grID Information

Summary

grID: hs025713237
Sequence (23-mer): CGGGCGGAGAGAAACCCGGGAGG
grID Score: moderate (600)
Doench (2014) Score: 0.32661
Doench (2016) Score: 0.76636
Cas9: S. pyogenes

Genomic Context

Genomic Location: chr12:6643743-6643765
Strand: +
gRNA location: gene:refGene(GAPDH)

Nearest Genes

refseqgenechromstartenddistance
NM_002046 GAPDHchr12664358466475370
NM_001256799 GAPDHchr1266444086647537643
NM_014865 NCAPD2chr12660329766411322611
NM_001039670 IFFO1chr12664869366652494928
NM_001193457 IFFO1chr12664869366652494928

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Sequence Analysis

Target Sequence (RNA): CGGGCGGAGAGAAACCCGGG
Target Sequence Occurrence: unique
PAM motif: AGG
Homopolymeric Runs: none
Pol III Terminator: none

Thermodynamic Properties

GC-content (%): 75
GC-score: high
Tm (°C): 66.78
Tm score: moderate
RNAfold (dot bracket): ((((..........))))..
deltaG (Kcal/mol): -5.30
Predicted Folding: moderate secondary structure

Offtarget Analysis

Total Predicted Genomic Targets: 8
Total Genomic Sites With 0 Mismatches:
Total Genomic Sites With 1 Mismatches:
Total Genomic Sites With 2 Mismatches:
Total Genomic Sites With 3 Mismatches: 8
1chr12:6643742-66437650
CGGGCGGAGAGAAACCCGGGAGG
|||||||||||||||||||||||
CGGGCGGAGAGAAACCCGGGAGG
2chr20:19192490-191925133
CGGGCGGAGAGAAACCCGGGAGG
*||||*|||*|||||||||||||
GGGGCAGAGGGAAACCCGGGAGG
3chr1:5490419-54904423
CCTCCCGGGTTTCTCTCCGCCCG
||||||||||*|||||||*||*|
CCTCCCGGGTATCTCTCCCCCGG
4chr1:207600746-2076007693
CGGGCGGAGAGAAACCCGGGAGG
*||||*|||||||||||*|||||
AGGGCAGAGAGAAACCCAGGAGG
5chr9:136474350-1364743733
CGGGCGGAGAGAAACCCGGGAGG
||||||**|||||*|||||||||
CGGGCGCTGAGAAGCCCGGGAGG
6chr14:55032722-550327453
CCTCCCGGGTTTCTCTCCGCCCG
||*||||||||*||||||*||||
CCACCCGGGTTACTCTCCCCCCG
7chr19:45946830-459468533
CGGGCGGAGAGAAACCCGGGAGG
*||||||||||*||||||||||*
GGGGCGGAGAGGAACCCGGGAGT
8chr11:62105231-621052543
CGGGCGGAGAGAAACCCGGGAGG
*||||||||||*|||*|||||||
GGGGCGGAGAGGAACGCGGGAGG
9chr20:61425628-614256513
CGGGCGGAGAGAAACCCGGGAGG
*||||||||||||*||||*||||
GGGGCGGAGAGAAGCCCGTGAGG
1
Number of Mismatches:0
Location:chr12:6643742-6643765
Genomic Sequence:CGGGCGGAGAGAAACCCGGGAGG
Strand:+
Genomic Region:gene(GAPDH)
3' PAM Orientation:CGGGCGGAGAGAAACCCGGGAGG
Alignment:
CGGGCGGAGAGAAACCCGGGAGG
|||||||||||||||||||||||
CGGGCGGAGAGAAACCCGGGAGG
Mismatch: 


2


Number of Mismatches:3


Location:chr20:19192490-19192513


Genomic Sequence:GGGGCAGAGGGAAACCCGGGAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GGGGCAGAGGGAAACCCGGGAGG


Alignment:
CGGGCGGAGAGAAACCCGGGAGG
*||||*|||*|||||||||||||
GGGGCAGAGGGAAACCCGGGAGG


Mismatch:

G......................
.....A.................
.........G.............
Distal mismatch
Distal mismatch
Distal seed mismatch


3


Number of Mismatches:3


Location:chr1:5490419-5490442


Genomic Sequence:CCGGGGGAGAGATACCCGGGAGG


Strand:-


Genomic Region:intergenic



3' PAM Orientation:CCGGGGGAGAGATACCCGGGAGG


Alignment:
CGGGCGGAGAGAAACCCGGGAGG
|*||*|||||||*||||||||||
CCGGGGGAGAGATACCCGGGAGG


Mismatch:

.C.....................
....G..................
............T..........
Distal mismatch
Distal mismatch
Proximal seed mismatch


4


Number of Mismatches:3


Location:chr1:207600746-207600769


Genomic Sequence:AGGGCAGAGAGAAACCCAGGAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:AGGGCAGAGAGAAACCCAGGAGG


Alignment:
CGGGCGGAGAGAAACCCGGGAGG
*||||*|||||||||||*|||||
AGGGCAGAGAGAAACCCAGGAGG


Mismatch:

A......................
.....A.................
.................A.....
Distal mismatch
Distal mismatch
Proximal seed mismatch


5


Number of Mismatches:3


Location:chr9:136474350-136474373


Genomic Sequence:CGGGCGCTGAGAAGCCCGGGAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:CGGGCGCTGAGAAGCCCGGGAGG


Alignment:
CGGGCGGAGAGAAACCCGGGAGG
||||||**|||||*|||||||||
CGGGCGCTGAGAAGCCCGGGAGG


Mismatch:

......C................
.......T...............
.............G.........
Distal mismatch
Distal seed mismatch
Proximal seed mismatch


6


Number of Mismatches:3


Location:chr14:55032722-55032745


Genomic Sequence:CGGGGGGAGAGTAACCCGGGTGG


Strand:-


Genomic Region:intergenic



3' PAM Orientation:CGGGGGGAGAGTAACCCGGGTGG


Alignment:
CGGGCGGAGAGAAACCCGGGAGG
||||*||||||*||||||||*||
CGGGGGGAGAGTAACCCGGGTGG


Mismatch:

....G..................
...........T...........
....................T..
Distal mismatch
Proximal seed mismatch
PAM N Offtarget


7


Number of Mismatches:3


Location:chr19:45946830-45946853


Genomic Sequence:GGGGCGGAGAGGAACCCGGGAGT


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GGGGCGGAGAGGAACCCGGGAGT


Alignment:
CGGGCGGAGAGAAACCCGGGAGG
*||||||||||*||||||||||*
GGGGCGGAGAGGAACCCGGGAGT


Mismatch:

G......................
...........G...........
......................T
Distal mismatch
Proximal seed mismatch
PAM mismatch


8


Number of Mismatches:3


Location:chr11:62105231-62105254


Genomic Sequence:GGGGCGGAGAGGAACGCGGGAGG


Strand:+


Genomic Region:gene(ASRGL1)



3' PAM Orientation:GGGGCGGAGAGGAACGCGGGAGG


Alignment:
CGGGCGGAGAGAAACCCGGGAGG
*||||||||||*|||*|||||||
GGGGCGGAGAGGAACGCGGGAGG


Mismatch:

G......................
...........G...........
...............G.......
Distal mismatch
Proximal seed mismatch
Proximal seed mismatch


9


Number of Mismatches:3


Location:chr20:61425628-61425651


Genomic Sequence:GGGGCGGAGAGAAGCCCGTGAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GGGGCGGAGAGAAGCCCGTGAGG


Alignment:
CGGGCGGAGAGAAACCCGGGAGG
*||||||||||||*||||*||||
GGGGCGGAGAGAAGCCCGTGAGG


Mismatch:

G......................
.............G.........
..................T....
Distal mismatch
Proximal seed mismatch
Proximal seed mismatch











Paired Nickase
Cas9(D10A)



	
PairOffsetOverhang

		
hs025713234943

		
hs0257132302559

		
hs0257132292862

		
hs0257132274579

		
hs0257132264680

		
hs0257132254983

		
hs0257132245589

		
hs0257132235690

		
hs02571322275109

		
hs02571322176110

		
hs02571322077111

		
hs02571321978112

		
hs02571321883117

		
hs02571321786120

		
hs02571321690124

		
hs02571321593127




Sequence



Surrounding genomic sequence (500bp upstream and downstream target site)


Note: Repeats and low complexity DNA is shown in lower case; non repeating sequence is shown in upper case.







	















Screening Analysis


Restriction EnzymeRecognition SiteMatchSequence


Pdi8503IIICCGGNAGCCGGGAGCGGGCGGAGAGAAACCCGGGAGG


PsuGIBBCGDGGCGGCGGGCGGAGAGAAACCCGGGAGG


PsuGIBBCGDCCCGGCGGGCGGAGAGAAACCCGGGAGG


HpaIICCGGCCGGCGGGCGGAGAGAAACCCGGGAGG


SecICCNNGGCCCGGGCGGGCGGAGAGAAACCCGGGAGG


AvaICYCGRGCCCGGGCGGGCGGAGAGAAACCCGGGAGG


CauIICCSGGCCCGGCGGGCGGAGAGAAACCCGGGAGG


ScrFICCNGGCCCGGCGGGCGGAGAGAAACCCGGGAGG


SmaICCCGGGCCCGGGCGGGCGGAGAGAAACCCGGGAGG




SNPs and Variation


Notes

	

        	×
        	Warning!  This gRNA contains a dinucleotide repeat sequence which can lead to greater off-targets.
    	




	

        	×
        	Warning!  This gRNA has a high GC content which can lead to greater off-targets.
    	



References



Jaskula-Ranga, V and Zack, DJ. 2016.  grID: A CRISPR-Cas9 guide RNA Database and Resource for Gene-Editing.
bioRxiv 097352; doi: https://doi.org/10.1101/097352


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