Ensembl GENE Annotation for Sheep

Ovis aries, the domestic sheep, is a livestock animal reared for meat, fleece and milk. The International Sheep Genome Consortium (ISGC) has produced a draft genome assembly for sheep (GCA_000298735.1) comprising 27 chromosomes and 5,670 unplaced scaffolds.

We have produced a gene set for this sheep genome assembly using the Ensembl automatic gene annotation system. Protein-coding models were generated by aligning vertebrate protein sequences from UniProt to the repeat-masked genome and by using RNA-Seq data provided by the ISGC. The final gene set includes models from both the UniProt alignments and the RNAseq data. It comprises 20921 protein-coding models, 3985 short noncoding RNAs and 291 pseudogenes.

The ISGC RNA-Seq data set includes a range of tissue samples shared between a trio: ram, ewe and their lamb. In total, we aligned >800 GB data from 89 tissue samples to the sheep genome assembly. This RNA-Seq data set is larger than for any other species in Ensembl.

Full annotation of the sheep genome will be made public in Ensembl release 74 (December 2013) and includes pairwise genome alignments with human, cow and pig. Users can view the indexed BAM files, tissue-specific gene models and the full set of splice junctions (introns) identified by the RNA-Seq pipeline alongside the sheep gene set on the Ensembl genome browser http://www.ensembl.org/Ovis_aries. We also provide gene orthologues, cross-references to external databases, and variations from dbSNP and selected genotyping chips. Data can be downloaded from our FTP site or queried using our Perl API or BioMart query system.