Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Erratum in

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.

Figures

Figure 1.
Figure 1.
A diagram showing the 28 Expert Databases imported into RNAcentral as of September 2018, organised according to their contents. The full list of databases is available at https://rnacentral.org/expert-databases.
Figure 2.
Figure 2.
Novel snoRNA Me18S-G1506 (URS0000A59F5E_7227) found in the ENA database that was mapped with 100% sequence identity to the Drosophila melanogaster genome using the new genome mapping pipeline.
Figure 3.
Figure 3.
Example secondary structure of tRNA-Ser-TGA-1-2 from Bacillus subtilis (URS000043457D_1423) visualized using Forna. The nucleotides in the Forna diagram are colored by secondary structure element, with helixes in green, hairpin loops in blue and red otherwise.
Figure 4.
Figure 4.
New section of the sequence report pages showing target proteins for miRNA hsa-miR-612 (URS0000759916_9606). The table provides links to Ensembl genes and TarBase summary pages and shows experimental methods.
Figure 5.
Figure 5.
(A) New text search interface options for filtering sequences by length (bottom) or changing the order of the results (top). (B) Structured snippets in text search results. The string matching the query (‘mir-100’) is highlighted in light-gray. The logos of expert databases annotating the sequence are displayed and additional information about the databases can be viewed on mouse hover. (C) A search result showing a sequence with a quality check failure. Here the red warning symbol indicates the sequence has an error, along with the type of issue detected, incomplete sequence here.
Figure 6.
Figure 6.
New section of the sequence report showing Rfam annotations. In this example, an ENA sequence URS00005B7DD8_9606, originally annotated as miscellaneous RNA (misc_RNA), matches a conserved domain of the MALAT1 Rfam family (RF01871) and MEN beta RNA (RF01684). The locations of the Rfam matches are shown in the feature viewer.
Figure 7.
Figure 7.
RNAcentral visualization of GO annotations for miRNA hsa-mir-126 (URS0000759B6D_9606) that is involved in heart development.

Similar articles

  • RNAcentral: a comprehensive database of non-coding RNA sequences.
    The RNAcentral Consortium, Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, Dinger ME. The RNAcentral Consortium, et al. 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.
    RNAcentral Consortium, Petrov AI, Kay SJE, Gibson R, Kulesha E, Staines D, Bruford EA, Wright MW, Burge S, Finn RD, Kersey PJ, Cochrane G, Bateman A, Griffiths-Jones S, Harrow J, Chan PP, Lowe TM, Zwieb CW, Wower J, Williams KP, Hudson CM, Gutell R, Clark MB, Dinger M, Quek XC, Bujnicki JM, Chua NH, Liu J, Wang H, Skogerbø G, Zhao Y, Chen R, Zhu W, Cole JR, Chai B, Huang HD, Huang HY, Cherry JM, Hatzigeorgiou A, Pruitt KD. RNAcentral Consortium, et al. 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.
    Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI. Kalvari I, et al. 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.
    Kalvari I, Nawrocki EP, Argasinska J, Quinones-Olvera N, Finn RD, Bateman A, Petrov AI. Kalvari I, et al. 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.
    Meng S, Brown DE, Ebbole DJ, Torto-Alalibo T, Oh YY, Deng J, Mitchell TK, Dean RA. Meng S, et al. 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.
See all similar articles

Cited by 9 articles

See all "Cited by" articles

References

    1. The RNAcentral Consortium RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res. 2017; 45:D128–D134. - PMC - PubMed
    1. The RNAcentral Consortium RNAcentral: an international database of ncRNA sequences. Nucleic Acids Res. 2015; 43:D123–D129. - PMC - PubMed
    1. Wheeler T.J., Eddy S.R. nhmmer: DNA homology search with profile HMMs. Bioinformatics. 2013; 29:2487–2489. - PMC - PubMed
    1. Hui J.H.L., Marco A., Hunt S., Melling J., Griffiths-Jones S., Ronshaugen M. Structure, evolution and function of the bi-directionally transcribed iab-4/iab-8 microRNA locus in arthropods. Nucleic Acids Res. 2013; 41:3352–3361. - PMC - PubMed
    1. Rinn J.L., Kertesz M., Wang J.K., Squazzo S.L., Xu X., Brugmann S.A., Goodnough L.H., Helms J.A., Farnham P.J., Segal E. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 2007; 129:1311–1323. - PMC - PubMed

Publication types

Feedback