Internal region of ERV1 endogenous retrovirus, Harlequin subfamily
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Harlequin is an internal part of an endogenous retrovirus-like element flanked by LTR2s. Its consensus sequence has been reconstructed based on eight full-length copies; they are ~92% similar to the consensus sequence. One copy has been inserted into Alu-Y repeat. Harlequin was built up from several different retroviruses including HERVE, HERVI, HERV17 and MER4I-group sequences. We suggest that shuffling of non-homologous endogenous retroviral sequences may generate mosaic retrovirus-like elements. Presumably, the shuffling occurs in virions where RNA genomes of different retroviruses could be packed in together. Self-catalytic RNA recombinations or jumping of reverse transcriptase between non-homologous RNA molecules may induce the shuffling.
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 6896 positions long. The average length of non-redundant hits to the model is 1708.7. This table shows the number of hits above score thresholds:
|non-redundant||all hits||non-redundant||all hits|
External Database Links
- Repbase : HARLEQUIN [Requires Repbase registration]