Flask Parent Template

Get a complete CRISPR plan for introducing an insertion

The Automated CRISPR Planner aims to streamline your CRISPR design process given only the gene name and the insertion you wish to introduce.

The tool is designed for insertions, both small and large, in the Caenorhabditis elegans genome. We recommend to use this tool for insertions not larger than ~1500nt (for larger insertions it’s better to use two guides – a design that this tool does not provide).
The tool has been built to generate CRISPR designs according to the methods described in Geraldine Seydoux's paper:

Paix A, Folkmann A, Goldman DH, et al. Precision genome editing using synthesis-dependent repair of Cas9-induced DNA breaks. Proc Natl Acad Sci U S A. 2017;114(50):E10745-E10754. doi:10.1073/pnas.1711979114

Automated CRISPR Planner for insertion

In order to use the service, please insert your worm gene name, insertion sequence, the insertion site (the amino acid immediately downstream to your insertion, or you can insert start/end if you wish the insertion to be before the first amino acid, then pay attention you need to start the insertion with start codon, or before the last amino acid, i.e. before the end codon), forward and reverse primers 5’ to 3’ (this is optional – only if you are planning to lift your insertion by PCR) and linker sequence (again optional – you can add a linker on both sides of the insertion, on one of the sides or none at all. You can add different linkers on either side).

If you don't have a valid crRNA sequence with which you wish to plan your CRISPR, please leave that box empty.
Once clicking the "Submit" button, you will be presented with all possible crRNA sequences relevant to your request.
Choose one of the RNA guides presented to you and then you will get the complete CRISPR design plan for your insertion.

For example: PDR-1 gene has 3 different isoforms: K08E3.7a.1 , K08E3.7b.1 , K08E3.7b.2 , K08E3.7c.1.
We'll never share your email with anyone else.
If you have the exact sequence, you can copy it or write 'INSERTION' if you prefer not the copy the whole sequence.
Choose strand: