What everybody should know about the rat genome and its online resources

Abstract

It has been four years since the original publication of the draft sequence of the rat genome. Five groups are now working together to assemble, annotate and release an updated version of the rat genome. As the prevailing model for physiology, complex disease and pharmacological studies, there is an acute need for the rat's genomic resources to keep pace with the rat's prominence in the laboratory. In this commentary, we describe the current status of the rat genome sequence and the plans for its impending 'upgrade'. We then cover the key online resources providing access to the rat genome, including the new SNP views at Ensembl, the RefSeq and Genes databases at the US National Center for Biotechnology Information, Genome Browser at the University of California Santa Cruz and the disease portals for cardiovascular disease and obesity at the Rat Genome Database.

Figure 1

GViewer visualization of rat genes and QTL associated with cardiovascular disease. The genes and are QTL are shown aligned with the rat genome which has been colored according to the corresponding syntenic regions in Human. 586 rat genes, 388 rat QTL and 127 rat strains have been associated with various types of cardiovascular disease. These are all available through the RGD Cardiovascular Disease Portal along with 588 Human and 559 Mouse genes and 49 Human QTL.