Autonomous Harbinger DNA transposon from zebrafish
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HARBINGER1_DR is an autonomous Harbinger-like DNA transposon. Given well preserved 16-bp TIRs, the TAA target site duplication, and encoded protein sequences, HARBINGER1_DR was active in the zebrafish genome recently. The zebrafish genome harbors multiple families of nonautonomous DNA transposons, for example HARBINGERN1_DR, that are derivates of autonomous HARBINGER1_DR-like elements. HARBINGER1_DR encodes two proteins, a 424-aa DNA transposase (2 exons, positions 190-419 and 1084-2128) and a 250-aa DNA-binding protein with the trihelix motif (positions 4001-3249). The latter is related to multiple DNA binding proteins and transcription factors identified in plants (GT-1 proteins), insects (GenBank, g7294624) and mammals (GenBank, g12844693). Presumably, the second protein is a former host gene captured by Harbinger in the past.
|Class||Cut and Paste|
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 4016 positions long. The average length of non-redundant hits to the model is 229.6. This table shows the number of hits above score thresholds:
|non-redundant||all hits||non-redundant||all hits|
External Database Links
- Repbase : HARBINGER1_DR [Requires Repbase registration]