Nucleic Acids Research, 1980, Vol. 8, No. 13 2967-2984
© 1980
MOLECULAR BIOLOGY |
The nucleotide sequence of an untranslated but conserved domain at the 3' end of the avian sarcoma virus genome
Department of Microbiology and Immunology, University of California San Francisco, CA 94143, USA *Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA
Received April 10, 1980. The genomes of numerous avian retroviruses contain at their 3' termini a conserved domain denoted "c". The precise boundaries and function of "c" have been enigmas. In an effort to resolve these issues, we determined the sequerce of over 900 nucleotides at the 3' end of the genome of the Schmidt-Ruppin subgroup A strain of avian sarcoma virus (ASV). We obtained the sequence from a Suitable fragment of ASV DNA that had been cloned into the single-stranded DNA phage M13mp2. Computer-assisted analysis of the sequence revealed the following structural features: i) the length of "C" - 473 nucleotides; ii) the 3' terminal domain of src, ending in an amber codon at the 5' boundary of "C"; iii) terminator codons that preclude continuous translation from "C"; iv) suitably located sequerces that may serve as signals for the initiation of viral RNA synthesis and for the processing and/or polyadenylation of viral mRNA;v) a repeated sequerce that flanks src and that could facilitate deletion of this gene; vi) repeated sequences within "c"; and vii) unexplained homologies between sequences in "c" and sequerces in several other nucleic acids, including the 5' terminal domain of the ASV genome tRNASS and its inversion, the complement of tRNASS and its inversion, and the 18S RNA of eukaryotic ribosomas. We cocnclude that "c" probably does not encode a protein, but its sequence may nevertheless serve several essential functions in viral replication.