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CRISPRdirect specifications


Unique identifier OMICS_06778
Name CRISPRdirect
Interface Web user interface
Restrictions to use None
Input data Single target region sequence
Computer skills Basic
Stability Stable
Maintained Yes


  • Invertebrates
    • Bombyx mori
  • Plants and Fungi
    • Arabidopsis thaliana
    • Zea mays
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus

Publication for CRISPRdirect

CRISPRdirect citations


Targeted mutagenesis in wheat microspores using CRISPR/Cas9

Sci Rep
PMCID: 5916876
PMID: 29695804
DOI: 10.1038/s41598-018-24690-8

[…] of regenerating successfully edited plants, designing highly specific and effective grnas is important. multiple bioinformatics tools, such as wheatcrispr (cram et al., submitted), e-crisp and crisprdirect, have been developed to facilitate the design of grnas targeting specific loci in the wheat genome and prediction of off-target sites. among these, the wheatcrispr tool offers a distinct […]


Expanding the genetic toolkit of Tribolium castaneum

PLoS One
PMCID: 5897005
PMID: 29649291
DOI: 10.1371/journal.pone.0195977

[…] numerical aperture of 1.40. light and fluorescent whole animal images were collected on a leicamz10f dissecting microscope. all pictures were processed in adobe photoshop., grnas were designed using crisprdirect [] using the tcas3 genome assembly for the specificity check. only high-quality grnas were selected. 20-mer protospacer sequences were cloned into bsai-digested pu6b-bsai-grna [] […]


Rapid CRISPR/Cas9 Mediated Cloning of Full Length Epstein Barr Virus Genomes from Latently Infected Cells

PMCID: 5923465
PMID: 29614006
DOI: 10.3390/v10040171

[…] plasmid, was used to make px330-sgebv, which introduces a single cut to the target site (). the target sequence of the crispr/cas9 plasmid was chosen by subjecting the 1088-bp sequence to crisprdirect ( so far, the crispr/cas9 plasmid did not show any off-target effects, which can be manifested by cell growth retardation or cell death of the host cells. […]


Genome wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

PMCID: 5879934
PMID: 29609617
DOI: 10.1186/s13072-018-0183-3

[…] drosophila stock center) (additional file : fig. 19). oligonucleotides that target the genomic region that contains mimic insert and cds of cg9879 were designed with crispr optimal finder and crisprdirect tools [, ]. each oligonucleotide pair (l1: 5′-cttcgacgatggtgacaggtgtct-3′, l2: 5′-aaacagacacctgtcaccatcgtc-3′, r1: 5′-cttcgtgccagtggttggcccgag-3′, r2: 5′-aaacctcgggccaaccactggcac-3′) […]


Multiple nuclear replicating viruses require the stress induced protein ZC3H11A for efficient growth

Proc Natl Acad Sci U S A
PMCID: 5910864
PMID: 29610341
DOI: 10.1073/pnas.1722333115

[…] adding preheated medium (42 °c) to the cells, which were then incubated at 42 °c for 1 h., zc3h11a was knocked out in hela cells using crispr/cas9. a specific grna for zc3h11a was designed using the crisprdirect tools (). a grna expression cassette containing the u6 promoter, the grna, a grna scaffold, and a termination signal () was synthesized by integrated dna technologies (fig. s1a). […]


Overexpression of OsNAC14 Improves Drought Tolerance in Rice

Front Plant Sci
PMCID: 5855183
PMID: 29593766
DOI: 10.3389/fpls.2018.00310

[…] caused by crispr/cas9 mediated mutagenesis, we performed computational analysis to select unique and specific sequence which can be used for grna target site on osnac14 coding sequence using crisprdirect software ( rice u6 promoter and 5′-region of grna was amplified by pcr reactions (f: 5′-cccaagcttaaggaatctttaaacatacga-3′, r: […]

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CRISPRdirect institution(s)
Database Center for Life Science (DBCLS), National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima, Shizuoka, Japan; Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
CRISPRdirect funding source(s)
Supported by the Life Science Database Integration Project, the National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (JST); a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan; and the Cell Innovation Program of MEXT.

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