Gene or accession: Accession number AE003722 genes CG7689 and CG6790 Missed gene Comments: I work on the fruitless gene and have cloned this gene from several species. I have been examining the genome sequence in comparison with the known cDNAs for D. melanogaster and the known genome structure for D. heteroneura and D. silvestris. (Both in Genbank af051662-af51670 and in press) The structure given in AE003722 is mostly OK except for the 3'terminal exon and the 5' male specific peptide and exons. I have given below a detailed annotation based upon the published D. melanogaster sequence data. Coordinates are from AE003722 complimentary strand. Accession number AF039231 is male specific fru (Ryner et al cell 1996) Exons: 159917..159742 129972..129681 (note start codon for male peptide 129961..129959) 50339..50192 50119..49919 49611..48784 47367..47113 45513..45381 31849..31326 (note stop codon 31828..31826) (note this is gene CG6790 fused to CG7689) Accession number U72492 is female fru sequence (Ryner et al cell 1996) exons: 159917..159742 129972..128080 50339..50192 (note female start codon 50317..50315) rest as for male seq above. Accession number D84437 female fru (Ito et al. 1997 PNAS) exons: 50339..50192 (note start codon 50317..50315) 50119..49919 49611..48784 47367..47113 45513..45381 41715..40694 (note stop codon 40696..40694) (note that the sequence D84437 hReferer: > Tue Jun 06 13:08:54 2000 Dear Dr. Davis, a while back (in April) you wrote to FlyBase with an error report for two CG's on the scaffold AE003722. I have included the mail you sent at the bottom of this e-mail. I am in the process of getting the information in your e-mail into FlyBase as a personal communication, so that when the re-annotation is done, it can be used by the molecular curators to correct the annotation of that part of the genome. I have a couple of questions: 1. you talk about the genes 'genes CG7689 and CG6790'. I think that 'CG6790' is a typo, and should read 'CG7690' \- please can you confirm whether this is the case. 2. I think that your message may have been truncated as it ends in the middle of a sentence. If that is the case and you have more information about these 2 genes, I would be grateful if you could send me the extra information and I will incorporate it into the personal communication. I look forward to hearing from you, Gillian copy of mail you sent: > Thu Apr 06 13:57:56 2000 Gene or accession: Accession number AE003722 genes CG7689 and CG6790 Missed gene Comments: I work on the fruitless gene and have cloned this gene from several species. I have been examining the genome sequence in comparison with the known cDNAs for D. melanogaster and the known genome structure for D. heteroneura and D. silvestris. (Both in Genbank af051662-af51670 and in press) The structure given in AE003722 is mostly OK except for the 3'terminal exon and the 5' male specific peptide and exons. I have given below a detailed annotation based upon the published D. melanogaster sequence data. Coordinates are from AE003722 complimentary strand. Accession number AF039231 is male specific fru (Ryner et al cell 1996) Exons: 159917..159742 129972..129681 (note start codon for male peptide 129961..129959) 50339..50192 50119..49919 49611..48784 47367..47113 45513..45381 31849..31326 (note stop codon 31828..31826) (note this is gene CG6790 fused to CG7689) Accession number U72492 is female fru sequence (Ryner et al cell 1996) exons: 159917..159742 129972..128080 50339..50192 (note female start codon 50317..50315) rest as for male seq above. Accession number D84437 female fru (Ito et al. 1997 PNAS) exons: 50339..50192 (note start codon 50317..50315) 50119..49919 49611..48784 47367..47113 45513..45381 41715..40694 (note stop codon 40696..40694) (note that the sequence D84437 hReferer: Subject: Re: FlyBase error report for fru Date sent: Tue, 6 Jun 2000 13:14:22 \+0100 > Dear Dr. Davis, > > a while back (in April) you wrote to FlyBase with an error report for > two CG's on the scaffold AE003722. I have included the mail you sent > at the bottom of this e-mail. I am in the process of getting the > information in your e-mail into FlyBase as a personal communication, so > that when the re-annotation is done, it can be used by the molecular > curators to correct the annotation of that part of the genome. I have > a couple of questions: > > 1. you talk about the genes 'genes CG7689 and CG6790'. I think that > 'CG6790' is a typo, and should read 'CG7690' \- please can you confirm > whether this is the case. Yes you are correct. The CG7690 is the 5 prime end of the fru gene and is spliced to CG7689. > 2. I think that your message may have been truncated as it ends in the > middle of a sentence. If that is the case and you have more > information about these 2 genes, I would be grateful if you could send > me the extra information and I will incorporate it into the personal > communication. I am not sure what I said and I have not the original message. I will summarise the info. The gene fru is complex and has many splice forms. The male and female specific forms mentioned first are from Ryner et al. they include CG7690 spliced to CG7689. The male form is spliced in the middle of the second exon. The 3 prime terminal from Ryner is 31849..31326. The female form mentioned in Ito et al. has the same exons (including the exons in CG7690 though this is not in the Genbank sequence D84437) as Ryner et al. except the last exon is 41715..40694 and NOT 31849..31326. The female form of the protein is the same except for its 3 prime terminal. Note that this corrects the terminal part of CG7689. Note that the male proteins differs from the female proteins due to the addition of the extra 5 prime amino acids in cds CG7689. I hope that this is not confusing. If you can check the references it should become clearer. Check also Davis et al (2000) Gene 246, p143-149. This is the Drosophila heteroneura fru gene but the exons and splice sites are identical though I didn't find the male specific exons (CG7690) in heteroneura. There are sevaral other splice variants of this gene but I will need to talk to my colleagues before I can annotate them. If I have confused you please contact me again. It is quite difficult to be clear over the e.mail. Sincerely Terry Davis > I look forward to hearing from you, > > Gillian > > > copy of mail you sent: > > Date: Thu, 6 Apr 2000 06:02:26 \-0700 (PDT) > > Error report from Terence Davis > Gene or accession: Accession number AE003722 genes CG7689 and CG6790 > Missed gene > Comments: I work on the fruitless gene and have cloned this gene > from several species. I have been examining the genome sequence > in comparison with the known cDNAs for D. melanogaster and > the known genome structure for D. heteroneura and D. silvestris. > (Both in Genbank af051662-af51670 and in press) > > The structure given in AE003722 is mostly OK except for the > 3'terminal exon and the 5' male specific peptide and exons. > > I have given below a detailed annotation based upon the > published D. melanogaster sequence data. > Coordinates are from AE003722 > complimentary strand. > > Accession number AF039231 is male specific fru (Ryner et al cell > 1996) > > Exons: > > 159917..159742 > 129972..129681 > (note start codon for male peptide 129961..129959) > 50339..50192 > 50119..49919 > 49611..48784 > 47367..47113 > 45513..45381 > 31849..31326 > (note stop codon 31828..31826) > > (note this is gene CG6790 fused to CG7689) > > Accession number U72492 is female fru sequence (Ryner et al > cell 1996) > > exons: > 159917..159742 > 129972..128080 > 50339..50192 > (note female start codon 50317..50315) > rest as for male seq above. > > Accession number D84437 female fru (Ito et al. 1997 > PNAS) > > exons: > 50339..50192 > (note start codon 50317..50315) > 50119..49919 > 49611..48784 > 47367..47113 > 45513..45381 > 41715..40694 > (note stop codon 40696..40694) > (note that the sequence D84437 hReferer: > Dr Terence Davis Department of Pathology University of Wales College of Medicine > Dear Terry, > > thanks for the e-mail with the extra information about the various fru > splice forms. I will include it with your original error report as a > personal communication to FlyBase and it will be used by the molecular > curators at FlyBase to correct the annotation for fru so that all the > correct splice forms are shown. It will be some time before the gene > structure is corrected, as we are working through the genome region by > region systematically to refine all of the annotations. Thanks again > for sending this information, > > Gillian Please also note that I sent a correction for the gene CG7688. This is actually one of the terminal ends of the fru gene (Ryner et al sequence) and is only a single exon (bases 31849..31326) in my previous message. I will try to get permission to annotate the other splice variants as there are several more (these are as yet unpublished and are not my data). Terry Dr Terence Davis Department of Pathology University of Wales College of Medicine
