TSS for a gene of interest

42 views
Skip to first unread message

Marilynn Chow

unread,
Mar 22, 2017, 11:59:47 AM3/22/17
to gen...@soe.ucsc.edu

To whom it may concern,

 

I have been interested in finding the transcription start site (TSS) for gene that I am studying. I came across some forums that described the Table Browser from UCSC’s website. I tried to use it for my gene (+ strand coordinates: ch19: 4903080-4962154) but I am unsure how to interpret the output data. I’ve attached screenshots from the process so you’ll have an idea of the parameters I was selecting.

 

Would you mind clarifying what the output data means? I’m not sure how to interpret the start and end values relative to my gene, and there are many “TSS” listed (a few of which are identical).

 

Let me know if you need any more information.

 

I appreciate your assistance in this matter.

 

Best,

Marilynn

UHRF1 TSS_ UCSC Table Browser.pdf

Christopher Lee

unread,
Mar 22, 2017, 1:42:57 PM3/22/17
to Marilynn Chow, gen...@soe.ucsc.edu
Hi Marilynn,

Thank you for your question about obtaining TSS location data via the
Table Browser. It looks like there is a small typo in the position box
in the first screenshot, there should be no dash (-) in the second
coordinate. If you instead input chr19:4903080-4962154 as a position
then you will return only the results for the 5 transcripts at
position chr19:4,903,080-4,962,154. The second dash in the position
field was causing the Table Browser to output all transcripts from the
knownGene table located on chr19, which is why you were seeing many
lines of output, and since multiple transcripts of a gene can have the
same start and stop positions (differing in number of exons or
positions of exons), there were some lines of identical positions.

The txStart and txEnd numbers are the genomic positions corresponding
to transcription starts and stops. However they can be tricky to
interpret because of strandedness. When a gene is on the positive
strand, then the txStart field refers to the actual transcription
start position, and the txEnd field refers to the transcription stop
position. However, because we store all of our coordinates in
reference to the positive strand, when a transcript is actually on the
negative strand, the txStart field refers to the transcription end
position, and the txEnd field refers to the transcription start
position.

If you are ever looking at data via the Table Browser and are confused
about what the fields of a table mean, you can click the "describe
table schema" button from the main Table Browser page to get a
description of each field in the table.

Please let us know if you have any further questions!

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
> --
>
> ---
> You received this message because you are subscribed to the Google Groups
> "UCSC Genome Browser discussion list" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to genome+un...@soe.ucsc.edu.
Reply all
Reply to author
Forward
0 new messages