From ozaki@XXXX Fri Aug 01  22:34:27  1997
Envelope-to: m.ashburner@XXXX
Delivery-date: Fri, 1 Aug 1997  22:34:27  +0100
Date: Fri, 1 Aug 1997  20:30:15  +0900
To: m.ashburner@XXXX
From: ozaki@XXXX (Koichi Ozaki)
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Subject: Re: Help FlyBase please
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Dear Professor Ashburner:
Thank you very much for your e-mail, and I would apologize to you for 
making your head confused.
In our recent paper (1997 FEBS Letters  404:65--69 ), we described the 
complete cDNA sequence of Drosophila Rab proteins, 
DRab 1,2,6,8,10,11,14, 
DRabRP3, RP4,
which we registered at DDBJ DNA databank (linking EMBL and Genebank) 
in April,1996 (except DRab10, we registered the sequence today to open
immediately).  I asked them to release these sequences, when our paper
in FEBS Lett. was published. But they did not. Today, I again asked DDBJ 
to open these sequence information, and I hope they will be released 
in a few days.   
Before the paper, we presented partial sequences of those DRabs at the 
meetings of Zoological Society of Japan (ZSJ) in 1993 and 1994. We also
presented the complete cDNA sequence of them in the 1995 meeting of ZSJ.
The following is the abstract of one of these meetings, where 'Kohno'
is the old name of 'Satoh', who changed her family name with marriage.
>An abstract by Kohno et al (1994 Zool. Sci., Tokyo Suppl. 11: 99.)
>also mentions:
>
>DRAB1,2,3,4,7,8,10,11,14
>&
>DRABR1,2,3,4
Other abstracts are as follows:
  Kono, A., Tokunaga, F. and Ozaki, K., (1993). Molecular cloning of 
  rab-family proteins from Drosophila retina. Zool. Sci., 10, supple., 119.
  Kono, A., Ozaki, K., Tokunaga, F. and Tanimura, T., (1995). Drosophila 
  Rab proteins; Determination of nucleotide sequences and gene loci, and 
  the production of their dominant negative mutants. Zool. Sci., 12,
  supple., 113.
In the above, DRab3, 4, 7, and DRabRP1, RP2 were not completely sequenced, 
when the paper in FEBS Lett. was published, and we did not register
them in a DNA databank.  However, partial sequence of DRab3 is completely
identical to that has been determined by Johnston et al.(1991, Neuron 7: 
101--109).  
The DRab genes from Hotta's Lab (DRab2 and DRab11) are the same as ours,
which were, however, independently sequenced. 
>Shetty et al., 1996, A. Conf. Dros. Res. 37: 360
>Shetty et al., 1997, A. Conf. Dros. Res. 38: 216A
>
>describe a rab6
I am sorry I do not know these reports, but I assume these may be from 
Joe O'Tousa's group. If so, above Rab6 must be identical to ours, because
we checked our sequences each other, last December.
>[Please note that, following Lindsley & Zill the Drosophila gene naming
>rules make it illegal to have D (=Drosophila) as a gene symbol prefix. All
>Drosophila genes would have this otherwise !
>
>I wonder if the time has not come to have a rational naming, after the 
>cytological position.
>eg Rab2 would become Rab42C
>Rab6 (of Satoh) Rab33B
>etc.
On the naming of Drosophila Rab gene, I do not think it good way to use
cytological position.  In Rab protein, the number following to the word 
'rab' has a significant meaning.  For example, rab1 forms very conservative
subfamily consisting of the members from yeast rab1 to human rab1.  These 
membaers have significantly different amino acid sequences from other 
subfamilies of Rab (e.g. Rab2, Rab3 ........).  Therefore, Rab protein 
named,for example, Rab42C, generally means a protein belonging to a 
Rab42 subfamily.  This would cause undesirable confusion.  I rather propose
the usage of the name 'rab1', 'rab2', 'rab3' ....... (Of course, I know 
'rab' is already used for 'rabbit', but 'rab1' et al. is usable, isn't it?)
Thank you again for your kind e-mail.  I would like to pay my sincere
respect to you for your great effort to flybase.
Sincerely yours, 
Koichi
==================================================
Koichi Ozaki, D.Sc.
Department of Biology, Graduate School of Science,
Osaka University
Toyonaka, Osaka 560, Japan
Ph & FAX : +81-6-850-5439
e-mail : ozaki@XXXX
WWW : http://www.bio.sci.osaka-u.ac.jp/~ozaki/
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