[Feedback] Site Feedback: wrongly annotated?

[Subbaiah Chalivendra]

Hi,

Since there is an active ticket, I may as well point out a minor
discrepancy with sucrose synthase nomenclature on the MaizeSequence.org
site. To be consistent with the recent literature (Chourey, PS. 2006. MNL.
80:11
http://mnl.maizegdb.org/mnl/80/35chourey.htm) and the MaizeGDB, these are
the correct annotations for the following gene models:

GRMZM2G152908 = ZmSUS1 (and *not* Zm"SUS2")
GRMZM2G318780 = ZmSUS2 (and *not* just "sucrose synthase").

I appreciate if this can be rectified to avoid confusion.

thanks very much,
Subbaiah Chalivendra


On Wed, Aug 13, 2014 at 8:55 PM, Subbaiah Chalivendra <
subbaiahchalivendra at gmail.com> wrote:

> Thank you very much for your reply. Sorry for the false alarm. I find now
> that it is a sucrose synthase. I made a mistake when I entered the
> coordinates.You may please cancel the ticket.
>
> Subbaiah
>
>
> On Wed, Aug 13, 2014 at 4:55 PM, <feedback at gramene.org> wrote:
>
>> URL         : http://tools.gramene.org/search?query=GRMZM2G152908
>>
>> Subject     : Site Feedback: wrongly annotated?
>>
>> Name        : Subbaiah Chalivendra
>>
>> Email       : schalivendra at lsu.edu
>>
>> Organization: none
>>
>> Comments    :
>>
>> Hi,
>>
>> I am trying to retrieve coding and upstream sequences for maize sucrose
>> synthase gene ZmSUS1 (gene model: GRMZM2G152908). It is mapped to chr9:
>> 122219990-122227063. When I downloaded the sequence and did a blastx search
>> on NCBI, I am getting alignment with putative transposase or transposon
>> protein sequences rather than sucrose synthase. I appreciate to know
>> whether the region has been mis-annotated. I also want to know how I can
>> obtain the correct SUS1 genomic sequence complete with its upstream
>> regulatory sequence.
>>
>> thanks very much,
>> Subbaiah
>>
>> http://www.warelab.org/bugs/view.php?id=5004
>>
>>
>
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