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Choosing a common exon in GOI to design your guides

Crisprexon guide RNA

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#1 Natalia KM

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Posted 11 October 2019 - 05:04 PM

Hi Im new to cloning. Previously who I did Crispr knock outs, the guides and plasmids were designed/made by a cloning team so I did the cell culture part of it.

 

Now I need to design my own guides and clone into appropriate vectors.

 

Right now I hav a very basic question, I know I need to target a common exon thats present in all splice/transcript variants of my gene of interest.

 

But when Im going on NCBI, I'm getting very confused about which ones are common exons. Can someone please help?

 

Let's take an example gene eg PPARGC1a, could someone tell me step by step how to find the common exon most 5' that I can target for a knockout?

 

Thanks 



#2 Jon Moulton

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Posted 18 December 2019 - 08:21 AM

Try the gene views in Ensembl.  The gene pages give a map that helps a lot for identifying which exons are present in which transcripts. 

 

Scroll down for the map.

 

http://uswest.ensemb...ENST00000498200

 

Here's a map for the example you cite, PPARGC1a:

 

http://uswest.ensemb...755041-23904089


Jon D. Moulton
Gene Tools, LLC
www.gene-tools.com




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