[Genome] cds info on mRNA track (human)

[Rachel Harte]

Hello Micha,

The GTF output is determined by the information in the PSL table
(all_mrna) which does not include the CDS position. We just use the
Genbank record CDS to determine how to draw the mRNAs in the Human mRNA
track. This information can be found by referring to the gbCdnaInfo table.
In the cds column, there is an integer which can be used to search the id
column of the cds table. The CDS region from the Genbank record is shown
in the name column.

The RefSeq genes and UCSC Genes (or Known Genes track on hg17) tables use
genePred format which include the coordinates of the CDS region so these
will appear in the GTF output for these gene tables.

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 Sat, 2 Jun 2007, Micha Sammeth wrote:

> Hi,
>
> (thank you Rachel for the very detailed and exhaustive explanations to
> my previous questions!!)
>
> When downloading an gtf export of the human (hg17) mRNA track via the
> table browser, it does not include information about ORF positions
> (feature cds). I also checked the table and didnt find a field that
> sounds to store this information. However, in the browser track I can
> see "CDSs" (thick start/end). Did I do something wrong or is there
> another way to obtain this information?
>
> Thank you, micha.
>