On 27 Jul 2011, at Wed27 Jul 12:58 , Wieczorek, Helmut wrote: Thank you very much. Although “Slc45-2” will be an unofficial synonym, it may be advantageous for the field. Helmut -- Dear Helmut, Yes, that's fine. I won't be able to give CG40467 the official symbol of 'Slc45-2' based on this correspondence - we only rename genes based on peer-reviewed, published papers (unless there are mitigating circumstances, as with CG4484) - but I will add 'Slc45-2' as an unofficial synonym of CG40467 if you think that would be helpful. Steven. -- On 27 Jul 2011, at Wed27 Jul 12:09 , Wieczorek, Helmut wrote: Dear Steven, actually I would prefer to name it “Slc45-1”. Would you accept this? Helmut -- Dear Helmut, I think there are two options : i) we give the Dmel genes different suffixes (such as 'Slc45a' and 'Slc45b', or 'Slc45-1' and 'Slc45-2') or ii) we steer clear of naming the Dmel genes based on orthology and name them based on their wild type function or mutant phenotype - just like you originally did in your paper. However, as I said, we can't use 'Scrt' because of a pre-existing gene with this symbol. Some other contraction based on the fullname of 'Sucrose transporter' would be perfectly acceptable. I suggested 'Suct' in my earlier email, but there are several other variations. Steven. -- On 27 Jul 2011, at Wed27 Jul 11:13 , Wieczorek, Helmut wrote: Dear Steven, in principle this would be okay. However, there appears to be another gene in the Drosophila genome, CG40467, with high similarity to the mammalian SLC45 family. How would we name this gene? Best, Helmut -- Dear Helmut, Thanks for your reply. FlyBase gene symbols never include 'D' or 'Dmel' or variants thereof to indicate the species - this can be ambiguous and is redundant with the fact that all genes in FlyBase are associated with a particular species anyway. (See section 2.2.7 of our nomenclature doc here: http://flybase.org/static_pages/docs/nomenclature/nomenclature3.html#2.2. ) So, I'm afraid we can't use "Slc45dmel" in this case. Based on previous similar cases, I suggest we use 'Slc45' as the official FlyBase gene symbol, and 'Slc45 ortholog' as the official gene fullname. As I say, the species of this gene is encoded by associations in the database (and the gene will actually appear as 'Dmel\Slc45' in the FlyBase Gene Report), while the orthology to mammalian SLC45 is explicitly noted in the 'Orthologs' section of the Gene Report page. Does this sound reasonable? Steven. -- On 27 Jul 2011, at Wed27 Jul 08:11 , Wieczorek, Helmut wrote: Dear Steven, if possible, I would like to have the SCRT named “Slc45dmel” in order to indicate its origin (dmel) and its relation with the SLC45 family. Would that be ok? Best regards, Helmut Dr. Helmut Wieczorek Professor of Animal Physiology Department of Biology/Chemistry -- On 12 Jul 2011, at Tue12 Jul 10:15 , Steven Marygold wrote: Dear Helmut Wieczorek, I have just finished curating your recent J. Cell Sci. paper "Identification of an animal sucrose transporter" in which you give the symbol 'scrt' to the previously uncharacterized gene CG4484. Unfortunately, I cannot change the FlyBase symbol of 'CG4484' to 'scrt' because there is already a gene in FlyBase with this symbol: http://flybase.org/reports/FBgn0004880.html Given your characterization of this gene, I'd like to give it a more meaningful symbol than 'CG4484' and I'd prefer to use a symbol that you're happy with. Since we can't use 'scrt', do you have any other suggestions? Maybe 'Suct' (for Sucrose transporter)? Or 'Slc45' (to reflect the orthology with mammalian SLC45 genes)? (Whatever the official FlyBase symbol, the symbol used in your paper ('scrt') will still be added to the FlyBase Gene Report as a synonym that FlyBase users will see and will be able to search with.) Thanks for your time, Steven Marygold. FlyBase
