Hello Drashti Patel,
A number of our gene prediction tracks include exon start and stop sites
and for any track of interest you can retrieve tabular data using our
Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables). For example to
retrieve exon start and stop sites from the UCSC genes track go to the
Table Browser and select:
group: Genes and Gene Prediction Tracks
track: UCSC Genes
table: knownGene
output format: "selected fields from primary and related tables"
Once you click on "get output" this will take you to a menu where you
can specify which fields you want to retrieve (in this case you can
select: exonCount, exonStarts, and exonEnds).
Note that if you click on "define regions" you can also input up to 1000
genomic regions of interest to refine your results.
Depending on what sort of splicing data you are interested in you may
also want to look at the Alt Events splicing track
(http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownAlt).
Hopefully this information is enough to get you started. 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
On 09/28/10 22:33, Drashti Patel wrote:
> Dear UCSE Genome Browser help desk,
>
> Greetings!!!
>
> We are an education and research institute working on
> Different sequencing profiles.
>
>>From our sequencing results, we are trying to identify the *splicing regions
> * for our contigs. We are using your browser for the same and we get results
> in form of the images and sequences. However, we want to point out the exact
> location for splicing for all our 5000 plus contigs. In this case, it would
> be highly cost effective if the data is somehow represented in excel file,
> i.e. contig X - splcing nucleotide no 5-9, 11-19 etc. Please provide us with
> the procedure to export the data into excel file.
>
> Thank you,
>
> Drashti Patel
>
> Research Fellow
> Department of Animal Biotechnology
> Anand Agricultural University
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