title: Organization and nucleotide sequence of the rat T cell receptor beta-chain complex.
abstract: We have characterized four overlapping genomic clones containing the DA rat TCR C beta complex, which span a total of 23 kb and bear two closely related complexes of gene segments. The D beta 1-J beta 1-C beta 1 and the D beta 2-J beta 2-C beta 2 complexes each contain a single diversity segment, six joining segments and four exons that encode the C region. All gene segments appear to be functional except J beta 2.5, which has a 5-bp frame-shifting deletion. This organizational pattern is identical to that of the mouse, and the homologous rat and mouse coding regions share about 92% nucleotide sequence identity. Our sequence comparisons indicate that a localized gene correction event has homogenized the sequences of the first exons of C beta 1 and C beta 2 in the evolutionary time since rats and mice became separate species. We have identified three repetitive elements, each flanked by short direct repeats, present in the region "brain-specific" identifier (ID) sequences, another is a truncated member of the LINE I class of repetitive elements, and the third is a member of the Alu type 2 family. The insertion of at least two, and probably all, of these elements has occurred since the time of rat/mouse divergence. We have identified a substantial number of "cryptic" rearrangement signals (heptamer/nonamer) in the C beta locus, which match the consensus sequence as well or better than authentic signals, and may represent sites of nonfunctional rearrangements.
authors.affiliation: Department of Microbiology and Molecular Genetics, California College of Medicine, University of California, Irvine 92717.
authors.forename: C B
authors.initials: CB
authors.lastname: Williams
authors.forename: E P
authors.initials: EP
authors.lastname: Blankenhorn
authors.forename: K E
authors.initials: KE
authors.lastname: Byrd
authors.forename: G
authors.initials: G
authors.lastname: Levinson
authors.forename: G A
authors.initials: GA
authors.lastname: Gutman
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D005091:Exons; D015329:Gene Rearrangement, T-Lymphocyte; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D051381:Rats; D011948:Receptors, Antigen, T-Cell / Q000235:genetics*; D016693:Receptors, Antigen, T-Cell, alpha-beta; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D011948:Receptors, Antigen, T-Cell; D016693:Receptors, Antigen, T-Cell, alpha-beta