Finding promoter regions - (Sep/20/2016 )

What is the best way to find promoter regions in my GOI? I've looked on UCSC genome browser to no avail. The ultimate purpose is to evaluate sgRNA sequences for CRISPRa. Thanks.

Why don't you use a CRISPR target finder then?

Check this one (I haven't used it though):

https://bitbucket.org/juanlmateo/cctop_standalone

PS: if your genome is from a commonly used species you can try these ones

(online version of the previous)

http://crispr.cos.uni-heidelberg.de/species.html

CRISPR target finder

http://tools.flycrispr.molbio.wisc.edu/targetFinder/

Which CRISPRa system are you using? Look at the publication for it, they probably describe the optimal sgRNA design parameters. Generally, targeting a pool of sgRNAs as close to the transcriptional start site as possible (<100bp) is the best.