grID Information

Summary

grID: hs025713215
Sequence (23-mer): ACCGGGGGCGCGGCGGCAGGCGG
grID Score: moderate (600)
Doench (2014) Score: 0.04552
Doench (2016) Score: 0.51494
Cas9: S. pyogenes

Genomic Context

Genomic Location: chr12:6643650-6643628
Strand: -
gRNA location: exon:refGene(NM_002046.exon0)

Nearest Genes

refseqgenechromstartenddistance
NM_002046 GAPDHchr12664358466475370
NM_001256799 GAPDHchr1266444086647537780
NM_014865 NCAPD2chr12660329766411322518
NM_001039670 IFFO1chr12664869366652495065
NM_001193457 IFFO1chr12664869366652495065

DNase I hypersensitive sites from ENCODE

DNase I hypersensitivity region:chr12:6643560-6643710
Numbers of Cell Types:123
Cell Types:8988t, A549, AG04449, AG04450, AG09309, AG09319, AG10803, Adult_CD4_Th0, AoAF, AoSMC, BE2_C, BJ, Caco-2, CD14+, CD20+, CD34+_Mobilized, CMK, Chorion, Cll, HSMM_emb, Fibrobl, Fibrop, GM06990, GM12864, GM12865, GM12878, Gliobla, Gm12891, Gm12892, Gm18507, Gm19238, Gm19239, Gm19240, H9es, HAEpiC, HAc, HA-h, HBMEC, HCF, HCFaa, HCM, HCPEpiC, HCT-116, HConF, HEEpiC, H1-hESC, HFF, HFF-Myc, HGF, HIPEpiC, HL-60, HMEC, HMF, HMVEC-LBl, HMVEC-LLy, HMVEC-dAd, HMVEC-dBl-Ad, HMVEC-dBl-Neo, HMVEC-dLy-Ad, HMVEC-dLy-Neo, HMVEC-dNeo, HNPCEpiC, HPAEC, HPAF, HPF, HPdLF, HRCEpiC, HRE, HRGEC, HRPEpiC, HSMM, HSMM_FSHD, HUVEC, HVMF, HeLa-S3, HeLa-S3s3Ifna4h, HepG2, Hepatocytes, HPDE6-E6E7, HTR8svn, Huh-7, Huh-7.5, Ips, Ishikawa, Ishikawa, Jurkat, K562, LNCap, LNCaP, MCF-7, MCF-7, Medullo, Melano, Myometr, NB4, NH-A, NHDF-Ad, NHDF-neo, NHEK, NHLF, NT2-D1, Osteobl, PanIsletD, Panislets, Phte, PrEC, Progfib, RPTEC, RWPE1, SAEC, SK-N-SH, SK-N-MC, SkMC, Stellate, T-47D, Urothelia, UrotheliaUt189, WERI-Rb-1, WI-38, WI-38_TAM, H1-hESC, Th1, Th2,

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Sequence Analysis

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

Thermodynamic Properties

GC-content (%): 90
GC-score: very high
Tm (°C): 72.94
Tm score: high
RNAfold (dot bracket): .(((......))).......
deltaG (Kcal/mol): -4.00
Predicted Folding: moderate secondary structure

Offtarget Analysis

Total Predicted Genomic Targets: 13
Total Genomic Sites With 0 Mismatches: 1
Total Genomic Sites With 1 Mismatches:
Total Genomic Sites With 2 Mismatches: 1
Total Genomic Sites With 3 Mismatches: 11
1chr12:6643627-66436500
CCGCCTGCCGCCGCGCCCCCGGT
|||||||||||||||||||||||
CCGCCTGCCGCCGCGCCCCCGGT
2chr17:18022467-180224902
CCGCCTGCCGCCGCGCCCCCGGT
||||||||*|||||||*||||||
CCGCCTGCGGCCGCGCGCCCGGT
3chr1:227058659-2270586823
CCGCCTGCCGCCGCGCCCCCGGT
|||||||||||||*|||||*|*|
CCGCCTGCCGCCGGGCCCCGGCT
4chr1:2136024-21360473
CCGCCTGCCGCCGCGCCCCCGGT
|||||*|||||||*||||||||*
CCGCCAGCCGCCGGGCCCCCGGA
5chr22:38142288-381423113
ACCGGGGGCGCGGCGGCAGGCGG
*||||*|||||||||||*|||||
GCCGGAGGCGCGGCGGCGGGCGG
6chr7:36406644-364066673
ACCGGGGGCGCGGCGGCAGGCGG
**||||||||||||||*||||||
GGCGGGGGCGCGGCGGGAGGCGG
7chr8:130951953-1309519763
ACCGGGGGCGCGGCGGCAGGCGG
|*||||||*||||||||||*|||
AGCGGGGGAGCGGCGGCAGCCGG
8chr9:94186010-941860333
ACCGGGGGCGCGGCGGCAGGCGG
*||||||*||||||||*||||||
TCCGGGGCCGCGGCGGGAGGCGG
9chr14:97263828-972638513
ACCGGGGGCGCGGCGGCAGGCGG
*||||||||||||*|||*|||||
GCCGGGGGCGCGGAGGCGGGCGG
10chr16:639640-6396633
ACCGGGGGCGCGGCGGCAGGCGG
*|||||||||*||||||*|||||
GCCGGGGGCGGGGCGGCCGGCGG
11chr6:108489648-1084896713
CCGCCTGCCGCCGCGCCCCCGGT
||||||||*||*|||||||||*|
CCGCCTGCGGCGGCGCCCCCGCT
12chr1:225965357-2259653803
ACCGGGGGCGCGGCGGCAGGCGG
|||||||||||*|*|||||*|||
ACCGGGGGCGCTGTGGCAGCCGG
13chr15:85259033-852590563
CCGCCTGCCGCCGCGCCCCCGGT
||||*|*|||||*||||||||||
CCGCGTCCCGCCCCGCCCCCGGT
1
Number of Mismatches:0
Location:chr12:6643627-6643650
Genomic Sequence:ACCGGGGGCGCGGCGGCAGGCGG
Strand:-
Genomic Region:exon(NM_002046.exon0)
3' PAM Orientation:ACCGGGGGCGCGGCGGCAGGCGG
Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
|||||||||||||||||||||||
ACCGGGGGCGCGGCGGCAGGCGG
Mismatch: 


2


Number of Mismatches:2


Location:chr17:18022467-18022490


Genomic Sequence:ACCGGGCGCGCGGCCGCAGGCGG


Strand:-


Genomic Region:exon(NM_016239.exon1)



3' PAM Orientation:ACCGGGCGCGCGGCCGCAGGCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
||||||*|||||||*||||||||
ACCGGGCGCGCGGCCGCAGGCGG


Mismatch:

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


3


Number of Mismatches:3


Location:chr1:227058659-227058682


Genomic Sequence:AGCCGGGGCCCGGCGGCAGGCGG


Strand:-


Genomic Region:gene(PSEN2)



3' PAM Orientation:AGCCGGGGCCCGGCGGCAGGCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
|*|*|||||*|||||||||||||
AGCCGGGGCCCGGCGGCAGGCGG


Mismatch:

.G.....................
...C...................
.........C.............
Distal mismatch
Distal mismatch
Distal seed mismatch


4


Number of Mismatches:3


Location:chr1:2136024-2136047


Genomic Sequence:TCCGGGGGCCCGGCGGCTGGCGG


Strand:-


Genomic Region:gene(C1orf86)



3' PAM Orientation:TCCGGGGGCCCGGCGGCTGGCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
*||||||||*|||||||*|||||
TCCGGGGGCCCGGCGGCTGGCGG


Mismatch:

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


5


Number of Mismatches:3


Location:chr22:38142288-38142311


Genomic Sequence:GCCGGAGGCGCGGCGGCGGGCGG


Strand:+


Genomic Region:exon(NM_007032.exon0)



3' PAM Orientation:GCCGGAGGCGCGGCGGCGGGCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
*||||*|||||||||||*|||||
GCCGGAGGCGCGGCGGCGGGCGG


Mismatch:

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


6


Number of Mismatches:3


Location:chr7:36406644-36406667


Genomic Sequence:GGCGGGGGCGCGGCGGGAGGCGG


Strand:+


Genomic Region:exon(NM_001199707.exon0)



3' PAM Orientation:GGCGGGGGCGCGGCGGGAGGCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
**||||||||||||||*||||||
GGCGGGGGCGCGGCGGGAGGCGG


Mismatch:

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


7


Number of Mismatches:3


Location:chr8:130951953-130951976


Genomic Sequence:AGCGGGGGAGCGGCGGCAGCCGG


Strand:+


Genomic Region:exon(NR_046359.exon0)



3' PAM Orientation:AGCGGGGGAGCGGCGGCAGCCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
|*||||||*||||||||||*|||
AGCGGGGGAGCGGCGGCAGCCGG


Mismatch:

.G.....................
........A..............
...................C...
Distal mismatch
Distal seed mismatch
Proximal seed mismatch


8


Number of Mismatches:3


Location:chr9:94186010-94186033


Genomic Sequence:TCCGGGGCCGCGGCGGGAGGCGG


Strand:+


Genomic Region:exon(NM_005384.exon0)



3' PAM Orientation:TCCGGGGCCGCGGCGGGAGGCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
*||||||*||||||||*||||||
TCCGGGGCCGCGGCGGGAGGCGG


Mismatch:

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


9


Number of Mismatches:3


Location:chr14:97263828-97263851


Genomic Sequence:GCCGGGGGCGCGGAGGCGGGCGG


Strand:+


Genomic Region:gene(VRK1)



3' PAM Orientation:GCCGGGGGCGCGGAGGCGGGCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
*||||||||||||*|||*|||||
GCCGGGGGCGCGGAGGCGGGCGG


Mismatch:

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


10


Number of Mismatches:3


Location:chr16:639640-639663


Genomic Sequence:GCCGGGGGCGGGGCGGCCGGCGG


Strand:+


Genomic Region:gene(RAB40C)



3' PAM Orientation:GCCGGGGGCGGGGCGGCCGGCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
*|||||||||*||||||*|||||
GCCGGGGGCGGGGCGGCCGGCGG


Mismatch:

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


11


Number of Mismatches:3


Location:chr6:108489648-108489671


Genomic Sequence:AGCGGGGGCGCCGCCGCAGGCGG


Strand:-


Genomic Region:gene(NR2E1)



3' PAM Orientation:AGCGGGGGCGCCGCCGCAGGCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
|*|||||||||*||*||||||||
AGCGGGGGCGCCGCCGCAGGCGG


Mismatch:

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


12


Number of Mismatches:3


Location:chr1:225965357-225965380


Genomic Sequence:ACCGGGGGCGCTGTGGCAGCCGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:ACCGGGGGCGCTGTGGCAGCCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
|||||||||||*|*|||||*|||
ACCGGGGGCGCTGTGGCAGCCGG


Mismatch:

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


13


Number of Mismatches:3


Location:chr15:85259033-85259056


Genomic Sequence:ACCGGGGGCGGGGCGGGACGCGG


Strand:-


Genomic Region:gene(SEC11A)



3' PAM Orientation:ACCGGGGGCGGGGCGGGACGCGG


Alignment:
ACCGGGGGCGCGGCGGCAGGCGG
||||||||||*|||||*|*||||
ACCGGGGGCGGGGCGGGACGCGG


Mismatch:

..........G............
................G......
..................C....
Proximal seed mismatch
Proximal seed mismatch
Proximal seed mismatch











Paired Nickase
Cas9(D10A)



	
PairOffsetOverhang

		
hs0257132286498

		
hs02571323173107

		
hs02571323274108

		
hs02571323377111

		
hs02571323589123

		
hs02571323690124

		
hs02571323793127

		
hs02571323898132

		
hs02571323999133




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


HhaIGCGCGCGCACCGGGGGCGCGGCGGCAGGCGG


HpaIICCGGCCGGACCGGGGGCGCGGCGGCAGGCGG


Cac8IGCNNGCGCAGGCACCGGGGGCGCGGCGGCAGGCGG


BisIGCNGCGCGGCACCGGGGGCGCGGCGGCAGGCGG


PsuGIBBCGDCGCGGACCGGGGGCGCGGCGGCAGGCGG


PsuGIBBCGDGGCGGACCGGGGGCGCGGCGGCAGGCGG


Fnu4HIGCNGCGCGGCACCGGGGGCGCGGCGGCAGGCGG


RlaIVCWGCAACCGGGGGCGCGGCGGCAGGCGG


FnuDIICGCGCGCGACCGGGGGCGCGGCGGCAGGCGG


ScrFICCNGGCCGGGACCGGGGGCGCGGCGGCAGGCGG


SecICCNNGGCCGGGGACCGGGGGCGCGGCGGCAGGCGG


TauIGCSGCGCGGCACCGGGGGCGCGGCGGCAGGCGG


GlaIGCGCGCGCACCGGGGGCGCGGCGGCAGGCGG


CauIICCSGGCCGGGACCGGGGGCGCGGCGGCAGGCGG




SNPs and Variation


Notes

	

        	×
        	Warning!  This gRNA contains polymeric runs which can lead to greater off-targets.
    	




	

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



	

        	×
        	Warning!  This gRNA has a high Tm 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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