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'with' field contents for IPI annotations
camon at ebi.ac.uk
Wed Mar 1 06:40:01 PST 2006
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
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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