grID Information

Summary

grID: hs025713240
Sequence (23-mer): GAAACCCGGGAGGCTAGGGACGG
grID Score: high (700)
Doench (2014) Score: 0.12292
Doench (2016) Score: 0.60832
Cas9: S. pyogenes

Genomic Context

Genomic Location: chr12:6643753-6643775
Strand: +
gRNA location: gene:refGene(GAPDH)

Nearest Genes

refseqgenechromstartenddistance
NM_002046 GAPDHchr12664358466475370
NM_001256799 GAPDHchr1266444086647537633
NM_014865 NCAPD2chr12660329766411322621
NM_001039670 IFFO1chr12664869366652494918
NM_001193457 IFFO1chr12664869366652494918

Browser View

Sequence Analysis

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

Thermodynamic Properties

GC-content (%): 65
GC-score: high
Tm (°C): 68.30
Tm score: moderate
RNAfold (dot bracket): ....(((((....)).))).
deltaG (Kcal/mol): -4.40
Predicted Folding: moderate secondary structure

Offtarget Analysis

Total Predicted Genomic Targets: 6
Total Genomic Sites With 0 Mismatches:
Total Genomic Sites With 1 Mismatches:
Total Genomic Sites With 2 Mismatches:
Total Genomic Sites With 3 Mismatches: 6
1chr12:6643752-66437750
GAAACCCGGGAGGCTAGGGACGG
|||||||||||||||||||||||
GAAACCCGGGAGGCTAGGGACGG
2chr9:39027436-390274593
CCGTCCCTAGCCTCCCGGGTTTC
||*||||||||||||||*||*||
CCCTCCCTAGCCTCCCGCGTATC
3chr9:40075265-400752883
GAAACCCGGGAGGCTAGGGACGG
||*||*||||||||||||||*||
GATACTCGGGAGGCTAGGGAAGG
4chr9:40384002-403840253
GAAACCCGGGAGGCTAGGGACGG
||*||*||||||||||||||*||
GATACTCGGGAGGCTAGGGAAGG
5chr15:101601761-1016017843
GAAACCCGGGAGGCTAGGGACGG
||*||||*||||||||||||||*
GAGACCCAGGAGGCTAGGGACGT
6chr21:46222167-462221903
CCGTCCCTAGCCTCCCGGGTTTC
|||||||*||||**|||||||||
CCGTCCCAAGCCAGCCGGGTTTC
7chr4:37978731-379787543
CCGTCCCTAGCCTCCCGGGTTTC
*||||||*|||||||*|||||||
GCGTCCCAAGCCTCCGGGGTTTC
1
Number of Mismatches:0
Location:chr12:6643752-6643775
Genomic Sequence:GAAACCCGGGAGGCTAGGGACGG
Strand:+
Genomic Region:gene(GAPDH)
3' PAM Orientation:GAAACCCGGGAGGCTAGGGACGG
Alignment:
GAAACCCGGGAGGCTAGGGACGG
|||||||||||||||||||||||
GAAACCCGGGAGGCTAGGGACGG
Mismatch: 


2


Number of Mismatches:3


Location:chr9:39027436-39027459


Genomic Sequence:GATACGCGGGAGGCTAGGGAGGG


Strand:-


Genomic Region:intergenic



3' PAM Orientation:GATACGCGGGAGGCTAGGGAGGG


Alignment:
GAAACCCGGGAGGCTAGGGACGG
||*||*||||||||||||||*||
GATACGCGGGAGGCTAGGGAGGG


Mismatch:

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


3


Number of Mismatches:3


Location:chr9:40075265-40075288


Genomic Sequence:GATACTCGGGAGGCTAGGGAAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GATACTCGGGAGGCTAGGGAAGG


Alignment:
GAAACCCGGGAGGCTAGGGACGG
||*||*||||||||||||||*||
GATACTCGGGAGGCTAGGGAAGG


Mismatch:

..T....................
.....T.................
....................A..
Distal mismatch
Distal mismatch
PAM N Offtarget


4


Number of Mismatches:3


Location:chr9:40384002-40384025


Genomic Sequence:GATACTCGGGAGGCTAGGGAAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GATACTCGGGAGGCTAGGGAAGG


Alignment:
GAAACCCGGGAGGCTAGGGACGG
||*||*||||||||||||||*||
GATACTCGGGAGGCTAGGGAAGG


Mismatch:

..T....................
.....T.................
....................A..
Distal mismatch
Distal mismatch
PAM N Offtarget


5


Number of Mismatches:3


Location:chr15:101601761-101601784


Genomic Sequence:GAGACCCAGGAGGCTAGGGACGT


Strand:+


Genomic Region:gene(LRRK1)



3' PAM Orientation:GAGACCCAGGAGGCTAGGGACGT


Alignment:
GAAACCCGGGAGGCTAGGGACGG
||*||||*||||||||||||||*
GAGACCCAGGAGGCTAGGGACGT


Mismatch:

..G....................
.......A...............
......................T
Distal mismatch
Distal seed mismatch
PAM mismatch


6


Number of Mismatches:3


Location:chr21:46222167-46222190


Genomic Sequence:GAAACCCGGCTGGCTTGGGACGG


Strand:-


Genomic Region:intergenic



3' PAM Orientation:GAAACCCGGCTGGCTTGGGACGG


Alignment:
GAAACCCGGGAGGCTAGGGACGG
|||||||||**||||*|||||||
GAAACCCGGCTGGCTTGGGACGG


Mismatch:

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


7


Number of Mismatches:3


Location:chr4:37978731-37978754


Genomic Sequence:GAAACCCCGGAGGCTTGGGACGC


Strand:-


Genomic Region:gene(TBC1D1)



3' PAM Orientation:GAAACCCCGGAGGCTTGGGACGC


Alignment:
GAAACCCGGGAGGCTAGGGACGG
|||||||*|||||||*||||||*
GAAACCCCGGAGGCTTGGGACGC


Mismatch:

.......C...............
...............T.......
......................C
Distal seed mismatch
Proximal seed mismatch
PAM mismatch











Paired Nickase
Cas9(D10A)



	
PairOffsetOverhang

		
hs025713241-133

		
hs0257132341953

		
hs0257132303569

		
hs0257132293872

		
hs0257132275589

		
hs0257132265690

		
hs0257132255993

		
hs0257132246599

		
hs02571322366100

		
hs02571322285119

		
hs02571322186120

		
hs02571322087121

		
hs02571321988122

		
hs02571321893127

		
hs02571321796130

		
hs025713216100134




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


Csp2014IGGAGGCGGAGGCGAAACCCGGGAGGCTAGGGACGG


SecICCNNGGCCCGGGGAAACCCGGGAGGCTAGGGACGG


FinIGGGACGGGACGAAACCCGGGAGGCTAGGGACGG


SmaICCCGGGCCCGGGGAAACCCGGGAGGCTAGGGACGG


CviJIRGCYGGCTGAAACCCGGGAGGCTAGGGACGG


HpaIICCGGCCGGGAAACCCGGGAGGCTAGGGACGG


AvaICYCGRGCCCGGGGAAACCCGGGAGGCTAGGGACGG


CauIICCSGGCCCGGGAAACCCGGGAGGCTAGGGACGG


PsuGIBBCGDCCCGGGAAACCCGGGAGGCTAGGGACGG


MaeICTAGCTAGGAAACCCGGGAGGCTAGGGACGG


ScrFICCNGGCCCGGGAAACCCGGGAGGCTAGGGACGG


RlaIVCWGCTGAAACCCGGGAGGCTAGGGACGG


Pdi8503IIICCGGNAGCCGGGAGGAAACCCGGGAGGCTAGGGACGG




SNPs and Variation




NamestartendstrandrefNCBIrefUCSCobservedclassfunction


rs18440711666437726643773+CCC/Gsingleintron,near-gene-5,untranslated-5




Notes


	

        	×
        	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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