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Cow assembly and gene annotation

Assembly

The UMD 3.1 assembly (NCBI assembly accesion GCA_000003055.3), released in December 2009, is the third release of the cow (Bos taurus) assembly from the Center for Bioinformatics and Computational Biology (CBCB) at University of Maryland. The genome sequences were generated using a combination of BAC-by-BAC hierarchical (~11 million reads) and whole-genome shotgun (~24 million reads) sequencing methods, assembled using the Celera Assembler version 5.2.

The total length of the UMD3.1 assembly is 2.65Gb. The N50 size is the median sequence length, i.e. 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size for contigs in the UMD3.1 assembly is 103785.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000003055.3

Gene annotation

Gene annotation in cow has been generated by alignment of proteins from three major sources (in descending order of their contribution to the final gene set):

  • Bos taurus (cow) proteins from UniProtKB and NCBI RefSeq and Bos taurus cDNAs from INSDC. For proteins, UniProtKB proteins were filtered to keep only those of protein existence (PE) levels 1 and 2 (i.e. with protein or transcript level evidence), and only curated RefSeq proteins (accessions starting with "NP_") were used. For cDNAs, they were also filtered to keep curated RefSeq mRNAs (accessions starting with "NM_") and to remove those associated with PE level 3-5 UniProt proteins.
  • UniProt mammalian and vertebrate proteins of PE levels 1 and 2; and
  • Translations of Ensembl human genes which have one-to-one orthologues in mouse (taken from Ensembl release 62 data).
The alignment of UniProt and RefSeq proteins were aligned to the cow genome followed procedures in the standard Ensembl genebuild pipeline using Genewise. Ensembl human translations were aligned to the cow genome using Exonerate. The gene-building procedure on the UMD3.1 assembly identified 19981 protein coding genes and 797 pseudogenes.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyUMD3.1, INSDC Assembly GCA_000003055.3, Nov 2009
Base Pairs2,649,685,036
Golden Path Length2,670,422,299
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedApr 2011
Genebuild releasedSep 2011
Genebuild last updated/patchedSep 2011
Database version94.31

Gene counts

Coding genes19,994
Non coding genes3,825
Small non coding genes3,650
Misc non coding genes175
Pseudogenes797
Gene transcripts26,740

Other

Genscan gene predictions47,100
Short Variants102,499,615
Structural variants18,942

About this species