Internal sequence of a Gypsy LTR retrotransposon from zebrafish
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Flanked by Gypsy-17-LTR_DR LTRs. The consensus sequence was reconstructed based on multiple alignment of two proviral copies (they are less than 1% divergent from the consensus sequence). Gypsy-17_DR retrotransposons are characterized by 4-bp target-site duplications. The internal portion contains two ORFs encoding a 572-aa gag protein (pos. 85-1799) and a 1578-aa pol protein (pos. 1794-6527) 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. One proviral copy is flanked by identical 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 6546 positions long. The average length of non-redundant hits to the model is 3089.9. This table shows the number of hits above score thresholds:
|non-redundant||all hits||non-redundant||all hits|
External Database Links
- Repbase : Gypsy-17-I_DR [Requires Repbase registration]