title: TROMB, a new retrotransposon of the gypsy-Ty3 group from the fly Megaselia scalaris.
abstract: We describe TROMB, a new LTR retrotransposon, from the phorid fly Megaselia scalaris. Three full-length copies (4226, 4160 and 4129bp) and a truncated one (319bp) have been isolated. The target site consensus is TATAT, with a 4bp target site duplication TATA. The LTRs are short (142bp) and contain a TATA-box and a polyadenylation signal. The isolated copies are degenerate to different degrees and presumably inactive. The polyprotein coding sequence contains scattered stop codons and deletions/insertions at non-homologous positions. The consensus sequence among the three full-length copies, however, has an uninterrupted open reading frame and, presumably, represents the original sequence of the active element. Southern hybridization experiments showed TROMB to be present at a low copy number in two wild-type strains of M. scalaris and absent in a related species, M. abdita. The order of domains in the polyprotein coding region, the target site specificity for AT-rich sequences, and the protein sequence similarity to blastopia, mdg3 and micropia place TROMB in the gypsy-Ty3 group of LTR retrotransposons.
authors.affiliation: Institut für Biologie, Medizinische Universität zu Lübeck, D-23538, Lübeck, Germany.
authors.forename: G
authors.initials: G
authors.lastname: Suck
authors.forename: W
authors.initials: W
authors.lastname: Traut
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics; D004175:Diptera / Q000235:genetics*; D019143:Evolution, Molecular; D005260:Female; D018628:Gene Dosage; D008297:Male; D008969:Molecular Sequence Data; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D020079:Terminal Repeat Sequences
chemical_list: D018626:Retroelements; D004247:DNA