5' and 3' UTR coordinates

[Brian Smith]

Hi,

For all refseq genes (Humans), I wanted to download data that should contain:

1. Gene start and end positions
2. Exon start and end positions
3. 5' and 3' UTR start and end positions.

I tried by using track as 'refseq Genes', and selected 'all fields from selected table', but didn't get all the data. Is there something else that I need to do? Also, is there a way that I can also have the HGNC gene ids/names in this file/download?

many thanks!

[Brooke Rhead]

Hi Brian,

If you selected the "refGene" table in the Table Browser, and also chose
to get "all fields from selected table", your data should contain all of
the chromosome locations you describe. To see a description of the
fields in the table, hit the "describe table schema" button.

The gene start and end positions correspond to txStart and txEnd (note
that if this is a gene on the negative strand, txStart specifies the 3'
end of the gene, and txEnd specifies the 5'end).

The exon start and end positions are in the exonStarts and exonEnds fields.

For a + strand gene, a 5' UTR (if there is one) would be specified by
the region between txStart and cdsStart. A 3' UTR would be the region
between cdsEnd and txEnd.

Note that start coordinates in tables differ from the coordinates
displayed in the Genome Browser by one base. See these pages for an
explanation:
http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms

There is a way to include HGNC gene IDs and names in your output, but
the information comes from data that we update when we build the UCSC
Genes track, which is not updated as frequently as the RefSeq Genes
track, so some HGNC info may be out of date or missing.

Also, there was a bug that recently got fixed in the Table Browser
functionality that relates the relevant table to the UCSC Genes track,
which is in turn related to the RefSeq Genes track. We corrected the
bug, but for the next week you will need to use our preview server to
follow this method: http://genome-preview.ucsc.edu/. Be aware that
there is a lot of untested and experimental data on the preview server.

To relate RefSeq Genes to HGNC identifiers and names, keep the "refGene"
table selected in the Table Browser, but choose to get "selected fields
from primary and related tables" as the output format. Hit get output,
and then scroll down and check the box for the hg19.kgXref table. Hit
the "allow selection from checked tables" button at the bottom of the
page. Now you should see more tables listed in the "Linked tables"
section. Scroll down and select the proteome.hgncXref table, then hit
the "allow selection from checked tables" button again. Now you should
be able to get all of the fields from the refGene table, plus the symbol
and hgncId fields from the proteome table.

I hope this information is helpful. If you have further questions,
please reply to gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

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