Photo courtesy of Michael MacNeil, USDA
(NHGRI Press Photos)
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Bos Taurus Photo courtesy of Michael MacNeil, USDA (NHGRI Press Photos) |
The Nov. 2009 Bos taurus draft assembly (UMD_3.1, NCBI project 32899, GenBank GCA_000003055.3) was produced by the Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD. This browser also includes the mitochondrial genome with NCBI accession NC_006853. For more information about this assembly, see Bos_taurus_UMD_3.1 in the NCBI Assembly database.
A genome position can be specified by the accession number of a sequenced genomic region, an mRNA or EST, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the bovine genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| chr28 | Displays all of chromosome 28 | |
| chr28:1-1000000 | Displays first million bases of chromosome 28 | |
| chr28:1000000+2000 | Displays a region of chr 28 that spans 2000 bases, starting with position 1000000 | |
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| BC140604 | Displays region of mRNA with GenBank accession number BC140604 | |
| EE384456 | Displays region of EST with GenBank accession EE384456 on chr X | |
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BC122573; BC102169 | Displays region between genome landmarks, such as the mRNA markers BC122573 and BC102169. This syntax may also be used for other range queries, such as between uniquely determined ESTs, STSs, refSeqs, etc. | |
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| pseudogene mRNA | Lists transcribed pseudogenes, but not cDNAs | |
| homeobox caudal | Lists mRNAs for caudal homeobox genes | |
| zinc finger | Lists many zinc finger mRNAs | |
| kruppel zinc finger | Lists only kruppel-like zinc fingers | |
| zahler | Lists mRNAs deposited by scientist named Zahler | |
| Evans,J.E. | Lists mRNAs deposited by co-author J.E. Evans | |
| Use this last format for author queries. Although GenBank requires the search format Evans JE, internally it uses the format Evans,J.E.. | ||
The UMD_3.1 assembly, which is based on reads downloaded from the NCBI Trace Archive, has a coverage of 9.5X. Approximately 91% of the sequence has been anchored to thirty chromosomes: 1-29 and X. The remaining unanchored contigs are contained in 3286 scaffolds (labeled chrUn_GJnnnnnn). The sequence length is approximately 2.67 Gb, of which about 20.7 Mb are 'N' bases in gaps. The mitochondrial sequence (chrM) was obtained from GenBank (accession NC_006853).
The University of Maryland Center for Bioinformatics and Computational Biology (UMD CBCB) reports that they applied assembly improvement techniques to produce a version that is substantially more accurate and complete than existing alternative versions, as evaluated using independent metrics. Based on UMD statistics, this assembly provides more genome coverage, closes thousands of gaps, corrects many erroneous inversions, deletions, and translocations, and fixes thousands of single-nucleotide errors. For more information, see Zimin AV et al., A whole-genome assembly of the domestic cow, Bos taurus, Genome Biol. 2009;10(4):R42. Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page.
The UMD cow browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.