Internal sequence of a Gypsy LTR retrotransposon from zebrafish
A brief description of the entry. Suggestions for modification to this description can be submitted using the adjacent pencil icon.
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.
Number of matches to this model that meet the "Gathering" threshold and more stringent "Trusted" threshold. For each threshold, two numbers are shown: (1) the number of matches to this model after removing redundant hits to other models ("non-redundant"), and (2) the total number of matches above threshold, including those with better scoring matches to other models ("all hits").
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:
|non-redundant||all hits||non-redundant||all hits|
External Database Links
- Repbase : Gypsy-16-I_DR [Requires Repbase registration]