CRISPOR

CRISPOR (citation) is a program that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. CRISPOR Manual
July 2023: A faster server has arrived and should come online within 2-3 months. Python3 upgrade on hold, the ML models output different scores on Py3. 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>Avoid using cDNA sequences as input, CRISPR guides that straddle splice sites are unlikely to work.<br>You can paste a single >23bp sequence and even multiple sequences, separated by N characters.

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.<br>You can paste a single >23bp sequence and even multiple sequences, separated by N characters.

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 1020 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</i>. The VRER and VQR mutants were described by <a href='http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature14592.html' target='_blank'>Kleinstiver et al</a>, Cas9-HF1 by <a href='https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851738/'>Kleinstiver 2016</a>, eSpCas1.1 by <a href='https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4714946/'>Slaymaker 2016</a>, Cpf1 by <a href='http://www.cell.com/abstract/S0092-8674(15)01200-3'>Zetsche 2015</a>, SaCas9 by <a href='https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25830891/'>Ran 2015</a> and KKH-SaCas9 by <a href='https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/26524662/'>Kleinstiver 2015</a>, modified As-Cpf1s by <a href='http://biorxiv.org/content/early/2016/12/04/091611'>Gao et al. 2017</a>.

Select a Protospacer Adjacent Motif (PAM)

See notes on enzymes in the manual.

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