The miRBase Sequence Database — Release 13.0

by Chris on March 10, 2009

in miRBase

UPDATE August 2012:  Current Version is miRBase 19

The miRBase Sequence Database — Release 13.0
———————————————

1. SUMMARY

The miRBase Sequence Database provides a searchable online repository
for published microRNA sequences and associated annotation,
functionality previously provided by the microRNA Registry. miRBase
also contains predicted miRNA target genes in miRBase Targets, and
provides a gene naming and nomenclature function in the miRBase
Registry.

Release 13.0 of the database contains 9539 entries representing
hairpin precursor miRNAs, expressing 9169 mature miRNA products, in
103 species. The data are freely available to all through the web
interface at http://microrna.sanger.ac.uk/sequences/ and in flatfile
form from ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/.

2. CHANGES SINCE RELEASE 12.0

937 new hairpin sequences and 1005 novel mature miR and miR* products
have been added. See the miRNA.diff file for the full description of
changes. Sequences from Amphimedon queenslandica, Branchiostoma
floridae, Capitella sp. I, Cerebratulus lacteus, Haliotis rufescens,
Hydra magnipapillata, Ixodes scapularis, Locusta migratoria, Lottia
gigantea, Lotus japonicus, Nematostella vectensis, Saccoglossus
kowalevskii, Schistosoma japonicum, Schistosoma mansoni,
Strongylocentrotus purpuratus, and Vigna unguiculata are included for
the first time.

3. FILES

The following files are available from the above ftp site:

miRNA.dat – all entries in (almost) EMBL format
hairpin.fa – predicted miR stem-loop sequences in fasta format
mature.fa – mature sequences in fasta format
maturestar.fa – minor miR* sequences in fasta format
miRNA.dead – entries removed from the database
miRNA.diff – differences between the current and last release
miFam.dat – family classification of related hairpin sequences

The genomes/ directory contains gff files of genome coordinates for,
based on the following genome assemblies:

aga.gff – A. gambiae (AGAMP3)
ame.gff – A. mellifera (AMEL4.0)
ath.gff – A. thaliana (TAIR8)
bfl.gff – B. floridae (Braf2)
bmo.gff – B. mori (SILKDB2.0)
bna.gff – B. napus (BrassicaDB-20080411)
bta.gff – B. taurus (BTAU4.0)
cap.gff – Capitella sp. I (Capca1)
cbr.gff – C. briggsae (CB25.AGP8)
cel.gff – C. elegans (WormBase WS190)
cfa.gff – C. familiaris (CANFAM2.0)
cin.gff – C. intestinalis (JGI2.0)
cre.gff – C. reinhardtii (JGI Chlre3.1)
csa.gff – C. savignyi (CSAV2.0)
dme.gff – D. melanogaster (BDGP5.0)
dps.gff – D. pseudoobscura (DPSE2.0)
dre.gff – D. rerio (WTSI Zv7)
fru.gff – F. rubripes (FUGU4)
gga.gff – G. gallus (WASHUC2)
gma.gff – G. max (JGI Glyma0)
hsa.gff – H. sapiens (NBCI36)
lgi.gff – L. gigantia (JGI1)
mdo.gff – M. domestica (MONDOM5.0)
mml.gff – M. mulata (MMUL1.0)
mmu.gff – M. musculus (NCBIM37)
mtr.gff – M. truncatula (Mt2.0)
nve.gff – N. vectensis (Nemve1)
oan.gff – O. anatinus (OANA4)
osa.gff – O. sativa (TIGR4.0)
ptc.gff – P. trichocarpa (Poptr1.0)
ptr.gff – P. troglodytes (PANTRO2.1)
rno.gff – R. norvegicus (RGSC3.4)
sme.gff – S. mediterranea (WUSTL2.0)
tca.gff – T. casteneum (TCAS2.0)
tae.gff – T. aestivum (TIGR tae2)
tni.gff – T. nigroviridis (TETRAODON7)
vvi.gff – V. vinifera (Genoscope 20070911)
xtr.gff – X. tropicalis (JGI4.1)
zma.gff – Z. mays (TIGR AZM5)
ebv.gff – Epstein Barr virus (EMBL:AJ507799.2)
hcmv.gff – Human cytomegalovirus (EMBL:X17403.1)
kshv.gff – Kaposi sarcoma-associated herpesvirus (EMBL:U75698.1)
mghv.gff – Mouse gammaherpesvirus 68 (EMBL:U97553.1)

The database_files/ directory contains dumps of the MySQL relational
database that is used to generate the web pages. The documentation
for this subset of files is non-existent – use at your peril!

4. LICENSE

miRBase is in the public domain. It is not copyrighted. You may
freely modify, redistribute, or use it for any purpose. See
ftp://ftp.sanger.ac.uk/pub/mirbase/CURRENT/LICENSE for details.

5. HOW TO CITE THE miRNA DATABASE

The miRBase Sequence database is described in the following articles:

miRBase: tools for microRNA genomics.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.
Nucleic Acids Res. 2008 36:D154-D158

miRBase: microRNA sequences, targets and gene nomenclature.
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ.
Nucleic Acids Res. 2006 34:D140-D144

The miRNA Registry.
Griffiths-Jones S.
Nucleic Acids Res. 2004 32:D109-D111

Please cite us if you use the data we distribute, but also be sure to
cite the primary sources of miRNA sequences in your work.

Guidelines to miRNA annotation are published here:

A uniform system for microRNA annotation.
Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X,
Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M,
Ruvkun G, Tuschl T.
RNA 2003 9(3):277-279

6. FEEDBACK

Any queries about data, web services, naming requests or other
feedback should be directed to microrna@sanger.ac.uk.

7. HISTORY

Version Date Entries

1.0 12/02 218
1.1 01/03 262
1.2 04/03 295
1.3 05/03 332
1.4 07/03 345
2.0 07/03 506
2.1 09/03 558
2.2 11/03 593
3.0 01/04 719
3.1 04/04 899
4.0 07/04 1185
5.0 09/04 1345
5.1 12/04 1420
6.0 04/05 1650
7.0 06/05 2909
7.1 10/05 3424
8.0 02/06 3518
8.1 05/06 3963
8.2 07/06 4039
9.0 10/06 4361
9.1 02/07 4449
9.2 05/07 4584
10.0 08/07 5071
10.1 12/07 5395
11.0 04/08 6396
12.0 09/08 8619
13.0 03/09 9539

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