[Gramene] Converting Rice locus IDs to Swissprot ACs

[Pankaj Jaiswal]

Dear Sara

This can be done easily at Gramene Database site, whcih is the source 
for the O. sativa GO annotations in Gene Ontology website. Here is what 
you need  to follow.

Use the GrameneMart query:

-visit http://www.gramene.org
-from the search menu select 'All-GrameneMart'
-once on the GrameneMart page select choose the database 'gramene# 
(Gramene 27)'
-choose dataset 'oryza sativa japonica genes (TIGR5)'
-hit the 'count' button in the navigation bar in black color
-then click on 'attributes' link in the grey colored column
-open 'EXTERNAL' menu and check the desired info e.g. UniProt/SPTrembl ID
-after selecting all the desired fields click the 'result' button in the 
navigation bar in black color
-it will give you a results table.
-select your export format to get the complete results.

Let us know if you need more help. In the meantime we will try to fix 
the GO association files to get the corresponding locus IDs  in it.

Pankaj



Sara Movahedi wrote:
> Dear,
> I am looking for a conversion table that links some gene_IDs mentioned 
> in the GO association file (http://geneontology.org ; Downloads ; 
> Annotations ; Oryza sativa) to locus names provided in the TIGR annotation.
> 
> _for example we have:_
> 
>     /*gene_association.gramene_oryza*
>     CVS Version: Revision: 1.49
>     GOC Validation Date: 05/03/2008
>     Submission Date: 9/19/2007/
> 
> /GR_protein    P35683    *Os06g0701100, LOC_Os06g48750    *    
> GO:0003676    GR_REF:8030    RCA    
> InterPro:IPR001650|InterPro:IPR000629    F    Eukaryotic initiation 
> factor 4A    eIF-4A|eIF4A    protein    taxon:4530    20060831    GR
> GR_protein    Q9AVL8    *OsRPA70a*        GO:0003676    GR_REF:8030    
> RCA    InterPro:IPR004365    F    Replication protein A 70kDa        
> protein    taxon:4530    20060831    GR /
> 
> So how can I find the LOC_ID corresponding to "*OsRPA70a*" ?
> Is there any conversion table available?
> 
> Thanks,
> Sara
> 
> -- 
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> Sara Movahedi 
> 
> Tel:+32 (0)9 331 38 22                        fax:+32 (0)9 3313809
> VIB Department of Plant Systems Biology, Ghent University
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