How to report a new gene

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

How to report a new gene

Post by ksaville » Wed Apr 24, 2013 6:58 pm

We believe we have found a duplictaed copy of a gene in D. anananasse. The fosmid is 3L control fosmid_1479A08 and the gene is CG32395. The D mel protein track identified CG32395 and there was a genscan prediction just upstream of this that didn't have a correponding d mel blast hit. A blastp search using the genscan protein matched CG32395. Also when blasting the CG32395 exons against the fosmid DNA it matched two places. That identified by the blast track and a new one.

We annotated this new gene based on the exon-exon blast and checked it in Gene Model Checker CG32395 as our reference.

However, Because we had to call both genes CG32395, they show up as one gene, when we merge the GFF files.

and - because it isn't a new isoform, we weren't sure what to do - so we just sort of described it in the report.

I just wanted to ask here in case any one else runs into this situation

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

Re: How to report a new gene

Post by wleung » Wed Apr 24, 2013 10:34 pm

If your analysis indicates that there might be a novel paralog in D. ananassae, you can pick an unique name for the feature (i.e. a gene symbol that has not been used in D. melanogaster). For example, a novel paralog of CG32395 could be called CG32395-2. When you check the gene model using the Gene Model Checker, it will issue a warning indicating that the gene is not found in D. melanogaster.

Using the peptide sequence generated by the Gene Model Checker, you can perform a bl2seq blastp alignment against the gene from each the paralog was derived (i.e. CG32395). In the annotation report, please include the analysis that lead you to conclude that the feature is a paralog as well as the protein alignment and the dot plot from the bl2seq blastp search.

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