Subject: Re: FlyBase Query (cy901a)
CG9841 contains obvious EFTU-like sequence, but we did worry that portions
of the two CG's should perhaps be merged. We got conflicting evidence on
this. As we said in the paper, running the region through the Sanger
Genefinder (fgenesh) predicted a single gene instead of the two you listed
(if you want I can send you the predicted exons). And while the portion of
that prediction that corresponds to the 'second' gene (CG10795) is not
obviously similar to EFTU, it does have some similarity to GTP-binding
proteins, and EFTUs bind GTP.
On the other hand, other gene predictors split this up into two different
genes. And the LD27358 EST sequence corresponds only to CG10795, and
contains what looks like 5' UTR sequence sitting between the two genes. So
either there really are two genes, or LD27358 contains some unspliced
intron sequence. There don't seem to be any other ESTs for this gene.
Beyond that, we did not do anything to figure out which was right.
Sorry, wish I could be of more help. Certainly not strong enough evidence
to say your prediction is in error.
Also, just curious about one thing. Do the cDNA Fasta's in Gadfly
correspond only to the ORF? The release 1 CG10795 starts with an ATG, but
there's a stop shortly after it, and the translation Fasta starts much later.
Seth
Seth S. Blair
Department of Zoology
University of Wisconsin