Extracting promoter regions alignment

Question

[prosvirov.k]

Greetings, everyone!

I`m trying to extract promoter regions alignment from UCSC Table Browser. I can get promoter regions for any species using output format as "sequence", also I can get alignments of "CDS" I guess, using output as "CDS FASTA....". So my question is divided into two:

1. Can I possibly combine these two options to acquire alignments of promoter regions uptream of XXX nc?
2. If not, could I possibly use "define regions" option with promoterscoordinates in human genome to acquire alignments using "CDS FASTA...." option? If its possible, could you tell me where to get promoter coordinates?

Thank you in advance for your answers/advice/tips!

Answer 1

[Sam]

Promoter regions aren't stonely defined I believe. Essentially you would look at the TSS of a gene and then choose a region (~3k+/3k- ... promoter region definitions vary) from there and that would be considered your promoter region. You can do this on the UCSC Table Browser I think, if not you could definitely do it using a combination of the Table Browser and slopBed from bedtools.