[Feedback] Site Feedback: regarding GRMZM no and Zm00001 no

[Marcela K. Monaco]

Dear Rachel,

As noted in http://ensembl.gramene.org/Zea_mays/Info/Annotation/#annotation,
we followed the new standard of Maize Genetics Nomenclature:
http://www.maizegdb.org/nomenclature#GENEMODEL to name RefGen_v4 gene
models.  Please note that the genes in RefGen_v3 with exactly the same
genomics sequences were linked (projected on) to the RefGen_v4 annotations
(in a separate genome browser track).

MaizeGDB will eventually also move to the newest v4 coordinate system.

<http://www.warelab.org/bugs/view.php?id=5468>Hope this helps!

Marcela



On Fri, Sep 16, 2016 at 7:56 PM, feedback at gramene.org <feedback at gramene.org>
wrote:

> URL         :
>
> Subject     : Site Feedback: regarding GRMZM no and Zm00001 no
>
> Name        : Rachel Wang
>
> Email       : rwang at gate.sinica.edu.tw
>
> Organization: Academia Sinica
>
> Comments    :
>
> Hi
> We usually use and see gene model (in papers) as GRMZM.... numbers.  Why
> the new genome assembly uses different nomenclature as Zm00001...
>
> What are the difference? one from MaizeGDB and the other from Gramene?  Do
> they exactly correspond? where we can get the corresponding table?  which
> one we should use for analyses, for example RNAseq dataset?
> Thank you so much.
>
>
> http://www.warelab.org/bugs/view.php?id=5468
>
>
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-- 

Marcela Karey Tello-Ruiz, PhD
Gramene Project Manager
Cold Spring Harbor Laboratory
One Bungtown Road, Williams #5
Cold Spring Harbor, NY 11724
Phone: 516-367-8808
Fax: 516-367-6851
E-mail: telloruiz at cshl.edu
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