Knock-in Atlas (Human)

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↩︎ Knockin Atlas home

Genes

HEK293 TPM: 45 – 300

Gene	chromosome	start_pos	end_pos	HEK293T_TPM	HeLa_TPM	HAP1_TPM	THP1_TPM	gene_function

gRNAs for the selected gene

pLDDT: 0 – 80

Gene	IntronID	pLDDT	chromosome	start_pos	end_pos

Download gRNAs for selected gene (CSV)

UCSC Genome Browser

gRNAs for the selected intron

Gene	IntronID	IntronPhase	gRNAID	gRNA_strand	gRNA_spacer	gRNA_PAM	gRNA_score

Download selected intron gRNAs (CSV)

(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

(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: Download CSV for the selected intron

Options: Set TPM or pLDDT scores

Default TPM and pLDDT are 45 and 80, respectively

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.

Introns step

Download CSV files

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

2. Design gRNAs

gRNA design

Download CSV files

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

3. AlphaFold mapping

AlphaFold mapping

Download CSV files

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

4. Visualize feature tracks

Download BigBed files (Note: large ~1GB)

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

References

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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

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