RNAcentral: a hub of information for non-coding RNA sequences.

The RNAcentral Consortium
Author Information

Abstract

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org.

References

  1. Nat Genet. 2000 May;25(1):25-9 [PMID: 10802651]
  2. Genome Res. 2002 Apr;12(4):656-64 [PMID: 11932250]
  3. Cell. 2007 Jun 29;129(7):1311-23 [PMID: 17604720]
  4. Bioinformatics. 2009 Nov 15;25(22):3045-6 [PMID: 19744993]
  5. Nucleic Acids Res. 2013 Mar 1;41(5):3352-61 [PMID: 23335784]
  6. Bioinformatics. 2013 Oct 1;29(19):2487-9 [PMID: 23842809]
  7. Bioinformatics. 2013 Nov 15;29(22):2933-5 [PMID: 24008419]
  8. BMC Res Notes. 2013 Oct 23;6:426 [PMID: 24148649]
  9. Nucleic Acids Res. 2014 Jan;42(Database issue):D68-73 [PMID: 24275495]
  10. Nucleic Acids Res. 2015 Jan;43(Database issue):D123-9 [PMID: 25352543]
  11. Nucleic Acids Res. 2015 Jan;43(Database issue):D743-50 [PMID: 25355511]
  12. Nucleic Acids Res. 2015 Jan;43(Database issue):D174-80 [PMID: 25378313]
  13. Bioinformatics. 2015 May 15;31(10):1592-8 [PMID: 25609791]
  14. Nucleic Acids Res. 2015 Apr 20;43(7):3490-7 [PMID: 25800743]
  15. Bioinformatics. 2015 Oct 15;31(20):3377-9 [PMID: 26099263]
  16. Mamm Genome. 2015 Oct;26(9-10):366-78 [PMID: 26187010]
  17. Nucleic Acids Res. 2016 Jan 4;44(D1):D574-80 [PMID: 26578574]
  18. Nucleic Acids Res. 2016 Jan 4;44(D1):D48-50 [PMID: 26657633]
  19. Nucleic Acids Res. 2016 Jan 4;44(D1):D184-9 [PMID: 26673694]
  20. RNA. 2016 May;22(5):667-76 [PMID: 26917558]
  21. Database (Oxford). 2016 Jun 23;2016: [PMID: 27337980]
  22. Nucleic Acids Res. 2017 Jan 4;45(D1):D128-D134 [PMID: 27794554]
  23. Nucleic Acids Res. 2017 Jan 4;45(D1):D663-D671 [PMID: 27799470]
  24. Nucleic Acids Res. 2017 Jan 4;45(D1):D619-D625 [PMID: 27799471]
  25. Nucleic Acids Res. 2017 Jan 4;45(D1):D635-D642 [PMID: 27899575]
  26. Nucleic Acids Res. 2018 Jan 4;46(D1):D836-D842 [PMID: 29092072]
  27. Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342 [PMID: 29112718]
  28. BMC Bioinformatics. 2017 Nov 15;18(1):487 [PMID: 29141608]
  29. Nucleic Acids Res. 2018 Jan 4;46(D1):D239-D245 [PMID: 29156006]
  30. Mol Ecol. 2018 Jan;27(2):403-418 [PMID: 29218749]
  31. Int J Oncol. 2018 Jun;52(6):1765-1776 [PMID: 29620157]
  32. BMC Genomics. 2018 May 30;19(1):417 [PMID: 29848285]
  33. Noncoding RNA. 2015 Jul 13;1(2):139-150 [PMID: 29861420]
  34. RNA. 2018 Aug;24(8):1005-1017 [PMID: 29871895]

Grants

  1. R01 HG006753/NHGRI NIH HHS
  2. RG/13/5/30112/British Heart Foundation
  3. R01 HL064541/NHLBI NIH HHS
  4. U41 HG002273/NHGRI NIH HHS
  5. U41 HG000739/NHGRI NIH HHS
  6. U41 HG007234/NHGRI NIH HHS
  7. BB/N019199/1/Biotechnology and Biological Sciences Research Council
  8. U41 HG000330/NHGRI NIH HHS

Links to CNCB-NGDC Resources

Database Commons: DBC000016 (RNAcentral)

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