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.
RNAcentral: a comprehensive database of non-coding RNA sequences.Nucleic Acids Res. 2017 Jan 4;45(D1):D128-D134. doi: 10.1093/nar/gkw1008. Epub 2016 Oct 28. Nucleic Acids Res. 2017. PMID: 27794554 Free PMC article.
RNAcentral: an international database of ncRNA sequences.Nucleic Acids Res. 2015 Jan;43(Database issue):D123-9. doi: 10.1093/nar/gku991. Epub 2014 Oct 28. Nucleic Acids Res. 2015. PMID: 25352543 Free PMC article.
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342. doi: 10.1093/nar/gkx1038. Nucleic Acids Res. 2018. PMID: 29112718 Free PMC article.
Non-Coding RNA Analysis Using the Rfam Database.Curr Protoc Bioinformatics. 2018 Jun;62(1):e51. doi: 10.1002/cpbi.51. Epub 2018 Jun 5. Curr Protoc Bioinformatics. 2018. PMID: 29927072 Free PMC article.
Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae.BMC Microbiol. 2009 Feb 19;9 Suppl 1(Suppl 1):S8. doi: 10.1186/1471-2180-9-S1-S8. BMC Microbiol. 2009. PMID: 19278556 Free PMC article. Review.
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Formation of human long intergenic non-coding RNA genes, pseudogenes, and protein genes: Ancestral sequences are key players.PLoS One. 2020 Mar 26;15(3):e0230236. doi: 10.1371/journal.pone.0230236. eCollection 2020. PLoS One. 2020. PMID: 32214344 Free PMC article.
A guide to naming human non-coding RNA genes.EMBO J. 2020 Mar 16;39(6):e103777. doi: 10.15252/embj.2019103777. Epub 2020 Feb 24. EMBO J. 2020. PMID: 32090359 Free PMC article. Review.
Initial Virome Characterization of the Common Cnidarian Lab Model Nematostella vectensis.Viruses. 2020 Feb 15;12(2):218. doi: 10.3390/v12020218. Viruses. 2020. PMID: 32075325 Free PMC article.
DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts.Nucleic Acids Res. 2020 Jan 8;48(D1):D101-D110. doi: 10.1093/nar/gkz1036. Nucleic Acids Res. 2020. PMID: 31732741 Free PMC article.
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update.Nucleic Acids Res. 2020 Jan 8;48(D1):D504-D510. doi: 10.1093/nar/gkz949. Nucleic Acids Res. 2020. PMID: 31665520 Free PMC article.
- U41 HG003345/HG/NHGRI NIH HHS/United States
- R01 HL064541/HL/NHLBI NIH HHS/United States
- U41 HG002273/HG/NHGRI NIH HHS/United States
- U41 HG000739/HG/NHGRI NIH HHS/United States
- U41 HG007234/HG/NHGRI NIH HHS/United States