Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

isoform IDS: dash not dot

Evelyn Camon camon at ebi.ac.uk
Wed Mar 1 06:45:32 PST 2006


btw I should have said...UniProt Isoform Ids (P00001-1, P00001-2)
and not (P00001.1, P00001.2)the latter will be used as sequence version 
numbers, revision numbers...

Evelyn

Evelyn Camon wrote:
> Hi David,
> 
> The main sequence does not always represent isoform 1 but it usually 
> does. TrEMBL records create problems for us also and so we annotate 
> isoforms only when they are Swiss-Prot records. I am ccing 
> Michele/Eleanor to confirm. At the time you look at a TrEMBL record the 
> sequence might represent a specific isoform...later it will be merged 
> with other entries and a different perhaps longer sequence might be 
> chosen as the representative sequence in the Swiss-Prot record. The 
> TrEMBL identifier might then become secondary to this new accession I am 
> not aware of a way of linking the new isoform ids to the old TrEMBL 
> accessions but it may be possible???? Michele or Eleanor can confirm. I 
> believe once an isoform ID is assigned it is stable??(Ele).
> 
> Some minutes of our discussion on the topic for your information.
> 
> Evelyn
> 
> ****************
> The information that is manually annotated to UniProtKB/Swiss-Prot 
> record represents the characterisation of all splicing variants. However 
> each splicing variant is designated a unique isoform id e.g 
> (P12345.1)and it is possible using a script to separate the sequences 
> into those that represent the individual isoforms.
> 
> Up to Novemeber 2005 GOA had no method of annotating directly to splice 
> variants and so all possible annotations were assigned to the main 
> protein accession i.e P12345. This meant that it was impossible for 
> biologists to extract the specific variant GO annotation. The ability to 
> annotate to splice variants allows GOA also to experimentally validate 
> the splicing variants as in UniProtKB they are not all experimentally 
> verified.
> 
> DECISION at GOA Meeting 7-11-2005
> 
> If you know specific variant GO annotation then annotate to the 
> variant/isoform accession(P12345-1).
> 
> If you don't know which specific variant GO annotation should apply then 
> annotate to the main entry(P12345). These are ok to generally transfer 
> to other species by ISS.
> 
> If you know specific isoform has a match in another species then can 
> transfer by ISS from isoform to isoform (wait until David updates tool)
> Notes: No need to try an summarise GO annotation to higher level terms 
> from specific variants in main entry. Eleanor made point that isoform.1 
> is not always the sequence on display in UniProtKb.
> ****************
> 
> 
> 
> 
> David Hill wrote:
> 
>> Actually, if an author is looking at a specific isoform, it is usually 
>> easy to tell which Uniprot-# it goes with by looking at the sequence. 
>> The probelm I run across is when the isoform corresponds to a Trembl 
>> record. Is that record just rolled into the generic uniprot id or does 
>> it actually become associated with the correct isoform?
>>
>> David
>>
>>>
>>>
>>> We will also accept UniProt Isoform Ids (P00001.1, P00001.2) if you 
>>> can figure out which is the correct one in the paper and its has an 
>>> id in UniProt..bit of an awkward one at the moment.
>>
>>
>>
>>
>>
>>
> 
> 


-- 
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




More information about the go-discuss mailing list