Arabidopsis genes & rice orthologues

[Fowler.JohnE at epamail.epa.gov]

Hello,

I noticed, while searching through your Gramene database, that there are a 
number of Arabidopsis genes that are apparently not present at all (eg 
At1g02790).

Does this mean that these genes do not have rice orthologs, or that they 
have not been evaluated in the Ensembl compara pipeline?


There are other Arabidopsis genes that are present, but do not have rice 
orthologues predicted - I take it that these HAVE been evaluated, but that 
either there is no rice ortholog, or it is impossible to predict the 
ortholog using the Ensembl procedure.

thank you for clearing this up.


I am also interested in more information on how far along the rice - maize 
gene orthology comparison is - I have a copy of your latest paper from 
NAR, but it was unclear to me how exactly the rice - maize comparisons 
were done.  Can you point me to any help information in the database?  I 
would be particularly interested to find out whether your database has 
information that would help define orthology between the maize genes 
represented on the U. Arizona 70-mer oligo array and rice, and possibly 
then on to Arabidopsis.

thanks!
John

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
John E. Fowler
Associate Professor, OSU Botany and Plant Pathology Dept.
On Sabbatical at the EPA Western Ecology Division, Corvallis
email:  fowler.johne at epamail.epa.gov
Phone: (541) 754-4866
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