grID Information

Summary

grID: hs025713245
Sequence (23-mer): GGGACGGCCTGAAGGCGGCAGGG
grID Score: moderate (600)
Doench (2014) Score: 0.28762
Doench (2016) Score: 0.51098
Cas9: S. pyogenes

Genomic Context

Genomic Location: chr12:6643769-6643791
Strand: +
gRNA location: gene:refGene(GAPDH)

Nearest Genes

refseqgenechromstartenddistance
NM_002046 GAPDHchr12664358466475370
NM_001256799 GAPDHchr1266444086647537617
NM_014865 NCAPD2chr12660329766411322637
NM_001039670 IFFO1chr12664869366652494902
NM_001193457 IFFO1chr12664869366652494902

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Sequence Analysis

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

Thermodynamic Properties

GC-content (%): 75
GC-score: high
Tm (°C): 70.47
Tm score: high
RNAfold (dot bracket): ....(.(((....))).)..
deltaG (Kcal/mol): -5.00
Predicted Folding: moderate secondary structure

Offtarget Analysis

Total Predicted Genomic Targets: 9
Total Genomic Sites With 0 Mismatches:
Total Genomic Sites With 1 Mismatches:
Total Genomic Sites With 2 Mismatches: 1
Total Genomic Sites With 3 Mismatches: 8
1chr12:6643768-66437910
GGGACGGCCTGAAGGCGGCAGGG
|||||||||||||||||||||||
GGGACGGCCTGAAGGCGGCAGGG
2chr17:80039270-800392932
GGGACGGCCTGAAGGCGGCAGGG
|||||||||||*|*|||||||||
GGGACGGCCTGTATGCGGCAGGG
3chr11:129149384-1291494073
CCCTGCCGCCTTCAGGCCGTCCC
|||||*|||||||*|||||*|||
CCCTGGCGCCTTCTGGCCGACCC
4chr15:66316236-663162593
GGGACGGCCTGAAGGCGGCAGGG
|||*|||*||||||||*||||||
GGGTCGGTCTGAAGGCTGCAGGG
5chr15:101348032-1013480553
GGGACGGCCTGAAGGCGGCAGGG
||||*|||||||||||*|||||*
GGGAGGGCCTGAAGGCTGCAGGC
6chr14:64254540-642545633
CCCTGCCGCCTTCAGGCCGTCCC
*|||||*|||||||||||*||||
GCCTGCGGCCTTCAGGCCCTCCC
7chr3:127292513-1272925363
CCCTGCCGCCTTCAGGCCGTCCC
||||||*||||*||||||*||||
CCCTGCGGCCTACAGGCCCTCCC
8chr2:135476062-1354760853
GGGACGGCCTGAAGGCGGCAGGG
|||*||||||||||||*||*|||
GGGTCGGCCTGAAGGCAGCTGGG
9chr6:37225865-372258883
GGGACGGCCTGAAGGCGGCAGGG
|||||*|||||**||||||||||
GGGACTGCCTGGTGGCGGCAGGG
10chr1:201108201-2011082243
CCCTGCCGCCTTCAGGCCGTCCC
|||||***|||||||||||||||
CCCTGGGCCCTTCAGGCCGTCCC
1
Number of Mismatches:0
Location:chr12:6643768-6643791
Genomic Sequence:GGGACGGCCTGAAGGCGGCAGGG
Strand:+
Genomic Region:gene(GAPDH)
3' PAM Orientation:GGGACGGCCTGAAGGCGGCAGGG
Alignment:
GGGACGGCCTGAAGGCGGCAGGG
|||||||||||||||||||||||
GGGACGGCCTGAAGGCGGCAGGG
Mismatch:
2
Number of Mismatches:2
Location:chr17:80039270-80039293
Genomic Sequence:GGGACGGCCTGTATGCGGCAGGG
Strand:+
Genomic Region:gene(FASN)
3' PAM Orientation:GGGACGGCCTGTATGCGGCAGGG
Alignment:
GGGACGGCCTGAAGGCGGCAGGG
|||||||||||*|*|||||||||
GGGACGGCCTGTATGCGGCAGGG
Mismatch:
...........T...........
.............T.........
Proximal seed mismatch
Proximal seed mismatch
3
Number of Mismatches:3
Location:chr11:129149384-129149407
Genomic Sequence:GGGTCGGCCAGAAGGCGCCAGGG
Strand:-
Genomic Region:intergenic
3' PAM Orientation:GGGTCGGCCAGAAGGCGCCAGGG
Alignment:
GGGACGGCCTGAAGGCGGCAGGG
|||*|||||*|||||||*|||||
GGGTCGGCCAGAAGGCGCCAGGG
Mismatch:
...T...................
.........A.............
.................C.....
Distal mismatch
Distal seed mismatch
Proximal seed mismatch
4
Number of Mismatches:3
Location:chr15:66316236-66316259
Genomic Sequence:GGGTCGGTCTGAAGGCTGCAGGG
Strand:+
Genomic Region:gene(MEGF11)
3' PAM Orientation:GGGTCGGTCTGAAGGCTGCAGGG
Alignment:
GGGACGGCCTGAAGGCGGCAGGG
|||*|||*||||||||*||||||
GGGTCGGTCTGAAGGCTGCAGGG
Mismatch:
...T...................
.......T...............
................T......
Distal mismatch
Distal seed mismatch
Proximal seed mismatch
5
Number of Mismatches:3
Location:chr15:101348032-101348055
Genomic Sequence:GGGAGGGCCTGAAGGCTGCAGGC
Strand:+
Genomic Region:intergenic
3' PAM Orientation:GGGAGGGCCTGAAGGCTGCAGGC
Alignment:
GGGACGGCCTGAAGGCGGCAGGG
||||*|||||||||||*|||||*
GGGAGGGCCTGAAGGCTGCAGGC
Mismatch:
....G..................
................T......
......................C
Distal mismatch
Proximal seed mismatch
PAM mismatch
6
Number of Mismatches:3
Location:chr14:64254540-64254563
Genomic Sequence:GGGAGGGCCTGAAGGCCGCAGGC
Strand:-
Genomic Region:intergenic
3' PAM Orientation:GGGAGGGCCTGAAGGCCGCAGGC
Alignment:
GGGACGGCCTGAAGGCGGCAGGG
||||*|||||||||||*|||||*
GGGAGGGCCTGAAGGCCGCAGGC
Mismatch:
....G..................
................C......
......................C
Distal mismatch
Proximal seed mismatch
PAM mismatch
7
Number of Mismatches:3
Location:chr3:127292513-127292536
Genomic Sequence:GGGAGGGCCTGTAGGCCGCAGGG
Strand:-
Genomic Region:CDS(NM_001136053.cds10)
3' PAM Orientation:GGGAGGGCCTGTAGGCCGCAGGG
Alignment:
GGGACGGCCTGAAGGCGGCAGGG
||||*||||||*||||*||||||
GGGAGGGCCTGTAGGCCGCAGGG
Mismatch:
....G..................
...........T...........
................C......
Distal mismatch
Proximal seed mismatch
Proximal seed mismatch
8
Number of Mismatches:3
Location:chr2:135476062-135476085
Genomic Sequence:GGGTCGGCCTGAAGGCAGCTGGG
Strand:+
Genomic Region:gene(TMEM163)
3' PAM Orientation:GGGTCGGCCTGAAGGCAGCTGGG
Alignment:
GGGACGGCCTGAAGGCGGCAGGG
|||*||||||||||||*||*|||
GGGTCGGCCTGAAGGCAGCTGGG
Mismatch:
...T...................
................A......
...................T...
Distal mismatch
Proximal seed mismatch
Proximal seed mismatch
9
Number of Mismatches:3
Location:chr6:37225865-37225888
Genomic Sequence:GGGACTGCCTGGTGGCGGCAGGG
Strand:+
Genomic Region:exon(NM_001162900.exon0)
3' PAM Orientation:GGGACTGCCTGGTGGCGGCAGGG
Alignment:
GGGACGGCCTGAAGGCGGCAGGG
|||||*|||||**||||||||||
GGGACTGCCTGGTGGCGGCAGGG
Mismatch:
.....T.................
...........G...........
............T..........
Distal mismatch
Proximal seed mismatch
Proximal seed mismatch
10
Number of Mismatches:3
Location:chr1:201108201-201108224
Genomic Sequence:GGGACGGCCTGAAGGGCCCAGGG
Strand:-
Genomic Region:gene(TMEM9)
3' PAM Orientation:GGGACGGCCTGAAGGGCCCAGGG
Alignment:
GGGACGGCCTGAAGGCGGCAGGG
|||||||||||||||***|||||
GGGACGGCCTGAAGGGCCCAGGG
Mismatch:
...............G.......
................C......
.................C.....
Proximal seed mismatch
Proximal seed mismatch
Proximal seed mismatch

Paired Nickase

Cas9(D10A)
PairOffsetOverhang
hs0257132411549
hs0257132343569
hs0257132305185
hs0257132295488
hs02571322771105
hs02571322672106
hs02571322575109
hs02571322481115
hs02571322382116

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
Ssp6803IVGAAGGCGAAGGCGGGACGGCCTGAAGGCGGCAGGG
Fnu4HIGCNGCGCGGCGGGACGGCCTGAAGGCGGCAGGG
BsiYICCNNNNNNNGGCCTGAAGGCGGGGGACGGCCTGAAGGCGGCAGGG
CviJIRGCYGGCCGGGACGGCCTGAAGGCGGCAGGG
BisIGCNGCGCGGCGGGACGGCCTGAAGGCGGCAGGG
TauIGCSGCGCGGCGGGACGGCCTGAAGGCGGCAGGG
PsuGIBBCGDGGCGGGGGACGGCCTGAAGGCGGCAGGG
RlaIVCWCCTGGGACGGCCTGAAGGCGGCAGGG
RlaIVCWGCAGGGACGGCCTGAAGGCGGCAGGG
HaeIIIGGCCGGCCGGGACGGCCTGAAGGCGGCAGGG
FinIGGGACGGGACGGGACGGCCTGAAGGCGGCAGGG

SNPs and Variation

NamestartendstrandrefNCBIrefUCSCobservedclassfunction
rs18440711666437726643773+CCC/Gsingleintron,near-gene-5,untranslated-5
rs57102823866437846643785+GGA/Gsingleintron,near-gene-5,untranslated-5

Notes

× 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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