Subject: Re: BDGP gene annotation
A word document is attached to this message explaining my arguments for the
annotation of 10 Drosophila genes as members of the syntaxin family involved
in vesicle fusion.
Thank you.
Ross McLennan
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Ross McLennan
Division of Molecular Genetics
Anderson College
University of Glasgow
Glasgow
G11 6NU
Scotland
Analysis of the completed Drosophila melanogaster genome sequence has
revealed that there are putatively 10 syntaxin genes in this species.
Several of these genes have already been studied in great detail, in
particular the Drosophila homologue of syntaxin 1A. However, the vast
majority of this family of genes has not been ananlysed in any great
detail.
I suggest the following nomenclature for the members of the Drosophila
syntaxin gene family (see table below) based on the homology of the
predicted products of the Drosophila genes to proteins which have
previously been characterised in other species (although the same
phylogenies are seen at the nucleotide level). The closest homolgues
of each of the Drosophila syntaxin gene products (using the BLASTp
2.1.1 programme at http://www.ncbi.nlm.nih.gov/blast/blast.cgi) were
found to be mammalian syntaxin proteins (see attached table and
phylogenetic tree) and I suggest that the Drosophila genes be named
corresponding to their closest mammalian orthologue.
In particular, I question the naming of Drosophila Syx7 and Syx6/10 as
this does not agree with the nomenclature system described above. In
reality the closest homologue of CG7736 (currently named syx7) is human
syntaxin6, whist the closest homologue of CG5081 (currently named
Syx6/10) is rat syntaxin 7.
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Drosophila gene | Current Drosophila | Closest orthologue | Proposed |
accession number | gene name | (species) | Drosophila |
| (Flybase 21.05.2001) | | gene name |
\----------------------------------------------------------------------------
CG5448 | Syx1A | Syntaxin 1A (rat) | DmSyx1A |
\----------------------------------------------------------------------------
CG2715 |  EG:95B7.1  | Syntaxin 4 (mouse) | DmSyx4 |
\----------------------------------------------------------------------------
CG4214 | Sed5 | Syntaxin 5 (human) | DmSyx5 |
\----------------------------------------------------------------------------
CG7736 | Syx7 | Syntaxin 6 (human) | DmSyx6 |
\----------------------------------------------------------------------------
CG5081 | Syx6/10 | Syntaxin 7 (rat) | DmSyx7 |
\----------------------------------------------------------------------------
CG4109 | \- | Syntaxin 8 (human) | DmSyx8 |
\----------------------------------------------------------------------------
CG11278 | \- | Syntaxin 13 (rat) | DmSyx13 |
\----------------------------------------------------------------------------
CG1467 | Syx16 | Syntaxin 16 (human) | DmSyx16 |
\----------------------------------------------------------------------------
CG7452 | \- | Syntaxin 17 (rat) | DmSyx17 |
\----------------------------------------------------------------------------
CG13626 | \- | Syntaxin 18 (human) | DmSyx18 |
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<up>FlyBase curator comment: copy of phylogenetic tree is archived</up>