Internal sequence of a Gypsy LTR retrotransposon from zebrafish
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Flanked by Gypsy39-LTR_DR. 4-bp target site duplications. The internal portion encodes one 1585-aa polyprotein (pos. 181-4935) composed of gag, protease, reverse transcriptase, and integrase domains. Some insertions are fairly recent, considering the high identity between their flanking LTRs. Consensus obtained after the alignment of at least nine 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 5049 positions long. The average length of non-redundant hits to the model is 1445. This table shows the number of hits above score thresholds:
|non-redundant||all hits||non-redundant||all hits|
External Database Links
- Repbase : Gypsy39-I_DR [Requires Repbase registration]