GO Help query (from website)

[Evelyn Camon]

Hi,

I'm looking up AK110615 in EMBL via SRS...it has no cDNA annotated 
however SRS links this entry to AP protein ID BAF27994.1 which brings 
you to AP008217.1
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+5YN2E1UScjH+-e+[EMBLCDS:'BAF27994']+-qnum+1+-enum+3
click on GOA cross reference
http://www.ebi.ac.uk/ego/QuickGO?query=Q53LC7&mode=search&entry=&querytype=protein&showcontext=false
There are two InterPro2GO IEA assignments, zinc ion binding and 
oxidoreductase activity ....

cheers,

Evelyn

Pankaj Jaiswal wrote:
> Hi Eurie,
> 
> Thanks for the help. I have replied the the person off the GO list with 
> some more tips on querying the same at Gramene database.
> 
> BTW one aspect that I find from this query is that, more and more people 
> want to know GO annotations using their source sequences from ESTs, GSS, 
> cDNAs, UniGenes etc. Using the BLAST is a very effective way of doing 
> this, but certainly not a good practice to ask everyone to perform 
> BLAST. The solution, I see lies in mapping the  ESTs, GSS, cDNAs, 
> UniGenes to the object we have in our Association files. This will give 
> them a straight forward answer. I also agree that it is beyond the scope 
> of GO, but is there a way the source dbs can provide the data (I am sure 
> many of the have this kind of mapping), that can be used by GO to 
> facilitate this query.
> 
> Pankaj
> 
> Eurie Hong wrote:
> 
>> Hello,
>>
>> It appears that the cDNA clone with the GenBank accession AK110615 is 
>> currently not annotated.   You can BLAST the sequence of AK110615 
>> against the sequences available in AmiGO to identify if the gene that 
>> encodes this cDNA has been annotated:
>>
>> http://amigo.geneontology.org/cgi-bin/gost/gost.cgi
>>
>> A BLASTX using the cDNA sequence hits the Oryza sativa (japonica 
>> cultivar-group) gene Os11g0255500:
>>
>> http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?search_constraint=gp&view=details&session_id=3361b1172551729&gp=Q53LC7 
>>
>>
>> I am cc'ing the staff at Gramene (http://www.gramene.org/) who provide 
>> GO annotations for Oryza sativa (japonica cultivar-group) so that they 
>> can answer any further questions you might have.
>>
>> Cheers,
>> Eurie
>>
>> *******************************************
>> Eurie L. Hong, Ph.D.
>> Scientific Curator
>> Saccharomyces Genome Database: http://www.yeastgenome.org/
>> Gene Ontology: http://www.geneontology.org/
>> *******************************************
>>
>>
>> On Feb 25, 2007, at 5:33 AM, noreply at genome.stanford.edu wrote:
>>
>>> contactName: psrao
>>> contactEmail: psrao at ccmb.res.in
>>> contactText: Please ley me know how can I get GO terms(Go:7275) from 
>>> NCBI Gene Accession numbers(AK110615)
>>>
>>
>>
> 


-- 
Evelyn Camon
GOA Coordinator
Senior Scientific Curator
European Bioinformatics Institute
Tel:01223-494465
Fax:01223-494468
E-mail: camon at ebi.ac.uk
URL: http://www.ebi.ac.uk/goa