
hsa-mir-424 chrX: 133508375-133508397 4161 TTCAAAACATGAATTGCTGCTG
Yes Yes Yes Yes Yes hsa-mir-518c* chr19: 58903823-58903846 4162
TCTCTGGAGGGAAGCACTTTCTG Yes Yes No No No hsa-mir-543 chr14:
100568122-100568144 4163 AAACATTCGCGGTGCACTTCTT Yes Yes Yes Yes Yes
hsa-mir-18a chr13: 90801010-90801033 4164 TAAGGTGCATCTAGTGCAGATAG
Yes Yes Yes Yes Yes hsa-mir-138-1* chr3: 44130769-44130791 4165
GCTACTTCACAACACCAGGGCC No No Yes Yes Yes hsa-let-7e* chr19:
56887902-56887924 4166 CTATACGGCCTCCTAGCTTTCC Yes Yes Yes Yes Yes
hsa-mir-545 chrX: 73423685-73423707 4167 GCACACAATAAATGTTTGCTGA Yes
Yes No No No hsa-mir-549 chr15: 78921388-78921409 4168
AGAGCTCATCCATAGTTGTCA Yes Yes No No No hsa-mir-549 chr15:
78921423-78921444 4169 TGACAACTATGGATGAGCTCT Yes Yes No No No
hsa-mir-133a chr20: 60572621-60572643 4170 TTTGGTCCCCTTCAACCAGCTG
Yes Yes Yes Yes Yes hsa-mir-133a chr18: 17659670-17659692 4171
CAGCTGGTTGAAGGGGACCAAA Yes Yes Yes Yes Yes hsa-mir-574-3p chr4:
38546107-38546129 4172 CACGCTCATGCACACACCCACA No No Yes Yes No
hsa-mir-133b chr6: 52121744-52121766 4173 TTTGGTCCCCTTCAACCAGCTA
Yes Yes Yes Yes Yes hsa-mir-1237 chr11: 63892730-63892751 4174
TCCTTCTGCTCCGTCCCCCAG Yes Yes No No No hsa-mir-220c chr19:
53755391-53755413 4175 AGTCTTCACAACAGCCCTGTGT Yes No No No No
hsa-mir-369-3p chr14: 100601730-100601751 4176
AATAATACATGGTTGATCTTT Yes Yes Yes Yes Yes hsa-mir-518e chr19:
58924956-58924977 4177 AAAGCGCTTCCCTTCAGAGTG Yes No No No No
hsa-mir-519e* chr19: 58875018-58875040 4178 TTCTCCAAAAGGGAGCACTTTC
Yes Yes No No No hsa-mir-15a chr13: 49521303-49521325 4179
CACAAACCATTATGTGCTGCTA Yes Yes Yes Yes No hsa-mir-769-5p chr19:
51214058-51214080 4180 TGAGACCTCTGGGTTCTGAGCT No No No No No
hsa-mir-15b chr3: 161605088-161605110 4181 TAGCAGCACATCATGGTTTACA
Yes Yes Yes Yes Yes hsa-mir-453 chr14: 100592322-100592345 4182
AGGTTGTCCGTGGTGAGTTCGCA Yes Yes Yes No Yes hsa-mir-876-5p chr9:
28853672-28853694 4183 TGGTGATTCACAAAGAAATCCA Yes Yes Yes Yes Yes
hsa-mir-1226 chr3: 47866101-47866123 4184 TCACCAGCCCTGTGTTCCCTAG
Yes Yes No No Yes hsa-mir-802 chr21: 36014899-36014922 4185
CAGTAACAAAGATTCATCCTTGT Yes Yes Yes Yes Yes hsa-mir-520a-5p chr19:
58885960-58885981 4186 CTCCAGAGGGAAGTACTTTCT Yes Yes No No No
hsa-mir-552 chr1: 34907801-34907822 4187 TTGTCTAACCAGTCACCTGTT Yes
Yes No No No hsa-mir-147b chr15: 43512587-43512609 4188
GTGTGCGGAAATGCTTCTGCTA Yes Yes
Yes Yes Yes hsa-mir-432* chr14: 100420633-100420654 4189
CTGGATGGCTCCTCCATGTCT Yes Yes Yes Yes No hsa-mir-650 chr22:
21495284-21495305 4190 AGGAGGCAGCGCTCTCAGGAC Yes Yes No No No
hsa-mir-146a* chr5: 159844992-159845014 4191 CCTCTGAAATTCAGTTCTTCAG
No No Yes Yes No hsa-mir-335 chr7: 129923202-129923225 4192
TCAAGAGCAATAACGAAAAATGT Yes Yes Yes Yes No hsa-mir-520d-3p chr19:
58915214-58915236 4193 AAAGTGCTTCTCTTTGGTGGGT Yes Yes No No No
hsa-mir-19b-1* chr13: 90801461-90801484 4194
AGTTTTGCAGGTTTGCATCCAGC Yes Yes Yes Yes Yes hsa-mir-1231 chr1:
200044365-200044385 4195 GTGTCTGGGCGGACAGCTGC No Yes No No No
hsa-mir-146b-3p chr10: 104186302-104186324 4169
TGCCCTGTGGACTCAGTTCTGG Yes No No No No hsa-mir-875-5p chr8:
100618233-100618255 4197 CACCTGATAAAACTGAGGTATA Yes Yes Yes Yes Yes
hsa-mir-874 chr5: 137011169-137011191 4198 TCGGTCCCTCGGGCCAGGGCAG
Yes Yes Yes Yes Yes hsa-mir-873 chr9: 28878922-28878943 4199
AGGAGACTCACAAGTTCCTGC Yes Yes Yes Yes Yes hsa-mir-15b* chr3:
161605126-161605148 4200 CGAATCATTATTTGCTGCTCTA Yes Yes Yes Yes Yes
hsa-mir-25* chr7: 99529168-99529189 4201 CAATTGCCCAAGTCTCCGCCT Yes
Yes Yes Yes Yes hsa-mir-1185 chr14: 100579080-100579101 4202
AGAGGATACCCTTTGTATGTT Yes Yes Yes No No hsa-mir-1185 chr14:
100580301-100580322 4203 AGAGGATACCCTTTGTATGTT Yes Yes Yes No No
hsa-mir-720 chr3: 165541848-165541865 4204 TCTCGCTGGGGCCTCCA Yes No
No No No hsa-mir-409-3p chr14: 100601435-100601457 4205
GAATGTTGCTCGGTGAACCCCT Yes Yes Yes Yes Yes hsa-mir-1182 chr1:
229222209-229222232 4206 GTCACATCCCTCCCAAGACCCTC Yes Yes No No No
hsa-mir-1179 chr15: 86952355-86952376 4207 AAGCATTCTTTCATTGGTTGG
Yes Yes No No No hsa-mir-1178 chr12: 118635836-118635857 4208
CTAGGGAAGAACAGTGAGCAA Yes Yes No No No hsa-mir-367* chr4:
113788519-113788541 4209 AGAGTTGCATATTAGCAACAGT Yes Yes Yes Yes No
hsa-mir-150 chr19: 54695900-54695922 4210 CACTGGTACAAGGGTTGGGAGA
Yes Yes Yes Yes Yes hsa-mir-153 chr7: 157059801-157059823 4211
GATCACTTTTGTGACTATGCAA Yes Yes Yes Yes Yes hsa-mir-153 chr2:
219867091-219867113 4212 GATCACTTTTGTGACTATGCAA No Yes Yes No No
hsa-mir-152 chr17: 43469538-43469559 4213 CCAAGTTCTGTCATGCACTGA Yes
Yes Yes Yes Yes hsa-mir-155 chr21: 25868165-25868188 4214
TTAATGCTAATCGTGATAGGGGT Yes Yes Yes Yes No hsa-mir-154 chr14:
100595858-100595880 4215 TAGGTTATCCGTGTTGCCTTCG Yes Yes No Yes Yes
hsa-mir-634 chr17: 62213711-62213733 4216 AACCAGCACCCCAACTTTGGAC
Yes No No No No hsa-mir-377* chr14: 100598145-100598167 4217
AGAGGTTGCCCTTGGTGAATTC Yes Yes Yes Yes Yes hsa-mir-1228 chr12:
55874604-55874624 4218 TCACACCTGCCTCGCCCCCC No Yes No No No
hsa-mir-199a-5p chr1: 170380354-170380377 4219
GAACAGGTAGTCTGAACACTGGG Yes Yes Yes Yes Yes hsa-mir-199a-5p chr19:
10789144-10789167 4220 GAACAGGTAGTCTGAACACTGGG Yes Yes Yes Yes No
hsa-mir-767-5p chrX: 151312608-151312631 4221
CATGCTCAGACAACCATGGTGCA No Yes No Yes Yes hsa-mir-151-3p chr8:
141811867-141811888 4222 CCTCAAGGAGCTTCAGTCTAG Yes Yes Yes No No
hsa-mir-154* chr14: 100595894-100595916 4223 AATCATACACGGTTGACCTATT
Yes Yes No Yes Yes hsa-mir-483-5p chr11: 2111986-2112008 4224
CTCCCTTCTTTCCTCCCGTCTT No No No Yes Yes hsa-mir-33a chr22:
40626898-40626919 4225 GTGCATTGTAGTTGCATTGCA Yes No Yes Yes Yes
hsa-mir-33b chr17: 17657935-17657955 4226 GCAATGCAACAGCAATGCAC Yes
Yes Yes No No hsa-mir-1304 chr11: 93106537-93106559 4227
CACATCTCACTGTAGCCTCAAA Yes Yes No No No hsa-mir-25 chr7:
99529129-99529151 4228 TCAGACCGAGACAAGTGCAATG Yes Yes Yes Yes Yes
hsa-mir-1306 chr22: 18453634-18453652 4229 ACGTTGGCTCTGGTGGTG Yes
Yes Yes Yes Yes hsa-mir-1307 chr10: 105144047-105144069 4230
CACGACCGACGCCACGCCGAGT Yes Yes Yes No No hsa-mir-1300 chr15:
51017866-51017884 4231 CAGCAGCCTCCTTCTCAA Yes No Yes Yes Yes
hsa-mir-21 chr17: 55273415-55273437 4232 TAGCTTATCAGACTGATGTTGA Yes
Yes Yes Yes Yes hsa-mir-22 chr17: 1563957-1563979 4233
ACAGTTCTTCAACTGGCAGCTT Yes No Yes Yes Yes hsa-mir-596 chr8:
1752818-1752839 4234 AAGCCTGCCCGGCTCCTCGGG Yes Yes No No No
hsa-mir-599 chr8: 100618054-100618074 4235 GTTTGATAAACTGACACAAC Yes
Yes Yes Yes No hsa-mir-598 chr8: 10930140-10930162 4236
TGACGATGACAACGATGACGTA Yes No No Yes Yes hsa-mir-610 chr11:
28034990-28035011 4237 TCCCAGCACACATTTAGCTCA Yes No No No No
hsa-mir-610 chr11: 28034952-28034973 4238 TGAGCTAAATGTGTGCTGGGA Yes
No No No No hsa-mir-611 chr11: 61316547-61316570 4239
GTCAGACCCCGAGGGGTCCTCGC Yes Yes No No No hsa-mir-616 chr12:
56199232-56199254 4240 CTGCTCAAACCCTCCAATGACT Yes Yes No No No
hsa-mir-617 chr12: 79750502-79750524 4241 GCCACCTTCAAATGGGAAGTCT
Yes Yes No No No hsa-mir-614 chr12: 12960082-12960105 4242
GAACGCCTGTTCTTGCCAGGTGG Yes No No No No hsa-mir-517c chr19:
58936434-58936456 4243 ATCGTGCATCCTTTTAGAGTGT Yes Yes No No No
hsa-mir-517b chr19: 58916184-58916206 4244 TCGTGCATCCCTTTAGAGTGTT
Yes No No No No hsa-mir-517a chr19: 58907386-58907408 4245
ATCGTGCATCCCTTTAGAGTGT Yes Yes No No No hsa-mir-495 chr14:
100569893-100569915 4246 AAACAAACATGGTGCACTTCTT Yes Yes Yes Yes Yes
hsa-mir-671-3p chr7: 150566506-150566527 4247 TCCGGTTCTCAGGGCTCCACC
Yes Yes Yes Yes Yes hsa-mir-135a* chr3: 52303287-52303309 4248
CGCCACGGCTCCAATCCCTATA Yes Yes Yes Yes No hsa-mir-513a-3p chrX:
146102707-146102730 4249 CCTTCTCAGAAAGGTGAAATTTA Yes No No No No
hsa-mir-513a-3p chrX: 146115069-146115092 4250
CCTTCTCAGAAAGGTGAAATTTA Yes Yes No No No hsa-mir-525-5p chr19:
58892612-58892633 4251 CTCCAGAGGGATGCACTTTCT Yes Yes No No No
hsa-mir-758 chr14: 100562160-100562182 4252 TTTGTGACCTGGTCCACTAACC
Yes Yes Yes Yes Yes hsa-mir-187* chr18: 31738831-31738853 4253
GCCCGGGTCCTGTGTTGTAGCC No Yes Yes Yes Yes hsa-mir-520d-5p chr19:
58915176-58915196 4254 CTACAAAGGGAAGCCCTTTC Yes Yes No No No
hsa-mir-522* chr19: 58946291-58946313 4255 CTCTAGAGGGAAGCGCTTTCTG
Yes Yes No No No hsa-mir-101 chr9: 4840344-4840365 4256
TACAGTACTGTGATAACTGAA Yes Yes Yes Yes Yes hsa-mir-101 chr1:
65296712-65296733 4257 TTCAGTTATCACAGTACTGTA Yes Yes Yes Yes Yes
hsa-mir-299-3p chr14: 100559921-100559943 4258
TATGTGGGATGGTAAACCGCTT Yes Yes Yes Yes Yes hsa-mir-107 chr10:
91342492-91342515 4259 TGATAGCCCTGTACAATGCTGCT Yes Yes Yes Yes Yes
hsa-mir-1278 chr1: 191372304-191372326 4260 TAGTACTGTGCATATCATCTAT
Yes Yes Yes No No hsa-mir-1279 chr12: 67953234-67953251 4261
AGAAAGAAGCAATATGA Yes No Yes Yes Yes hsa-mir-219-1-3p chr6:
33283650-33283672 4262 AGAGTTGAGTCTGGACGTCCCG Yes Yes Yes No No
hsa-mir-541 chr14: 100600637-100600659 4263 TGGTGGGCACAGAATCTGGACT
Yes Yes Yes No No hsa-mir-1270 chr19: 20371127-20371150 4264
ACACAGCTCTTCCATATCTCCAG No No No No No hsa-mir-1271 chr5:
175727568-175727590 4265 CTTGGCACCTAGCAAGCACTCA Yes Yes Yes Yes Yes
hsa-mir-1272 chr15: 62841722-62841748 4266
TTTCAGAATTTGCTGCCATCATCATC Yes No No No No hsa-mir-1273 chr8:
101105388-101105413 4267 AAGAAAGAGTCTTGCTTTGTCGCCC Yes No No No No
hsa-mir-1275 chr6: 34075772-34075789 4268 GACAGCCTCTCCCCCAC Yes Yes
No No No hsa-mir-1276 chr15: 84114782-84114802 4269
TGTCTCCACAGGGCTCTTTA Yes No No No No hsa-mir-1277 chrX:
117404430-117404452 4270 TACGTAGATATATATGTATTTT No Yes Yes No No
hsa-mir-488* chr1: 175265170-175265191 4271 TTGAGAGTGCCATTATCTGGG
Yes Yes Yes Yes Yes
hsa-mir-219-2-3p chr9: 130194731-130194753 4272
ACAGATGTCCAGCCACAATTCT Yes Yes Yes Yes Yes hsa-mir-142-5p chr17:
53763642-53763663 4273 AGTAGTGCTTTCTACTTTATG Yes Yes Yes Yes Yes
hsa-mir-615-3p chr12: 52714060-52714082 4274 TCCGAGCCTGGGTCTCCCTCTT
Yes Yes Yes Yes Yes hsa-mir-130b chr22: 20337642-20337664 4275
CAGTGCAATGATGAAAGGGCAT Yes Yes Yes Yes Yes hsa-mir-506 chrX:
146119962-146119983 4276 TCTACTCAGAAGGGTGCCTTA Yes Yes Yes No No
hsa-mir-507 chrX: 146120211-146120232 4277 TTCACTCCAAAAGGTGCAAAA
Yes Yes No No No hsa-mir-504 chrX: 137577586-137577608 4278
GATAGAGTGCAGACCAGGGTCT Yes Yes Yes Yes Yes hsa-mir-885-5p chr3:
10411214-10411236 4279 AGAGGCAGGGTAGTGTAATGGA Yes Yes Yes No No
hsa-mir-944 chr3: 191030457-191030479 4280 AAATTATTGTACATCGGATGAG
Yes Yes No No No hsa-mir-500 chrX: 49659790-49659813 4281
TAATCCTTGCTACCTGGGTGAGA Yes Yes Yes Yes No hsa-let-7d* chr9:
95980997-95981019 4282 CTATACGACCTGCTGCCTTTCT Yes Yes Yes Yes Yes
hsa-mir-545* chrX: 73423723-73423745 4283 TCATCTAATAAACATTTACTGA
Yes Yes No No Yes hsa-mir-942 chr1: 117438799-117438821 4284
TCTTCTCTGTTTTGGCCATGTG Yes Yes No No No hsa-mir-200a* chr1:
1093120-1093142 4285 CATCTTACCGGACAGTGCTGGA Yes Yes Yes Yes Yes
hsa-mir-130a* chr11: 57165266-57165288 4286 TTCACATTGTGCTACTGTCTGC
Yes Yes Yes Yes Yes hsa-mir-1266 chr15: 50356654-50356677 4287
AGCCCTGTTCTACAGCCCTGAGG Yes Yes No No No hsa-mir-548a-3p chr6:
18680053-18680075 4288 CAAAACTGGCAATTACTTTTGC Yes No No No No
hsa-mir-548a-3p chr6: 135602050-135602072 4289
CAAAACTGGCAATTACTTTTGC Yes No No No No hsa-mir-548a-3p chr8:
105565787-105565809 4290 GCAAAAGTAATTGCCAGTTTTG No Yes No No No
hsa-mir-557 chr1: 166611445-166611468 4291 GTTTGCACGGGTGGGCCTTGTCT
Yes No No No No hsa-mir-1238 chr19: 10523858-10523878 4292
CTTCCTCGTCTGTCTGCCCC No No No No No hsa-mir-920 chr12:
24256671-24256691 4293 GGGGAGCTGTGGAAGCAGTA Yes Yes No No No
hsa-mir-921 chr1: 164390633-164390658 4294
GAATCCTGGTTCTGTCCCTCACTAG Yes Yes No No No hsa-mir-922 chr3:
198885765-198885788 4295 GACGTAGTCCTATTCTCTGCTGC Yes Yes No No No
hsa-mir-923 chr17: 30502320-30502341 4296 AGTTTCTTTTCCTCCGCTGAC Yes
No No No No hsa-mir-924 chr18: 35456114-35456134 4297
GCAAGACATCACAAGACTCT Yes Yes No No No hsa-mir-193b* chr16:
14305337-14305359 4298 CGGGGTTTTGAGGGCGAGATGA Yes Yes Yes Yes No
hsa-mir-378 chr5: 149092622-149092643 4299 ACTGGACTTGGAGTCAGAAGG
Yes Yes Yes No No hsa-mir-320c chr18: 20155677-20155697 4300
AAAAGCTGGGTTGAGAGGGT Yes No Yes Yes Yes hsa-mir-320c chr18:
17517517-17517537 4301 AAAAGCTGGGTTGAGAGGGT Yes Yes Yes Yes No
hsa-mir-320b chr1: 222511373-222511395 4302 TTGCCCTCTCAACCCAGCTTTT
Yes Yes No No No hsa-mir-320b chr1: 117015931-117015953 4303
AAAAGCTGGGTTGAGAGGGCAA Yes Yes Yes Yes Yes hsa-mir-320a chr8:
22158432-22158454 4304 TCGCCCTCTCAACCCAGCTTTT Yes Yes Yes Yes Yes
hsa-mir-324-3p chr17: 7067350-7067370 4305 CCAGCAGCACCTGGGGCAGT Yes
Yes Yes Yes Yes hsa-mir-370 chr14: 100447275-100447297 4306
GCCTGCTGGGGTGGAACCTGGT Yes Yes Yes Yes Yes hsa-mir-431* chr14:
100417158-100417180 4307 CAGGTCGTCTTGCAGGGCTTCT Yes Yes Yes Yes Yes
hsa-mir-372 chr19: 58982996-58983019 4308 AAAGTGCTGCGACATTTGAGCGT
Yes Yes Yes No Yes hsa-mir-375 chr2: 219574613-219574635 4309
TCACGCGAGCCGAACGAACAAA Yes Yes Yes Yes Yes hsa-mir-422a chr15:
61950240-61950262 4310 GCCTTCTGACCCTAAGTCCAGT Yes Yes No No No
hsa-mir-377 chr14: 100598183-100598205 4311 ATCACACAAAGGCAACTTTTGT
Yes Yes Yes Yes Yes hsa-mir-362-3p chrX: 49660352-49660374 4312
AACACACCTATTCAAGGATTCA Yes Yes Yes Yes Yes hsa-mir-579 chr5:
32430254-32430277 4313 AATCGCGGTTTATACCAAATGAA Yes Yes No No No
hsa-mir-578 chr4: 166526903-166526924 4314 CTTCTTGTGCTCTAGGATTGT
Yes Yes No No No hsa-mir-24-2* chr19: 13808139-13808161 4315
CTGTGTTTCAGCTCAGTAGGCA Yes Yes Yes Yes Yes hsa-mir-573 chr4:
24130972-24130996 4316 CTGATCAGTTACACATCACTTCAG Yes Yes No No No
hsa-mir-572 chr4: 10979608-10979628 4317 GTCCGCTCGGCGGTGGCCCA Yes
Yes No No No hsa-mir-571 chr4: 334005-334026 4318
TGAGTTGGCCATCTGAGTGAG Yes Yes No No No hsa-mir-570 chr3:
196911510-196911532 4319 CGAAAACAGCAATTACCTTTGC No No No No No
hsa-mir-577 chr4: 115797378-115797399 4320 TAGATAAAATATTGGTACCTG
Yes Yes No No No hsa-mir-520c-3p chr19: 58902571-58902593 4321
AAAGTGCTTCCTTTTAGAGGGT Yes Yes No No No hsa-mir-509-3-5p chrX:
146148905-146148927 4322 CATGATTGCCACGTCTGCAGTA Yes No No No Yes
hsa-mir-23a* chr19: 13808443-13808465 4323 AAATCCCATCCCCAGGAACCCC
Yes Yes Yes Yes Yes hsa-mir-518f* chr19: 58895095-58895117 4324
CTCTAGAGGGAAGCACTTTCTC Yes Yes No No No hsa-mir-195* chr17:
6861670-6861692 4325 GGAGCAGCACAGCCAATATTGG Yes Yes Yes Yes Yes
hsa-mir-576-5p chr4: 110629317-110629339 4326
ATTCTAATTTCTCCACGTCTTT Yes Yes No No No hsa-mir-575 chr4:
83893528-83893547 4327 GCTCCTGTCCAACTGGCTC Yes No No No No
hsa-mir-21* chr17: 55273453-55273474 4328 CAACACCAGTCGATGGGCTGT Yes
Yes No Yes Yes hsa-mir-27b* chr9: 96887565-96887587 4329
AGAGCTTAGCTGATTGGTGAAC Yes Yes Yes Yes Yes hsa-mir-217 chr2:
56063658-56063681 4330 TCCAATCAGTTCCTGATGCAGTA Yes Yes Yes Yes Yes
hsa-mir-214 chr1: 170374578-170374600 4331 ACTGCCTGTCTGTGCCTGCTGT
Yes Yes Yes Yes Yes hsa-mir-215 chr1: 218357880-218357901 4332
GTCTGTCAATTCATAGGTCAT Yes Yes Yes Yes Yes hsa-mir-212 chr17:
1900333-1900354 4333 GGCCGTGACTGGAGACTGTTA No Yes Yes Yes Yes
hsa-mir-210 chr11: 558111-558133 4334 TCAGCCGCTGTCACACGCACAG Yes
Yes Yes Yes Yes hsa-mir-211 chr15: 29144589-29144611 4335
AGGCGAAGGATGACAAAGGGAA Yes Yes Yes Yes Yes hsa-mir-92a chrX:
133131239-133131261 4336 ACAGGCCGGGACAAGTGCAATA Yes Yes Yes Yes Yes
hsa-mir-92a chr13: 90801615-90801637 4337 TATTGCACTTGTCCCGGCCTGT
Yes Yes Yes Yes Yes hsa-mir-92b chr1: 153431651-153431673 4338
TATTGCACTCGTCCCGGCCTCC No Yes Yes Yes Yes hsa-mir-218 chr4:
20139019-20139040 4339 TTGTGCTTGATCTAACCATGT Yes Yes Yes Yes Yes
hsa-mir-218 chr5: 168127793-168127814 4340 ACATGGTTAGATCAAGCACAA
Yes Yes Yes Yes Yes hsa-mir-515-3p chr19: 58874118-58874140 4341
GAGTGCCTTCTTTTGGAGCGTT Yes No No No No hsa-mir-515-3p chr19:
58880124-58880146 4342 GAGTGCCTTCTTTTGGAGCGTT Yes No No No No
hsa-mir-1 chr18: 17662973-17662995 4343 ATACATACTTCTTTACATTCCA Yes
Yes Yes Yes Yes hsa-mir-1 chr20: 60562002-60562024 4344
TGGAATGTAAAGAAGTATGTAT Yes Yes Yes Yes Yes hsa-mir-425* chr3:
49032595-49032617 4345 GGGCGGACACGACATTCCCGAT Yes Yes Yes Yes Yes
hsa-mir-522 chr19: 58946329-58946351 4346 AAAATGGTTCCCTTTAGAGTGT
Yes Yes No No No hsa-mir-7 chr9: 85774546-85774569 4347
ACAACAAAATCACTAGTCTTCCA Yes Yes Yes Yes Yes hsa-mir-7 chr15:
86956090-86956113 4348 TGGAAGACTAGTGATTTTGTTGT Yes Yes Yes Yes Yes
hsa-mir-7 chr19: 4721711-4721734 4349 TGGAAGACTAGTGATTTTGTTGT Yes
Yes Yes Yes Yes hsa-mir-9 chr15: 87712266-87712289 4350
TCTTTGGTTATCTAGCTGTATGA Yes Yes Yes Yes Yes hsa-mir-9 chr1:
154656807-154656830 4351 TCATACAGCTAGATAACCAAAGA Yes Yes Yes Yes
Yes hsa-mir-9 chr5: 87998475-87998498 4352 TCATACAGCTAGATAACCAAAGA
Yes Yes Yes Yes Yes hsa-mir-615-5p chr12: 52714017-52714039 4353
GGGGGTCCCCGGTGCTCGGATC Yes Yes Yes Yes Yes hsa-mir-512-3p chr19:
58861794-58861816 4354 AAGTGCTGTCATAGCTGAGGTC Yes No No No No
hsa-mir-512-3p chr19: 58864278-58864300 4355 AAGTGCTGTCATAGCTGAGGTC
No Yes No No No
hsa-mir-202* chr10: 134911066-134911088 4356 CAAAGAAGTATATGCATAGGAA
Yes No Yes Yes Yes hsa-mir-888* chrX: 144884003-144884025 4357
TTCACCCAAAGAGGTGTCAGTC No Yes No No No hsa-mir-143* chr5:
148788699-148788721 4358 GGTGCAGTGCTGCATCTCTGGT Yes Yes Yes Yes Yes
hsa-mir-526b chr19: 58889471-58889494 4359 CTCTTGAGGGAAGCACTTTCTGT
Yes Yes No No No hsa-mir-656 chr14: 100602855-100602876 4360
AATATTATACAGTCAACCTCT Yes Yes Yes No No hsa-mir-657 chr17:
76713685-76713708 4361 CCTAGAGAGGGTGAGAACCTGCC Yes Yes No No No
hsa-mir-655 chr14: 100585699-100585721 4362 ATAATACATGGTTAACCTCTTT
Yes No Yes No No hsa-mir-652 chrX: 109185272-109185293 4363
AATGGCGCCACTAGGGTTGTG Yes Yes No No No hsa-mir-653 chr7:
92950070-92950091 4364 CAGTAGAGATTGTTTCAACAC Yes Yes Yes Yes Yes
hsa-mir-518a-3p chr19: 58926121-58926143 4365
GAAAGCGCTTCCCTTTGCTGGA Yes No No No No hsa-mir-518a-3p chr19:
58934450-58934472 4366 GAAAGCGCTTCCCTTTGCTGGA Yes No No No No
hsa-mir-651 chrX: 8055020-8055042 4367 TTTAGGATAAGCTTGACTTTTG Yes
No No No No hsa-mir-302f chr18: 26132899-26132916 4368
TAATTGCTTCCATGTTT Yes Yes Yes Yes Yes hsa-mir-1184 chrX:
154265958-154265981 4369 GGAAGCCATCAAGTCGCTGCAGG Yes Yes Yes Yes
Yes hsa-mir-1184 chrX: 154340431-154340454 4370
CCTGCAGCGACTTGATGGCTTCC Yes Yes Yes Yes Yes hsa-mir-1184 chrX:
153768844-153768867 4371 GGAAGCCATCAAGTCGCTGCAGG Yes Yes Yes Yes
Yes hsa-mir-302d chr4: 113788610-113788633 4372
ACACTCAAACATGGAAGCACTTA Yes Yes Yes Yes No hsa-mir-302c chr4:
113788970-113788993 4373 CCACTGAAACATGGAAGCACTTA Yes Yes Yes Yes No
hsa-mir-302b chr4: 113789093-113789116 4374 CTACTAAAACATGGAAGCACTTA
Yes Yes Yes Yes No hsa-mir-1180 chr17: 19188418-19188440 4375
ACACACCCACGCGAGCCGGAAA Yes Yes Yes No No hsa-mir-1181 chr19:
10375180-10375201 4376 CGGCTCGGGTGGCGGCGACGG Yes Yes No No No
hsa-mir-629* chr15: 68158779-68158801 4377 GCTGGGCTTACGTTGGGAGAAC
No No No No No hsa-mir-302e chr11: 7212577-7212594 4378
TAAGTGCTTCCATGCTT Yes Yes No No No hsa-mir-103 chr5:
167920486-167920509 4379 TCATAGCCCTGTACAATGCTGCT Yes Yes Yes Yes
Yes hsa-mir-103 chr20: 3846187-3846210 4380 AGCAGCATTGTACAGGGCTATGA
Yes Yes Yes Yes Yes hsa-mir-100 chr11: 121528192-121528214 4381
CACAAGTTCGGATCTACGGGTT Yes Yes Yes Yes Yes hsa-mir-138-2* chr16:
55449986-55450008 4382 GCTATTTCACGACACCAGGGTT Yes Yes Yes Yes Yes
hsa-mir-122* chr18: 54269335-54269357 4383 AACGCCATTATCACACTAAATA
Yes Yes Yes Yes Yes hsa-mir-105 chrX: 151311392-151311415 4384
ACCACAGGAGTCTGAGCATTTGA Yes Yes Yes No No hsa-mir-105 chrX:
151313585-151313608 4385 ACCACAGGAGTCTGAGCATTTGA Yes Yes Yes No No
hsa-mir-223* chrX: 65155461-65155483 4386 CGTGTATTTGACAAGCTGAGTT
Yes Yes Yes Yes Yes hsa-mir-363* chrX: 133131120-133131142 4387
AAATTGCATCGTGATCCACCCG No Yes Yes Yes Yes hsa-mir-28-5p chr3:
189889275-189889297 4388 AAGGAGCTCACAGTCTATTGAG Yes Yes Yes Yes Yes
hsa-mir-150* chr19: 54695865-54695887 4389 CTGTCCCCCAGGCCTGTACCAG
Yes Yes Yes Yes Yes hsa-mir-99a* chr21: 16833328-16833350 4390
CAAGCTCGCTTCTATGGGTCTG Yes Yes Yes Yes Yes hsa-mir-1825 chr20:
30289293-30289311 4391 TCCAGTGCCCTCCTCTCC Yes Yes No No No
hsa-mir-129* chr7: 127635208-127635230 4392 AAGCCCTTACCCCAAAAAGTAT
Yes Yes Yes Yes Yes hsa-mir-556-3p chr1: 160579013-160579035 4393
ATATTACCATTAGCTCATCTTT Yes No No No No hsa-mir-10b chr2:
176723302-176723325 4394 TACCCTGTAGAACCGAATTTGTG Yes Yes Yes Yes
Yes hsa-mir-1827 chr12: 99107840-99107858 4395 TGAGGCAGTAGATTGAAT
Yes Yes No No No hsa-mir-10a chr17: 44012264-44012287 4396
CACAAATTCGGATCTACAGGGTA Yes Yes Yes Yes Yes hsa-mir-623 chr13:
98806400-98806423 4397 ATCCCTTGCAGGGGCTGTTGGGT Yes Yes No No No
hsa-mir-622 chr13: 89681496-89681517 4398 ACAGTCTGCTGAGGTTGGAGC Yes
No No No No hsa-mir-621 chr13: 40282961-40282982 4399
GGCTAGCAACAGCGCTTACCT Yes No No No No hsa-mir-620 chr12:
115070762-115070782 4400 ATTTCTATATCTATCTCCAT Yes No No No No
hsa-mir-127-5p chr14: 100419090-100419112 4401
CTGAAGCTCAGAGGGCTCTGAT Yes Yes Yes Yes Yes hsa-mir-626 chr15:
39771134-39771153 4402 AGCTGTCTGAAAATGTCTT Yes No No No No
hsa-mir-625 chr14: 65007622-65007643 4403 GGACTATAGAACTTTCCCCCT Yes
No No No No hsa-mir-625 chr14: 65007586-65007607 4404
AGGGGGAAAGTTCTATAGTCC Yes No No No No hsa-mir-182* chr7:
129197481-129197502 4405 TAGTTGGCAAGTCTAGAACCA Yes Yes Yes Yes No
hsa-mir-1292 chr20: 2581424-2581449 4406 TGGGAACGGGTTCCGGCAGACGCTG
Yes No No No No hsa-mir-342-3p chr14: 99645804-99645827 4407
TCTCACACAGAAATCGCACCCGT Yes Yes Yes Yes Yes hsa-mir-1290 chr1:
19096158-19096177 4408 TCCCTGATCCAAAAATCCA Yes Yes No No No
hsa-mir-1291 chr12: 47334543-47334567 4409 ACTGCTGGTCTTCAGTCAGGGCCA
Yes Yes Yes No No hsa-mir-1296 chr10: 64802777-64802799 4410
GGAGATGGAGCCAGGGCCCTAA Yes Yes Yes No No hsa-mir-1297 chr13:
53784116-53784133 4411 CACCTGAATTACTTGAA Yes Yes Yes No No
hsa-mir-1294 chr5: 153706905-153706927 4412 TGTGAGGTTGGCATTGTTGTCT
Yes No No No No hsa-mir-1225-5p chr16: 2080264-2080286 4413
CCCCCCACTGGGCCGTACCCAC Yes Yes Yes Yes Yes hsa-mir-509-5p chrX:
146148020-146148041 4414 TGATTGCCACTGTCTGCAGTA Yes Yes Yes Yes Yes
hsa-mir-509-5p chrX: 146149795-146149816 4415 TGATTGCCACTGTCTGCAGTA
Yes Yes No Yes Yes hsa-mir-1224-3p chr3: 185441950-185441971 4416
CCCCACCTCCTCTCTCCTCAG Yes Yes Yes Yes Yes hsa-mir-140-3p chr16:
68524545-68524566 4417 TACCACAGGGTAGAACCACGG Yes Yes Yes Yes Yes
hsa-mir-532-3p chrX: 49654549-49654571 4418 CCTCCCACACCCAAGGCTTGCA
Yes Yes Yes Yes Yes hsa-mir-1298 chrX: 113855922-113855944 4419
TTCATTCGGCTGTCCAGATGTA Yes Yes Yes Yes Yes hsa-mir-26b chr2:
218975623-218975644 4420 TTCAAGTAATTCAGGATAGGT Yes Yes Yes Yes Yes
hsa-let-7f-2* chrX: 53600881-53600903 4421 GGAAAGACAGTAGACTGTATAG
Yes Yes Yes Yes Yes hsa-mir-585 chr5: 168623197-168623216 4422
TAGCATACAGATACGCCCA Yes No No No No hsa-mir-490-5p chr7:
136238491-136238511 4423 CCATGGATCTCCAGGTGGGT Yes Yes Yes Yes Yes
hsa-mir-519c-3p chr19: 58881587-58881609 4424
AAAGTGCATCTTTTTAGAGGAT Yes Yes No No No hsa-mir-513a-5p chrX:
146115109-146115127 4425 ATGACACCTCCCTGTGAA Yes Yes Yes No No
hsa-mir-513a-5p chrX: 146102747-146102765 4426 ATGACACCTCCCTGTGAA
Yes Yes Yes No No hsa-mir-591 chr7: 95686969-95686989 4427
ACAATGAGAACCCATGGTCT Yes No No No No hsa-mir-191* chr3:
49033067-49033089 4428 GGGGACGAAATCCAAGCGCAGC Yes Yes Yes No No
hsa-mir-1305 chr4: 183327489-183327511 4429 TTTTCAACTCTAATGGGAGAGA
No No No Yes No hsa-mir-624 chr14: 30553625-30553646 4430
AGGTAATACCAATACCTTGTG Yes No No No No hsa-mir-593 chr7:
127509226-127509245 4431 TGTCTCTGCTGGGGTTTCT Yes Yes No No No
hsa-mir-302a chr4: 113788790-113788813 4432 TCACCAAAACATGGAAGCACTTA
Yes Yes Yes Yes No hsa-mir-592 chr7: 126485437-126485459 4433
ACATCATCGCATATTGACACAA Yes Yes Yes Yes Yes hsa-mir-1293 chr12:
48914231-48914253 4434 GCACAAATCTCCAGACCACCCA Yes Yes No No No
hsa-mir-30e* chr1: 40992671-40992693 4435 CTTTCAGTCGGATGTTTACAGC
Yes Yes Yes Yes Yes hsa-mir-432 chr14: 100420585-100420608 4436
TCTTGGAGTAGGTCATTGGGTGG Yes Yes Yes Yes No hsa-mir-629 chr15:
68158819-68158840 4437 AGTTCTCCCAACGTAAACCCA No No No No No
hsa-mir-96* chr7: 129201772-129201794 4438 CATATTGGCACTGCACATGATT
Yes Yes Yes Yes Yes hsa-mir-1301 chr2: 25405023-25405047 4439
GAAGTCACTCCCAGGCAGCTGCAA No No
Yes Yes Yes hsa-mir-200b* chr1: 1092366-1092388 4440
CATCTTACTGGGCAGCATTGGA No No Yes Yes Yes hsa-mir-181c* chr19:
13846576-13846598 4441 AACCATCGACCGTTGAGTGGAC Yes Yes Yes Yes Yes
hsa-mir-508-3p chrX: 146126154-146126177 4442
TCTACTCCAAAAGGCTACAATCA Yes No No No No hsa-mir-1303 chr5:
154045579-154045601 4443 TTTAGAGACGGGGTCTTGCTCT Yes Yes No No No
hsa-mir-539 chr14: 100583418-100583440 4444 GGAGAAATTATCCTTGGTGTGT
Yes Yes Yes Yes Yes hsa-mir-10b* chr2: 176723341-176723363 4445
ACAGATTCGATTCTAGGGGAAT Yes Yes Yes Yes Yes hsa-mir-612 chr11:
64968519-64968544 4446 GCTGGGCAGGGCTTCTGAGCTCCTT Yes Yes No No No
hsa-mir-613 chr12: 12808909-12808929 4447 AGGAATGTTCCTTCTTTGCC Yes
No No No No hsa-mir-1295 chr1: 169337502-169337523 4448
TCACCCAGATCTGCGGCCTAA Yes Yes No No No hsa-mir-196a chr17:
44064892-44064914 4449 CCCAACAACATGAAACTACCTA Yes Yes Yes Yes Yes
hsa-mir-196a chr12: 52671812-52671834 4450 TAGGTAGTTTCATGTTGTTGGG
Yes Yes Yes Yes Yes hsa-mir-196b chr7: 27175671-27175693 4451
CCCAACAACAGGAAACTACCTA Yes Yes Yes Yes Yes hsa-mir-296-3p chr20:
56826075-56826097 4452 GGAGAGCCTCCACCCAACCCTC Yes Yes Yes Yes Yes
hsa-mir-518d-3p chr19: 58929994-58930015 4453 CAAAGCGCTTCCCTTTGGAGC
Yes Yes No No No hsa-mir-1308 chrX: 21990211-21990229 4454
CCACTGAACCACCCATGC No No No No No hsa-mir-92a-2* chrX:
133131278-133131300 4455 GTAATGCAACAAATCCCCACCC Yes Yes No No No
hsa-mir-658 chr22: 36570239-36570264 4456 ACCAACGGACCTACTTCCCTCCGCC
Yes No No Yes Yes hsa-mir-106b* chr7: 99529560-99529582 4457
GCAGCAAGTACCCACAGTGCGG Yes Yes Yes Yes Yes hsa-mir-374a* chrX:
73423854-73423876 4458 AATTACAATACAATCTGATAAG Yes Yes Yes No No
hsa-mir-595 chr7: 158018185-158018206 4459 AGACACACCACGGCACACTTC
Yes Yes No No No hsa-mir-518d-5p chr19: 58929957-58929979 4460
CTCTAGAGGGAAGCACTTTCTG Yes No No No No hsa-mir-590-5p chr7:
73243478-73243500 4461 GAGCTTATTCATAAAAGTGCAG Yes Yes Yes No No
hsa-mir-448 chrX: 113964342-113964364 4462 TTGCATATGTAGGATGTCCCAT
Yes Yes Yes Yes Yes hsa-mir-326 chr11: 74723799-74723819 4463
CTGGAGGAAGGGCCCAGAGG Yes No Yes Yes Yes hsa-mir-325 chrX:
76142279-76142302 4464 ACACTTACTGGACACCTACTAGG No Yes Yes Yes Yes
hsa-mir-632 chr17: 27701300-27701319 4465 GTGTCTGCTTCCTGTGGGA Yes
Yes Yes No No hsa-mir-328 chr16: 65793730-65793752 4466
ACGGAAGGGCAGAGAGGGCCAG Yes No Yes Yes Yes hsa-mir-329 chr14:
100563240-100563262 4467 AACACACCTGGTTAACCTCTTT Yes Yes Yes No Yes
hsa-mir-329 chr14: 100562923-100562945 4468 AACACACCTGGTTAACCTCTTT
Yes Yes Yes Yes Yes hsa-mir-659 chr22: 36573645-36573667 4469
TGGGGACCCTCCCTGAACCAAG Yes Yes No No No hsa-mir-214* chr1:
170374619-170374641 4470 GCACAGCAAGTGTAGACAGGCA Yes Yes Yes Yes Yes
hsa-mir-483-3p chr11: 2111947-2111968 4471 AAGACGGGAGGAGAGGAGTGA No
No Yes Yes Yes hsa-mir-376a* chr14: 100576877-100576899 4472
GTAGATTCTCCTTCTATGAGTA Yes Yes Yes Yes Yes hsa-mir-218-1* chr4:
20139062-20139084 4473 ATGGTTCCGTCAAGCACCATGG Yes Yes Yes Yes Yes
hsa-mir-302d* chr4: 113788649-113788671 4474 GCAAGTGCCTCCATGTTAAAGT
Yes Yes Yes Yes No hsa-mir-887 chr5: 15988337-15988359 4475
GTGAACGGGCGCCATCCCGAGG No Yes No No No hsa-mir-380* chr14:
100561110-100561132 4476 TGGTTGACCATAGAACATGCGC Yes Yes Yes Yes Yes
hsa-mir-32* chr9: 110848331-110848353 4477 AAATATCACACACACTAAATTG
Yes Yes Yes Yes Yes hsa-mir-889 chr14: 100584038-100584059 4478
TTAATATCGGACAACCATTGT Yes Yes Yes No No hsa-mir-768-5p chr16:
70349860-70349886 4479 ATCACTCCGTACTTTCATCCTCCAAC Yes Yes Yes No No
hsa-mir-501-3p chrX: 49661119-49661141 4480 AATGCACCCGGGCAAGGATTCT
Yes No Yes Yes Yes hsa-mir-485-3p chr14: 100591553-100591575 4481
GTCATACACGGCTCTCCTCTCT Yes Yes Yes Yes Yes hsa-mir-1234 chr8:
145596285-145596307 4482 GTGGGGTGGGTGGTCAGGCCGA Yes Yes No No No
hsa-mir-22* chr17: 1563995-1564017 4483 TAAAGCTTGCCACTGAAGAACT Yes
No Yes Yes Yes hsa-mir-125a-5p chr19: 56888332-56888356 4484
TCCCTGAGACCCTTTAACCTGTGA Yes Yes Yes Yes Yes hsa-mir-643 chr19:
57476921-57476943 4485 ACTTGTATGCTAGCTCAGGTAG Yes Yes No No No
hsa-mir-147 chr9: 122047083-122047103 4486 GCAGAAGCATTTCCACACAC Yes
Yes No Yes No hsa-mir-144 chr17: 24212691-24212711 4487
AGTACATCATCTATACTGTA Yes Yes Yes Yes Yes hsa-mir-145 chr5:
148790416-148790439 4488 GTCCAGTTTTCCCAGGAATCCCT Yes Yes Yes Yes
Yes hsa-mir-143 chr5: 148788733-148788754 4489
TGAGATGAAGCACTGTAGCTC Yes Yes Yes Yes Yes hsa-mir-597 chr8:
9636606-9636628 4490 TGTGTCACTCGATGACCACTGT Yes Yes No No No
hsa-mir-141 chr12: 6943578-6943600 4491 TAACACTGTCTGGTAAAGATGG Yes
Yes Yes Yes Yes hsa-mir-512-5p chr19: 58864241-58864264 4492
CACTCAGCCTTGAGGGCACTTTC Yes Yes No No No hsa-mir-512-5p chr19:
58861757-58861780 4493 CACTCAGCCTTGAGGGCACTTTC Yes Yes No No No
hsa-mir-323-5p chr14: 100561836-100561858 4494
AGGTGGTCCGTGGCGCGTTCGC Yes Yes Yes Yes Yes hsa-mir-224 chrX:
150877758-150877779 4495 AACGGAACCACTAGTGACTTG Yes Yes Yes Yes Yes
hsa-mir-223 chrX: 65155503-65155525 4496 TGTCAGTTTGTCAAATACCCCA Yes
Yes Yes Yes Yes hsa-mir-222 chrX: 45491385-45491406 4497
ACCCAGTAGCCAGATGTAGCT No Yes Yes Yes Yes hsa-mir-221 chrX:
45490551-45490574 4498 GAAACCCAGCAGACAATGTAGCT Yes Yes Yes Yes Yes
hsa-mir-149 chr2: 241044104-241044127 4499 TCTGGCTCCGTGTCTTCACTCCC
Yes Yes Yes Yes No hsa-mir-520a-3p chr19: 58885998-58886020 4500
AAAGTGCTTCCCTTTGGACTGT Yes Yes No No No hsa-mir-548c-5p chr12:
63302579-63302601 4501 AAAAGTAATTGCGGTTTTTGCC Yes Yes No No No
hsa-mir-374b chrX: 73355146-73355168 4502 CACTTAGCAGGTTGTATTATAT
Yes Yes Yes Yes Yes hsa-mir-26a chr12: 56504707-56504729 4503
AGCCTATCCTGGATTACTTGAA Yes Yes Yes Yes Yes hsa-mir-26a chr3:
37985907-37985929 4504 TTCAAGTAATCCAGGATAGGCT Yes Yes Yes Yes Yes
hsa-mir-374a chrX: 73423884-73423906 4505 CACTTATCAGGTTGTATTATAA
Yes Yes Yes Yes No hsa-mir-1302 chr9: 99165698-99165719 4506
TTTAGCATAAGTATGTCCCAA Yes Yes No No No hsa-mir-1302 chr15:
100318229-100318250 4507 TTTAGCATAAGTATGTCCCAA Yes Yes No No No
hsa-mir-1302 chr12: 111617269-111617290 4508 TTTAGCATAAGTATGTCCCAA
Yes No No No No hsa-mir-1302 chr8: 142865522-142865543 4509
TTTAGCATAAGTATGTCCCAA Yes Yes No No No hsa-mir-1302 chr2:
114057050-114057071 4510 TTTAGCATAAGTATGTCCCAA Yes Yes No No No
hsa-mir-1302 chr1: 20300-20321 4511 TTGGGACATACTTATGCTAAA Yes Yes
No No No hsa-mir-1302 chr7: 18133381-18133402 4512
TTTAGCATAAGTATGTCCCAA Yes Yes No No No hsa-mir-1302 chr19:
23044-23065 4513 TTGGGACATACTTATGCTAAA Yes Yes No No No
hsa-mir-1302 chr2: 207842296-207842317 4514 TTTAGCATAAGTATGTCCCAA
Yes Yes No No No hsa-mir-1302 chr9: 20215-20236 4515
TTGGGACATACTTATGCTAAA Yes Yes No No No hsa-mir-1302 chr20:
48664632-48664653 4516 TTTAGCATAAGTATGTCCCAA No No No No No
hsa-mir-624* chr14: 30553662-30553684 4517 TGAACACAAGGTACTGGTACTA
Yes Yes No No No hsa-mir-619 chr12: 107754827-107754851 4518
ACTGGGCACAAACATGTCCAGGTC Yes No No No No hsa-mir-586 chr6:
45273448-45273470 4519 GGACCTAAAAATACAATGCATA Yes Yes No No No
hsa-mir-587 chr6: 107338707-107338728 4520 TTTCCATAGGTGATGAGTCAC
Yes No No No No hsa-mir-584 chr5: 148422128-148422150 4521
CTCAGTCCCAGGCAAACCATAA Yes Yes No No No hsa-mir-30d* chr8:
135886303-135886325 4522 GCAGCAAACATCTGACTGAAAG Yes Yes Yes Yes
Yes
hsa-mir-450a chrX: 133502088-133502110 4523 ATATTAGGAACACATCGCAAAA
Yes Yes Yes Yes Yes hsa-mir-450a chrX: 133502259-133502281 4524
ATATTAGGAACACATCGCAAAA Yes Yes Yes Yes Yes hsa-mir-583 chr5:
95440612-95440633 4525 CAAAGAGGAAGGTCCCATTAC Yes Yes No No No
hsa-mir-580 chr5: 36183765-36183787 4526 CCTAATGATTCATCATTCTCAA Yes
Yes No No No hsa-mir-581 chr5: 53283150-53283171 4527
ACTGATCTAGAGAACACAAGA Yes Yes No No No hsa-mir-129-3p chr11:
43559575-43559597 4528 AAGCCCTTACCCCAAAAAGCAT Yes Yes Yes Yes Yes
hsa-mir-331-5p chr12: 94226351-94226373 4529 CTAGGTATGGTCCCAGGGATCC
Yes Yes Yes Yes Yes hsa-mir-665 chr14: 100411164-100411184 4530
ACCAGGAGGCTGAGGCCCCT Yes Yes Yes Yes Yes hsa-mir-664 chr1:
218440513-218440536 4531 TGTAGGCTGGGGATAAATGAATA Yes Yes No Yes Yes
hsa-mir-663 chr20: 26136878-26136900 4532 GCGGTCCCGCGGCGCCCCGCCT
Yes No No No No hsa-mir-662 chr16: 760243-760264 4533
TCCCACGTTGTGGCCCAGCAG No Yes Yes Yes Yes hsa-mir-588 chr6:
126847484-126847505 4534 TTGGCCACAATGGGTTAGAAC Yes No No No No
hsa-mir-589 chr7: 5502029-5502051 4535 CTCAGAGCAGACGTGGTTCTCA Yes
Yes Yes No No hsa-mir-220a chrX: 122523693-122523714 4536
AAAGTGTCAGATACGGTGTGG Yes Yes No No No hsa-mir-220b chr19:
6446968-6446989 4537 CCACCACCGTGTCTGACACTT Yes Yes Yes Yes No
hsa-mir-371-3p chr19: 58982781-58982804 4538
AAGTGCCGCCATCTTTTGAGTGT Yes Yes Yes No Yes hsa-mir-744 chr17:
11925950-11925972 4539 TGCGGGGCTAGGGCTAACAGCA Yes Yes Yes Yes No
hsa-mir-934 chrX: 135460716-135460738 4540 TGTCTACTACTGGAGACACTGG
Yes Yes No No No hsa-mir-628-5p chr15: 53452480-53452502 4541
CCTCTAGTAAATATGTCAGCAT Yes Yes Yes No Yes hsa-mir-888 chrX:
144884039-144884060 4542 TGACTGACAGCTTTTTGAGTA Yes Yes No No No
hsa-mir-126* chr9: 138684888-138684909 4543 CATTATTACTTTTGGTACGCG
Yes Yes Yes Yes Yes hsa-mir-99b* chr19: 56887720-56887742 4544
CAAGCTCGTGTCTGTGGGTCCG Yes Yes Yes Yes Yes hsa-mir-137 chr1:
98284234-98284257 4545 CTACGCGTATTCTTAAGCAATAA Yes Yes Yes Yes Yes
hsa-mir-136 chr14: 100420805-100420828 4546 ACTCCATTTGTTTTGATGATGGA
Yes Yes Yes Yes Yes hsa-mir-149* chr2: 241044145-241044166 4547
AGGGAGGGACGGGGGCTGTGC Yes Yes Yes Yes No hsa-mir-134 chr14:
100590783-100590805 4548 TGTGACTGGTTGACCAGAGGGG Yes Yes Yes Yes Yes
hsa-mir-138 chr16: 55449939-55449962 4549 AGCTGGTGTTGTGAATCAGGCCG
Yes Yes Yes Yes Yes hsa-mir-138 chr3: 44130729-44130752 4550
AGCTGGTGTTGTGAATCAGGCCG No No Yes Yes Yes hsa-mir-1269 chr4:
66825202-66825224 4551 CTGGACTGAGCCGTGCTACTGG Yes Yes No No No
hsa-mir-1268 chr15: 20014622-20014640 4552 CCCCCACCACCACGCCCG No No
No No No hsa-mir-196a* chr12: 52671849-52671871 4553
CGGCAACAAGAAACTGCCTGAG Yes Yes Yes Yes Yes hsa-mir-20b* chrX:
133131508-133131530 4554 CTGGAAGTGCCCATACTACAGT Yes Yes Yes No No
hsa-mir-199a-3p chr19: 10789104-10789126 4555
TAACCAATGTGCAGACTACTGT Yes Yes Yes Yes Yes hsa-mir-199a-3p chr1:
170380316-170380338 4556 TAACCAATGTGCAGACTACTGT Yes Yes Yes Yes Yes
hsa-mir-1263 chr3: 165372004-165372026 4557 ACTCAGTATGCCAGGGTACCAT
Yes No No No No hsa-mir-1262 chr1: 68421846-68421868 4558
ATCCTTCTACAAATTCACCCAT Yes Yes No No No hsa-mir-1261 chr11:
90241995-90242014 4559 AAGCCAAAGCCTTATCCAT Yes Yes No No No
hsa-mir-1260 chr14: 76802326-76802344 4560 ATCCCACCTCTGCCACCA Yes
Yes No No No hsa-mir-1267 chr13: 106981565-106981586 4561
TGGGGATTACACTTCAACAGG Yes Yes No No No hsa-mir-151-5p chr8:
141811903-141811924 4562 ACTAGACTGTGAGCTCCTCGA Yes Yes Yes No No
hsa-mir-1265 chr10: 14518593-14518615 4563 CAGGATGTGGTCAAGTGTTGTT
Yes Yes No No No hsa-mir-1264 chrX: 113793426-113793449 4564
CAAGTCTTATTTGAGCACCTGTT Yes Yes Yes No Yes hsa-mir-125b-2* chr21:
16884480-16884502 4565 TCACAAGTCAGGCTCTTGGGAC Yes Yes Yes Yes Yes
hsa-mir-33a* chr22: 40626938-40626960 4566 CAATGTTTCCACAGTGCATCAC
Yes No Yes Yes Yes hsa-mir-339-5p chr7: 1029151-1029174 4567
CGTGAGCTCCTGGAGGACAGGGA Yes Yes Yes Yes No hsa-mir-708* chr11:
78790723-78790745 4568 CTAGAAGCTCACAGTCTAGTTG Yes Yes Yes Yes Yes
hsa-mir-1255a chr4: 102470544-102470567 4569
AATCTACTTTCTTTGCTCATCCT Yes Yes No No No hsa-mir-1255b chr4:
36104421-36104443 4570 AACCACTTTCTTTGCTCATCCG Yes No No No No
hsa-mir-1255b chr1: 166234526-166234548 4571 CGGATGAGCAAAGAAAGTGGTT
Yes No No No No hsa-mir-7-1* chr9: 85774505-85774527 4572
TATGGCAGACTGTGATTTGTTG Yes Yes Yes Yes Yes hsa-mir-199b-3p chr9:
130046844-130046866 4573 TAACCAATGTGCAGACTACTGT Yes Yes Yes Yes No
hsa-mir-641 chr19: 45480349-45480373 4574 GAGGTGACTCTATCCTATGTCTTT
Yes No No No No hsa-mir-193a-3p chr17: 26911181-26911203 4575
AACTGGCCTACAAAGTCCCAGT Yes Yes Yes Yes Yes hsa-mir-186* chr1:
71305912-71305934 4576 CCCAAAAAATTCACCTTTGGGC Yes Yes Yes No Yes
hsa-mir-139-5p chr11: 72003794-72003816 4577 CTGGAGACACGTGCACTGTAGA
Yes Yes Yes Yes Yes hsa-mir-671-5p chr7: 150566467-150566490 4578
AGGAAGCCCTGGAGGGGCTGGAG Yes Yes Yes Yes Yes hsa-mir-582-3p chr5:
59035212-59035234 4579 GGTTCAGTTGTTCAACCAGTTA Yes Yes Yes Yes Yes
hsa-mir-548d-5p chr17: 62898117-62898139 4580
GGCAAAAACCACAATTACTTTT Yes No No No No hsa-mir-548d-5p chr8:
124429505-124429527 4581 GGCAAAAACCACAATTACTTTT No Yes No No No
hsa-mir-130b* chr22: 20337604-20337625 4582 ACTCTTTCCCTGTTGCACTAC
Yes Yes Yes Yes Yes hsa-let-7f-1* chr9: 95978511-95978533 4583
CTATACAATCTATTGCCTTCCC Yes Yes Yes Yes Yes hsa-mir-767-3p chrX:
151312574-151312597 4584 AGAAACCATGGGGTATGAGCAGA No Yes Yes Yes Yes
hsa-mir-363 chrX: 133131077-133131099 4585 TACAGATGGATACCGTGCAATT
No Yes Yes Yes Yes hsa-mir-32 chr9: 110848372-110848394 4586
TGCAACTTAGTAATGTGCAATA Yes Yes Yes Yes Yes hsa-mir-31 chr9:
21502156-21502177 4587 AGCTATGCCAGCATCTTGCCT Yes Yes Yes Yes Yes
hsa-mir-525-3p chr19: 58892649-58892671 4588 GAAGGCGCTTCCCTTTAGAGCG
Yes Yes No No No hsa-mir-181d chr19: 13646723-13846746 4589
AACATTCATTGTTGTCGGTGGGT Yes Yes Yes Yes Yes hsa-mir-568 chr3:
115518071-115518091 4590 GTGTGTATACATTTATACAT Yes Yes Yes Yes Yes
hsa-mir-548b-5p chr6: 119431961-119431983 4591
GGCCAAAACCACAATTACTTTT Yes No No No No hsa-mir-559 chr2:
47458332-47458353 4592 TAAAGTAAATATGCACCAAAA Yes No No No No
hsa-mir-559 chr2: 47458372-47458393 4593 TTTTGGTGCATATTTACTTTA Yes
No No No No hsa-mir-181a chr9: 126494579-126494602 4594
AACATTCAACGCTGTCGGTGAGT Yes Yes Yes Yes Yes hsa-mir-181a chr1:
197094859-197094882 4595 ACTCACCGACAGCGTTGAATGTT Yes Yes Yes Yes
Yes hsa-mir-181b chr9: 126495824-126495847 4596
AACATTCATTGCTGTCGGTGGGT Yes Yes Yes Yes Yes hsa-mir-181b chr1:
197094676-197094699 4597 ACCCACCGACAGCAATGAATGTT Yes Yes Yes Yes
Yes hsa-mir-181c chr19: 13646538-13846560 4598
AACATTCAACCTGTCGGTGAGT Yes Yes Yes Yes Yes hsa-mir-34b* chr11:
110888884-110888907 4599 TAGGCAGTGTCATTAGCTGATTG Yes Yes Yes Yes
Yes hsa-mir-188-5p chrX: 49654862-49654883 4600
CATCCCTTGCATGGTGGAGGG Yes Yes Yes Yes Yes hsa-mir-367 chr4:
113788481-113788503 4601 TCACCATTGCTAAAGTGCAATT Yes Yes Yes Yes No
hsa-mir-365 chr17: 26926609-26926631 4602 TAATGCCCCTAAAAATCCTTAT
Yes Yes Yes Yes Yes hsa-mir-365 chr16: 14310697-14310719 4603
TAATGCCCCTAAAAATCCTTAT Yes Yes Yes Yes Yes hsa-mir-449b chr5:
54502290-54502312 4604 GCCAGCTAACAATACACTGCCT Yes Yes Yes No Yes
hsa-mir-29a* chr7: 130212084-130212106 4605 CTGAACACCAAAAGAAATCAGT
Yes Yes Yes Yes Yes hsa-let-7c* chr21: 16834050-16834072 4606
TAGAGTTACACCCTGGGAGTTA Yes Yes Yes Yes Yes
hsa-mir-558 chr2: 32610783-32610802 4607 TGAGCTGCTGTACCAAAAT Yes
Yes No No No hsa-mir-10a* chr17: 44012224-44012246 4608
TATTCCCCTAGATACGAATTTG Yes Yes Yes Yes Yes hsa-mir-518e* chr19:
58924918-58924940 4609 CTCTAGAGGGAAGCGCTTTCTG Yes Yes No No No
hsa-mir-561 chr2: 188870523-188870545 4610 CAAAGTTTAAGATCCTTGAAGT
Yes Yes No No No hsa-mir-562 chr2: 232745666-232745686 4611
AAAGTAGCTGTACCATTTGC Yes Yes No No No hsa-mir-563 chr3:
15890332-15890351 4612 AGGTTGACATACGTTTCCC Yes No No No No
hsa-mir-361-5p chrX: 85045341-85045363 4613 GTACCCCTGGAGATTCTGATAA
Yes Yes Yes Yes Yes hsa-mir-566 chr3: 50185777-50185796 4614
GGGCGCCTGTGATCCCAAC Yes Yes No No No hsa-mir-567 chr3:
113314352-113314375 4615 AGTATGTTCTTCCAGGACAGAAC Yes No No No No
hsa-mir-642 chr19: 50870040-50870062 4616 GTCCCTCTCCAAATGTGTCTTG
Yes Yes No No No hsa-mir-192* chr11: 64415206-64415226 4617
CTGTGACCTATGGAATTGGCAG Yes Yes Yes Yes No hsa-mir-92a-1* chr13:
90801578-90801601 4618 AGGTTGGGATCGGTTGCAATGCT Yes No Yes No No
hsa-mir-27a* chr19: 13808300-13808322 4619 TGCTCACAAGCAGCTAAGCCCT
Yes Yes Yes Yes Yes hsa-mir-564 chr3: 44878398-44878417 4620
AGGCACGGTGTCAGCAGGC Yes Yes No No No hsa-mir-106a* chrX:
133131903-133131925 4621 GTAAGAAGTGCTTACATTGCAG Yes Yes Yes No No
hsa-mir-26a-1* chr3: 37985946-37985968 4622 CCTATTCTTGGTTACTTGCACG
Yes Yes Yes Yes Yes hsa-mir-498 chr19: 58869295-58869318 4623
TTTCAAGCCAGGGGGCGTTTTTC Yes Yes No No No hsa-mir-454* chr17:
54569970-54569992 4624 GCAGAGACAATATTGATAGGGT Yes Yes Yes No No
hsa-mir-502-5p chrX: 49665960-49665981 4625 ATCCTTGCTATCTGGGTGCTA
Yes Yes Yes Yes Yes hsa-mir-218-2* chr5: 168127750-168127772 4626
CGCGGTGCTTGACAGAACCATG Yes Yes Yes Yes Yes hsa-mir-30c-2* chr6:
72143387-72143409 4627 AGAGTAAACAGCCTTCTCCCAG Yes Yes Yes Yes Yes
hsa-mir-526b* chr19: 58889508-58889530 4628 GAAAGTGCTTCCTTTTAGAGGC
Yes Yes No No No hsa-mir-542-5p chrX: 133503095-133503118 4629
TCTCGTGACATGATGATCCCCGA No Yes Yes Yes Yes hsa-mir-433 chr14:
100418038-100418060 4630 ATCATGATGGGCTCCTCGGTGT Yes Yes Yes Yes Yes
hsa-mir-27a chr19: 13808260-13808281 4631 GCGGAACTTAGCCACTGTGAA Yes
Yes Yes Yes Yes hsa-mir-27b chr9: 96887607-96887628 4632
TTCACAGTGGCTAAGTTCTGC Yes Yes Yes Yes Yes hsa-mir-330-3p chr19:
50834106-50834129 4633 TCTCTGCAGGCCGTGTGCTTTGC Yes Yes Yes Yes Yes
hsa-mir-431 chr14: 100417115-100417136 4634 TGTCTTGCAGGCCGTCATGCA
Yes Yes Yes Yes Yes hsa-mir-520c-5p chr19: 58902533-58902555 4635
CTCTAGAGGGAAGCACTTTCTG Yes No No No No hsa-mir-708 chr11:
78790768-78790791 4636 CCCAGCTAGATTGTAAGCTCCTT Yes Yes Yes Yes Yes
hsa-mir-17* chr13: 90800909-90800931 4637 ACTGCAGTGAAGGCACTTGTAG
Yes No Yes Yes Yes hsa-mir-1197 chr14: 100561709-100561730 4638
TAGGACACATGGTCTACTTGCT Yes Yes Yes Yes Yes hsa-mir-548a-5p chr8:
105565823-105565845 4639 GGTAAAACTCGCAATTACTTTT No Yes No No No
hsa-mir-1248 chr3: 187987157-187987184 4640
ACCTTCTTGTATAAGCACTGTGCTAAA Yes Yes Yes Yes Yes hsa-mir-208b chr14:
22957045-22957067 4641 ACAAACCTTTTGTTCGTCTTAT Yes Yes Yes Yes Yes
hsa-mir-208a chr14: 22927650-22927672 4642 ACAAGCTTTTTGCTCGTCTTAT
Yes Yes Yes Yes Yes hsa-mir-499-5p chr20: 33041871-33041892 4643
TTAAGACTTGCAGTGATGTTT Yes Yes Yes Yes Yes hsa-mir-29b-1* chr7:
130212805-130212829 4644 TCTAAACCACCATATGAAACCAGC Yes Yes Yes Yes
Yes hsa-mir-378* chr5: 149092584-149092606 4645
CTCCTGACTCCAGGTCCTGTGT Yes Yes Yes No Yes hsa-mir-16-1* chr13:
49521121-49521143 4646 TCAGCAGCACAGTTAATACTGG Yes Yes Yes Yes No
hsa-mir-338-3p chr17: 76714281-76714303 4647 CAACAAAATCACTGATGCTGGA
Yes Yes Yes Yes Yes hsa-mir-145* chr5: 148790454-148790476 4648
GGATTCCTGGAAATACTGTTCT Yes Yes Yes Yes Yes hsa-mir-3373p chr14:
100410642-100410664 4649 CTCCTATATGATGCCTTTCTTC Yes Yes No Yes Yes
hsa-mir-593* chr7: 127509163-127509188 4650
AGGCACCAGCCAGGCATTGCTCAGC Yes No No No No hsa-mir-130a chr11:
57165300-57165322 4651 CAGTGCAATGTTAAAAGGGCAT Yes Yes Yes Yes Yes
hsa-mir-627 chr15: 40279119-40279141 4652 TCCTCTTTTCTTAGAGACTCAC
Yes Yes No No No hsa-mir-892b chrX: 144886417-144886439 4653
TCTACCCAGAAAGGAGCCAGTG Yes Yes No No No hsa-mir-892a chrX:
144885888-144885909 4654 CTACGCAGAAAGGACACAGTG Yes Yes No No No
hsa-mir-548n chr7: 34946940-34946962 4655 ACAAAATCCACAATTACTTTTG
Yes No No No No hsa-mir-768-3p chr16: 70349813-70349841 4656
GTCAGCAGTTTGAGTGTCAGCATTGTGA Yes Yes Yes No No hsa-mir-630 chr15:
70666671-70666693 4657 AGTATTCTGTACCAGGGAAGGT Yes Yes No No No
hsa-mir-631 chr15: 73433043-73433064 4658 GCTGAGGTCTGGGCCAGGTCT Yes
Yes Yes No No hsa-mir-1287 chr10: 100145017-100145039 4659
GACTCGAACCACTGATCCAGCA Yes Yes Yes No No hsa-mir-633 chr17:
58375367-58375390 4660 CTAATAGTATCTACCACAATAAA Yes Yes No No No
hsa-mir-1281 chr22: 39818494-39818511 4661 TCGCCTCCTCCTCTCCC Yes
Yes Yes Yes Yes hsa-mir-635 chr17: 63932246-63932269 4662
GGACATTGTTTCAGTGCCCAAGT Yes No No No No hsa-mir-636 chr17:
72244142-72244165 4663 TGCGGGCGGGACGAGCAAGCACA Yes Yes No No No
hsa-mir-637 chr19: 3912426-3912450 4664 ACGCAGAGCCCGAAAGCCCCCAGT
Yes No No No No hsa-mir-638 chr19: 10690094-10690119 4665
AGGGATCGCGGGCGGGTGGCGGCCT No Yes Yes No No hsa-mir-639 chr19:
14501414-14501437 4666 ATCGCTGCGGTTGCGAGCGCTGT No No No No No
hsa-mir-1289 chr5: 132791205-132791228 4667 AAAATGCAGATTCCTGGACTCCA
Yes Yes No No No hsa-mir-1289 chr20: 33505225-33505248 4668
AAAATGCAGATTCCTGGACTCCA Yes Yes No No No hsa-mir-1288 chr17:
16126096-16126117 4669 TGGACTGCCCTGATCTGGAGA Yes Yes No No No
hsa-mir-548j chr22: 25281239-25281261 4670 ACCAAAGACCGCAATTACTTTT
Yes No No No No hsa-mir-518b chr19: 58897852-58897874 4671
CAAAGCGCTCCCCTTTAGAGGT Yes Yes No No No hsa-let-7c chr21:
16834028-16834050 4672 TGAGGTAGTAGGTTGTATGGTT Yes Yes Yes Yes Yes
hsa-let-7a chr22: 44887295-44887317 4673 TGAGGTAGTAGGTTGTATAGTT Yes
Yes Yes Yes Yes hsa-let-7a chr11: 121522485-121522507 4674
AACTATACAACCTACTACCTCA Yes Yes Yes Yes Yes hsa-let-7a chr9:
95978064-95978086 4675 TGAGGTAGTAGGTTGTATAGTT Yes Yes Yes Yes Yes
hsa-let-7f chrX: 53600931-53600953 4676 AACTATACAATCTACTACCTCA Yes
Yes Yes Yes Yes hsa-let-7f chr9: 95978455-95978477 4677
TGAGGTAGTAGATTGTATAGTT Yes Yes Yes Yes Yes hsa-let-7g chr3:
52277391-52277413 4678 AACTGTACAAACTACTACCTCA Yes Yes Yes Yes No
hsa-let-7d chr9: 95980943-95980965 4679 AGAGGTAGTAGGTTGCATAGTT Yes
Yes Yes Yes Yes hsa-let-7e chr19: 56887857-56887879 4680
TGAGGTAGGAGGTTGTATAGTT Yes Yes Yes Yes Yes hsa-mir-516a-3p chr19:
58956258-58956276 4681 TGCTTCCTTTCAGAGGGT Yes No No No No
hsa-mir-516a-3p chr19: 58951866-58951884 4682 TGCTTCCTTTCAGAGGGT
Yes No No No No hsa-let-7i chr12: 61283737-61283759 4683
TGAGGTAGTAGTTTGTGCTGTT Yes Yes Yes Yes Yes hsa-mir-503 chrX:
133508066-133508089 4684 CTGCAGAACTGTTCCCGCTGCTA Yes Yes Yes Yes
Yes hsa-mir-494 chr14: 100565770-100565792 4685
TGAAACATACACGGGAAACCTC Yes Yes Yes Yes Yes hsa-mir-519b-3p chr19:
58890328-58890350 4686 AAAGTGCATCCTTTTAGAGGTT Yes Yes No No No
hsa-mir-1207-5p chr8: 129130586-129130607 4687
TGGCAGGGAGGCTGGGAGGGG Yes No No No No hsa-let-7b* chr22:
44888288-44888310 4688 CTATACAACCTACTGCCTTCCC Yes Yes Yes Yes Yes
hsa-mir-181a* chr1: 197094820-197094842 4689 GGTACAATCAACGGTCGATGGT
Yes Yes Yes Yes Yes hsa-mir-548e chr10: 112738725-112738747 4690
AAAAACTGAGACTACTTTTGCA Yes No
No No No hsa-mir-125b chr21: 16884443-16884465 4691
TCCCTGAGACCCTAACTTGTGA Yes Yes Yes Yes Yes hsa-mir-125b chr11:
121475726-121475748 4692 TCACAAGTTAGGGTCTCAGGGA Yes Yes Yes Yes Yes
hsa-mir-9* chr1: 154656769-154656791 4693 ACTTTCGGTTATCTAGCTTTAT
Yes Yes Yes Yes Yes hsa-mir-9* chr5: 87998439-87998461 4694
ACTTTCGGTTATCTAGCTTTAT Yes Yes Yes Yes Yes hsa-mir-9* chr15:
87712305-87712327 4695 ATAAAGCTAGATAACCGAAAGT Yes No Yes Yes Yes
hsa-mir-301b chr22: 20337313-20337336 4696 CAGTGCAATGATATTGTCAAAGC
Yes Yes Yes Yes Yes hsa-mir-301a chr17: 54583291-54583314 4697
GCTTTGACAATACTATTGCACTG Yes Yes Yes Yes Yes hsa-mir-98 chrX:
53599984-53600006 4698 AACAATACAACTTACTACCTCA Yes Yes Yes Yes Yes
hsa-mir-550* chr7: 30295994-30296016 4699 TGTCTTACTCCCTCAGGCACAT
Yes Yes No No No hsa-mir-550* chr7: 32739177-32739199 4700
TGTCTTACTCCCTCAGGCACAT Yes Yes No No No hsa-mir-505* chrX:
138834020-138834042 4701 ACATCAATACTTCCTGGCTCCC Yes Yes Yes Yes Yes
hsa-mir-142-3p chr17: 53763604-53763627 4702
TCCATAAAGTAGGAAACACTACA Yes Yes Yes Yes Yes hsa-mir-487a chr14:
100588583-100588605 4703 AATCATACAGGGACATCCAGTT Yes Yes Yes No No
hsa-mir-93 chr7: 99529373-99529396 4704 CTACCTGCACGAACAGCACTTTG Yes
Yes Yes Yes Yes hsa-mir-95 chr4: 8057938-8057960 4705
TGCTCAATAAATACCCGTTGAA Yes Yes Yes No No hsa-mir-96 chr7:
129201814-129201837 4706 AGCAAAAATGTGCTAGTGCCAAA Yes Yes Yes Yes
Yes hsa-mir-200c* chr12: 6943126-6943148 4707
CGTCTTACCCAGCAGTGTTTGG No Yes Yes Yes Yes hsa-mir-527 chr19:
58949096-58949116 4708 CTGCAAAGGGAAGCCCTTTC Yes No No No No
hsa-mir-521 chr19: 58943754-58943776 4709 AACGCACTTCCCTTTAGAGTGT
Yes No No No No hsa-mir-521 chr19: 58911712-58911734 4710
AACGCACTTCCCTTTAGAGTGT Yes No No No No hsa-mir-127-3p chr14:
100419124-100419146 4711 TCGGATCCGTCTGAGCTTGGCT Yes Yes Yes Yes Yes
hsa-mir-523 chr19: 58893502-58893525 4712 GAACGCGCTTCCCTATAGAGGGT
Yes No No No No hsa-mir-135b chr1: 203684111-203684134 4713
TCACATAGGAATGAAAAGCCATA Yes Yes Yes Yes Yes hsa-mir-135a chr3:
52303325-52303348 4714 TCACATAGGAATAAAAAGCCATA Yes Yes Yes Yes Yes
hsa-mir-135a chr12: 96481742-96481765 4715 TATGGCTTTTTATTCCTATGTGA
Yes Yes Yes Yes Yes hsa-mir-146b-5p chr10: 104186266-104186288 4716
TGAGAACTGAATTCCATAGGCT Yes No Yes Yes Yes hsa-mir-509-3p chrX:
146148871-146148893 4717 CTACCCACAGACGTACCAATCA Yes Yes No No No
hsa-mir-509-3p chrX: 146147984-146148006 4718
CTACCCACAGACGTACCAATCA Yes Yes No No No hsa-mir-509-3p chrX:
146149759-146149781 4719 CTACCCACAGACGTACCAATCA Yes Yes No No No
hsa-mir-33b* chr17: 17657895-17657917 4720 GGGCTGCACTGCCGAGGCACTG
Yes Yes Yes No No hsa-mir-744* chr17: 11926007-11926029 4721
CTGTTGCCACTAACCTCAACCT Yes Yes Yes Yes No hsa-mir-1274a chr5:
41511503-41511521 4722 GTCCCTGTTCAGGCGCCA Yes Yes No No No
hsa-mir-532-5p chrX: 49654512-49654534 4723 CATGCCTTGAGTGTAGGACCGT
Yes Yes Yes Yes Yes hsa-mir-1274b chr19: 62716222-62716239 4724
TGGCGCCCGAACAGGGA Yes No No No No hsa-let-71* chr12:
61283793-61283815 4725 CTGCGCAAGCTACTGCCTTGCT Yes Yes No Yes Yes
hsa-mir-132 chr17: 1899972-1899994 4726 CGACCATGGCTGTAGACTGTTA No
Yes Yes Yes Yes hsa-mir-20a* chr13: 90801362-90801384 4727
ACTGCATTATGAGCACTTAAAG Yes No Yes Yes Yes hsa-mir-23a chr19:
13808408-13808429 4728 GGAAATCCCTGGCAATGTGAT Yes Yes Yes Yes Yes
hsa-mir-23b chr9: 96887367-96887388 4729 ATCACATTGCCAGGGATTACC Yes
Yes Yes Yes Yes hsa-mir-542-3p chrX: 133503059-133503081 4730
TTTCAGTTATCAATCTGTCACA No Yes Yes Yes Yes hsa-mir-148b chr12:
53017328-53017350 4731 TCAGTGCATCACAGAACTTTGT Yes Yes Yes Yes Yes
hsa-mir-148a chr7: 25956066-52956088 4732 ACAAAGTTCTGTAGTGCACTGA
Yes Yes Yes Yes No hsa-mir-886-3p chr5: 135444086-135444107 4733
AAGGGTCAGTAAGCACCCGCG Yes Yes No No No hsa-mir-24 chr19:
13808102-13808124 4734 CTGTTCCTGCTGAACTGAGCCA Yes Yes Yes Yes Yes
hsa-mir-24 chr9: 96888166-96888188 4735 TGGCTCAGTTCAGCAGGAACAG Yes
Yes Yes Yes Yes hsa-mir-330-5p chr19: 50834146-50834168 4736
GCCTAAGACACAGGCCCAGAGA Yes Yes Yes Yes Yes hsa-mir-497* chr17:
6861980-6862002 4737 TCTAACACCACAGTGTGGTTTG Yes Yes Yes Yes Yes
hsa-mir-451 chr17: 24212546-24212568 4738 AACTCAGTAATGGTAACGGTTT
Yes Yes Yes Yes Yes hsa-mir-452 chrX: 150878805-150878827 4739
TCAGTTTCCTCTGCAAACAGTT Yes Yes Yes Yes No hsa-mir-340* chr5:
179374924-179374946 4740 GCTATAAAGTAACTGAGACGGA Yes Yes Yes Yes No
hsa-mir-454 chr17: 54569929-54569952 4741 ACCCTATAAGCAATATTGCACTA
Yes Yes Yes No No hsa-mir-890 chrX: 144883530-144883551 4742
CAACTGATGCCTTTCCAAGTA Yes No No No No hsa-mir-135b* chr1:
203684073-203684095 4743 CCCATGGCTTTTAGCCCTACAT Yes Yes Yes Yes Yes
hsa-mir-875-3p chr8: 100618200-100618221 4744 CACAACCTCAGTGTTTCCAGG
Yes Yes Yes No No hsa-mir-541* chr14: 100600593-100600618 4745
AAAGGATTCTGCTGTCGGTCCCACT No Yes No No No hsa-mir-26a-2* chr12:
56504669-56504691 4746 GAAACAAGTAATCAAGAATAGG Yes Yes Yes No No
hsa-mir-302c* chr4: 113789006-113789028 4747 CAGCAGGTACCCCCATGTTAAA
Yes Yes Yes Yes No hsa-mir-885-3p chr3: 10411182-10411204 4748
TATCCACTACACCCCGCTGCCT Yes Yes Yes No No hsa-mir-450b-3p chrX:
133501889-133501911 4749 TATGGATGCAAAATGATCCCAA Yes Yes Yes No No
hsa-mir-296-5p chr20: 56826110-56826131 4750 ACAGGATTGAGGGGGGGCCCT
Yes Yes No Yes Yes hsa-mir-221* chrX: 45490592-45490614 4751
AAATCTACATTGTATGCCAGGT Yes Yes Yes Yes Yes hsa-mir-100* chr11:
121528157-121528179 4752 CATACCTATAGATACAAGCTTG Yes Yes Yes Yes Yes
hsa-mir-302b* chr4: 113789130-113789152 4753 GAAAGCACTTCCATGTTAAAGT
Yes Yes Yes No No hsa-mir-487b chr14: 100582594-100582616 4754
AATCGTACAGGGTCATCCACTT Yes Yes Yes Yes Yes hsa-mir-607 chr10:
98578430-98578451 4755 GTTATAGATCTGGATTTGAAC Yes No No No No
hsa-mir-625* chr14: 65007623-65007645 4756 GACTATAGAACTTTCCCCCTCA
Yes No No No No hsa-mir-625* chr14: 65007684-65007606 4757
TGAGGGGGAAAGTTCTATAGTC Yes No No No No hsa-mir-141* chr12:
6943536-6943558 4758 CATCTTCCAGTACAGTGTTGGA Yes Yes Yes Yes Yes
hsa-mir-606 chr10: 76982281-76982302 4759 AAACTACTGAAAATCAAAGAT Yes
Yes No No No hsa-mir-155* chr21: 25868204-25868226 4760
CTCCTACATATTAGCATTAACA Yes Yes Yes No No hsa-mir-146a chr5:
159844956-159844978 4761 TGAGAACTGAATTCCATGGGTT Yes Yes Yes Yes Yes
hsa-mir-1183 chr7: 21477247-21477244 4762
CACTGTAGGTGATGGTGAGAGTGGGCA Yes Yes No No No
Sequence CWU 0 SQTB SEQUENCE LISTING The patent application
contains a lengthy "Sequence Listing" section. A copy of the
"Sequence Listing" is available in electronic form from the USPTO
web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20140171484A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
0 SQTB SEQUENCE LISTING The patent application contains a lengthy
"Sequence Listing" section. A copy of the "Sequence Listing" is
available in electronic form from the USPTO web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20140171484A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
* * * * *
References