RTE-like non-LTR retrotransposon from zebrafish
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EXPANDER1_DR is a family of RTE-like non-LTR retrotransposons and it was active in zebrafish a few million years ago. There are several thousand copies of EXPANDER1_DR fossilized in the zebrafish genome; they are ~91% identical with the consensus sequence. The 5' portion of EXPANDER1_DR is incomplete. The consensus encodes a 3' portion of the reverse transcriptase. EXPANDER1_DR is 87% identical to EXPANDER1 from the fugu genome. Such a high nucleotide identity between non-LTR retrotransposons from the species diverged more than 100 million years ago strongly indicates that horizontal transfer events were involved in evolution of EXPANDERs. The full-length sequence is >74% identical to RTE elements in fugu, medaka, stickleback, and even lamprey.
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 3365 positions long. The average length of non-redundant hits to the model is 490.2. This table shows the number of hits above score thresholds:
|non-redundant||all hits||non-redundant||all hits|
External Database Links
- Repbase : EXPANDER1_DR [Requires Repbase registration]