Rattus norvegicus
(NHGRI Press Photos)

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.

Sample position queries

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.

   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..

Assembly details

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.

GenBank Pipeline Details

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