DNA sequence analysis of a rat RT1 class II A beta gene.

The rat major histocompatibility complex (RT1) encodes twin sets of class II molecules, each consisting of two polypeptide chains referred to as A alpha and A beta, and E alpha and E beta. A gene encoding the RT1.A beta chain was isolated from a rat genomic library using an HLA-DQ beta chain cDNA as a probe. The nucleotide sequence of the coding regions of this gene was determined. Comparison of this sequence with those of the corresponding genes of mouse (H-2A beta) and human (HLA-DQ beta) revealed that this gene has been highly conserved during evolution, and that some parts of the molecule are more conserved than others. Analysis of the nucleotide sequence encoding the two external domains suggests that the membrane proximal domain has been subject to conservative selection, whereas replacement substitutions have been selected positively at certain residues within the amino terminal domain. The overall organization of the RT1.A beta gene is similar to that of the H-2A beta gene.