Date: Wed, 28 Feb 2007  15:33:24  +0900
To: rd120@XXXX
From: Yuji Kageyama <kageyama@XXXX>
Subject: Re: Helping FlyBase: ADRC-60426
Cc: s-inagakXXXX, ta-kondoXXXX
Dear Rachel,
Thank you for e-mail.
Regarding annotations for MRE genes, we need your help to add
some description to Flybase.
MRE31 and MRE32 are annotated as CR30009 and CR32730
in Flybase (please cite Inagaki et al. [Genes. Cells, 2005, 10 (12),
1163-1173] as a reference).  Since MRE are arbitrary name and
we do not have any data on their function (we only published their
expression patterns during embryogenesis), it may be better to
handle MRE31 and MRE32 as synonyms of these CR entries.
MRE3 is also annotated as  pncr013:4 , based on Tupy et al.
[Proc Natl Acad Sci U S A, 2005, 102(15), 5495-5500].  Since
they published 6 mo. earlier than we, MRE3 should be a synonym of
 pncr013:4 .
For MRE16 and other MREs, EST sequences have already been
registered in GenBank.  Therefore, instead of sequence deposition
to GenBank, we would like to register them as new entries into
Flybase.  Would you tell us how to add new entries to Flybase?
For example, as shown below, if we submit a gene name,
corresponding EST clone name and the reference, is it enough to
register new genes?
MRE1	GH22170
MRE2	GH23165
MRE3/ pncr013:4 	GM01028
MRE4	GM01267
MRE5	GM03914
MRE6	GM04458
MRE7	GM05777
MRE8	GM07040
MRE9	GM07660
MRE10	GM08676
MRE11	GM09444
MRE12	GM09534
MRE13	GM09828
MRE14	GM10545
MRE15	GM13095
MRE16	GM31309
MRE17	HL01663
MRE18	HL05775
MRE19	LD03248
MRE20	LD07701
MRE21	LD11130
MRE22	LD33458
MRE23	RE65620
MRE24	RH66459
MRE25	RH66770
MRE26	SD04448
MRE27/CR31972	GH10270
MRE28/CR32646	HL02010
MRE29/CR33327/ pncr001:3R 	LD11162
MRE30/CR32028	LD13080
MRE31/CR30009	RE30084
MRE32/CR32730	RE54930
MRE33/CR31808	RE70695
* Modfied from Inagaki et al., Genes. Cells, 2005, 10 (12),
   1163-1173, Table 2)
Again, since we do not have any data for their function, it may be
better to define these genes as CR entries with MRE numbers,
similar to MRE31/32.
We know our requests are bit complicated and troublesome
but we believe these info are helpful for fly people (at least,
much better than nothing).  And, If you know more appropriate
person to handle these stuffs, please let me know.
Regards,
--
Yuji Kageyama, PhD  <kageyama@XXXX>
PREST Investigator
Japan Science and Technology Agency
4-1-8 Honcho
Kawaguchi, Saitama 332-0012
Assistant Professor
Graduate School of Biological Sciences
Nara Institute of Science and Technology
8916-5 Takayama
Ikoma, Nara 630-0192, Japan
phone: +81-743-72-5552
fax: +81-743-72-5559
>From: "Rachel Drysdale (Genetics)" <rd120@XXXX>
>Date: 2007G/27n26F|  5:56:46:JST 
>To: s-inagak@XXXX
>Subject: Helping FlyBase: ADRC-60426
>
>Dear Sachi,
>
>We are currently curating the abstracts for the upcoming 48th
>(Philadelphia) Annual Drosophila Research Conference, for FlyBase.
>I am writing in connection with your abstract:
>Characterization and functional analysis of mRNA-like non-coding RNAs in
>Drosophila.
>
>The abstracts mention four interesting genes new to FlyBase - MRE3,
>MRE16, MRE31 and MRE32 - which I will enter into FlyBase with those
>symbols and the full names mRNA-like ncRNA in embryogenesis 3, 16, 31
>and 32 respectively.
>
>I am presuming that these genes are not yet described in terms of the
>gene models.  If you have not already done so I would urge you to
>submit the sequences of these genes to DDBJ/EMBL/GenBank, so that they
>will eventually be incorporated into the genome annotation.
>
>Best regards,
>
>Rachel.
>
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>Rachel Drysdale.
>
>FlyBase (Cambridge),
>Department of Genetics,
>University of Cambridge,
>Downing Street,                       email: rd120@XXXX
>Cambridge,  CB2 3EH,                  Ph : 01223-333963
>UK.                                   FAX: 01223-333992
>
>http://flybase.org/
>http://www.gen.cam.ac.uk/Research/flybase.htm
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~