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Cow assembly and gene annotation

Cattle —colloquially cows— are the most common type of large domesticated ungulates. They are a prominent modern member of the subfamily Bovinae, are the most widespread species of the genus Bos, and are most commonly classified collectively as Bos taurus. In 2009, cattle became one of the first livestock animals to have a fully mapped genome.

Archeozoological and genetic data indicate that cattle were first domesticated from wild aurochs (Bos primigenius) approximately 10,500 years ago. There were two major areas of domestication: one in the Near East, giving rise to the taurine line, and a second in the area that is now Pakistan, resulting in the indicine line. Modern mitochondrial DNA variation indicates the taurine line may have arisen from as few as 80 aurochs tamed in the upper reaches of Mesopotamia near the villages of Çayönü Tepesi in what is now southeastern Turkey and Dja'de el-Mughara in what is now northern Iraq.

Assembly

The ARS-UCD1.2 assembly was submitted by Usda Ars on April 2018. The assembly is on chromosome level, consisting of 2,597 contigs assembled into 2,211 scaffolds. From these sequences, 30 chromosomes have been built. 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 25,896,116 while the scaffold N50 is 103,308,737.

Gene annotation

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). 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. lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

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

AssemblyARS-UCD1.2, INSDC Assembly GCA_002263795.2, Apr 2018
Base Pairs2,715,853,792
Golden Path Length2,715,853,792
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2018
Genebuild releasedDec 2018
Genebuild last updated/patchedNov 2018
Database version100.12

Gene counts

Coding genes21,880
Non coding genes5,235
Small non coding genes3,375
Long non coding genes1,488
Misc non coding genes372
Pseudogenes492
Gene transcripts43,984

Other

Genscan gene predictions46,441
Short Variants98,844,739
Structural variants18,942

About this species

HASH(0x25bc27e0)