Automated RNA gene annotation

Most gene sets that are imported into Ensembl Metazoa do not have RNA gene annotation, and in these cases we perform automated annotation. For release 36 of Ensembl Metazoa RNA genes were annotated on all species except those imported from FlyBase, VectorBase, and WormBase. The RNA gene annotation uses three sources:

• miRBase provide genomic locations of precursor microRNA genes for a subset of species (Apis mellifera, Heliconius melpomene, Nasonia vitripennis, Strongylocentrotus purpuratus).
• tRNAscan-SE is used to predict tRNA genes (with a score threshold of 65).
• Rfam covariance model alignments are used to annotate RNA genes of all classes except tRNA. Models are restricted to those that are taxonomically appropriate, and are filtered to prevent overlapping genes (on either strand).

RNA genes have been updated for 26 species (21 of which had out-dated RNA gene annotation from earlier Ensembl Metazoa releases, the remaining 5 having partial annotation from the geneset provider); and added to 11 species which previously had no RNA gene annotation.

The chart below shows the numbers of RNA genes annotated, broken down by biotype, across all 37 species (click image for a larger version).

What's New in Release 36

• New data
  • Alignment of Rfam 12.2 covariance models for all species
  • Automated RNA gene annotation for 37 species (i.e. all species that have not been imported from FlyBase, VectorBase or WormBase)
• Updated data
  • Updated cross references
  • Updated protein features (new sources added: CDD, MobiDB, SFLD)
  • Updated BioMarts