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Willis, J. (2007.1.3). Drosophila genes that have the R&R consensus. 
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FBrf0199281
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Personal communication to FlyBase
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Date: Wed, 3 Jan 2007  14:51:05  -0500
From: FB_HelpMail_checked@XXXX
To: flybase-help@XXXX
Subject: FB Help Mailer: 096 Personal communication
 comments:    I am in the process of compiling all of the D. melanogaster genes that have the R&R consensus indicating that they are cuticular proteins (also recognized by pfam00379 or IPR000618.  There are about 100 such genes, only 26 have been given names (i.e. LCP65A, pcp, Ccp84Ag).  Almost all of them are on a database we set up (CuticleDB), and someone from Mike Ashburner's lab has been asking for the past 2 years for us to allow her to incorporate them into some Drosophila database.  But until now, no one has checked the sequences for accuracy, and a few have been incorrectly annotated, i.e. they lack a signal peptide that is essential for secretion into the cuticle.  I have corrected such errors by hand.
I am turning to FlyBase for permission to name (designate as a Symbol) the unnamed ones CPRXXx  with XXx representing the chromosome band with a small letter indicating the order within the band.  For example, CG9079 would become CPR47Ea and CG13224 would become CPR47Eb.  
    This nomenclature combines what I have been using for Anopheles where we now have annotated, and submitted to Ensembl, over 140 genes with this consensus -- i.e. CPR1 to CPR140 with the previous convention in Drosophila using band names. Cuticle DB will use the names AgamCPR1 and DmelCPR47Ea, so there will never be confusion about names among species.  I do not plan to rename the ones that already have been named, as some of the genes have been discussed in research papers.  
    I have been asked to submit a MS for a symposium volume honoring Lynn Riddiford (R&R stands for Rebers and Riddiford Consensus)so this seemed to be a good time to compile the Drosophila cuticular proteins.  The MS will be short, but, with your permission for naming, will include a table giving Symbols and Annotation Symbols. 
    I will be pleased to talk to someone about this.
    706-542-0802.
    Thank you very much.
    Judy Willis
    P.S.  If you wonder if the consensus is sufficient to identify a protein as a cuticular protein, we have worried about this too.  We have a paper in press (Insect Biochem. Molec. Biol.)where cleaned Anopheles cuticles were trypsin digested and the extracts examined with tandem MS.  We have already confirmed about half of the putative Anopheles cuticular proteins as being authentic constituents of the cuticle. So this is the right time to compile a list of all the comparable Drosophila cuticular proteins.
 realname: Judy Willis
 reply-to: jhwillis@XXXX
 source: FB Help Mailer:
Sent from computer 128.192.13.87 
Date: Fri, 5 Jan 2007  11:43:18  +0000 (GMT)
From: "Rachel Drysdale (Genetics)" <rd120@XXXX>
Subject: Re: FB Help Mailer: 096 Personal communication
To: flybase-helpXXXX, jhwillisXXXX
Hi Judy,
your suggestion seems unproblematic in that we have no existing gene
symbols of that format.
To comply with existing nomenclature guidelines the initial letter, but
not the following two, would be capitalized, thus Cpr47Ea and Cpr47Eb
rather than CPR47Ea and CPR47Eb.
(Guidelines are at
http://www.flybase.org/static_pages/docs/nomenclature/nomenclature3.html#1.7.)
We do have a gene Cpr (Cytochrome P450 reductase, FBgn0015623), so all
would require a suffix to avoid confusion, but that is already in your
plan.
It would be sensible for you to run your table by us before the
publication to avoid any confusion e.g. some of the CGs may
have got symbols since FlyBase was last updated.
We would, with your permission, curate the table as a personal
communication from you to FlyBase, to make sure that the information
gets into FlyBase promptly.
With best regards,
Rachel.
for FlyBase.
From: "Judy Willis" <jhwillis@XXXX>
To: "Rachel Drysdale (Genetics)" <rd120@XXXX>
Date: Sun, 07 Jan 2007  11:07:39  -0500
Rachel:
Attached are two files.  The Excell sheet has all of the Drosophila 
genes that have the R&R consensus indicating that they code for 
cuticular proteins in this family.
The Word file has details on the genes whose sequences I modified 
as well as the genomic region that shows that there are two identical 
CG18777 genes.  But my genomic region came from Ensembl 
annotation 4.1 I believe.  Is the duplicate real?  
.
.
.
The sequences marked with red stars are associated with another 
gene.  CG3440 was already known to reside in the intron of a 
constitutively expressed enzyme.  But the two others have a totally 
different gene in their first exons.  I learned this from FlyBase.
.
.
.
One you have approved these names, I will see that they get 
incorporated into CuticleDB.  
Many thanks.
Judy Willis 
DOI
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File date: 2007.1.16 ; File size: 378880 ; File format: xls ; File name: Willis.2007.1.16.xls
File date: 2007.1.17 ; File size: 178688 ; File format: doc ; File name: Willis.2007.1.17.doc
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