The gag coding region of the Drosophila telomeric retrotransposon, HeT-A, has an internal frame shift and a length polymorphic region.

A major component of Drosophila telomeres is the retrotransposon HeT-A, which is clearly related to other retrotransposons and retroviruses. This retrotransposon is distinguished by its exclusively telomeric location, and by the fact that, unlike other retrotransposons, it does not encode its own reverse transcriptase. HeT-A coding sequences diverge significantly, even between elements within the same genome. Such rapid divergence has been noted previously in studies of gag genes from other retroelements. Sequence comparisons indicate that the entire HeT-A coding region codes for gag protein, with regions of similarity to other insect retrotransposon gag proteins found throughout the open reading frame (ORF). Similarity is most striking in the zinc knuckle region, a region characteristic of gag genes of most replication-competent retroelements. We identify a subgroup of insect non-LTR retrotransposons with three zinc knuckles of the form: (1) CX2CX4HX4C, (2) CX2CX3HX4C, (3) CX2CX3HX6C. The first and third knuckles are invariant, but the second shows some differences between members of this subgroup. This subgroup includes HeT-A and a second Drosophila telomeric retrotransposon, TART. Unlike other gag regions, HeT-A requires a -1 frameshift for complete translation. Such frameshifts are common between the gag and pol sequences of retroviruses but have not before been seen within a gag sequence. The frameshift allows HeT-A to encode two polypeptides; this mechanism may substitute for the post-translational cleavage that creates multiple gag polypeptides in retroviruses. D. melanogaster HeT-A coding sequences have a polymorphic region with insertions/deletions of 1-31 codons and many nucleotide changes. None of these changes interrupt the open reading frame, arguing that only elements with translatable ORFs can be incorporated into the chromosomes. Perhaps HeT-A translation products act in cis to target the RNA to chromosome ends.