(NHGRI Press Photos)
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Felis catus (NHGRI Press Photos) |
The Dec. 2008 Felis catus draft assembly, catChrV17e, was produced by the NHGRI Genome Technology Branch and NIH Intramural Sequencing Center, Maryland; Agencourt Bioscience Corporation, Massachusetts; NCI Laboratory of Genomic Diversity, Maryland; and Hill's Pet Nutrition, Inc, Kansas. The mitochondrial genome was sequenced by NCI Laboratory of Genomic Diversity. For more information about this assembly, see catChrV17e 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 cat genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| chrA3 | Displays all of chromosome A3 | |
| chrA3:1-1000000 | Displays first million bases of chr A3 | |
| chrA3:1000000+2000 | Displays a region of chr A3 that spans 2000 bases, starting with position 1000000 | |
| | ||
| GQ247880 | Displays region of mRNA with GenBank accession number GQ247880 | |
| CV794675 | Displays region of EST with GenBank accession CV794675 on chr A3 | |
| | ||
| 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 | |
| pathak | Lists mRNAs deposited by scientist named Pathak | |
| Kapil,S. | Lists mRNAs deposited by co-author S. Kapil | |
| Use this last format for author queries. Although GenBank requires the search format Kapil S, internally it uses the format Kapil,S.. | ||
This assembly adds a coverage improvement of 0.9X to the previous 1.9X Cinnamon assembly (UCSC felCat3). The increased coverage was achieved by adding paired-end fosmid ABI 3730 reads obtained from six other breeds and one wild cat. All 2.8X coverage was assembled and mapped using the techniques described for the 1.9X felCat3 assembly.
The felCat4 assembly has 19 chromosomes: chrA1-3, chrB1-4, chrC1-2, chrD1-4, chrE1-3, chrF1-2, and chrX. The mitochondrial sequence chrM was obtained from GenBank accession NC_001700. The total sequence length is approximately 2.87 Gb, of which about 1.17 Gb are 'N' bases in gaps, resulting in approximately 1.7 Gb of ACGT. For more information about the techniques used to produce this assembly, see the paper Mullikin, JC et al. Light whole genome sequence for SNP discovery across domestic cat breeds, BMC Genomics 2010 Jun 24;11:406 and the NCBI Entrez Felis catus genome project web page.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page.
The cat Genome Browser and its 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.