The Feb. 2008 Caenorhabditis brenneri (PB2801) draft assembly was produced by the Washington University in St. Louis (WUSTL) School of Medicine Genome Sequencing Center. The UCSC caePb2 assembly corresponds to WUSTL version 6.0.1. For more information about this assembly, see C_brenneri-6.0.1 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 C. brenneri genome. Note that the search results may include organisms other than the current genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| chrUn:1-1000000 | Displays first million bases of chrUn | |
| chrUn:1000000+2000 | Displays a region of chrUn that spans 2000 bases, starting with position 1000000 | |
| | ||
| EU677736 | Displays region of mRNA with GenBank accession number EU677736 | |
| FF084898 | Displays region of EST with GenBank accession FF084898 | |
| tnc-1 | Displays regions of tnc-1 mRNA | |
| | ||
| pseudogene | Lists pseudogene mRNAs | |
| homeobox caudal | Lists mRNAs for caudal homeobox genes | |
| zinc finger | Lists many zinc finger mRNAs | |
| kruppel zinc finger | Lists only kruppel-like zinc fingers | |
| | ||
| nemeroff | Lists mRNAs deposited by scientist named Nemeroff | |
| Hughes,K.J. | Lists mRNAs deposited by co-author K.J. Hughes | |
| Use this last format for author queries. Although GenBank requires the search format Hughes KJ, internally it uses the format Hughes,K.J.. | ||
This assembly is a 20X inbred (one gravid female per generation) derivative of LKC28, which is conspecific with CB5161. This species was renamed to C. brenneri in 2007. Other conspecific strains include SB129 and SB280. For more information, see Sudhaus W and Kiontke K. Comparison of the cryptic nematode species Caenorhabditis brenneri sp. n. and C. remanei (Nematoda: Rhabditidae) with the stem species pattern of the Caenorhabditis Elegans group. Zootaxa 25 Apr. 2007;1456:45-62.
The assembly has been sequenced to 9.5X WGS coverage. The 3,510 supercontigs are displayed in the UCSC Genome browser as a single artificial chromosome chrUn with artificial gaps of 1,000 Ns inserted between supercontigs. The largest supercontig is 4,147,112 bp; 121 supercontigs larger than 377,562 bp (N50) contain over 50% of the sequence. For more information about the assembly, see the WUSTL C. brenneri project page.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use.
The worm 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.