A repetitive DNA sequence in the salmonid fishes similar to a retroviral long terminal repeat.

We describe the characteristics of a repetitive DNA sequence from the rainbow trout and related salmonid fishes that is similar to a retroviral long terminal repeat (LTR). The repeat is 160 bp long and contains a region of homology to the LTR of the avian sarcoma virus. Two clones with this repeat from the chum salmon also have a polypurine tract and tRNA binding site, respectively, and these clones may represent the two LTRs of a retrovirus or retroviral-like repetitive element. Copies of the repeat are also adjacent to rainbow trout and chum salmon protamine genes. These repeats may be "solo" LTRs. There appears to be some polymorphism in restriction sites between individual rainbow trout and considerable differences between salmonid fish species when the repeat is used as a probe.