[Feedback] Site Feedback: Gene Annotation

[Marcela K. Monaco]

Hola Omar,

I am so sorry that your query fell trough the cracks...

Gramene displays AraPort11 <https://www.araport.org/data/araport11> gene
annotations (see
http://ensembl.gramene.org/Arabidopsis_thaliana/Info/Annotation/#assembly),
which in the case of your gene looks almost identical to the one for TAIR10:

https://www.arabidopsis.org/servlets/TairObject?id=30613&type=locus

TAIR would probably have the best curated genes, if you wish to contact
them directly.

As far as the phylogeny, the gene is found to be among a transmembrane
family of proteins known as Cornichon (see protein domains summary here:
http://ensembl.gramene.org/Arabidopsis_thaliana/Transcript/ProteinSummary?db=core;g=AT1G12340;r=1:4197396-4198310;t=AT1G12340.1).


It closely matches grape and brachy peptides, and a predicted peptide in A.
lyrata with >90% protein identity:

http://ensembl.gramene.org/Arabidopsis_thaliana/Gene/Compara_Ortholog/Alignment?db=core;g=AT1G12340;g1=VIT_02s0025g05160;hom_id=68752272;r=1:4197396-4198310;t=AT1G12340.1
http://ensembl.gramene.org/Arabidopsis_thaliana/Gene/Compara_Ortholog/Alignment?db=core;g=AT1G12340;g1=Bo8g064800;hom_id=68608610;r=1:4197396-4198310;t=AT1G12340.1
http://ensembl.gramene.org/Arabidopsis_thaliana/Gene/Compara_Ortholog/Alignment?db=core;g=AT1G12340;g1=scaffold_101356.1;hom_id=68606680;r=1:4197396-4198310;t=AT1G12340.1

Let us know if you have further questions or contact TAIR (Phoenix
Bioinformatics) to suggest changes in the existing gene annotation.

Hope this helps!  :)

Marcela









On Wed, Aug 15, 2018 at 8:49 PM, feedback at gramene.org <feedback at gramene.org>
wrote:

> URL         :
> https://urldefense.proofpoint.com/v2/url?u=http-3A__webmail.ibt.unam.mx_correoweb_-3F-5Ftask-3Dmail-26-5Fframed-3D1-26-5Faction-3Dpreview-26-5Fuid-3D381651-26-5Fmbox-3DINBOX-26-5Fsafe-3D1&d=DwIBaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=hVLPv2-I8XRCe1DdWdxWGxz_NG3gbDC9wsq9SNoQLCc&s=oGPN2Q3uC6snyqzsmAA1dV2c247n3JMp9OFLghva5Sg&e=
>
> Subject     : Gene Annotation
>
> Name        : Omar Pantoja
>
> Email       : omar at ibt.unam.mx
>
> Organization: Instituto de Biotecnologia, UNAM
>
> Comments    : Hi, I would like to make a comment regarding the annotation
> of the gene At1g12340, which I thin is incorrectly annotated. I have been
> working on the phylogeny of this gene family and according to my analyses,
> the region assigned to that gene does not code for a protein. I wonder if
> you could check this. Thank you
>
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.warelab.org_bugs_view.php-3Fid-3D5753&d=DwIBaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=hVLPv2-I8XRCe1DdWdxWGxz_NG3gbDC9wsq9SNoQLCc&s=uE-1FjnX1af9wqRdY8FFjZFsmpQci4IimeNKuJt-WsE&e=
>



-- 

Marcela Karey Tello-Ruiz, PhD
Gramene Project Manager and Education, Outreach & Training Lead
Cold Spring Harbor Laboratory
One Bungtown Road, Williams #5
Cold Spring Harbor, NY 11724
Phone: 516-367-6977
Fax: 516-367-6851
E-mail: telloruiz at cshl.edu
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