Find common and unique CRISPR guide RNA targets for different transcripts of one gene

Search for common and specific CRISPR guide RNA targets for different transcripts of one gene

5' dinucleotide
Target length
PAM sequence orientation 5' 3'
PAM sequence NGG (scoring is available*) Your own PAM sequence

*Scoring is available for 20-nt type II sgRNAs. See Doench et al., 2014 for details. High scores may indicate more potent sgRNAs. However, some potent sgRNAs have scores < 0.1 and a number of successful sgRNAs had scores between 0.1 and 0.2. Therefore, potential experimental utility and subsequent experimental verification should guide the choice of sgRNAs.

Off-target analysis parameters:
GT-Scan : No restrictions on PAM sequence or target length. Adjust the target rule on the submission form.
Cas-OFFinder : Length should be 20bp for SpCas9 (PAM = 'NGG'), 18bp for StCas9 (PAM = 'NNAGAAW'), and 24bp for NmCas9 (PAM = 'NNNNGMTT').

Organism (species name)

Choose the type of gene identifier Gene symbols Ensembl Gene IDs

Enter a gene identifier:

Demo input

CRISPR MultiTargeter was developed by Sergey Prykhozhij at the IWK Health Centre and Dalhousie University. The design of the logo and the buttons was by Vinothkumar Rajan. The latest update was in May 2019.