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When doing an annotation of a contig31 of Drosophila biarmipes genome, the gene predictions(in orange, red, green, tan, blue, brown, and gray) picked up numerous possible genes in the area circled in blue below:

GEP genome browser on *D.biarmipes*, dot chromosome, contig 31

So according to the GEP(genomic education partnership) guide I was reading, I was to then BLASTP the amino acid sequence from these predicted genes to a non-redundant protein database. Using NCBI BLAST I did just that, and observed alot of results of significance (E value < 1 X 10^-5).

Many of the BLASTP results were somthing like:

First BLASTP result, possible TE?

Reading up on gag proteins I found they were related to transposable element activity, specifically reverse transcriptase activity. So then should I conclude that these regoins are showing a gene because they are a Transposable element, or the remenats of one?

I also found:

enter image description here

And reading on Wolbachia I found that there is Horizontal gene transfer with its genome and Drosophila in general, according to wikipedia: http://en.wikipedia.org/wiki/Wolbachia#Horizontal_gene_transfer_and_genomics

So then, can I conclude the area circled in blue is a result of Transposable element, and not an actual gene belonging to D. biarmipes?

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  • $\begingroup$ Do a nucleotide BLAST first. This seems to be just a partial match. You cannot conclude that this is a transposable element. Also see if RNAseq data is available. $\endgroup$ – WYSIWYG May 7 '15 at 10:06
  • $\begingroup$ @WYSIWYG THe RNA seq data is in the first picture, under the blue circle, there are black peaks that correlate with RNA seq data, the first is labeled "RNA-Seq alignment summary for mixed embryos". As for the nucleotide BLAST, i did a tBLASTn, since I only had an amino acid file to work with. The results were still a same link to the pol gag protein. The title of the highest significance match was: "Drosophila ananassae retrotransposon putative gag-pol protein gene" . $\endgroup$ – Ro Siv May 7 '15 at 18:43

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