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Horse assembly and gene annotation


The EquCab2 assembly is a Whole Genome Shotgun (WGS) assembly at 6.79x. A female thoroughbred named "Twilight" was selected as the representative horse for genome sequencing. The project coordination and genome sequencing and assembly is provided by the Broad Institute.

The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size of the contigs is 112.38 kb, and the total length of all contigs is 2.43 Gb. When the gaps between contigs in scaffolds are included, the total span of the assembly is 2.68 Gb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000002305.1

Gene annotation

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).

More information

General information about this species can be found in Wikipedia.



AssemblyEqu Cab 2, INSDC Assembly GCA_000002305.1, Sep 2007
Base Pairs2,428,790,173
Golden Path Length2,474,929,062
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2007
Genebuild releasedMar 2008
Genebuild last updated/patchedNov 2012
Database version94.2

Gene counts

Coding genes20,449
Non coding genes2,142
Small non coding genes1,967
Misc non coding genes175
Gene transcripts29,196


Genscan gene predictions107,701
Short Variants21,744,737
Structural variants193,747

About this species