[Genome] gene promoters

[Ann Zweig]

Hello Chris,

	If you are interested in getting the upstream sequence for your regions of 
interest, you can do this by creating a Custom Track, then using the Table 
Browser to get the upstream sequence.

	If, on the other hand, you are interested in determining the exact location of 
the promoter regions, we have a few annotation tracks in the browser that may be 
useful to you.  We have an annotation track on the latest human assembly (hg18) 
called "Transcription Factor Binding Sites" (table name: tfbsConsSites).  This 
track contains the location and score of transcription factor binding sites 
conserved in the human/mouse/rat alignment. A binding site is considered to be 
conserved across the alignment if its score meets the threshold score for its 
binding matrix in all 3 species. The score and threshold are computed with the 
Transfac Matrix Database (v7.0) created by Biobase. The data are purely 
computational, and as such not all binding sites listed here are biologically 
functional binding sites.

	Other annotation tracks that may be helpful to you (as with the TFBS track, you 
will find them in the "Expression and Regulation" track group) are:

- FirstEF: First-Exon and Promoter Prediction (table: firstEF)
- ESPERR Regulatory Potential (table: regPotential7X)
- TargetScan miRNA Regulatory Sites (table: targetScanS)
- Eponine Predicted Transcription Start Sites (table: eponine)

	Once you determine which of these tracks will be most useful to you, you can do 
an intersection in the Table Browser tool with the underlying table and your 
Custom Track.  Read more about using the Table Browser tool here: 
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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Christine J. Jung wrote:
> Hello,
> 
> I have a list of the coordinates of the transcripts of genes that I am
> interested in studying (about 100 of them).  Could someone give me some
> advice on the best way to capture the promoter regions of these genes?
> Thank you.  chris
> 
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