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PITCh KnockIn
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PITCh designer 2.1
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PITCh designer 2.1
A free online tool to design sgRNA and microhomologies for gene knock-in.
Citation information
PITCh designer (previous version : version 1.0):
Nakamae, Kazuki, et al. "Establishment of expanded and streamlined pipeline of PITCh knock-in - a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO."
Bioengineered
(2017).
Designing JavaScript library :
KnockIn.js
PITCh systems:
Nakade, Shota, et al. "Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9."
Nature communications
5
(2014).
Sakuma, Tetsushi, et al. "MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems."
Nature protocols
11.1
(2016): 118-133.
Visit the old version of PITCh designer:
version 1.0
version 2.0
*We do not recommend using Internet Explorer to use PITCh designer 2.1.
1. Enter nucleotide sequence
Paste nucleotide sequence (100-15,000 bp) [FASTA format]:
>sample sequence GTGACGTTTCAACACAGACCTGAGGGAGGGAGAGAGCCCCCAAGAGGAACACAGCACAGGCTCTGGAGTGGCGGCAGGAACCAGACCCCAGGGGGTACAT GGTCTCACTCAGGATCACACGGACAGGCTTGGAACCCACATCTGCCACCCACCCCTGAGGGGCCCAGGCCCTGGGGACTCACAGGACAGAGGGCTCCGGC AGCTTCGGGGAGGGGGTCGGGGTAATTCTGGCAAGACGGAGCTCCTTGGCCTGTGTGGAGAGGAGAAGGGGAGGAAGGGGCAGTTCCCTCGACTGGGCAG GGGCCTGGGCCTGGACCCGGCCCAACCCTCACTCACCTGAGTGGAGGTCCCTTCCAGCCAGGAGGAGGAAGCCGAGCGCTGCAGCCCAGCCCCAGGGGCT CCCTCCGCTGTCCGCCTTTCAGGGGGACCCAGGGCACCAGAACTCCCTGTCTTCAGGAGGCCAAAGCGCCTGGAGAAGGGGGCCTCTTCAAGCTGCTGGG AGAAGGAGGAGGTCTCAGTTAGAGAGAAAGGATCCCTCTTCTCAGACCTCAAGGGTTAGCCCCCAAAGGACTGCAACAAACTACAATTCCCATCAGCCCC CGGGGCAGGCACAGCCTAAAAAGGAAGCCGGTTGTCCAGGACGACTCTGGGAACTATAGTCTTCCCCCTATCTGCCCCTGCCAGAGGTTCACAGGCTGTA TGGAATCCCACCTCCGGGCCCTCCCAGCCTCACAGGACCTCTCAGGGCATCCACTCACCACGGGACTCTTAGGGCTGGGGTGCGGCGGGGAGGAGACGCC ATTGAGGGTTCTGGGTTCTGCAGGGGGTGGTTCTGTGATGTGGGAACACCGGGCAGGTCACAGAAGATGCCAGTTGCCTCTAGATTCAGAG
Reading frame:
Frame 1
Frame 2
Frame 3
No frame
Adjustment of reading frame:
C-insertion method
Codon deletion method
Knock-in cassette:
EGFP2APuroR (Sakuma et al.,2016)
CMV-EGFP2APuroR-polyA (Nakamae et al., 2017)
User defined insert
Paste insert sequence (20-15,000 bp) [FASTA format]:
> User defined insert atggtgagcaagggcgaggagctgttcaccggggtggtgcccatcctggtcgagctggacggcgacgtaaacggccacaagttcagcgtgtccggcgagg gcgagggcgatgccacctacggcaagctgaccctgaagttcatctgcaccaccggcaagctgcccgtgccctggcccaccctcgtgaccaccctgaccta cggcgtgcagtgcttcagccgctaccccgaccacatgaagcagcacgacttcttcaagtccgccatgcccgaaggctacgtccaggagcgcaccatcttc ttcaaggacgacggcaactacaagacccgcgccgaggtgaagttcgagggcgacaccctggtgaaccgcatcgagctgaagggcatcgacttcaaggagg acggcaacatcctggggcacaagctggagtacaactacaacagccacaacgtctatatcatggccgacaagcagaagaacggcatcaaggtgaacttcaa gatccgccacaacatcgaggacggcagcgtgcagctcgccgaccactaccagcagaacacccccatcggcgacggccccgtgctgctgcccgacaaccac tacctgagcacccagtccgccctgagcaaagaccccaacgagaagcgcgatcacatggtcctgctggagttcgtgaccgccgccgggatcactctcggca tggacgagctgtacaagtaa
Length of left microhomology (10-40 bp):
PAM sequence requirement:
*PITCh system using Cpf1 is unconfirmed
Length of right microhomology (10-40 bp):
Species:
none
Advanced options >>>
Tm value
CG %
Primers for genotyping :
Min (0-100 ℃):
Max (0-100 ℃):
Min (0-100 %):
Max (0-100 %):
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