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RatMap


NAR Molecular Biology Database Collection entry number 625
StÅhl F.1,2, Levan G.1, Ilenius N.1, Johnson P.1, Petersen G.1, Andersson L.1, Klinga-Levan K.3 and GÓmez-Fabre P.M.1
1 Department of Cell and Molecular Biology - Genetics, GÖteborg University, Box 462, 40530 GÖteborg, Sweden
2 School of Health Sciences, University College of Boras, Sweden
3 School of Life Sciences, University of SkÖvde, Box 408, SE 54128 SkÖvde, Sweden

Database Description

The rat is particularly well suited as a genetic model organism for complex human diseases such as diabetes, rheumatoid arthritis, hypertension, and cancer. In order to facilitate the exploitation of the rat model, the rat genome database RatMap was launched in 1994 with the clear objective of collecting, curating and presenting rat gene localization data. The data presented on rat genes, DNA-markers and QTLs (Quantitative Trait Loci) are mainly obtained from the literature as well as from other databases and by electronic submission. RatMap has, together with the US rat genome database RGD (http://rgd.mcw.edu), been appointed by the Rat Genome and Nomenclature Committee (RGNC) to be the official web site for rat gene nomenclature.

All references recorded in RatMap can be queried from a simple form and the result is presented as a single report including: description, chromosomal position, bibliographic references as well as links to other relevant databases such as PubMed, GenBank, LocusLink (http://www.ncbi.nlm.nih.gov/) and the genome databases RGD and MGD (http://www.informatics.jax.org/). Information on gene orthologies between rat and human and rat and mouse are also displayed.

A number of tools are available from RatMap facilitating the finding and characterisation of rat QTL (called "QTL") and Candidate Gene Capture (called "CGC"). "RatMapped" is another tool that combines an integrated linkage map with gene sequence positions and QTLs in a single interface. "BACFinder" enables a quick characterisation of number and sizes of exons by comparing mRNA sequences with full-length sequences from rat BAC sequences.

Also comparative databases for rat-mouse ("mouseGAPP") and rat-human ("humanGAPP") are available. These comparative maps are independently developed at RatMap, based on the occurrence of orthologous gene pairs. Thus they serve as an independent complement to similar comparative maps.

Acknowledgements

This work was supported by the Swedish Medical Research Council, the SWEGENE Foundation, the Sven and Lilly Lawski Foundation, the Royal Society of Arts and Sciences in Goteborg, the Swedish Cancer Society, the Erik Philip-SÖrensen Foundation, the Wilhelm and Martina Lundgren Research Foundation, and the Royal Hvitfeldtska Foundation.


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