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Design CRISPR sgRNA and DNA templates for HDR knock-in experiments

EasyEdit sgRNA Now Starting at Only $79/2nmol!

User Guide Watch How to Video

Please enter 19-20nt guide RNA sequence (exclude PAM). RNA sequence of guide RNA, or DNA sequence for target sequence are both acceptable.

Frequently Asked Question

Exon (negative direction) Exon (positive direction) Deletion Insertion sgRNA Translation Previous translation
Sequence Flip Tool

Please note the GFP sequence insertion does not contain a stop codon. A stop codon like TAA should be added if the insertion is at the end of the protein translated.

Output for Gene Symbol (Gene ID )

Download Design Result

For HDR template exceeding 20kb, please contact us for technical support (crispr@genscript.com)

Input Sequence

Output Sequence

Please enter 17-23nt guide RNA sequence.

Getting Started with GenCRISPR HDR Design Tool

Thanks for choosing our HDR design tool for your knock-in project.

Our tool designs sgRNA as well as HDR knock-in templates for CRISPR Cas9 based gene insertion projects in human and mouse.

5 EASY STEPS AND SIT BACK!

  1. Provide target species, gene or sequence information
  2. Confirm your start editing site by entering or pinpointing genome site on the interactive slider bar
  3. Specify mutation sequence (select region to be deleted, enter new sequence to be inserted, or directly select commonly used protein tags to be inserted)
  4. Define homology arm length on each side or use recommended default setting
  5. Select number of designs to return and sit back for recommended sgRNA and HDR donor template designs with detailed on/off target score analysis and ordering options

GenScript offers high quality sgRNA/Cas9, as well as long linear GenExactTM ssDNA, linear closed-end GenWandTM dsDNA, and miniaturized circular GenCircleTM dsDNA to help you expedite your projects. Any questions, please send Email to crispr@genscript.com.

Select editing position:

  • The green label represents the targeted editing site.
  • When the mouse is placed on both ends of the green label and changes into a cross shape, press and hold the left mouse button to adjust the position on the left and right ends of the green label, and select a suitable editing position.

Go through sequence map:

  • By placing the mouse cursor on the sequence map and scrolling the mouse wheel, you can zoom in on the sequence map to display each base and amino acid.
  • Press and hold the left mouse button to move the sequence map freely to the left or right.

Here is our default HA length for deletion within 70bp:

  • 70nt HA for ≤100bp inserts
  • 300nt HA for >100bp inserts
  • Our suggestions: If insertion length ≤2kb, HA is recommended as 250nt for ssDNA, HA is recommended as 150bp-200bp dsDNA. If insertion length>2kb, HA is recommended as 300bp-500bp

Here is our default HA length for deletion over 70bp:

  • Deletion length 70-299 nt: HA=300nt
  • Deletion length 300-499 nt: HA=500nt
  • Deletion length 500-1500 nt: HA=700nt
The ranking is based on “distance to mutation” of different sgRNA, the smaller this parameter is, the higher the ranking is. If the “distance to mutation” is the same, the higher the “on target score” of sgRNA is, the higher the ranking is. Please select design according to your most important parameter.

Please enter the information according to your request:

  • Point mutation: select the codon or base need to be mutated in the sequence map by move the green label and deleted it directly. Then enter the new codon or base you want change to.
  • Knock-in: Select your desired deletion sequence in the sequence map by move the green label and deleted it directly. Then enter the sequence to be inserted.
  • Deletion: Select your desired deletion sequence in the sequence map by move the green label and deleted it directly. You may choose HDR template to increase precise knock out or not according to your request in following step.

Higher score represent the higher on target editing efficiency. Reference: Doench-score.
The ranking order represent overall evaluation according to on/off target score etc.

Higher score represent the higher off target editing efficiency. Reference: Doench-score.
The ranking order represent overall evaluation according to on/off target score etc.