Internal sequence of an endogenous retrovirus from zebrafish
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CATCH1I_DR is an internal portion of the CATCH1_DR endogenous retrovirus, which belongs to the BEL/Pao superfamily. It is flanked by identical long terminal repeats, deposited in Repbase as CATCH1LTR_DR, and is characterized by 5-bp target site duplication. It is possible that CATCH1_DR is still active in zebrafish. CATCH1I_DR encodes one polyprotein, 2029-aa CATCH1_DRp (positions 190-419). CATCH1_DRp includes gag-like, reverse transcriptase and endonuclease domains similar to other retroviruses from the BEL/Pao superfamily. N-terminal region of CATCH1_DRp (positions 20-250) is similar to coiled coil domains present in various myosins. Gag-like domain (including zinc fingers) is located at ~420-770.
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 6170 positions long. The average length of non-redundant hits to the model is 1767.5. This table shows the number of hits above score thresholds:
|non-redundant||all hits||non-redundant||all hits|
External Database Links
- Repbase : CATCH1I_DR [Requires Repbase registration]