finding TSS in GB

[Kaarthik John]

I don't have a whole lot of experience with the use of the Genome Browser. I have a couple of questions:

1. When genome browser lists the co-ordinates of a gene (eg: chr4: 75,310,853 - 75,490,485 for AREG from H. sapiens) is this also inclusive of the promoter of the gene? In other words is the starting co-ordinate, 75,310,853 inclusive of the promoter as well or is this just the position of where TRANSCRIPTION starts? 

2. Is there a way that Genome browser can be used to show the approximate transcription start site and provide the approximate position/ co-ordinate for this site?

Using Table browser I was able to get Tx start as 75,310,853 and Tx stop as 75,490,485. But is this the length of the gene or the point where transcription starts and stops, respectively.

Thanks!

[Brooke Rhead]

Hi John,

If you are new to the Genome Browser, the free Open Helix tutorials here
at http://www.openhelix.com/ucsc are a nice way to quickly get
acquainted with the most popular features.

The gene tracks in the Genome Browser follow the display conventions
here:
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GeneDisplay.
The gene coordinates do not include promoter regions; they start and end
where transcription starts and ends.

One thing to be aware of when looking at coordinates in the Genome
Browser vs. in tables is that the first coordinate in the table is one
lower than what is displayed in the Genome Browser. See:
http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms

To visualize transcription start sites, one thing you could do is use
the Table Browser to make a custom track consisting of regions just
before the start site of each transcript. To do this, select a gene
track in the Table Browser, make sure "region: genome" is selected, and
set the output format to "custom track." Hit "get output." On the next
page, you can choose to create one BED record for each upstream region.
Enter whatever number of bases you would like to see to represent the
regions just upstream of each TSS, and then hit "get custom track in
genome browser." You should see one solid block for each region that
precedes a transcription start site by the number of bases you
specified. Note that you can read about how each of the gene tracks we
display was made by clicking on the track name on the main Genome
Browser page (http://genome.ucsc.edu/cgi-bin/hgTracks). If you would
rather see a single TSS for all of the isoforms in a cluster of gene
annotations, you can select the UCSC Genes set and select the
knownCanonical table (instead of knownGene) from the drop-down menu when
you make your custom track.

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

--
Brooke Rhead
UCSC Genome Bioinformatics Group

On 2/27/13 8:43 AM, Kaarthik John wrote:
> I don't have a whole lot of experience with the use of the Genome
> Browser. I have a couple of questions:
> 1. When genome browser lists the co-ordinates of a gene (eg: chr4:

> *75,310,853 - 75,490,485* for AREG from H. sapiens) is this also

> inclusive of the promoter of the gene? In other words is the starting
> co-ordinate, 75,310,853 inclusive of the promoter as well or is this
> just the position of where TRANSCRIPTION starts?
>
> 2. Is there a way that Genome browser can be used to show the
> approximate transcription start site and provide the approximate
> position/ co-ordinate for this site?
> Using Table browser I was able to get Tx start as 75,310,853 and Tx stop

> as *75,490,485*. But is this the length of the gene or the point where

> transcription starts and stops, respectively.
> Thanks!
>

> --
>
>
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