CRISPOR (
citation
) is a program that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system.
CRISPOR Manual
June 2020: saCas9 primer fixes, Snapgene/Geneious improvements, better export for Cpf1
Full list of changes
Step 1
Planning a lentiviral gene knockout screen? Use
CRISPOR Batch
Sequence name (optional):
Enter a single genomic sequence, < 2000 bp, typically an exon
Clear Box
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Reset to default
ATTCTACTTTTCAACAATAATACATAAACatattggcttgtggtagCAACACTATCATGGTATCACTAACGTAAAAGTTCCTCAATATTGCAATTTGCTTGAACGGATGCTATTTCAGAATATTTCGTACTTACACAGGCCATACATTAGAATAATATGTCACATCACTGTCGTAACACTCT
Text case is preserved, e.g. you can mark ATGs with lowercase.
Instead of a sequence, you can paste a chromosome range, e.g. chr1:11,130,540-11,130,751
Step 2
Select a genome
-- No Genome: no specificity, only cleavage efficiency scores (max. len 25kbp)
Saccharum hybrid cultivar - sugarcane - NCBI GCA_900465005.1 (MTP)
Note: pre-calculated exonic guides for this species are on the
UCSC Genome Browser
.
We have 1 genomes, but not yours? Search
NCBI assembly
and send a GCF_/GCA_ ID to
CRISPOR support
.
Step 3
Select a Protospacer Adjacent Motif (PAM)
20bp-NGG - Sp Cas9, SpCas9-HF1, eSpCas9 1.1
20bp-NNG - Cas9 S. canis
20bp-NNGT - Cas9 S. canis - high efficiency PAM, recommended
20bp-NAA - iSpyMacCas9
21bp-NNG(A/G)(A/G)T - Cas9 S. Aureus
20bp-NNG(A/G)(A/G)T - Cas9 S. Aureus with 20bp-guides
20bp-NG(G/T) - xCas9, high efficiency PAM, recommended
20bp-NGN or GA(A/T) - xCas9, low efficiency PAM
21bp-NNN(A/G)(A/G)T - KKH SaCas9
20bp-NNN(A/G)(A/G)T - KKH SaCas9 with 20bp-guides
20bp-NGA - Cas9 S. Pyogenes mutant VQR
24bp-NNNNCC - Nme2Cas9
20bp-NGCG - Cas9 S. Pyogenes mutant VRER
20bp-NNAGAA - Cas9 S. Thermophilus
20bp-NGGNG - Cas9 S. Thermophilus
20bp-NNNNG(A/C)TT - Cas9 N. Meningitidis
20bp-NNNNACA - Cas9 Campylobacter jejuni, original PAM
22bp-NNNNRYAC - Cas9 Campylobacter jejuni, revised PAM
22bp-NNNVRYAC - Cas9 Campylobacter jejuni, opt. efficiency
20bp-TTCN - CasX
TTT(A/C/G)-23bp - Cas12a (Cpf1) - recommended, 23bp guides
TTT(A/C/G)-21bp - Cas12a (Cpf1) - 21bp guides recommended by IDT
TTTN-23bp - Cas12a (Cpf1) - low efficiency
ATTN-23bp - BhCas12b v4
NGTN-23bp - ShCAST/AcCAST, Strecker et al, Science 2019
T(C/T)C(A/C/G)-23bp - TYCV As-Cpf1 K607R
TAT(A/C/G)-23bp - TATV As-Cpf1 K548V
TTTA-23bp - TTTA LbCpf1
TCTA-23bp - TCTA LbCpf1
TCCA-23bp - TCCA LbCpf1
CCCA-23bp - CCCA LbCpf1
GGTT-23bp - CCCA LbCpf1
YTTV-20bp - MAD7 Nuclease, Lui, Schiel, Maksimova et al, CRISPR J 2020
Version 4.98 -
Documentation
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Contact us
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Downloads/local installation
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Citation
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License
CRISPR/Cas9 Guide Designer for chordate vertebrate ecdysozoans lophotrochozoans protostomes spongi corals plants butterflies metazoans genomes fruitflies insects nematodes mammals.
