Constitutive exon

[VG]

Hi Everyone,

I am trying to get a list of all the constitutive exon's coordinates in human genome(hg19). How can I get that information from UCSC?

Thanks

Regards

Varun

[Christopher Lee]

Hi Varun,

Thank you for your question about constitutive exon coordinates.

We have recently released a video to our YouTube channel on exactly this topic:
https://www.youtube.com/watch?v=6JoUqM1iKxQ

In summary:
1. Navigate to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables)
2. Select your assembly of interest
3. For the "group", "track" and "table" drop-downs, select "Genes and Genes Predictions", "UCSC Genes", and "knownGene"
4. In the "output format" drop-down, select "BED - browser extensible data"
5. Click "Get Output"
6. In the "Create one BED record per" section, select "Exons plus"
7. Click get BED

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any
further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address
are archived on a publicly-accessible forum. If your question includes sensitive data, you
may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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[VG]

Hi Christopher,

I did the same thing but then I guess I wrote a script to remove all those exon's which are repeating themselves, because each gene can have more than 1 transcript. Right?

Regards

Varun

[Luvina Guruvadoo]

Hello Varun,

Yes, each gene may have more than one transcript.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

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Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

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