Question: is this insect nucleotide sequence transpon (SINE family)? Need help with transposon.
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gravatar for lijunmin
6 months ago by
lijunmin0
lijunmin0 wrote:

sequences inserted into insect genome and potential tranposon identified in Repbase

Hello everyone, I've tried to confirm a sequence which is transposon or not. I've identified a sequences with the length around 200 bp that is widely integrated into a insect genome (distributed in the same or different contigs) as shown in the figure (more than a thousand insertion identified). I've tried to confirm that this is the transposon or not. So I put the sequence into Repbase and I got three homology of transposon homology, SINE3-1_TC, Polinton-6_NVi and Zator-N1_RPr as shown in the figure.

Since most of the sequences cover the range of SINE3-1_TC, so I extracted all of these inserted sequences and extend with 500 bp with 5' and 3' for each sequence, respectively. And I use SINE_Scan software to identify if these sequences are belong to the family of SINE transposon. The results indicated that most of them are identified as SINE family of transposon.

Since I'm not familiar with transposon, I've got several questions. One is that from these results, can I confirm that this sequence is transposon of the insect? Second is that when a transposon inserted into the genome, will it have different homology length for the insertion?

I'm really appreciated any help with this problem, Thank you very much in advance!

Best wishes

genome • 180 views
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