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

Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA.
Nature Genetics (Impact Factor: 29.35). 06/2008; 40(5):523-7. DOI: 10.1038/ng0508-523
Source: PubMed


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.

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Available from: Xose M Fernandez-Suarez
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    • "; Rat Genome Sequencing Project Consortium 2004; Chimpanzee Sequencing and Analysis Consortium 2005; Levy et al. 2007; Rhesus Macaque Genome Sequencing and Analysis Consortium 2007; Bentley et al. 2008; Twigger et al. 2008; Wang et al. 2008; Li et al. 2010; Gnerre et al. 2011; Kim et al. 2011; Lindblad-Toh et al. 2011; Locke et al. 2011; Xu et al. 2011; Yan et al. 2011; Perry et al. 2012; Prüfer et al. 2012; Scally et al. 2012 "
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    • "RNA-Seq offers the potential for de novo definition of intron-exon boundaries, 5′- and 3′-untranslated regions, splice variants, single nucleotide polymorphisms (SNPs), and potentially new transcripts at a highly accurate level of quantitation, all of which are crucial for the analysis of differential gene expression [3], [4], [5]. The laboratory rat is an important experimental animal model for the study of chemically-induced diseases but RNA-Seq studies of rat tissues [6], [7], [8], [9], [10], [11] are still rather limited in part because its complete genomic sequence and annotation are still being refined [12], [13]. Published rat transcript profiling studies have focused on effects in the ageing cerebral cortex [10], neurons in the nucleus accumbens [6], the hippocampus of alcohol-addicted rats [7], functional compartments in the rat placentation site [9], the ventricular myocardium from SHR rats, [8] and kidneys from aristolochic acid exposed animals [14]. "
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    • "Rat has been the traditional model for the study of ventilatory response to hypoxia (Powell et al., 2000). Accompanied by its resolved genome and a broad base of supporting information regarding genetic polymorphism, rat represents a supreme model for the study of genetic background effect in respect to hypoxia (Twigger et al., 2008). Previous data showed that among the inbred rat strains, BN, but not SS, is robust against hypoxia (Hodges et al., 2002). "
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