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Explore the Equus caballus genome

Karyotype

Click on a chromosome for a closer view

chromosome 1 chromosome 2 chromosome 3 chromosome 4 chromosome 5 chromosome 6 chromosome 7 chromosome 8 chromosome 9 chromosome 10 chromosome 11 chromosome 12 chromosome 13 chromosome 14 chromosome 15 chromosome 16 chromosome 17 chromosome 18 chromosome 19 chromosome 20 chromosome 21 chromosome 22 chromosome 23 chromosome 24 chromosome 25 chromosome 26 chromosome 27 chromosome 28 chromosome 29 chromosome 30 chromosome 31 chromosome X Horse karyotype selector

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About the Equus caballus genome

Assembly

Neigh, lad! 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.

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-vertebrate mammals. The set of predictions was been compared to 1:1 homologues genes in human and mouse, and missing homologs in the horse annotation have been recovered using exonerate. Horse and human cDNAs have been used to add UTRs to protein based predictions. The final gene-set comprises 20,737 protein-coding genes, 2,863 identified as pseudogenes and 1,580 classified as retro-transposed genes.

What's New in Ensembl 50

Equus caballus News

  • Non-coding genes
    These have been updated for most species, including an miRNA update and HGNC names where possible.
  • Horse assembly fix
    Chromosome 27 of Ensembl Horse has been shortened, in line with the latest Equus caballus assembly.
  • Multiple alignments

    The multiple alignments are being extended with new species and 2X genomes.
    Read more...

General News

  • Canonical Transcripts

    Canonical transcripts have been defined for all genes in the core databases.
    Read more...

  • SSAHA
    From release 50 we will no longer be providing SSAHA sequence search. If you wish to run your own SSAHA sequence search you can download the files to generate the search hashes from our FTP site.

More news...

Statistics

Assembly: Equ Cab 2, Sep 2007
Genebuild: Ensembl, Sep 2007
Database version: 50.2a
Known protein-coding genes: 723
Projected protein-coding genes: 14,844
Novel protein-coding genes: 4,755
Pseudogenes: 4,400
RNA genes: 1,438
Genscan gene predictions: 107,701
Gene exons: 206,391
Gene transcripts: 26,690
Base Pairs: 2,428,773,513
Golden Path Length: 2,474,912,402
Most common InterPro domains: Top 40 Top 500

How the statistics are calculated

 

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GermOnline based on Ensembl release 50 - Jul 2008
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