[Genome] How to find out Alternative Splicing

[Anton Kratz]

Hi Archana,

thank you very much for this answer, the knownIsoforms table looks very
interesting.

I need to distinguish gene isoforms which are a result of alternative
splicing to gene isoform with are a result of another process (alternative
TSS selection, alternative promoter).

Are the isoforms in knownIsoforms all a result of alt. splicing or is this a
table listing all isoforms? (also the ones which are a result of alt.
promoter etc)?

Because I need to somehow distinguish alt. splicing isoforms from the rest.

Best regards,
Anton

P.S.: Just as a side note, I am using hg17 because of other internal data
for which I have only coordinates in respect to hg17 and which can not
easily be re-mapped to hg18



2007/6/12, Archana Thakkapallayil <archanat at soe.ucsc.edu>:
>
> Hello Anton,
>
> You could get this information using the table 'knownIsoforms',which is
> located under the 'group: Genes and Gene Prediction Tracks'; 'track:
> UCSC Genes' for the hg18 assembly. This table links together various
> transcripts of a gene into a cluster.
>
> So first, you need to find out the clusterId for your gene of interest
> by using either the 'filter' option or the 'paste/upload' list fetaure
> if you have a list of gene ids. If the genes belongs to same cluster,
> then they are the alternate transcripts of the same gene.
>
> I hope this information is helpful to you. Please let us know if you
> have further question.
>
> Regards,
>
> Archana
> UCSC Genome Bioinformatics Group
>
>
> Anton Kratz wrote:
> > Dear UCSC Team,
> >
> > I sorted a list of UCSC KnownGene IDs into groups, groups consisting of
> > genes with sequences that overlap or are included in each other.
> > Now I would like to find out for each gene in each group if it is a
> result
> > of alternative splicing or another process (alternative promoter,
> > alternative TSS selection).
> >
> > In other words, I want to find out if a gene is an alternative splice of
> > another gene or not.
> >
> > Can I get this information from the table browser?
> >
> > I wrote a script which checks for missing exons to detect alt. splicing,
> but
> > I'm not too sure if I'm doing it right and would like to counter-check
> my
> > results
> >
> > Thanks for your help,
> > Anton
> > _______________________________________________
> > Genome maillist  -  Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
> >
>
>


-- 
Dipl.-Inf. Anton Kratz

mobile phone:  +81 [0]80-309-489-78
email: anton.kratz at googlemail.com
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