grID Information

Summary

grID: hs025713214
Sequence (23-mer): CGCGGCGGCAGGCGGTGACTCGG
grID Score: moderate (500)
Doench (2014) Score: 0.02590
Doench (2016) Score: 0.41910
Cas9: S. pyogenes

Genomic Context

Genomic Location: chr12:6643642-6643620
Strand: -
gRNA location: exon:refGene(NM_002046.exon0)

Nearest Genes

refseqgenechromstartenddistance
NM_002046 GAPDHchr12664358466475370
NM_001256799 GAPDHchr1266444086647537788
NM_014865 NCAPD2chr12660329766411322510
NM_001039670 IFFO1chr12664869366652495073
NM_001193457 IFFO1chr12664869366652495073

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): CGCGGCGGCAGGCGGUGACU
Target Sequence Occurrence: unique
PAM motif: CGG
Homopolymeric Runs: none
Pol III Terminator: none

Thermodynamic Properties

GC-content (%): 80
GC-score: high
Tm (°C): 66.05
Tm score: moderate
RNAfold (dot bracket): (((.((.....)).)))...
deltaG (Kcal/mol): -7.10
Predicted Folding: high secondary structure

Offtarget Analysis

Total Predicted Genomic Targets: 2
Total Genomic Sites With 0 Mismatches: 1
Total Genomic Sites With 1 Mismatches:
Total Genomic Sites With 2 Mismatches:
Total Genomic Sites With 3 Mismatches: 1
1chr12:6643619-66436420
CCGAGTCACCGCCTGCCGCCGCG
|||||||||||||||||||||||
CCGAGTCACCGCCTGCCGCCGCG
2chr17:1106897-11069203
CCGAGTCACCGCCTGCCGCCGCG
|*|||||||||||*||||||||*
CGGAGTCACCGCCAGCCGCCGCC
1
Number of Mismatches:0
Location:chr12:6643619-6643642
Genomic Sequence:CGCGGCGGCAGGCGGTGACTCGG
Strand:-
Genomic Region:exon(NM_002046.exon0)
3' PAM Orientation:CGCGGCGGCAGGCGGTGACTCGG
Alignment:
CGCGGCGGCAGGCGGTGACTCGG
|||||||||||||||||||||||
CGCGGCGGCAGGCGGTGACTCGG
Mismatch:
2
Number of Mismatches:3
Location:chr17:1106897-1106920
Genomic Sequence:GGCGGCGGCTGGCGGTGACTCCG
Strand:-
Genomic Region:intergenic
3' PAM Orientation:GGCGGCGGCTGGCGGTGACTCCG
Alignment:
CGCGGCGGCAGGCGGTGACTCGG
*||||||||*|||||||||||*|
GGCGGCGGCTGGCGGTGACTCCG
Mismatch:
G......................
.........T.............
.....................C.
Distal mismatch
Distal seed mismatch
PAM mismatch

Paired Nickase

Cas9(D10A)
PairOffsetOverhang
hs02571322872106
hs02571323181115
hs02571323282116
hs02571323385119
hs02571323597131
hs02571323698132

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
RlaIVCWGCACGCGGCGGCAGGCGGTGACTCGG
RlaIVCWACTCGCGGCGGCAGGCGGTGACTCGG
HinfIGANTCGACTCCGCGGCGGCAGGCGGTGACTCGG
Fnu4HIGCNGCGCGGCCGCGGCGGCAGGCGGTGACTCGG
Tsp45IGTSACGTGACCGCGGCGGCAGGCGGTGACTCGG
MaeIIIGTNACGTGACCGCGGCGGCAGGCGGTGACTCGG
Cac8IGCNNGCGCAGGCCGCGGCGGCAGGCGGTGACTCGG
BisIGCNGCGCGGCCGCGGCGGCAGGCGGTGACTCGG
TauIGCSGCGCGGCCGCGGCGGCAGGCGGTGACTCGG
PsuGIBBCGDCGCGGCGCGGCGGCAGGCGGTGACTCGG
PsuGIBBCGDGGCGGCGCGGCGGCAGGCGGTGACTCGG
PsuGIBBCGDCTCGGCGCGGCGGCAGGCGGTGACTCGG
FnuDIICGCGCGCGCGCGGCGGCAGGCGGTGACTCGG

SNPs and Variation

Notes

× Warning! This gRNA has a high GC content which can lead to greater off-targets.
× Warning! This gRNA has a low delta G which can lead to greater secondary structures.

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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