[Genome] CCDS genes

[Rachel Harte]

Jittima,

Yes, you can obtain this information through the Table Browser. The
description is obtained by using the CCDS gene's RefSeq accession to
query the refLink table. First, go to the Table Browser and select the
hg17 Human assembly (May 2004). Then follow these steps:

1) Select "Genes and Gene Predictions" as the group. Select CCDS Genes as
the track and ccdsGene as the table.
2) Select genome as the region, then either paste in a list or upload a
list of the CCDS identifiers using the buttons next to
"identifiers(names/accessions".
3) Select "select fields from primary and related tables" and click on
"get output". Then you can select fields from the ccdsGene table and the
ccdsInfo table. For ccdsInfo select mrnaAcc and srcDb.
4)Then from the Linked Tables, select hg17.refLink and click on the
"Allow Selection From Checked Tables" button at the bottom of the page.
Select "product" from the refLink table to get the description.

The output should give you all the CCDS information and the RefSeq
accession and description.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Sun, 21 Jan 2007, Jittima Piriyapongsa wrote:

> Hi,
>
> I have a set of CCDS gene accession numbers (i.e. CCDS9953.1). Is there any
> way to use table browser for finding the gene name and gene description of
> these CCDS genes by using their accession numbers?
>
> Thank you,
> Jittima
>
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