miRBase 18 Released

by Christoph on November 3, 2011

in miRBase

miRBase 18UPDATE: miRBase version 19 is the current version
********

As promised – miRBase 18 was just released: Release 18 of the database contains 18226 entries representing hairpin precursor miRNAs, expressing 21643 mature miRNA products, in 168 species. As compared to miRBase version 17 a total of 1488 new hairpin sequences and 1929 novel mature products have been added.

Apart from the the usual addition and corrections this release continues to improve adaption of the newer nomenclature: In mirBase version 18 all miR/miR* pairs for mature miRNAs from human, mouse and C. elegans were replaced with the -5p/-3p nomenclature. More species to follow in future releases. For a detailed article about the miRNA nomenclature see: miRBase Nomenclature – a few changes.

A partial list of changes in terms of mature miRNAs:

Acacia auriculiformis -wattle (aau)
7 new sequences

Anolis carolinensis – Carolina anole (aca)
416 new sequences

Arabidopsis thaliana – mouse-ear cress (ath)
62 new sequences, 2 name changes

Ascaris suum – large roundworm of pigs (asu)
416 new sequences

Caenorhabditis elegans – roundworm (cel)
28 new sequences, 247 name changes

Ciona intestinalis – sea squirt (cin)
38 new sequences

Drosophila melanogaster – fruit fly (dme)
4 new sequences, 4 sequence changes, 1 deletion

Glycine max – soybean (gma)
188 new sequences, 12 name changes

Homo sapiens – human (hsa)
190 new sequences, 5 sequence changes, 450 name changes, 2 deletions

Medicago truncatula – Barrel Medic or Barrel Medick or Barrel Clover (mtr)
291 new sequences, 1name change

Mus musculus – mouse (mmu)
48 new mnature miRNAs, 2 sequence changes, 646 name changes, 2 deletions

Oryza sativa – rice (osa)
115 new sequences, 15 name changes, 2 deletions

Oryzias latipes – Medaka and Japanese killifish (ora)
144 new sequences

Rhesus lymphocryptovirus (rlcv)
20 name changes

Rhipicephalus microplus – cattle tick (rmi)
24 new sequences

Sarcophilus harrisii – Tasmanian devil (sha)
65 new sequences

Sorghum bicolor – sorghum  (sbi)
24 new sequences, 1 name change

Sam from miRBase talks about the addition of sequencing data, new features and request user feedback – so, let him know what you think:
http://www.mirbase.org/blog/2011/11/mirbase-18-released/

For the official release notes for miRBase 18 see: ftp://mirbase.org/pub/mirbase/CURRENT/README

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{ 4 comments… read them below or add one }

Katelin November 3, 2011 at 8:29 am

Does this mean we should also expect an update on the prediction at microRNA.org?

Christoph November 3, 2011 at 12:04 pm

Katelin, microRNA.org is maintained be an entirely different group – so I would contact them directly. Their data are based on miRBase 15 – so let’s hope.

Nutan Prakash January 20, 2012 at 8:48 am

Dear Sir/Madam!
How i can download all the miRNA of plants. Kindly share your ideas with me.
Thanks and regards

Christoph January 25, 2012 at 11:14 am

Nutan, You can download all known sequences for all species directly from miRBase: http://www.mirbase.org/ftp.shtml
AFAIK there is no specific file with only plant miRNAs.
If you want to include predicted sequences you can dowload those from the plant miRNA database: http://bioinformatics.cau.edu.cn/PMRD/

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