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Goat assembly and gene annotation

Assembly

The ARS1 assembly was submitted by USDA ARS on 24/08/2016. The assembly is on the Chromosome level, consisting of 30,399 contigs assembled into 29,907 scaffolds. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 26,244,591 while the scaffold N50 is 87,277,232.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_001704415.1

Gene annotation

The domestic goat (Capra aegagrus hircus) is a subspecies of goat domesticated from the wild goat of southwest Asia and Eastern Europe. The goat is a member of the family Bovidae and is closely related to the sheep as both are in the goat-antelope subfamily Caprinae. There are over 300 distinct breeds of goat. Goats are one of the oldest domesticated species, and have been used for their milk, meat, hair, and skins over much of the world. In 2011, there were more than 924 million live goats around the globe, according to the UN Food and Agriculture Organization.

The gene annotation process was carried out using a combination of alignments to UniProt proteins and RNA-seq alignments (to RNASeq data from 39 tissues). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments. Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.

In accordance with the Fort Lauderdale Agreement , please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyARS1, INSDC Assembly GCA_001704415.1, Aug 2016
Base Pairs2,922,813,246
Golden Path Length2,922,813,246
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2017
Genebuild releasedMar 2018
Genebuild last updated/patchedMar 2018
Database version94.1

Gene counts

Coding genes21,361
Non coding genes5,688
Small non coding genes2,623
Long non coding genes2,713
Misc non coding genes352
Pseudogenes222
Gene transcripts41,794

Other

Genscan gene predictions58,693
Short Variants34,116,678

About this species