How to separate promoter regions and coding regions from a gene sequence?

Question

[udarika1990]

I want to analyze promoter regions and coding regions separately using multiple sequence alignment. Is there a online tool for that? If so how to do? Can I use Biomart martview tool and how?

Answer 1

[Joseph Pearson]

The UCSC genome browser, under the "Table Browser", allows you to extract BED files for all exons, coding exons, 5'UTR exons, 3' exons, or upstream of each gene.

Select the Genes and Gene Predictions Group under "Group", specify a region (or set of regions for genes of interest, using "define regions"), or just use whole genome. Under output format, select "BED", then click "get output". The next page will give you options on getting BED intervals.

These intervals can then be used to either get sequences, or sequence alignments, again through UCSC.