gene identification

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gene identification

Postby cnavarro » Mon Jan 28, 2008 4:40 pm

:?: Hello. :?:
I want to know if have been identified the gene of the receptor of ccap and receptor of the eth in the others 11 drosophila species.
If this has not been done, know if doing a blast would be enough for finding these genes in the others 11 species.

Apologies for my English. :oops:
cnavarro
 
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Re: gene identification

Postby andy » Wed Feb 06, 2008 10:17 am

Hi,

If you look at the Gbrowse view of the CCAP receptor in Gbrowse and select to view the similarity:synteny features tracks you will see the predicted consensus models from a number of species for genes that are putative orthologs of this gene. You can click on these prediction tracks and will be brought to a Gbrowse view of the other species gene and then you can access the gene report for that gene from there.

This should give you some clues as to which models in the other species encode the CCAP receptor but remember that these are automated predictions so must be treated with caution.

cheers,
Andy
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Re: gene identification

Postby Papanikolaou » Mon Feb 25, 2008 1:50 pm

Hello,

I am a "cancer" person and, in an effort to infer protein function(s) I have BLASTED a human male germ cell-specific mRNA and protein, which is encoded in human Xq28 and expressed only in testis spermatogonial stem cells, against the Dmel cDNA dbase to identify orthologues. I have done this using an E value of 10 or 1 and I retrieve 4 hits in the Dmel X and 2L chromsoomes. The identity is ~62% but in alow complexity region in the N-terminus. The stringency was high in order to get distant relatives. The proteins align between 52-56% in the same regions. What is your advise?
Note that there are no mouse counterparts to my protein and the human genome contains paralogs.

Thanks for any help on how to proceed.

Nick
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