grID Information

Summary

grID: hs025713229
Sequence (23-mer): GCGGCTGACTGTCGAACAGGAGG
grID Score: high (700)
Doench (2014) Score: 0.13921
Doench (2016) Score: 0.62884
Cas9: S. pyogenes

Genomic Context

Genomic Location: chr12:6643715-6643693
Strand: -
gRNA location: exon:refGene(NM_002046.exon0)

Nearest Genes

refseqgenechromstartenddistance
NM_002046 GAPDHchr12664358466475370
NM_001256799 GAPDHchr1266444086647537715
NM_014865 NCAPD2chr12660329766411322583
NM_001039670 IFFO1chr12664869366652495000
NM_001193457 IFFO1chr12664869366652495000

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): GCGGCUGACUGUCGAACAGG
Target Sequence Occurrence: unique
PAM motif: AGG
Homopolymeric Runs: none
Pol III Terminator: none

Thermodynamic Properties

GC-content (%): 65
GC-score: high
Tm (°C): 60.99
Tm score: moderate
RNAfold (dot bracket): .((((.....))))......
deltaG (Kcal/mol): -4.20
Predicted Folding: moderate secondary structure

Offtarget Analysis

Total Predicted Genomic Targets: 12
Total Genomic Sites With 0 Mismatches: 1
Total Genomic Sites With 1 Mismatches: 1
Total Genomic Sites With 2 Mismatches: 2
Total Genomic Sites With 3 Mismatches: 8
1chr12:6643692-66437150
CCTCCTGTTCGACAGTCAGCCGC
|||||||||||||||||||||||
CCTCCTGTTCGACAGTCAGCCGC
2chrX:39647433-396474561
GCGGCTGACTGTCGAACAGGAGG
||||||||||||*||||||||||
GCGGCTGACTGTAGAACAGGAGG
3chr15:64821908-648219312
GCGGCTGACTGTCGAACAGGAGG
|*|||||*|||||||||||||||
GTGGCTGTCTGTCGAACAGGAGG
4chr15:64920803-649208262
GCGGCTGACTGTCGAACAGGAGG
|||||||*||||*||||||||||
GCGGCTGTCTGTAGAACAGGAGG
5chr22:41070493-410705163
GCGGCTGACTGTCGAACAGGAGG
||*||||*|*|||||||||||||
GCAGCTGTCAGTCGAACAGGAGG
6chr1:215044015-2150440383
CCTCCTGTTCGACAGTCAGCCGC
||||||*||||||||*|||||*|
CCTCCTCTTCGACAGACAGCCCC
7chr5:159378543-1593785663
GCGGCTGACTGTCGAACAGGAGG
||*||||*|||||||||*|||||
GCAGCTGTCTGTCGAACGGGAGG
8chr13:29880853-298808763
CCTCCTGTTCGACAGTCAGCCGC
*||||||||||||||*|||||*|
GCTCCTGTTCGACAGACAGCCCC
9chr6:80663766-806637893
GCGGCTGACTGTCGAACAGGAGG
||*||||*|||||*|||||||||
GCAGCTGTCTGTCAAACAGGAGG
10chr5:173940243-1739402663
CCTCCTGTTCGACAGTCAGCCGC
|||||*|||||||||*|||||*|
CCTCCAGTTCGACAGACAGCCCC
11chr16:28252015-282520383
GCGGCTGACTGTCGAACAGGAGG
|||||||*||||||||**|||||
GCGGCTGTCTGTCGAATGGGAGG
12chr19:47061826-470618493
CCTCCTGTTCGACAGTCAGCCGC
|||||*||||*||||*|||||||
CCTCCAGTTCCACAGACAGCCGC
1
Number of Mismatches:0
Location:chr12:6643692-6643715
Genomic Sequence:GCGGCTGACTGTCGAACAGGAGG
Strand:-
Genomic Region:exon(NM_002046.exon0)
3' PAM Orientation:GCGGCTGACTGTCGAACAGGAGG
Alignment:
GCGGCTGACTGTCGAACAGGAGG
|||||||||||||||||||||||
GCGGCTGACTGTCGAACAGGAGG
Mismatch: 


2


Number of Mismatches:1


Location:chrX:39647433-39647456


Genomic Sequence:GCGGCTGACTGTAGAACAGGAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GCGGCTGACTGTAGAACAGGAGG


Alignment:
GCGGCTGACTGTCGAACAGGAGG
||||||||||||*||||||||||
GCGGCTGACTGTAGAACAGGAGG


Mismatch:

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


3


Number of Mismatches:2


Location:chr15:64821908-64821931


Genomic Sequence:GTGGCTGTCTGTCGAACAGGAGG


Strand:+


Genomic Region:gene(ZNF609)



3' PAM Orientation:GTGGCTGTCTGTCGAACAGGAGG


Alignment:
GCGGCTGACTGTCGAACAGGAGG
|*|||||*|||||||||||||||
GTGGCTGTCTGTCGAACAGGAGG


Mismatch:

.T.....................
.......T...............
Distal mismatch
Distal seed mismatch


4


Number of Mismatches:2


Location:chr15:64920803-64920826


Genomic Sequence:GCGGCTGTCTGTAGAACAGGAGG


Strand:+


Genomic Region:gene(ZNF609)



3' PAM Orientation:GCGGCTGTCTGTAGAACAGGAGG


Alignment:
GCGGCTGACTGTCGAACAGGAGG
|||||||*||||*||||||||||
GCGGCTGTCTGTAGAACAGGAGG


Mismatch:

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


5


Number of Mismatches:3


Location:chr22:41070493-41070516


Genomic Sequence:GCAGCTGTCAGTCGAACAGGAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GCAGCTGTCAGTCGAACAGGAGG


Alignment:
GCGGCTGACTGTCGAACAGGAGG
||*||||*|*|||||||||||||
GCAGCTGTCAGTCGAACAGGAGG


Mismatch:

..A....................
.......T...............
.........A.............
Distal mismatch
Distal seed mismatch
Distal seed mismatch


6


Number of Mismatches:3


Location:chr1:215044015-215044038


Genomic Sequence:GGGGCTGTCTGTCGAAGAGGAGG


Strand:-


Genomic Region:intergenic



3' PAM Orientation:GGGGCTGTCTGTCGAAGAGGAGG


Alignment:
GCGGCTGACTGTCGAACAGGAGG
|*|||||*||||||||*||||||
GGGGCTGTCTGTCGAAGAGGAGG


Mismatch:

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


7


Number of Mismatches:3


Location:chr5:159378543-159378566


Genomic Sequence:GCAGCTGTCTGTCGAACGGGAGG


Strand:+


Genomic Region:gene(ADRA1B)



3' PAM Orientation:GCAGCTGTCTGTCGAACGGGAGG


Alignment:
GCGGCTGACTGTCGAACAGGAGG
||*||||*|||||||||*|||||
GCAGCTGTCTGTCGAACGGGAGG


Mismatch:

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


8


Number of Mismatches:3


Location:chr13:29880853-29880876


Genomic Sequence:GGGGCTGTCTGTCGAACAGGAGC


Strand:-


Genomic Region:gene(MTUS2)



3' PAM Orientation:GGGGCTGTCTGTCGAACAGGAGC


Alignment:
GCGGCTGACTGTCGAACAGGAGG
|*|||||*||||||||||||||*
GGGGCTGTCTGTCGAACAGGAGC


Mismatch:

.G.....................
.......T...............
......................C
Distal mismatch
Distal seed mismatch
PAM mismatch


9


Number of Mismatches:3


Location:chr6:80663766-80663789


Genomic Sequence:GCAGCTGTCTGTCAAACAGGAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GCAGCTGTCTGTCAAACAGGAGG


Alignment:
GCGGCTGACTGTCGAACAGGAGG
||*||||*|||||*|||||||||
GCAGCTGTCTGTCAAACAGGAGG


Mismatch:

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


10


Number of Mismatches:3


Location:chr5:173940243-173940266


Genomic Sequence:GGGGCTGTCTGTCGAACTGGAGG


Strand:-


Genomic Region:intergenic



3' PAM Orientation:GGGGCTGTCTGTCGAACTGGAGG


Alignment:
GCGGCTGACTGTCGAACAGGAGG
|*|||||*|||||||||*|||||
GGGGCTGTCTGTCGAACTGGAGG


Mismatch:

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


11


Number of Mismatches:3


Location:chr16:28252015-28252038


Genomic Sequence:GCGGCTGTCTGTCGAATGGGAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GCGGCTGTCTGTCGAATGGGAGG


Alignment:
GCGGCTGACTGTCGAACAGGAGG
|||||||*||||||||**|||||
GCGGCTGTCTGTCGAATGGGAGG


Mismatch:

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


12


Number of Mismatches:3


Location:chr19:47061826-47061849


Genomic Sequence:GCGGCTGTCTGTGGAACTGGAGG


Strand:-


Genomic Region:gene(PPP5D1)



3' PAM Orientation:GCGGCTGTCTGTGGAACTGGAGG


Alignment:
GCGGCTGACTGTCGAACAGGAGG
|||||||*||||*||||*|||||
GCGGCTGTCTGTGGAACTGGAGG


Mismatch:

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











Paired Nickase
Cas9(D10A)



	
PairOffsetOverhang

		
hs025713228-133

		
hs025713231842

		
hs025713232943

		
hs0257132331246

		
hs0257132352458

		
hs0257132362559

		
hs0257132372862

		
hs0257132383367

		
hs0257132393468

		
hs0257132403872

		
hs0257132424680

		
hs0257132434983

		
hs0257132445387

		
hs0257132455488

		
hs0257132465589

		
hs0257132475892

		
hs0257132485993

		
hs0257132516599

		
hs02571325269103

		
hs02571325489123

		
hs02571325590124

		
hs02571325691125

		
hs02571325794128

		
hs02571325895129

		
hs025713259100134




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


TaqITCGATCGAGCGGCTGACTGTCGAACAGGAGG


OspHL35IIIYAGGAGCAGGAGGCGGCTGACTGTCGAACAGGAGG


CviJIRGCYGGCTGCGGCTGACTGTCGAACAGGAGG


RlaIVCWGCTGCGGCTGACTGTCGAACAGGAGG


RlaIVCWACTGCGGCTGACTGTCGAACAGGAGG


RlaIVCWACAGCGGCTGACTGTCGAACAGGAGG


Tsp4CIACNGTACTGTGCGGCTGACTGTCGAACAGGAGG


BisIGCNGCGCGGCGCGGCTGACTGTCGAACAGGAGG


Fnu4HIGCNGCGCGGCGCGGCTGACTGTCGAACAGGAGG


TauIGCSGCGCGGCGCGGCTGACTGTCGAACAGGAGG


PsuGIBBCGDGTCGAGCGGCTGACTGTCGAACAGGAGG




SNPs and Variation


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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