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:

Summary table of all sgRNAs within gene/location
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 FlyBase release 6.14 -> 6.24 (Oct 2018)
Variant search & sgRNA SNP count (Feb 2019)
Updated JBrowse to version 1.16.9 (May 2020)
Added linkouts for relevant designs to TRiP sgRNA Stock Database (Sept 2020)

Search by sequence

Search for Variants

1. Select dataset and
variant type

Dataset Variant Type

2. Search by gene, sequence, or genomic location

Gene Search

Search by gene location.

Gene:

Location Search

Search by genomic location.

Chromosome:

Start:

Stop:

Batch Search Sequences

Enter one sequence per line. Example

Batch Search Locations

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.

Stock Genotypes:

CRIMIC_iso2_18
- Genotype: y w; iso; attP2(y+){nos-Cas9(v+)}
CRIMIC_iso3_5
- Genotype: y w ;attP40(y+){nos-Cas9(v+)}/CyO; iso
CRIMIC_iso3_29
- Genotype: y w ;attP40(y+){nos-Cas9(v+)}/CyO; iso
CRIMIC_isoX_6
- Genotype: y w iso; ; attP2(y+){nos-Cas9(v+)}
TRiP_Cas9_attP40
- Genotype: y[1] sc[*] v[1] sev[21]; P{y[+t7.7] v[+t1.8]=nos-Cas9.R}attP40
- BDSC Stock ID: 78781
TRiP_Cas9_attP2
- Genotype: y[1] sc[*] v[1] sev[21]; P{y[+t7.7] v[+t1.8]=nos-Cas9.R}attP2
- BDSC Stock ID: 78782

Genome Variants Data Sources:

S2R+/NPT005 was sequenced and analyzed by Dr. Casey Bergman at University of Georgia
CRIMIC injection stocks were sequenced and analyzed by Dr. Hugo Bellen from Baylor Medical School
3 samples of each Cas9 injection stock were sequenced and analyzed by Dr. Benjamin White at NIH while one sample was sequenced and analyzed by TRiP

Other Data Sources:

Genome coordinates of domain annotations from FlyBase

Find CRISPRs

Search by gene

Batch search by gene

Search by sequence

Search for Variants