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 }
Does this mean we should also expect an update on the prediction at microRNA.org?
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.
Dear Sir/Madam!
How i can download all the miRNA of plants. Kindly share your ideas with me.
Thanks and regards
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/