Harlequin (DF0000017)

Internal region of ERV1 endogenous retrovirus, Harlequin subfamily


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.


Accession Name Wikipedia
Type Retrotransposon Article
Class LTR Article
Superfamily ERV1 Article

Hit Statistics

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:

Species Gathering Trusted
non-redundant all hits non-redundant all hits
Homo sapiens 430 7915 334 4327

External Database Links

  • Repbase : HARLEQUIN [Requires Repbase registration]