Physical mapping and evolution of the centromeric class I gene-containing region of the rat MHC

Abstract.

We physically mapped the centromeric part of the BN rat MHC (RT1ⁿ haplotype) in a contig of overlapping P1-derived artificial chromosome (PAC) clones encompassing about 300 kb. The following genes were identified and ordered as: (Syngap, Hset, Daxx, Bing1)–Tapbp–Rgl2–Ke2–Bing4–B3galt4–Rps18–Sacm2l–RT1-A1–RT1-A2–RT1-A3–Ring1–Ring2–Ke4–Rxrb–Col11a2–RT1-Hb–Ring3–RT1-DMb. Thus, in contrast to other RT1 haplotypes, RT1ⁿ contains three class I genes, RT1-A1, RT1-A2, and RT1-A3, mapping between the Sacm2l and Ring1 genes. Comparisons of the sequences flanking the Sacm2l and Ring1 genes in rat, human, and mouse suggest that the class I gene-containing region was inserted between these genes in rat and mouse at a similar position. Thus, this insertion is likely to have occurred in a common ancestor of these rodents, although the presence of a site particularly permissive for insertions cannot be excluded.