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The June 2003 rat (Rattus norvegicus) genome assembly is based on version 3.1 produced by the Atlas group at Baylor Human Genome Sequencing Center (HGSC) as part of the Rat Genome Sequencing Consortium.
A genome position can be specified by the accession number of a sequenced genomic clone, an mRNA or EST or STS marker, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the rat 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|
|chr16:1000000+2000||Displays a region of chr 16 that spans 2000 bases, starting with position 1000000|
|RNOR03233282;RNOR03233294||Displays region between Assembly IDs RNOR03233282 and RNOR03233294|
|AI501130||Displays region of EST with GenBank accession AI501130|
|AF199335||Displays region of mRNA with GenBank accession AF199335|
|apoe||Displays region of genome with gene identifier apoE|
|NM_145881||Displays region of genome with RefSeq identifier NM_145881|
|25728||Displays region of genome with Entrez Gene identifier 25728|
|pseudogene mRNA||Lists transcribed pseudogenes but not cDNAs|
|zinc finger||Lists many zinc finger mRNAs|
|kruppel zinc finger||Lists only kruppel-like zinc fingers|
|huntington||Lists candidate genes associated with Huntington's disease|
|Jones,R.||Lists mRNAs deposited by co-author R. Jones|
Use this last format for author queries. Although GenBank requires the search format Jones R, internally it uses the format Jones,R..
This sequence was assembled using a hybrid approach that combines the clone-by-clone and whole genome shotgun methods. This assembly is a minor update to the 3.0 release. Sequence changes affect only chromosomes 7 and X. No additional assembly releases are planned prior to the publication of the rat genome analysis papers.
The 3.x assemblies reflect several sequence additions and software improvements over the previous 2.x assemblies, including the sequencing of over 1100 new BACs to cover gaps, an improved marker set from the Medical College of Wisconsin, a new FPC map from the BC Cancer Agency Genome Sciences Centre, and improved linking of bactigs. For detailed information and statistics about the 3.x assemblies, see the Baylor HGSC Rat Genome Project web page.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data are made available with specific conditions for use. The rn3 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.