Internal sequence of a Gypsy LTR retrotransposon from zebrafish - fossilize
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Flanked by Gypsy-19-LTR_DR. The genome contains one copy of Gypsy-19-I_DR that is flanked by 2% diverged LTRs. The internal portion contains two ORFs encoding Gypsy-like gag and pol proteins. The first ORF contains one frame shift and encodes the 601-aa Gypsy-19_DR1p gag (pos. 94-1892). The second ORF encodes a 1566-aa pol protein (pos. 1847-6544) composed of protease, reverse transcriptase, and integrase domains.
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 6544 positions long. The average length of non-redundant hits to the model is 3454.9. This table shows the number of hits above score thresholds:
|non-redundant||all hits||non-redundant||all hits|
External Database Links
- Repbase : Gypsy-19-I_DR [Requires Repbase registration]