Extract promoters

To extract estimated promoter regions for the whole genome, select a track to base the analysis on (UCSC Genes, RefSeq Genes, etc.), then use the Table browser. Select output=sequence, sequence type=genomic, region=Promoter/Upstream by XXX bases (you decide the XXX). http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Sequence

The first base in the region is XXX bases upstream from the transcription start site of the transcript in the track (as determined by genome alignment). The last base in the region would be one base before the transcription start site.

Using hg18, there are a few tracks to consider. Starting at the Gateway page, select the genome hg18. Then use the button "configure" (instead of submit). The resulting page lists all tracks. Click on a track name to learn about the contents/methods.

In this section "Configure Tracks on UCSC Genome Browser: Human Mar. 2006 (NCBI36/hg18)" use the button "expand all" to view all track. Starting tracks to consider are in the Regulation group. Click on tracks to see which fit your needs. Suggested tracks to start with are Eponine TSS, SwitchGear TSS, and possibly FirstEF. Tracks in the Pilot ENCODE Transcription group may also be helpful (although the data is restricted to the pilot regions).