Long terminal repeat sequences of intracisternal A particle genes in the Syrian hamster genome: identification of tRNAPhe as a putative primer tRNA.

We have determined the nucleotide sequences of long terminal repeat (LTR) regions of Syrian hamster intracisternal A particle (IAP) genes. The size of the LTRs was 350 base-pairs (bp) and 376 bp in two clones, H10 and H18, respectively. Two LTRs at both ends of the IAP gene were linked to directly repeating 6 bp hamster sequences. Many structural features common to the integrated retroviral LTRs such as "CAT" box, "TATAA" box, polyadenylation signal, and terminal inverted repeat (3 bp), were present on each LTR. The estimated length of R region (about 60 bp) was similar to that of the murine leukemia-sarcoma virus. In contrast, the calculated U5 region of 54 bp was the shortest among those of the retroviruses so far studied. Furthermore, from the analysis of primer binding sites, phenylalanine tRNA was for the first time identified as a presumed primer tRNA for reverse transcription. These results clearly distinguish Syrian hamster IAP LTRs from other retroviral ones. Based on the comparison of the sequences between Syrian hamster and laboratory mouse LTRs, the structural features peculiar to the IAP LTRs and the origin of the IAP genes are discussed.