Subject: Helping FlyBase: ADRC-10357
Dear Sofia,
We are currently curating the abstracts for the upcoming 45th
(Washington DC) Annual Drosophila Research Conference, for FlyBase.
I am writing in connection with your abstract:
Identification and characterization of DSNX6, a sorting nexin that interacts
with 14-3-3.
You mention a gene symbol that is new to FlyBase, Dsnx6. 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. The CG symbols become synonyms when an
annotation is named with a more descriptive or functional name.
What does the D in the symbol stand for? Gene symbols should not be
prefixed with D for Drosophila (see nomenclature posting below) ...
should the valid gene symbol be Snx6 for 'Sorting nexin 6'?
With best wishes,
Rachel.
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Subject: Nomenclature
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Dear Colleagues,
We are writing with a suggestion about the nomenclature of Drosophila
genes.
It is now routine that a D. melanogaster gene is identified on the
basis of sequence homology with (or more rarely, functional
complementation for) a gene from another organism such as a yeast or a
vertebrate. Authors often prefix these Drosophila versions with 'D' or 'd'
for Drosophila, or 'Dm' for D. melanogaster. However in the absence of a
unifying pan-biological system of genetic nomenclature, to haphazardly
use 'D' or 'd' or 'Dm' is actually counterproductive. Think of Danio,
Dictyostelium, Daphnia magna .... there is room for confusion.
FlyBase uses a defined system of prefixes for denoting species other
than D. melanogaster. Examples are 'Dvir\' for D. virilis, 'Dsim\' for D.
simulans, etc. Examples of gene symbols are Dvir\Adh1 and Dsim\per
(see flybase/Documents/nomenclature/species-abbreviations.txt for full
listing of species abbreviations). We have not explicitly listed
melanogaster genes with the prefix 'Dmel\' since we consider that to be
implicit. However we would like to suggest that when meaning to
distinguish between a vertebrate gene and its Drosophila version that
would otherwise have the same symbol, authors prefix the symbol with
'Dmel\'. 'D', 'd', or 'Dm' ought NOT to be used as a prefix to a
D. melanogaster gene symbol \- this is a long-standing convention, having
been made explicit by Lindsley and Zimm in the 1992 edition of the Red
Book.
FlyBase
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Rachel Drysdale, Ph.D.
FlyBase (Cambridge),
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Subject: Re: Helping FlyBase: ADRC-10357
Hello,
I am very sorry for the delay and I hope that I didnt cause any problem.
Indeed the D in DSNX6 stands for Drosophila.
The CG number of the protein in the flybase is CG8282 and it appears to be
the homologue of sorting nexin 6.
Sofia Grammenoudi