CRISPOR (
paper
) is a program that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system.
CRISPOR Manual
May 2019: Added Lindel DSB-repair outcomes, Graf et al. motifs
Full list of changes
Step 1
Planning a lentiviral gene knockout screen? Use
CRISPOR Batch
Sequence name (optional):
Enter a single genomic sequence, < 10000 bp, typically an exon
Clear Box
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Reset to default
cttcctttgtccccaatctgggcgcgcgccggcgccccctggcggcctaaggactcggcgcgccggaagtggccagggcgggggcgacctcggctcacagcgcgcccggctattctcgcagctcaccatgGATGATGATATCGCCGCGCTCGTCGTCGACAACGGCTCCGGCATGTGCAAGGCCGGCTTCGCGGGCGACGATGCCCCCCGGGCCGTCTTCCCCTCCATCGTGGGGCGCC
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)
Felis catus - Domestic cat - Ensembl 89 (Felis_catus_6.2)
Homo sapiens - Human - UCSC Dec. 2013 (GRCh38/hg38)
Homo sapiens - Human - UCSC Feb. 2009 (GRCh37/hg19)
Mus musculus - Mouse (reference) - UCSC Dec. 2011 (mm10=C57BL/6J)
Saccharomyces cerevisiae - S. cerevisiae - UCSC Apr. 2011 (SacCer_Apr2011/sacCer3)
Spodoptera frugiperda - Fall armyworm - E. Joly 3.1
Spodoptera littoralis - African cotton leafworm - from Manue V2
Note: pre-calculated exonic guides for this species are on the
UCSC Genome Browser
.
We have 7 genomes, but not the one you need? Send its FASTA/GFF URL 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, NEW! 2019, A. Edraki
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
TTT(A/C/G)-23bp - Cas12a (Cpf1) Acidaminoc. / Lachnosp. - recommended
TTTN-23bp - Cas12a (Cpf1) Acidaminoc. / Lachnosp - low efficiency
Version 4.92 -
Documentation
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Contact us
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Downloads/local installation
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Paper
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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.
