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isoform IDS: dash not dot
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 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.
> 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
> 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?
>>> 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.
Senior Scientific Curator
European Bioinformatics Institute
E-mail: camon at ebi.ac.uk
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