CRISPOR

CRISPOR (citation) is a program that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. CRISPOR Manual
Jan 2025: The server went down a few times over the holidays, sorry. It is catching up today on submitted jobs. See Full list of changes

Step 1

Planning a lentiviral gene knockout screen? Use CRISPOR Batch
Sequence name (optional):
Enter a single genomic sequence, < 2300 bp, typically an exon CRISPOR conserves the lowercase and uppercase format of your sequence, allowing to highlight sequence features of interest such as ATG or STOP codons.<br

CRISPOR conserves the lowercase and uppercase format of your sequence, allowing to highlight sequence features of interest such as ATG or STOP codons.<br

Avoid using cDNA sequences as input, CRISPR guides that straddle splice sites are unlikely to work.
You can paste a single >23bp sequence and even multiple sequences, separated by N characters." class="tooltipster">
Clear Box - Reset to default

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

Note: pre-calculated exonic guides for this species are on the UCSC Genome Browser.

We have 1239 genomes, but not yours? Search NCBI assembly and send a GCF_/GCA_ ID to CRISPOR support.

Step 3

The most common system uses the NGG PAM recognized by Cas9 from S. <i

pyogenes. The VRER and VQR mutants were described by Kleinstiver et al, Cas9-HF1 by Kleinstiver 2016, eSpCas1.1 by Slaymaker 2016, Cpf1 by Zetsche 2015, SaCas9 by Ran 2015 and KKH-SaCas9 by Kleinstiver 2015, modified As-Cpf1s by Gao et al. 2017." class="tooltipsterInteract">

Select a Protospacer Adjacent Motif (PAM)

See notes on enzymes in the manual.

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