[Feedback] [Website feedback] Is Gramene in charge of the rice genome annotation?

[Marcela K. Monaco]

Hi Qunfeng,

Thanks for the generous compliments :)
As I understand, traditionally there have been 2 parallel assemblies for *Oryza
sativa japonica*, one by MSU (see http://rice.plantbiology.msu.edu/) and
one by RAP-DB (IRGSP, see http://rapdb.dna.affrc.go.jp/).
Gramene released the first merged version of both of these assemblies which
was generated by scientists of both of the above entities, and adopted
primarily the gene annotations of the IRGSP group.  However, we also
provide the MSU7 gene models in a separate browser track.  For more details
on this, see the annotation section in
http://ensembl.gramene.org/Oryza_sativa/Info/Annotation/#assembly

Marcela

PS: RAP-DB provide a gene conversion table at http://rapdb
.dna.affrc.go.jp/download/archive/RAP-MSU.txt.gz


==
Marcela Karey Monaco, PhD
Gramene Project Coordinator
Cold Spring Harbor Laboratory
One Bungtown Road, Williams #5
Cold Spring Harbor, NY 11724
Phone: 516-367-8808
Fax: 516-367-6851


On Tue, Mar 4, 2014 at 5:02 PM, qunfeng.dong at unt.edu
<qunfeng.dong at unt.edu>wrote:

> Qunfeng Dong (qunfeng.dong at unt.edu) sent a message using the contact form
> at
> http://www.gramene.org/contact.
>
> Dear Gramene team:
>
> I am always impressed by your excellent work.  Please do pardon my
> ignorance
> question, since it is difficult to track who is doing what these days.  My
> question is whether Gramene is charge of the rice genome annotations?  I
> know
> that Gramene is doing maize for sure, but can I trust that the rice genome
> annotation downloaded from Gramene is the latest official release for the
> community? Or Gramene just "imported" the rice annotation from somebody
> else?
>
> Thanks
>
> Qunfeng
>
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