Inbred rat strains provide a rich source of genetic diversity in immunologically relevant genes. We have characterized the alleles of one of these genes, encoding the rat T-cell receptor C/31 chain, by Southern blots and nucleic acid sequencing. The Cbl gene segments from DA and LEW rats display complex allotypic variation: both coding and noncoding regions contain multiple nucleotide substitutions. In addition, there is a polymorphic insertion of a rat repetitive LINE element 3' to the coding region. The Cbl alleles are one part of larger Tcrb haplotypes, containing V/3, D/3, and J/3 elements; complete Cbl genomic nucleotide sequences, and a partial list of the strain distribution of the two alleles, are described in this report.
Probes: DA genomic libraries were originally screened with a C/3specific Sau 3A fragment of 86T5, as described in Williams and coworkers (1991). LEW genomic libraries were screened with a mouse Tcrb-C region probe, KdD464 (see below) to identify Cb genes of the rat Tcr complex. Mouse DNA clones used for analyzing Southern blots m this study include RBL-5 (Caccia et al. 1984), representing the 3" region of the mouse Tcrb-C region; KdD464, the 5' end of the mouse Cb region (from Dr. R. Snodgrass); and genomic clones for mouse J/31 and J/32 (Kronenberg et al. 1985). All probes consisted of the vector-free insert radiolabelled by the random-primer fill-in reaction (Feinberg and Vogelstein 1983).