Subject: Re: FlyBase Query (cy721)
Hiya Chihiro,
..
To answer your questions:
what we have called alphaPS4 does correspond approximately to CG16827
what we have called alphaPS5 does correspond approximately to CG5372
Our predicted alpha subunits are longer than these predicted ORFs at the
N-terminus
Our argument for calling them alphaPS's is that they are so similar to
alphaPS3 we predict they will also form heterodimers with betaPS (mys).
However there is no biochemical data to support that. As far as naming the
genetic loci, as I indicated in the review I suspect that scab is a complex
locus that encodes both alphaPS3 and alphaPS4, but I do not have any data
to support this yet other then their close proximity and the weak phenotype
of apparent alphaPS3 molecular nulls. We do not know of any mutants in
alphaPS5 yet. You could just keep them as CG numbers until the mutants are
found and the genes named.
>
Paxillin is currently annotated as two overlapping genes CG18576 and CG18061
We have a different prediction for the gene structure but have not done any
experiments to confirm it.
>
To make the gene encoding the Filamin at 59A, combine exons from CG13525,
CG3550 and CG11605 going 5' to 3' Again this is based on sequence gazing
rather than additional data
>Any new info you give us I'll curate as a personal communication from
>you to FlyBase, if that's O.K. with you.
>
Thats fine.
..
Dr Nick Brown
Wellcome/CRC Institute
Tennis Court Road
Cambridge CB2 1QR
England
Subject: FlyBase Query (cy721)
Hiya Nick,
..
I'm curating a review of yours \- the Dev Biol one:
Brown et al, 2000, Dev. Biol. 223(1) 1-16
I've got a couple of questions I hope you can help me with.
1.<alpha>PS4&5
==============
You talk about <alpha>PS4 and <alpha>PS5. We have in our records 2 CGs
CG16827, and CG5372, that have been assigned gene product names
'integrin, α-subunit'. What you say about the relationship between
<alpha>PS4 and scab (on page 3) suggests that PS4 is CG16827 (having
had a look on Genescene). Can you confirm this? Which leaves by a
process of elimination <alpha>PS5 being CG5372. Is this true? Or are
there other <alpha> units that FlyBase doesn't know about?
Secondly these two don't have names (other than CGs) Do they have
names and symbols yet? If not I'll call them <alpha>PS4 and <alpha>PS5
(where <alpha> is the symbol alpha) though this would be a little odd
as PS1-3 have the mutant names as their Flybase names, with the PS
names as synonyms.
2. Paxillin
==========
I can't find any gene attributed with 'Paxillin' in our records. Do you
have a CG for this? Or if you don't know can you tell me where you
found out about this and give me a reference, so I can check it out?
3. Filamin 59A
==============
You mention a second filamin (not cheerio) AT 59A. I can't find any
other genes attributed with 'Filamin' in our records. Do you have a CG
for this? Or if you don't know can you tell me where you found out
about this and give me a reference, so I can check this out as well?
Any new info you give us I'll curate as a personal communication from
you to FlyBase, if that's O.K. with you.
Finally, FYI, whilst curating your review , I noticed that you didn't
know (at the time of writing anyway) that PINCH and steamer duck are in
fact the same gene. We have that merge attributed to:
Clark and Beckerle, 2000, A. Dros. Res. Conf. 41: 646C
Stay cool, say Hi to anyone I know.
Chihiro,
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Chihiro Yamada.
FlyBase (Cambridge),
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