Hello Gue Su,
I will try to answer your questions in turn:
1. We do not assign the protein ID "Q80TY4" you will have to consult
uniprot for their literature on criteria for assigning different
identifiers. We do generate the UCSC genes identifiers. You will notice
that each of the isoforms has a different UCSC genes identifiers (i.e.
uc007afy.1 and uc007afz.1).
2. To convert from a UCSC genes identifier (i.e. uc007afy.1) we have a
number of tables that list UCSC genes identifiers along with other
identifiers. To see some of these tables go to the table browser and select:
group: Genes and Gene Prediction Tracks
track: UCSC Genes
table: kgXref
kgXref contains a number of other popular identifiers but you may need
to use one of the other "knownTo..." tables depending which type of
identifier you are trying to convert.
Hopefully this information was helpful and answers your question. If you
have further questions or require clarification feel free to contact the
mailing list at [email protected].
Regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Gue Su Chang wrote:
> Dear UCSC browser;
>
> Hello, this is Gue-Su Chang. I am a graduate student at Penn State and I am
> working with Dr. Pugh in Wartik. May I ask several questions?
>
> Recently, I am using the UCSC Table browser to curate known genes from the
> mouse genome. I chose "UCSC Genes" track and the "knownGene" table. The
> following lines are a result example I now have. I would like to ask a
> question about them.
>
> -----------------------------------
> uc007afy.1 chr1 + 6720131 6851021 6758978 6848681 24
> 6720131,6727660,6742376,6743074,6758978,6761024,6785466,6792400,6797623,6799
> 357,6800654,6807683,6810014,6817856,6823643,6832219,6832953,6834201,6834371,
> 6835651,6838987,6845449,6847380,6848540,
> 6720321,6727738,6742449,6743117,6759033,6761055,6785657,6793186,6797758,6799
> 448,6800759,6807877,6810226,6818102,6823759,6832282,6833022,6834264,6834452,
> 6835873,6839076,6845553,6847524,6851021, Q80TY4 uc007afy.1
>
> uc007afz.1 chr1 + 6720131 6851021 6758978 6848681 23
> 6720131,6742376,6743074,6758978,6761024,6785466,6792400,6797623,6799357,6800
> 654,6807683,6810014,6817856,6823643,6832219,6832953,6834201,6834371,6835651,
> 6838987,6845449,6847380,6848540,
> 6720321,6742449,6743117,6759033,6761055,6785657,6793186,6797758,6799448,6800
> 759,6807877,6810226,6818102,6823759,6832282,6833022,6834264,6834452,6835873,
> 6839076,6845553,6847524,6851021, Q80TY4 uc007afz.1
> -----------------------------------
>
> Two questions are here, and it will be greatly appreciated if you could
> provide answers for me.
>
> (1) They are two isoforms of a protein which are processed differently by
> alternative splicing. Why do they have the same protein ID, like "Q80TY4"?
> They clearly consist of different exons.
>
> (2) I saw their ID names are "uc007afy.1" and "uc007afz.1". I would like to
> have their common names which are more familar with people. How can I
> retrieve this kind of information from UCSC?
>
> I am looking forward to your kind help.
>
> Best regards,
> Gue Su
>
>
> ----------------------------------------------------------------------
> Chang, Gue Su (E-mail: [email protected])
>
> Graduate student
> IBIOS Graduate Program Option in Bioinformatics and Genomics
> http://www.huck.psu.edu/IBIOS/
>
> PI: Dr. Frank B. Pugh
> Center for Eukaryotic Gene Regulation
> 331 South Frear
> Pennsylvania State University
> University Park PA, 16802
>
> http://www.bmb.psu.edu/faculty/pugh/pugh.html
> ----------------------------------------------------------------------
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
