grID Information

Summary

grID: hs025713230
Sequence (23-mer): GATGCGGCTGACTGTCGAACAGG
grID Score: high (700)
Doench (2014) Score: 0.09586
Doench (2016) Score: 0.46257
Cas9: S. pyogenes

Genomic Context

Genomic Location: chr12:6643718-6643696
Strand: -
gRNA location: exon:refGene(NM_002046.exon0)

Nearest Genes

refseqgenechromstartenddistance
NM_002046 GAPDHchr12664358466475370
NM_001256799 GAPDHchr1266444086647537712
NM_014865 NCAPD2chr12660329766411322586
NM_001039670 IFFO1chr12664869366652494997
NM_001193457 IFFO1chr12664869366652494997

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

Thermodynamic Properties

GC-content (%): 60
GC-score: moderate
Tm (°C): 58.63
Tm score: moderate
RNAfold (dot bracket): ....((((.....))))...
deltaG (Kcal/mol): -4.20
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: 1
Total Genomic Sites With 2 Mismatches:
Total Genomic Sites With 3 Mismatches: 11
1chr12:6643695-66437180
CCTGTTCGACAGTCAGCCGCATC
|||||||||||||||||||||||
CCTGTTCGACAGTCAGCCGCATC
2chrX:39647430-396474531
GATGCGGCTGACTGTCGAACAGG
|||||||||||||||*|||||||
GATGCGGCTGACTGTAGAACAGG
3chr13:29880856-298808793
CCTGTTCGACAGTCAGCCGCATC
||||||||||||*|||||*|||*
CCTGTTCGACAGACAGCCCCATG
4chr15:64821905-648219283
GATGCGGCTGACTGTCGAACAGG
*|||*|||||*||||||||||||
TATGTGGCTGTCTGTCGAACAGG
5chr6:80663763-806637863
GATGCGGCTGACTGTCGAACAGG
|||||*||||*|||||*||||||
GATGCAGCTGTCTGTCAAACAGG
6chr5:159378540-1593785633
GATGCGGCTGACTGTCGAACAGG
|||||*||||*|||||||||*||
GATGCAGCTGTCTGTCGAACGGG
7chr5:173940246-1739402693
CCTGTTCGACAGTCAGCCGCATC
||*|||||||||*|||||*||||
CCAGTTCGACAGACAGCCCCATC
8chr1:215044018-2150440413
CCTGTTCGACAGTCAGCCGCATC
|||*||||||||*|||||*||||
CCTCTTCGACAGACAGCCCCATC
9chr22:41070490-410705133
GATGCGGCTGACTGTCGAACAGG
|||||*||||*|*||||||||||
GATGCAGCTGTCAGTCGAACAGG
10chr15:64920800-649208233
GATGCGGCTGACTGTCGAACAGG
*|||||||||*||||*|||||||
TATGCGGCTGTCTGTAGAACAGG
11chr19:47061829-470618523
CCTGTTCGACAGTCAGCCGCATC
||*||||*||||*||||||||||
CCAGTTCCACAGACAGCCGCATC
12chr1:120102432-1201024553
GATGCGGCTGACTGTCGAACAGG
||||||||||*||||||||**||
GATGCGGCTGTCTGTCGAATGGG
13chr16:28252012-282520353
GATGCGGCTGACTGTCGAACAGG
||||||||||*||||||||**||
GATGCGGCTGTCTGTCGAATGGG
1
Number of Mismatches:0
Location:chr12:6643695-6643718
Genomic Sequence:GATGCGGCTGACTGTCGAACAGG
Strand:-
Genomic Region:exon(NM_002046.exon0)
3' PAM Orientation:GATGCGGCTGACTGTCGAACAGG
Alignment:
GATGCGGCTGACTGTCGAACAGG
|||||||||||||||||||||||
GATGCGGCTGACTGTCGAACAGG
Mismatch: 


2


Number of Mismatches:1


Location:chrX:39647430-39647453


Genomic Sequence:GATGCGGCTGACTGTAGAACAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GATGCGGCTGACTGTAGAACAGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
|||||||||||||||*|||||||
GATGCGGCTGACTGTAGAACAGG


Mismatch:

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


3


Number of Mismatches:3


Location:chr13:29880856-29880879


Genomic Sequence:CATGGGGCTGTCTGTCGAACAGG


Strand:-


Genomic Region:gene(MTUS2)



3' PAM Orientation:CATGGGGCTGTCTGTCGAACAGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
*|||*|||||*||||||||||||
CATGGGGCTGTCTGTCGAACAGG


Mismatch:

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


4


Number of Mismatches:3


Location:chr15:64821905-64821928


Genomic Sequence:TATGTGGCTGTCTGTCGAACAGG


Strand:+


Genomic Region:gene(ZNF609)



3' PAM Orientation:TATGTGGCTGTCTGTCGAACAGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
*|||*|||||*||||||||||||
TATGTGGCTGTCTGTCGAACAGG


Mismatch:

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


5


Number of Mismatches:3


Location:chr6:80663763-80663786


Genomic Sequence:GATGCAGCTGTCTGTCAAACAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GATGCAGCTGTCTGTCAAACAGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
|||||*||||*|||||*||||||
GATGCAGCTGTCTGTCAAACAGG


Mismatch:

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


6


Number of Mismatches:3


Location:chr5:159378540-159378563


Genomic Sequence:GATGCAGCTGTCTGTCGAACGGG


Strand:+


Genomic Region:gene(ADRA1B)



3' PAM Orientation:GATGCAGCTGTCTGTCGAACGGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
|||||*||||*|||||||||*||
GATGCAGCTGTCTGTCGAACGGG


Mismatch:

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


7


Number of Mismatches:3


Location:chr5:173940246-173940269


Genomic Sequence:GATGGGGCTGTCTGTCGAACTGG


Strand:-


Genomic Region:intergenic



3' PAM Orientation:GATGGGGCTGTCTGTCGAACTGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
||||*|||||*|||||||||*||
GATGGGGCTGTCTGTCGAACTGG


Mismatch:

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


8


Number of Mismatches:3


Location:chr1:215044018-215044041


Genomic Sequence:GATGGGGCTGTCTGTCGAAGAGG


Strand:-


Genomic Region:intergenic



3' PAM Orientation:GATGGGGCTGTCTGTCGAAGAGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
||||*|||||*||||||||*|||
GATGGGGCTGTCTGTCGAAGAGG


Mismatch:

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


9


Number of Mismatches:3


Location:chr22:41070490-41070513


Genomic Sequence:GATGCAGCTGTCAGTCGAACAGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GATGCAGCTGTCAGTCGAACAGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
|||||*||||*|*||||||||||
GATGCAGCTGTCAGTCGAACAGG


Mismatch:

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


10


Number of Mismatches:3


Location:chr15:64920800-64920823


Genomic Sequence:TATGCGGCTGTCTGTAGAACAGG


Strand:+


Genomic Region:gene(ZNF609)



3' PAM Orientation:TATGCGGCTGTCTGTAGAACAGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
*|||||||||*||||*|||||||
TATGCGGCTGTCTGTAGAACAGG


Mismatch:

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


11


Number of Mismatches:3


Location:chr19:47061829-47061852


Genomic Sequence:GATGCGGCTGTCTGTGGAACTGG


Strand:-


Genomic Region:gene(PPP5D1)



3' PAM Orientation:GATGCGGCTGTCTGTGGAACTGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
||||||||||*||||*||||*||
GATGCGGCTGTCTGTGGAACTGG


Mismatch:

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


12


Number of Mismatches:3


Location:chr1:120102432-120102455


Genomic Sequence:GATGCGGCTGTCTGTCGAATGGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GATGCGGCTGTCTGTCGAATGGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
||||||||||*||||||||**||
GATGCGGCTGTCTGTCGAATGGG


Mismatch:

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


13


Number of Mismatches:3


Location:chr16:28252012-28252035


Genomic Sequence:GATGCGGCTGTCTGTCGAATGGG


Strand:+


Genomic Region:intergenic



3' PAM Orientation:GATGCGGCTGTCTGTCGAATGGG


Alignment:
GATGCGGCTGACTGTCGAACAGG
||||||||||*||||||||**||
GATGCGGCTGTCTGTCGAATGGG


Mismatch:

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











Paired Nickase
Cas9(D10A)



	
PairOffsetOverhang

		
hs025713228-430

		
hs025713231539

		
hs025713232640

		
hs025713233943

		
hs0257132352155

		
hs0257132362256

		
hs0257132372559

		
hs0257132383064

		
hs0257132393165

		
hs0257132403569

		
hs0257132424377

		
hs0257132434680

		
hs0257132445084

		
hs0257132455185

		
hs0257132465286

		
hs0257132475589

		
hs0257132485690

		
hs0257132516296

		
hs02571325266100

		
hs02571325486120

		
hs02571325587121

		
hs02571325688122

		
hs02571325791125

		
hs02571325892126

		
hs02571325997131

		
hs02571326098132




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


PsuGIBBCGDTGCGGGATGCGGCTGACTGTCGAACAGG


PsuGIBBCGDGTCGAGATGCGGCTGACTGTCGAACAGG


BisIGCNGCGCGGCGATGCGGCTGACTGTCGAACAGG


TauIGCSGCGCGGCGATGCGGCTGACTGTCGAACAGG


Fnu4HIGCNGCGCGGCGATGCGGCTGACTGTCGAACAGG


RlaIVCWGCTGATGCGGCTGACTGTCGAACAGG


RlaIVCWACTGATGCGGCTGACTGTCGAACAGG


RlaIVCWACAGATGCGGCTGACTGTCGAACAGG


CviJIRGCYGGCTGATGCGGCTGACTGTCGAACAGG


Tsp4CIACNGTACTGTGATGCGGCTGACTGTCGAACAGG


TaqITCGATCGAGATGCGGCTGACTGTCGAACAGG




SNPs and Variation


Notes


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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