Find CRISPRs

» Search by gene
To find CRISPRs within a gene, enter the gene symbol, select tracks of interest, then click the 'Submit' button.

» Search by sequence
If you have a sequence and want to find nearby CRISPRs, enter the sequence into the textbox to BLAST it before viewing it on JBrowse. If the sequence is a significant hit, it will show as a highlight.


Both search functions will take you to a summary page with a table and embedded JBrowse view. If you want to zoom in or shift the location on the genome, click on "Full-screen view".

Miss the old version? Find CRISPRs 2017

**NEW** features:
  • Variant Search (data sources below)
  • Summary table of all CRISPRs within gene/location of interest
  • Search by sgRNA sequence
  • Batch search by gene or sequence
  • "seedScore" available for each CRISPR (ranging from 12 to 15), indicating its unique bp-end excluding PAM
  • Machine Learning based efficiency prediction
  • Updated JBrowse to version 1.13.0
  • Updated FlyBase release 6.14 -> 6.24

Search by gene


No Predicted Off-Targets (preferred)




1 - 3 Predicted Off-Targets
(Non-CDS Off-Targets)
(CDS Off-Targets)

>3 Predicted Off-Targets

(most stringent)

(least stringent)

Batch search by gene


No Predicted Off-Targets (preferred)




1 - 3 Predicted Off-Targets
(Non-CDS Off-Targets)
(CDS Off-Targets)

>3 Predicted Off-Targets

(most stringent)

(least stringent)

Search by sequence



Search for Variants







Search by gene location.





Search by genomic location.

Enter one sequence per line. Example



Enter comma seperated positions and chromosome, one per line. Example
Ex: 39131,41881,2L


Publication Citation: Benjamin E Housden, Alexander J Valvezan, Colleen Kelley, Richelle Sopko, Yanhui Hu, Charles Roesel, Shuailiang Lin, Michael Buckner, Rong Tao, Bahar Yilmazel, Stephanie E Mohr, Brendan D Manning, and Norbert Perrimon. 2015. “ Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi..” Sci Signal, 393, 8: rs9.


Genome Variants Data Sources:

Other Data Sources: