[Genome] The count of all annotated exons for a UCSC known gene ......

[Rileen]

Hi Ann,
             Thanks. I'm sorry, my question was ambiguous,  I already knew
how to do what you said. I wanted the number of exons per loci/"canonical" gene,
which is why I said

"By that I mean all exons that appear in at least one transcript - a sort of
"logical OR" of all exons in all transcripts."

which wasn't very clear, I admit.

To clarify - let's take an example, say the gene EDA. There are 8 Refseqs,
with varying numbers of exons - between 1 and 3. However, when you look
at them together, there 5 exons in this locus, each of which appears in at least
one Refgene. These are not exons which differ from each other by one splice site
etc., these are distinct, non-overlapping exons.

It is this number - 5 in this example - that I'm after.

Take care,
                   Yours,
                                  Rileen


On 01/06/07, Ann Zweig <ann at soe.ucsc.edu> wrote:
> Hello Rileen,
>
>         You can get the information you want by using the Table Browser tool
> ('Tables' in the blue navigation bar).  Configure it like so:
>
> clade:  Vertebrate
> genome: Human
> assembly: Mar 2006
> group:  Genes & Gene Prediction tracks
> track:  UCSC Genes
> table:  knownGene
> region: genome
> output format: selected fields from primary and related tables
>
>         Press "get output" button.
>
> Then, on the next page choose:
> name
> exonCount
> (and any other fields you would like)
>
>         Press "get output" button to see your list.
>
>         Do the same for the refGene table to get the exon counts for all of the
> Ref Seq Genes.
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
> Please feel free to search the Genome mailing list archives by visiting
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>
>
>
> Rileen Sinha wrote:
> > Hi,
> >        Is there some quick/convenient way of obtaining a list of the number
> > of annotated exons in each given gene in the UCSC known gene collection?
> >
> > By that I mean all exons that appear in at least one transcript - a sort of
> > "logical OR" of all exons in all transcripts.
> >
> > Is there also a corresponding solution for RefSeq genes?
> >
> > Thanks!
> >
> > Take care,
> >                    Yours,
> >                                   Rileen
> >
>