Download 5'UTR and 3'UTR coordinates for homo sapiens genes (hg19)

[Brian Smith]

Hi,

I wanted to download the 5'UTR and 3'UTR coordinates for all genes (homo sapiens-hg19), for all isoforms of the genes (hgnc_symbol as identifier).

How should I go about doing this?

many thanks!

[Luvina Guruvadoo]

Hello Brian,

You can do this using the Table Browser.  If you are unfamiliar with the Table Browser, please see the User's Guide here:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html. The best thing to do would be to select BED output which allows you to query coordinates for 5' UTR, 3' UTR, exons, introns, etc, but it doesn't allow you to select multiple items per query, so you will have to perform multiple queries.  Perform the following steps:

1.  Navigate to http://genome.ucsc.edu/cgi-bin/hgTables.

2.  Select the following options:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Predictions
Track: UCSC Genes or RefSeq Genes
Output format: BED - browser extensible data

3.  On the "region" line, select "genome" for the entire genome.

4.  Click the "get output" button .

5.  The following screen allows you to specify whether you want 5' UTR regions, 3' UTR regions, etc.  Choose your desired options and click the "get BED" button.

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.

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Luvina Guruvadoo
UCSC Genome Bioinformatics Group

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