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Help with first exon of CG10565 in Fosmid 18 of D. erecta

Posted: Wed May 09, 2012 8:33 pm
by bdanner
We are working with D. erecta Jan. 2008 (GEP/3L extended) Fosmid 18.

We found that exon 1 of gene CG10565 (PB/PA) has in-frame stop codons in all reading frames except the third reading frame, but the methionines are way downstream of where BLAST calls the gene. We are not sure where the start of this gene is. Should we start the gene at the first methionine in the third reading frame? We are aware that D. erecta should be fairly homologous to D. melanogaster, so we are expecting a 3 exon gene. Could you provide us any insight?
question.jpg
question.jpg (117.81 KiB) Viewed 4837 times
Thanks a bunch,
Nikie & Ben

Re: Help with first exon of CG10565 in Fosmid 18 of D. erect

Posted: Wed May 09, 2012 9:37 pm
by wleung
As you have noted, CG10565 is a 3-exon gene in D. melanogaster. Mapping the three coding exons against the fosmid18 sequence with bl2seq (using the BLASTX program) shows that all three exons are highly conserved.
gene_record_finder_CG10565.png
Gene record for CG10565
gene_record_finder_CG10565.png (33.54 KiB) Viewed 4834 times
The BLASTX alignment shows that the full-length match for the first coding exon (4_517_0) is located at 31465-31208. The region shown in the screenshot you have previously attached appears to correspond to the location of the CDS 1_517_2 (30488-28953), which is the third coding exon of CG10565.
blx_alignments_fosmid18_CG10565.png
BLASTX alignment of CG10565 CDS's against fosmid18
blx_alignments_fosmid18_CG10565.png (229.6 KiB) Viewed 4834 times

Re: Help with first exon of CG10565 in Fosmid 18 of D. erect

Posted: Fri May 11, 2012 8:28 pm
by bdanner
Thank you! The negative direction sequences always confuse me.