PLANT CRISPR TOOL
This tool is designed to identify potential CRISPR target(s) on a gene of your choice.
CRISPR targets (guide RNA targeting sites) are identified on exon sequences of the gene.
An appropriate target is 20bp long, starting with G, and ending with PAM site (e.g. NGG).
Each candidate CRISPR target is examined for homopolymer. Any targeted sequences with more than 4 base homopolymer repeats (e.g. AAAAA) are filtered out.
Each target sequence, including the PAM site, is then aligned to the reference genome using
Only targets that align uniquely back to the reference genome are listed.
To change the color of a feature type, click on its legend in the top-left corner and enter a
for your desired color.
To select only CRISPR targets that affect coding sequence, click on the 'CDS' button.
To select CRISPR targets on a specific region of the gene, click on the region of interest.
Exporting options only include entries that are listed on the output table. To export all entries, click 'Show all' and then export.
Features under development
Support more species, assembly, and PAM sequence. Requests are welcomed.
Allow bases other than 'G' for the target's first base.
More extensive check for off-targets.
This tool is under active development, bugs are to be expected. Use at your own risk. Independently verifying the results is strongly encouraged.
For any suggestions, or bug reports, please contact Ha Le
We identified and verified two maize glossy genes with the information of gene co-expression networks.
was accepted by the Plant Journal.
Honored to receive the NSF PGRP award to work on maize transformation. More in
New manuscript with Schnable labs in Molecular Biology and Evolution:
Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels.
: NIFA is funding, through NSF/NIFA Plant Biotic Interactions Program, our 3-year project to genetically dissect bacterial virulence and host resistance of maize Goss's wilt.
Our latest publication using XP-CNV to discover disease associated genes:
Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize
A new genotyping solution:
tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci
Our K-mer study to characterize genomes: A K-mer method for comparative genomics and genetic mapping of copy number variation:
Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement
Congratulations to Dr. Yanhai Yin who led the Rd26 work:
RD26 mediates crosstalk between drought and brassinosteroid signalling pathway
Great discovery, bacteria enhance fungal virulence, led by Dr. Frank White:
Dimorphic and Virulence-Enhancing Endosymbiont Bacterium Discovered in Rhizoctonia solani
Our PacBio publication:
Long reads to resolve complicated repetitive TAL gene assembly
Liu Lab 4022 Throckmorton Hall 1712 Claflin Rd Manhattan, KS 66502