About the project

The HGSC is sequencing the genome of the rat (Rattus norvegicus). The rat has been funded for a genome upgrade. This includes finishing some regions to high quality, addressing the Y chromosome, and producing an improved genome assembly (1).

Sample sequencing of eight strains to identify strain specific variants is also a part of the rat project (2).

This rodent is important as a model organism for cardiovascular and psychological research, and has a legacy of decades of study of its physiology in academia and industry.

The finished BAC sequences and the upgraded BAC sequences with ordered and oriented contigs are available from the NCBI.

The updated public release draft genome assembly (v.3.4) covering more than 90% of the estimated 2.8 Gb genome is available for download. This version incorporates 54.6 Mb of finished sequence into the draft genome assembly. Genome browsers for this data are listed in the resource section below. A brief description of the assembly is available.

The National Institutes of Health (NIH) Rat Genome Sequencing network is funded by the National Heart, Lung, and Blood Institute (NHLBI) and the National Human Genome Research Institute (NHGRI). See the press releases.

The Rat Genome Sequencing Consortium is led by the Baylor College of Medicine Human Genome Sequencing Center, and is a collaboration with Celera Genomics, Genome Therapeutics, The Institute for Genome Research, The University of Utah, Children's Hospital Oakland Research Institute, Medical College of Wisconsin, and BC Genome Sciences Center.

Access to the sequence

Genome Assembly

The genome assembly is available for download as linearized chromosome files and as contig files with assembly information.

A graphical view of the Rat Genome coverage in BACs available here.

BLAST Searches

• Assembled Genome (chromosome format)
• Assembled BAC clones enriched with whole genome sequence
• Assembled BAC clones

Individual matched sequences can be retrieved from the BCM FTP site using links in the output. Download the formatted BLAST database.

Overlapping BAC clones are arranged in Bactigs. The position of all of the BACs in a Bactig can be found under the Bactig tab at the top of the page.

Information on a set of projects associated with a particular set of Quantitative Trait Loci (QTL) can be viewed by selecting the location of that marker (RAT-SA) from the QTL Browser.

A three-way comparison of human and mouse to rat chromosomes found using Pash is available for browsing.

BAC-based Data Resources

Individual BAC clones can be searched using the Sequencing Project Browser with a query of:

• an Accession number (AC094151)
• a Clone name (CH230-2L21)
• or a Project name (GAWA)

in the appropriate query box.

A view of ENCODE BACs is available here.

A view of new BAC data produced in the last week can be found under the tab for Recent Assemblies.

Summary information for all BAC projects is available under the Clone Summary list.

Use the BAC Fisher to find Whole Genome Shotgun reads that overlap sequencing reads from a clone. This program finds similar sequences where the matches extend to the end of the query sequences . BAC-Fisher is tuned to reject repeat matches without masking repeats in the query.

Rat data access FAQ

International Genome Consortium Database

Conditions for use

Resources

NIH Rat Genomics and Genetics
Rat Genome Database - Medical College of Wisconsin
Rat Genome Data - Jackson Library
University of Iowa Rat EST Project
Fingerprint Database - BC Genome Sciences Center
Unigene - NCBI
BAC Resources - Children's Hospital Oakland Research Institute
Genome Browsers - NCBI, UCSC, Ensembl, LBL

Citations

Havlak P, et al. The Atlas genome assembly system. Genome Res. 2004 Apr;14(4):721-32.

Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521.