Ensembl: Non-Coding RNA Gene Annotation

Non-coding RNA (ncRNA) genes are genes that do not translate into proteins but instead produce functionally important RNA molecules. While some types of RNA (tRNAs, rRNAs and microRNA) have been studied for decades, others including long non-coding RNAs (lncRNAs), are less well studied. With the emergence and maturation of next generation sequencing, we now have more data and tools to capture and annotate the sequences from non-coding genes expressed in the genome.

Ensembl provide annotation for both small and long ncRNA genes. lncRNA genes are annotated based on transcriptomic data as follows: The Ensembl RNASeq pipeline produces a set of gene models, both protein coding and non-coding, from which we extract the lncRNA candidates. This is done by selecting the models that do not overlap annotated protein coding genes and do not have protein domains. Annotation for microRNAs may be imported from miRBase when available for the target species. To obtain an exhaustive set of ncRNAs, we run the small ncRNA pipeline which uses RFam and miRBase to predict the possible location of small ncRNAs.

Protein coding and ncRNA gene annotation from Ensembl are available on the cattle reference genome (UMD3.1). The lncRNA annotation was generated using a transcriptomic dataset containing multiple tissue samples. Small ncRNA annotation was generated using the public databases miRBase and RFam. All data in Ensembl are accessible through the website, www.ensembl.org, the Perl API and the REST API. Users can download data using our public FTP or view their own data alongside ours using Trackhubs.