(1-1) Step1: Search for the gene of interest

(1-2) Step2: Click and select to browse the gene of interest

(1-3) Step3: You can visually check pLDDT score and location of the pre-designed gRNA candidates on the genome browser

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(2-1) Step4: The pre-designed gRNAs with low pLDDT and gRNA score are listed in a table

(2-2) Pop up Genome Web Browser for the selected intron

(2-3) Step5: You can download the csv file and check the details of the pre-designed gRNAs for the selected introns; Time for the knock-in!!

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Options: Set TPM or pLDDT scores

Default TPM and pLDDT are 45 and 80, respectively

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FAQ: FORCE LOAD

Please click FORCE LOAD when you want to see large region

1. Select introns in CDS and organize intron phases

In this study, we referred to representative transcript isoform against each gene.

MANE Select v.1.0 for human and RefSeqSelect for mouse.

Download CSV files

Download genome-wide human introns Download genome-wide mouse introns

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2. Design gRNAs

Download CSV files

Download genome-wide human gRNAs Download genome-wide mouse gRNAs

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3. AlphaFold mapping

Download CSV files

Download genome-wide human pLDDTs Download genome-wide mouse pLDDTs

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4. Visualize feature tracks

Download BigBed files (Note: large ~1GB)

Download BigBed files (Note: large ~1GB)

Human gRNA BigBed Mouse gRNA BigBed Human pLDDT BigBed Mouse pLDDT BigBed

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References

• Morales & Pujar et al., A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature (2022)
• Goldfarb & Kodali et al., NCBI RefSeq: reference sequence standards through 25 years of curation and annotation. Nucleic Acids Res (2025)
• Labun et al., CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Res (2019)
• Doench et al., Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol (2016)
• Varadi et al., AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res (2024)
• Grant et al., The Bio3D packages for structural bioinformatics. Protein Sci (2020)

List of other links:

• Go to The Knock-in Atlas
• Go to Human intron gRNA Database
• Go to Mouse intron gRNA Database
• Go to Collection page of Knock-in cell lines

We would love to hear your feedback!

If you have any questions, suggestions, or feedback, feel free to contact us.

E-mail:

hanai.yuma.hv0@bs.naist.jp

okamurak@bs.naist.jp

Thank you for helping us improve!