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D. erecta 2nd 3L extended fosmid 32 changes

Posted: Wed Sep 12, 2012 10:09 pm
by cmackinnon
In June 2012, my students annotated fosmid 32 of D. erecta, 2nd 3L extended assembly. They selected the sls gene, isoform PD The Gene Record finder at that time showed the sls gene isoform RD started with exon 42. The gene model checker passed with flying colors. Today in class I had the students find all the exons in sls, and now there is an exon 43, and no 42, except in isoform PD. If you do a blastx with the exon 43 sequence, the first 21 amino acids aren't shown in the blastx report. After some hand waving, I said the annotation was probably updated to show a new exon that wasn't present in fosmid 32, but might have been in the adjacent fosmids. With all the information collected, the new model for sls now includes exon 43. What should I really have told them?

Re: D. erecta 2nd 3L extended fosmid 32 changes

Posted: Thu Sep 13, 2012 1:50 am
by wleung
As you have mentioned, the gene record for the D. melanogaster sls gene has changed in June 2012.
sls flybase update
flybase_sls_update.png (18.84 KiB) Viewed 4706 times
However, the most likely reason that you cannot detect the first exon (43_374_0) with blastx is that the low complexity filter and compositional adjustments were on when you performed the blastx search. Turning off both of these filters should allow you to detect the first exon of sls in fosmid32, as it is very highly conserved. Because the first exon consists of a high frequency of glutamine (Q), the low complexity filter and the compositional adjustments would likely have masked these regions.
blastx sls first exon against fosmid32
sls_first_exon_against_fosmid32.png (98.69 KiB) Viewed 4706 times
The putative location of the first exon as identified by BLASTX appears to be well supported by the RNA-Seq and gene predictors.
genome browser first exon fosmid32
sls_first_exon_fosmid32_browser.png (49.04 KiB) Viewed 4706 times

Re: D. erecta 2nd 3L extended fosmid 32 changes

Posted: Thu Sep 13, 2012 2:23 am
by cmackinnon
Thank you! I've been having trouble with blastx results--we keep getting error messages---and turning off the low complexity filter seemed to "fix" the problem, but created another one! I'll try a different browser than internet explorer; I tend to have more problems with it when accessing databases.