Horse assembly and gene annotation

Assembly

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.

Statistics

Summary

AssemblyEqu Cab 2, INSDC Assembly GCA_000002305.1, Sep 2007
Database version75.2
Base Pairs2,428,790,173
Golden Path Length2,474,929,062
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedSep 2007
Genebuild releasedMar 2008
Genebuild last updated/patchedNov 2012

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

20,449
Short non coding genes

Short non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as short non coding genes: miRNA, miscRNA, rRNA, tRNA, ncRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the short non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

2,142
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

4,400
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.29,196

Other

Genscan gene predictions107,701
Short Variants5,123,531
Structural variants387,240

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