Anananasee annotation -missing , extra exons

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ksaville
Posts: 45
Joined: Mon Aug 06, 2007 8:30 pm

Anananasee annotation -missing , extra exons

Post by ksaville » Wed Feb 27, 2013 9:52 pm

Are others finding more than usual cases of extra exons or fewer exons when compariing anananasee and melanogaster genes?

We are working on 5 fosmids and have already found 2 or 3 such cases.

K

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

Re: Anananasee annotation -missing , extra exons

Post by wleung » Thu Feb 28, 2013 12:02 am

Compared to D. erecta, genes in D. ananassae are less similar to genes in D. melanogaster. Consequently, BLAST might report multiple alignment blocks for a single exon because only parts of the exon is conserved with D. melanogaster. In these cases, you would still annotate the region as a single contiguous exon if there is a single open reading frame.

Because we have just started the annotation of D. ananassae projects this semester, we have not yet collected data on the frequency of changes in gene structure. Our previous analysis of the genes on the D. ananassae Muller F element suggests changes in gene structure are still relatively rare.

Please include an explanation of the changes in gene structure and supporting evidence (such as RNA-seq data, TopHat splice junction predictions, etc.) in the annotation report so that we can examine these annotations more closely during project reconciliation.

ksaville
Posts: 45
Joined: Mon Aug 06, 2007 8:30 pm

Re: Anananasee annotation -missing , extra exons

Post by ksaville » Thu Feb 28, 2013 12:15 am

Ok Thanks Wilson

I will have them include the evidence. I'm basing this on preliminary reports from students and haven't looked into it in detail myself yet, but it seems that a couple had different numbers of exons, with good protein alignments and only a "warn" message that the exon numbers differed. I'll keep an eye on it

K

pszauter
Posts: 1
Joined: Tue Jun 19, 2012 9:28 pm

Re: Anananasee annotation -missing , extra exons

Post by pszauter » Fri Mar 01, 2013 7:34 pm

I have a pretty good example of a gene with a missing intron in D. ananassae relative to D. melanogaster. I worked this up as an example for students to illustrate annotation of genes on the minus strand, then was surprised to find an intron missing.


http://www.discoveryandinnovation.com/b ... 49B07.html

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