The October 2004 frog (Xenopus tropicalis) whole genome shotgun (WGS) assembly release version 3.0 was sequenced and assembled by the DOE Joint Genome Institute (JGI).
A genome position can be specified by the accession number of a sequenced genomic clone, an mRNA or EST, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list provides examples of various types of position queries for the dog genome. See the User's Guide for more information.
| Request: |
Genome Browser Response: |
|
| chr16 | Displays all of chromosome 16 | |
| chr16:1-5000000 | Displays first 5 million bases of chr 16 | |
| AY572227 | Displays location of mRNA with GenBank accession AY572227 | |
| BM538765 | Displays location of EST with GenBank accession BM538765 | |
| chr6_8.29 | Displays location of Genscan gene prediction with identifier chr6_8.29 | |
| pseudogene mRNA | Lists transcribed pseudogenes but not cDNAs | |
| zinc finger | Lists zinc finger mRNAs | |
| breast cancer | Lists mRNAs associated with breast cancer susceptibility proteins | |
| evans | Lists mRNAs deposited by scientist named Evans | |
| Murphy,K.E. | Lists mRNAs deposited by co-author K.E. Murphy | |
| Use this last format for author queries. Although GenBank requires the search format Murphy KE, internally it uses the format Murphy,K.E.. | ||
The dog genome contains approximately 2.5 billion base pairs. This sequence is based on 7.6X coverage of the dog genome, assuming a WGS assembly size of 2.4 Gb. The assembly has an N50 contig length of 123 kb and an N50 supercontig length of 41.6 Mb. The boxer breed was selected for the initial sequencing effort based on the lower variation rate in its genome relative to other breeds. For more information about this assembly, see the NHGRI press release.
The canFam1 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. These data have specific conditions for use.
Many thanks to the Broad Institute of MIT/Harvard, NHGRI, and the many institutions who contributed to the sequencing and mapping effort for this release. The canFam1 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 the success of this release.