Subject: Helping FlyBase: ADRC-10855 Dear Kevin, We are currently curating the abstracts for the upcoming 44th (Chicago) Annual Drosophila Research Conference, for FlyBase. I am writing in connection with your abstract: Is extra eye a tyrosine phosphatase? You write about a gene, GEF, at 26CD. Is this Gef26 (FBgn0021873)? If not, do you know which of the Genome Project CG annotations your gene corresponds to? All the CGs have corresponding gene records in FlyBase already and we don't like to make duplicate records for what is actually the same gene unless we can't avoid it. Thank you very much for your help, with best wishes, Rachel. \---------------------------------------------------------------------- Rachel Drysdale, Ph.D. FlyBase (Cambridge), \---------------------------------------------------------------------- Subject: Re: Helping FlyBase: ADRC-10855 I was referring generically to the proteins encoded by genes to avoid using their names. The genes referred to are Gef26 and Ddr, which encodes the Discoidin Domain Receptor-class RTK. I was avoiding the name 'Gef26' since Qi He's lab uses the synonym 'dizzy' for this gene. We used 'dizzy' on his poster last year, but I will keep using the more descriptive 'Gef26' until 'dizzy' gets into the literature. Kevin \-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. Kevin A. Edwards Asst. Prof. of Genetics Dept. of Biological Sciences Illinois State University Box 4120 Normal, IL 61790-4120 \-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Subject: Re: Helping FlyBase: ADRC-10855 Hi Kevin, Thanks for this \- all very interesting. Your mail raises several things all of which give me a chance to improve the FlyBase files. First of all dizzy/Gef26. dizzy corresponds to CG9491 and, you say, is the same gene as Gef26 (for which a correlation with a genome annotation had not been established). Great. I will merge the gene records for Gef26 and dizzy (both of which currently exist in FlyBase). Your mail below indicates that you favour dizzy as the gene symbol. I notice that Gef26 has precedence but as far as I can see you are the only author to have used Gef26 so it can become dizzy if that is OK with you. Secondly \- I note that you have sent us a personal communication before (FBrf0149572) concerning the annotation of CG9488/CG9490 and things between, which you would like to see named Ddr for 'Discoidin Domain Receptor-class RTK'. The curator who dealt with that personal communication suffered from a lack of nerve and did not merge the five annotations into one gene record because you had not named each one explicitly. Are they CG9488, CG13985, CG11573, CG13984 and CG9490? When you confirm this to be the case I will finally bring about the merge and rename the merged gene Ddr. Sorry to answer your helpful reply with more questions, but if I have this all correct we will be able to reduce seven FlyBase gene records to two, both of which are tied to the genome, and that would be very satisfying. Best regards, Rachel. Subject: Re: Helping FlyBase: ADRC-10855 > >First of all dizzy/Gef26. dizzy corresponds to CG9491 and, you say, is >the same gene as Gef26 (for which a correlation with a genome >annotation had not been established). Great. I will merge the gene >records for Gef26 and dizzy (both of which currently exist in >FlyBase). Your mail below indicates that you favour dizzy as the gene >symbol. I notice that Gef26 has precedence but as far as I can see you >are the only author to have used Gef26 so it can become dizzy if that >is OK with you. I would not go with 'dizzy' until it is published and the name is clearly linked with the phenotype. Let's stick with Gef26 for now since that is more descriptive for the broader signaling community. > >Secondly \- I note that you have sent us a personal communication before >(FBrf0149572) concerning the annotation of CG9488/CG9490 and things >between, which you would like to see named Ddr for 'Discoidin Domain >Receptor-class RTK'. The curator who dealt with that personal >communication suffered from a lack of nerve and did not merge the five >annotations into one gene record because you had not named each one >explicitly. Let's call it 'Discoidin domain receptor (Ddr)'. >Are they CG9488, CG13985, CG11573, CG13984 and CG9490? My predicted aa seq (not based on cDNA, there still is no EST available) includes sequences from CG9488, CG13985, CG11573, and CG9490. It does not include CG13984, which may be a spurious ORF. I did not look in detail at the genomic arrangement of the predicted genes on a genome browser, you are probably better equipped to do that. I can resend my predicted aa seq if necessary.
