overlapping exons

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mspratt
Posts: 4
Joined: Fri Aug 17, 2007 5:15 pm

overlapping exons

Post by mspratt » Mon Apr 30, 2012 11:50 am

A student has Fosmid 30 in the 2nd 3L Control region of D. erecta. In the sls gene with its many exons and isoforms, there are adjacent exons in the isoforms that totally overlap for all practical purposes: 37_537_2 and 36_537_2; both are -2 orientation and reasonable splice sites are found. Of course gene checker won't pass this because the isoforms overlap--totally in this case. Is this a missprediction, or what am I missing? Alternate & lesser alignments don't appear any better.
Thanks much!
Mary Spratt

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: overlapping exons

Post by wleung » Mon Apr 30, 2012 2:25 pm

fosmid30 likely contains only part of the sls gene and that both 37_537_2 and 36_537_2 are located outside of the fosmid. For example, looking at the blastx alignment for sls-PJ, we find that only the latter part of the protein is mapped to the fosmid (starting at around 9475 of the protein). Note that the first four hits (e.g. 5639-5691, ... 8301-8327) have much lower percent identity than the rest of the protein and are likely spurious.
sls-PJ_blx_alignment.png
sls-PJ blastx alignment against fosmid30
sls-PJ_blx_alignment.png (73.63 KiB) Viewed 3868 times
The sls gene is quite large and it appears to span from fosmid32 to fosmid30. Hence the exons 37_537_2 and 36_537_2 are likely located in fosmid32.
Dere6_fosmid32_assembly_view.png
Dere6 fosmid32 genome browser view
Dere6_fosmid32_assembly_view.png (53.6 KiB) Viewed 3868 times
For example, mapping the exon 37_537_2 against fosmid32 with blastx, we find a highly conserved match to this exon from 32106-29311. Consequently, the matches to 37_537_2 and 36_537_2 are likely due to conserved immunoglobulin domains within the protein and do not correspond to the actual locations of these two exons.
sls_conserved_Ig_domains.png
sls conserved domain alignments
sls_conserved_Ig_domains.png (221.63 KiB) Viewed 3868 times

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