LTR retrotransposon from zebrafish: internal sequence
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The translation product of pos 18-401 match the Gypsy-gag-like protein from Copia-8_DR. Beware: from pos 1064 on this sequence is a VNTR, (accctccagagctgccag)n, (aatggccgccgcctcctgagcttcc)n and finally (acgctccaggccctccgcagctcc)n. It is dangerously skewed (very C-rich) and gives false positive matches to CpG islands like the promoter region of L1 in mammals, even with complexity adjusted scores.
Note: Uncertain classification.
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 3222 positions long. The average length of non-redundant hits to the model is 505.4. This table shows the number of hits above score thresholds:
|non-redundant||all hits||non-redundant||all hits|
External Database Links
- Repbase : Copia-7-I_DR [Requires Repbase registration]