C. remanei
Caenorhabditis remanei
Photo courtesy of Eric Haag, All Rights Reserved.

The Mar. 2006 Caenorhabditis remanei draft assembly was produced by the Washington University in St. Louis (WUSTL) School of Medicine Genome Sequencing Center. The UCSC caeRem2 version corresponds to WUSTL version 1.0.

Sample position queries

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. remanei 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
EU183219   Displays region of mRNA with GenBank accession number EU183219
DR775696   Displays region of EST with GenBank accession DR775696
kin-1   Displays regions of kin-1 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
Hamilton,K.   Lists mRNAs deposited by co-author K. Hamilton
Use this last format for author queries. Although GenBank requires the search format Hamilton K, internally it uses the format Hamilton,K..

Assembly details

The C. remanei genome was sequenced to a depth of 9X using whole-genome shotgun plasmid and fosmid libraries made from DNA extracted from a mixture of larvae and adult males and females. Coverage was based on an expected genome size of 100 Mb. The whole-genome shotgun plasmid and fosmid paired end reads were assembled using PCAP and submitted to GenBank under the accession number AAGD00000000.

The UCSC Genome Browser displays the 9,660 scaffolds as a single artificial chromosome, chrUn. The sequence contains 161,944,676 bases and 15,046,237 Ns in gaps. For more information on this assembly, see the WUSTL C. remanei 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 C. remanei 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.

GenBank Pipeline Details

For the purposes of the GenBank alignment pipeline, this assembly is considered to be: low-coverage.