The horse EquCab2 was annotated using a standard Ensembl mammalian pipeline. Predictions from vertebrate mammals as well as horse proteins have been given priority over predictions from non-mammalian vertebrates. 1:1 homologous genes in human and mouse were aligned to the horse genome using Exonerate. Alignments were compared to the set of predicted genes in horse to patch the horse gene set. Horse genes which had only been partially predicted previously were extended by additional exons. Single genes which had been mis-annotated as two distinct neighbouring genes were merged. Missing homologues in horse were also recovered. Horse and human cDNAs have been used to add UTRs to protein based predictions. The final gene-set comprises 20,436 protein-coding genes and 4400 pseudogenes (including retrotranposed genes).