Gypsy-16-I_DR (DF0003491)

Internal sequence of a Gypsy LTR retrotransposon from zebrafish

Description

Flanked by 100% identical LTRs (Gypsy-16-LTR_DR). The consensus sequence was reconstructed based on multiple alignment of nine proviral copies (they are less than 1% divergent from the consensus sequence). Gypsy-16_DR retrotransposons are characterized by 4-bp target site duplications. The internal portion contains two ORFs encoding a 645-aa gag protein (pos. 109-2043) and an 1601-aa Gypsy-15_DR2p pol proteins (pos. 1971-2043) composed of protease, reverse transcriptase, and integrase domains. The second protein, including the protease domain, does not start from Met. Presumably, the gag-pol fusion protein is formed originally due to a ribosomal frame shift. This family is likely still active in the genome: all nine proviral copies have perfect LTRs.

Classification

Accession Name Wikipedia
Type Retrotransposon Article
Class LTR Article
Superfamily Gypsy Article

Hit Statistics

The model is 6775 positions long. The average length of non-redundant hits to the model is 4870.9. This table shows the number of hits above score thresholds:

Species Gathering Trusted
non-redundant all hits non-redundant all hits
Danio rerio 25 1451 25 1128

External Database Links