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Finding promoter regions

crispr gene

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#1 Artemis2007

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Posted 20 September 2016 - 12:49 PM

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.



#2 El Crazy Xabi

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Posted 21 September 2016 - 03:39 PM

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

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

https://bitbucket.or...ctop_standalone

 

 

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

(online version of the previous)

http://crispr.cos.un...de/species.html

 

CRISPR target finder

http://tools.flycris...u/targetFinder/


Edited by El Crazy Xabi, 21 September 2016 - 03:41 PM.


#3 Ken S

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Posted 22 September 2016 - 01:37 PM

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.







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