RNAcentral is a new resource to organise data for non-protein coding RNA genes.
RNAcentral will offer integrated access to a comprehensive and up-to-date set of RNA sequences. These sequences will be provided by a collaborating group of expert databases and supplemented by sequences from the International Nucleotide Sequence Database archives (INSDC). The vision for RNAcentral is presented in the paper by Bateman et al, 2011.
The RNAcentral portal (available at this URL from late 2013) will provide access to the data via sequence and meta-data search, will link together the expert resources, and provide a defined identifier space for individual molecules. In a second phase of development, this reference data will be used to provide annotation for genome sequences from across the taxonomic space.
|ENA||comprehensive record of the world's nucleotide sequencing information|
|Comparative RNA Web (CRW) Site||comparative sequence and structure information for ribosomal, intron, and other RNAs|
|Genomic tRNA Database||tRNA predictions in genomes|
|HGNC||HUGO Gene Nomenclature Committee|
|lncRNAdb||annotations of eukaryotic long non-coding RNAs|
|miRBase||microRNA sequences and annotation|
|MODOMICS||RNA modification data|
|NONCODE||integrative annotation of long noncoding RNAs|
|NPInter||experimentally determined functional interactions between ncRNAs and proteins, mRNAs or genomic DNA|
|piRNABank||comprehensive resource on Piwi-interacting RNAs|
|RefSeq||comprehensive, integrated, non-redundant, well-annotated set of reference sequences|
|Rfam||collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models|
|Ribosomal Database Project||ribosome-related data and services|
|RNApathwaysDB||RNA maturation and decay pathways|
|SILVA||quality checked and aligned ribosomal RNA sequences|
|snoRNA Database||predicted snoRNA genes|
|SRPDB||aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP|
|tmRNA Website||tmRNA sequence data|
|VEGA||high quality manual annotation of vertebrate finished genome sequence|
November 27, 2013
RNAcentral is pleased to announce the import of 21,388 human lncRNA from the VEGA (Vertebrate Genome Annotation) expert database.
The set of VEGA lncRNA records is visible from http://www.ebi.ac.uk/ena/data/view/HG491497-HG512884, and the entire RNAcentral set is available at any time from http://www.ebi.ac.uk/ena/data/search?query=RNAcentral.
October 24, 2013
RNAcentral is pleased to announce the import of 3,661 transcriptome assembly contigs representing mature miRNA sequences from miRBase. The accessions are as follows:
August 22, 2013
July 8, 2013
The Non-coding product is the main feed source of sequence data for the RNAcentral database.
The Non-coding product contains nucleotide sequences of non-coding features annotated in the EMBL nucleotide sequence database in an analogous manner to that of the CDS product containing coding features. Features with the following feature names are included in this product:
Data are distributed in a flat-file format, similar to that of the EMBL database, but with each entry representing a single feature and with the sequence of only that entry.
Each entry's description comprises the organism name followed by the product or, if that is not given, the gene. All keywords from the parent entry that match a standard set are included, with the addition of the “RNAcentral” keyword for entries imported from expert databases. All citations from the entry within the range of the feature are included. If the parent entry has citations without a range these are also included. Database cross references to expert databases are also included.
The number of sequences of various classes in the latest release (r117) and in subsequent updates:
|RNA class||r117 release||Updates||Total (to 10/11/13)|
If you'd like to collaborate with us, please get in touch.
The development of RNAcentral is being coordinated by the European Bioinformatics Institute, and is funded by the United Kingdom Biotechnology and Biological Sciences Research Council grant BB/J019321/1.