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
Database version75.31
Base Pairs2,649,685,036
Golden Path Length2,670,422,299
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedApr 2011
Genebuild releasedSep 2011
Genebuild last updated/patchedSep 2011

Gene counts

Coding genes

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

19,994
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.

3,825
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.

797
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.26,740

Other

Genscan gene predictions47,100
Short Variants23,000,375
Structural variants12,251

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