Rat gene mapping in the post-genome sequencing era: the continued utility of cell hybrids to localize rat genes (Cks2, Ephb4, Fabp5, Il13ra1, Rpl10, Ssr4).
Finding the position of a gene is now easily done when the genome sequence is available: the gene position is generally found by a simple query of genomic databases such as those available at the Ensembl browser or the NCBI. We were interested in determining the position of 125 cancer-related rat genes and we found that the position of most of these genes (110) could indeed be identified in this manner. However, in 15 cases, the gene position was not available in these databases, or the results were ambiguous. We then explored a more specialized database, namely the Rat Genome Database, and experimentally mapped these genes using standard and radiation cell hybrids. The 15 genes in question could be localized unambiguously. In four cases, the radiation cell hybrids were indispensable: the sequence of these four genes could not be found in the rat genome sequence. On the basis of the sample we examined, it thus appears that a classical gene mapping method is still required to localize about 3% of the rat genes, as if 3% of the rat gene sequences were lacking in the current rat genome sequence.
Szpirer
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C
Institut de Biologie et de Médecine Moléculaires, Université libre de Bruxelles, Gosselies, Belgium. cszpirer@ulb.ac.be
Van Vooren
P
P
Rivière
M
M
Szpirer
J
J
D000818:Animals; D002135:Calcium-Binding Proteins / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D005136:Eye Proteins / Q000235:genetics*; D050556:Fatty Acid-Binding Proteins / Q000235:genetics*; D005796:Genes / Q000235:genetics*; D016678:Genome; D006822:Hybrid Cells; D053661:Interleukin-13 Receptor alpha1 Subunit / Q000235:genetics*; D008562:Membrane Glycoproteins / Q000235:genetics*; D051379:Mice; D009419:Nerve Tissue Proteins / Q000235:genetics*; D051381:Rats; D036224:Receptor, EphB4 / Q000235:genetics*; D018160:Receptors, Cytoplasmic and Nuclear / Q000235:genetics*; D018000:Receptors, Peptide / Q000235:genetics*; D012269:Ribosomal Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA
D002135:Calcium-Binding Proteins; D002352:Carrier Proteins; D005136:Eye Proteins; C107356:Fabp5 protein, rat; D050556:Fatty Acid-Binding Proteins; C508185:Il13ra1 protein, rat; D053661:Interleukin-13 Receptor alpha1 Subunit; D008562:Membrane Glycoproteins; D009419:Nerve Tissue Proteins; D018160:Receptors, Cytoplasmic and Nuclear; D018000:Receptors, Peptide; D012269:Ribosomal Proteins; C098998:Rpl10a protein, rat; C066973:signal sequence receptor; D036224:Receptor, EphB4