Long terminal repeat of a Gypsy LTR retrotransposon from zebrafish
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Flanked by 4-bp target site duplications.The internal portion encodes two proteins: a 536-aa gag protein (pos. 261-1868) and a 1546-aa polyprotein (pos. 1757-6394, conceptual translation) composed of protease, reverse transcriptase, and integrase domains. Some insertions are fairly recent, considering the high similarity between their flanking LTRs. Consensus obtained after the alignment of at least five independent insertions bearing at least 85% homology over at least 1000 bp.
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 6550 positions long. The average length of non-redundant hits to the model is 3003.4. This table shows the number of hits above score thresholds:
|non-redundant||all hits||non-redundant||all hits|
External Database Links
- Repbase : Gypsy4-I_DR [Requires Repbase registration]