scramble shRNA

Third generation lentiviral negative control vector with a scrambled shRNA.

Sequence Author: Sabatini Lab / Addgene #1864

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Explore Over 2.7k Plasmids: Viral Expression & Packaging Vectors | More Plasmid Sets
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HomePlasmidsViral Expression & Packaging Vectorsscramble shRNA
AscI BlpI SpeI XcmI EcoRI AgeI NdeI BspDI * - ClaI * KflI - PpuMI AleI BbvCI - Bpu10I MfeI EcoNI NruI * SphI AflIII - PciI PspFI HincII BamHI PflFI - Tth111I BsiWI RsrII BstEII CsiI - SexAI * NsiI Acc65I KpnI BbsI NcoI SfiI AvrII NgoMIV NaeI ScaI BseYI scramble shRNA 7085 bp
AscI  (7067)
1 site		 G G C G C G C C C C G C G C G G
BlpI  (7058)
1 site		 G C T N A G C C G A N T C G
Sticky ends from different BlpI sites may not be compatible.
SpeI  (6978)
1 site		 A C T A G T T G A T C A
XcmI  (6750)
1 site		 C C A N N N N N N N N N T G G G G T N N N N N N N N N A C C
The 1-base overhangs produced by XcmI may be hard to ligate.
Sticky ends from different XcmI sites may not be compatible.
EcoRI  (6515)
1 site		 G A A T T C C T T A A G
AgeI  (6456)
1 site		 A C C G G T T G G C C A
NdeI  (6388)
1 site		 C A T A T G G T A T A C
Prolonged incubation with NdeI may lead to removal of additional nucleotides.
BspDI  (6170)
1 site		 A T C G A T T A G C T A
* Blocked by Dam methylation.
ClaI  (6170)
1 site		 A T C G A T T A G C T A
* Blocked by Dam methylation.
KflI  (6081)
1 site		 G G G W C C C C C C W G G G
Sticky ends from different KflI sites may not be compatible.
PpuMI  (6081)
1 site		 R G G W C C Y Y C C W G G R
Sticky ends from different PpuMI sites may not be compatible.
AleI  (5724)
1 site		 C A C N N N N G T G G T G N N N N C A C
BbvCI  (5571)
1 site		 C C T C A G C G G A G T C G
Bpu10I  (5571)
1 site		 C C T N A G C G G A N T C G
Cleavage may be enhanced when more than one copy of the Bpu10I recognition sequence is present.
This recognition sequence is asymmetric, so ligating sticky ends generated by Bpu10I will not always regenerate a Bpu10I site.
Sticky ends from different Bpu10I sites may not be compatible.
MfeI  (5336)
1 site		 C A A T T G G T T A A C
EcoNI  (5317)
1 site		 C C T N N N N N A G G G G A N N N N N T C C
The 1-base overhangs produced by EcoNI may be hard to ligate.
Sticky ends from different EcoNI sites may not be compatible.
NruI  (4984)
1 site		 T C G C G A A G C G C T
* Blocked by Dam methylation.
SphI  (4468)
1 site		 G C A T G C C G T A C G
AflIII  (3965)
1 site		 A C R Y G T T G Y R C A
Sticky ends from different AflIII sites may not be compatible.
PciI  (3965)
1 site		 A C A T G T T G T A C A
PciI is inhibited by nonionic detergents.
PspFI  (3665)
1 site		 C C C A G C G G G T C G
HincII  (120)
1 site		 G T Y R A C C A R Y T G
BamHI  (150)
1 site		 G G A T C C C C T A G G
After cleavage, BamHI-HF® (but not the original BamHI) can remain bound to DNA and alter its electrophoretic mobility.
PflFI  (211)
1 site		 G A C N N N G T C C T G N N N C A G
The 1-base overhangs produced by PflFI may be hard to ligate.
Sticky ends from different PflFI sites may not be compatible.
Tth111I  (211)
1 site		 G A C N N N G T C C T G N N N C A G
The 1-base overhangs produced by Tth111I may be hard to ligate.
Sticky ends from different Tth111I sites may not be compatible.
BsiWI  (225)
1 site		 C G T A C G G C A T G C
BsiWI is typically used at 55°C, but is 50% active at 37°C.
RsrII  (285)
1 site		 C G G W C C G G C C W G G C
Efficient cleavage requires at least two copies of the RsrII recognition sequence.
Sticky ends from different RsrII sites may not be compatible.
For full activity, add fresh DTT.
BstEII  (303)
1 site		 G G T N A C C C C A N T G G
Sticky ends from different BstEII sites may not be compatible.
BstEII is typically used at 60°C, but is 50% active at 37°C.
CsiI  (736)
1 site		 A C C W G G T T G G W C C A
Sticky ends from different CsiI sites may not be compatible.
SexAI  (736)
1 site		 A C C W G G T T G G W C C A
* Blocked by Dcm methylation.
Sticky ends from different SexAI sites may not be compatible.
NsiI  (822)
1 site		 A T G C A T T A C G T A
Acc65I  (825)
1 site		 G G T A C C C C A T G G
KpnI  (829)
1 site		 G G T A C C C C A T G G
BbsI  (927)
1 site		 G A A G A C N N C T T C T G N N ( N ) 4
Sticky ends from different BbsI sites may not be compatible.
BbsI gradually loses activity when stored at -20°C.
NcoI  (1403)
1 site		 C C A T G G G G T A C C
SfiI  (1449)
1 site		 G G C C N N N N N G G C C C C G G N N N N N C C G G
Efficient cleavage requires at least two copies of the SfiI recognition sequence.
Sticky ends from different SfiI sites may not be compatible.
AvrII  (1496)
1 site		 C C T A G G G G A T C C
NgoMIV  (1829)
1 site		 G C C G G C C G G C C G
Efficient cleavage requires at least two copies of the NgoMIV recognition sequence.
NaeI  (1831)
1 site		 G C C G G C C G G C C G
Efficient cleavage requires at least two copies of the NaeI recognition sequence.
ScaI  (2596)
1 site		 A G T A C T T C A T G A
BseYI  (3661)
1 site		 C C C A G C G G G T C G
After cleavage, BseYI can remain bound to DNA and alter its electrophoretic mobility.
AmpR
2290 .. 3150  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 1:  signal sequence  
   2290 .. 2358  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
2290 .. 3150  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 2:  
   2359 .. 3150  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
2290 .. 3150  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
PuroR
169 .. 768  =  600 bp
199 amino acids  =  21.5 kDa
Product: puromycin N-acetyltransferase
confers resistance to puromycin
PuroR
169 .. 768  =  600 bp
199 amino acids  =  21.5 kDa
Product: puromycin N-acetyltransferase
confers resistance to puromycin
ori
3321 .. 3909  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
3321 .. 3909  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
hPGK promoter
6722 .. 147  =  511 bp
human phosphoglycerate kinase 1 promoter
hPGK promoter
6722 .. 147  =  511 bp
human phosphoglycerate kinase 1 promoter
f1 ori
1704 .. 2159  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
f1 ori
1704 .. 2159  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
U6 promoter
6210 .. 6450  =  241 bp
RNA polymerase III promoter for human U6 snRNA
U6 promoter
6210 .. 6450  =  241 bp
RNA polymerase III promoter for human U6 snRNA
3' LTR (ΔU3)
896 .. 1129  =  234 bp
self-inactivating 3' long terminal repeat (LTR) from HIV-1
3' LTR (ΔU3)
896 .. 1129  =  234 bp
self-inactivating 3' long terminal repeat (LTR) from HIV-1
RRE
5450 .. 5683  =  234 bp
The Rev response element (RRE) of HIV-1 allows for Rev-dependent mRNA export from the nucleus to the cytoplasm.
RRE
5450 .. 5683  =  234 bp
The Rev response element (RRE) of HIV-1 allows for Rev-dependent mRNA export from the nucleus to the cytoplasm.
RSV promoter
4378 .. 4604  =  227 bp
Rous sarcoma virus enhancer/promoter
RSV promoter
4378 .. 4604  =  227 bp
Rous sarcoma virus enhancer/promoter
5' LTR (truncated)
4605 .. 4785  =  181 bp
truncated 5' long terminal repeat (LTR) from HIV-1
5' LTR (truncated)
4605 .. 4785  =  181 bp
truncated 5' long terminal repeat (LTR) from HIV-1
SV40 ori
1362 .. 1497  =  136 bp
SV40 origin of replication
SV40 ori
1362 .. 1497  =  136 bp
SV40 origin of replication
HIV-1 Ψ
4832 .. 4957  =  126 bp
packaging signal of human immunodeficiency virus type 1
HIV-1 Ψ
4832 .. 4957  =  126 bp
packaging signal of human immunodeficiency virus type 1
SV40 poly(A) signal
1201 .. 1322  =  122 bp
SV40 polyadenylation signal
SV40 poly(A) signal
1201 .. 1322  =  122 bp
SV40 polyadenylation signal
cPPT/CTS
6556 .. 6673  =  118 bp
central polypurine tract and central termination sequence of HIV-1
cPPT/CTS
6556 .. 6673  =  118 bp
central polypurine tract and central termination sequence of HIV-1
AmpR promoter
2185 .. 2289  =  105 bp
AmpR promoter
2185 .. 2289  =  105 bp
shRNA
6462 .. 6509  =  48 bp
shRNA
6462 .. 6509  =  48 bp
ORF:  2290 .. 3150  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  1223 .. 1459  =  237 bp
ORF:  78 amino acids  =  8.6 kDa
ORF:  4307 .. 4552  =  246 bp
ORF:  81 amino acids  =  8.9 kDa
ORF:  6536 .. 6982  =  447 bp
ORF:  148 amino acids  =  17.0 kDa
ORF:  5328 .. 6185  =  858 bp
ORF:  285 amino acids  =  32.9 kDa
ORF:  7014 .. 768  =  840 bp
ORF:  279 amino acids  =  29.8 kDa
ORF:  6641 .. 170  =  615 bp
ORF:  204 amino acids  =  22.2 kDa
ORF:  2754 .. 3020  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  5243 .. 5623  =  381 bp
ORF:  126 amino acids  =  13.3 kDa
ORF:  7059 .. 819  =  846 bp
ORF:  281 amino acids  =  29.2 kDa
ORF:  4234 .. 4533  =  300 bp
ORF:  99 amino acids  =  10.9 kDa
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Individual Sequences & Maps

pAAV-AC-GFP
pLenti6.2 N-Lumio V5-DEST
pLVX-rHom-1
pRetroX-Tet3G
pAAV-AC-Myc-DDK
pLenti6.2 V5-DEST
pLVX-rHom-Nuc1
pRetroX-TetOne
pAAV-AC-RFP
pLenti6.3 TO V5-DEST
pLVX-rHom-Sec1
pRetroX-TetOne-Puro
pAAV2-EF1a-tGFP-WPRE
pLenti6.3 V5-DEST
pLVX-Tet-Off Advanced
pRetroX-Tight-Hyg
pAd BLOCK-iT-DEST
pLenti6.4 R4R2 V5-DEST
pLVX-Tet-On Advanced
pRetroX-Tight-Pur
pAd CMV V5-DEST
pLenti6 BLOCK-iT-DEST
pLVX-Tet3G
pRetroX-TRE3G
pAd PL-DEST
pLenti6 capTEV-CT-DEST
pLVX-TetOne
pRFP-C-RS
pAdenoX-CMV Linear
pLenti6 capTEV-NT-DEST1
pLVX-TetOne-Puro
pRFP-CB-shLenti
pAdenoX-DsRed-Express Linear
pLenti6 TR
pLVX-Tight-Puro
pRS
pAdenoX-PRLS Linear
pLenti6 UbC V5-DEST
pLVX-TRE3G
pRSGC1-U6-sg-HTS6-CMV-Cas9-2A-Puro
pAdenoX-PRLS-DsRed-Express Linear
pLenti6 V5-DEST
pLVX-TRE3G-Hom1
pRSGC2-U6-sg-HTS6-UbiC-Cas9-2A-Puro
pAdenoX-PRLS-ZsGreen1 Linear
pLenti7.3 V5-DEST
pLVX-TRE3G-IRES
pRSI12-U6-sh-HTS4-UbiC-TagRFP-2A-Puro
pAdenoX-Tet3G Linear
pLEX-MCS
pLVX-TRE3G-mCherry
pRSI16-U6-sh-HTS6-UbiC-TagRFP-2A-Puro
pAdenoX-ZsGreen1 Linear
pLHCX
pLVX-TRE3G-ZsGreen1
pRSI16cb-U6-sh-13kCB18-HTS6-UbiC-TagRFP-2A-Puro
pB-RS
pLKO.1
pLX301
pRSI17-U6-sh-HTS6-UbiC-TagGFP2-2A-Puro
pBABE-Hygro
pLKO.1 puro
pLX302
pRSI17cb-U6-sh-13kCB18-HTS6-UbiC-TagGFP2-2A-Puro
pBABE-Neo
pLMN-ZsGreen-Neomycin
pLX303
pRSIT12-U6Tet-sh-HTS4-CMV-TetRep-2A-TagRFP-2A-Puro
pBABE-Puro
pLMPd-Ametrine
pLX304
pRSIT16-U6Tet-sh-HTS6-CMV-TetRep-2A-TagRFP-2A-Puro
pBABE-Zeo
pLNCX2
pLX304-V5-Blast-Empty
pRSIT17-U6Tet-sh-HTS6-CMV-TetRep-2A-TagGFP2-2A-Puro
pCMV-VSV-G
pLP VSVG
pLXIN
pRSITEP-U6Tet-sh-noHTS-EF1-TetRep-2A-Puro
pGFP-B-RS
pLP1
pLXSN
pRSITUR-U6Tet-sh-HTS3-UbiC-TetRep-2A-TagRFP
pGFP-C-shLenti
pLP2
pMD2.G
pShuttle2
pGFP-V-RS
pLPCX
pMSCV16URP-U6-sh-HTS6-UbiC-TagRFP-2A-Puro
pSIREN-RetroQ
pGIPZ
pLVX-EF1alpha-IRES-mCherry
pMSCVhyg
pSIREN-RetroQ-DsRed-Express
pLenti-C-GFP
pLVX-EF1alpha-IRES-Puro
pMSCVneo
pSIREN-RetroQ-TetH
pLenti-C-mGFP
pLVX-EF1alpha-IRES-ZsGreen1
pMSCVpuro
pSIREN-RetroQ-TetP
pLenti-C-Myc-DDK
pLVX-EF1alpha-Tet3G
pQC-tTS-IN
pSIREN-RetroQ-ZsGreen1
pLenti-C-Myc-DDK-IRES-BSD
pLVX-Het-1
pQCXIH
psPAX2
pLenti-C-Myc-DDK-IRES-GFP
pLVX-Het-2
pQCXIN
pTRE3G-Hom1
pLenti-C-Myc-DDK-IRES-Neo
pLVX-Het-Mem1
pQCXIP
pTRIPZ
pLenti-C-Myc-DDK-IRES-Puro
pLVX-Het-Nuc1
pQCXIX
ptTS-Neo
pLenti-C-Myc-DDK-IRES-tRFP
pLVX-Hom-1
pRetro-Lib
pZIP-hCMV-RFP-Puro
pLenti-C-tRFP
pLVX-Hom-Mem1
pRetroQ-AcGFP1-C1
pZIP-hCMV-ZSGreen-Puro
pLenti-C-tYFP
pLVX-Hom-Nuc1
pRetroQ-AcGFP1-N1
pZIP-hEF1-alpha-RFP-Puro
pLenti-EF1a-C-mGFP
pLVX-IRES-Hyg
pRetroQ-DsRed-Monomer-C1
pZIP-hEF1-alpha-ZsGreen-Puro
pLenti-EF1a-C-Myc-DDK-IRES-Puro
pLVX-IRES-mCherry
pRetroQ-DsRed-Monomer-N1
pZIP-mCMV-RFP-Puro
pLenti-EF1a-C-tGFP
pLVX-IRES-Neo
pRetroQ-mCherry-C1
pZIP-mCMV-ZsGreen-Puro
pLenti-N-tGFP
pLVX-IRES-Puro
pRetroQ-mCherry-N1
pZIP-mEF1-alpha-RFP-Puro
pLenti-N-tRFP
pLVX-IRES-tdTomato
pRetroX-IRES-DsRedExpress
pZIP-mEF1-alpha-ZsGreen-Puro
pLenti-N-tYFP
pLVX-IRES-ZsGreen1
pRetroX-IRES-ZsGreen1
pZIP-SFFV-RFP-Puro
pLenti3.3 TR
pLVX-PTuner
pRetroX-PTuner
pZIP-SFFV-ZsGreen-Puro
pLenti4 BLOCK-iT-DEST
pLVX-PTuner Green
pRetroX-PTuner IRES
pZIP-TRE3G-ZsGreen-Puro
pLenti4 V5-DEST
pLVX-PTunerC
pRetroX-Tet-Off Advanced
pSIREN-Shuttle (linearized)
pLenti6.2 C-Lumio V5-DEST
pLVX-Puro
pRetroX-Tet-On Advanced
scramble shRNA

Plasmid Sets

Basic Cloning Vectors
I.M.A.G.E. Consortium Plasmids
pET & Duet Vectors (Novagen)
TA and GC Cloning Vectors
Coronavirus Resources
Insect Cell Vectors
pGEX Vectors (GE Healthcare)
TOPO Cloning Vectors
CRISPR Plasmids
Luciferase Vectors
Plant Vectors
Viral Expression & Packaging Vectors
Fluorescent Protein Genes & Plasmids
Lucigen Vectors
Qiagen Vectors
Yeast Plasmids
Gateway® Cloning Vectors
Mammalian Expression Vectors
Structural Genomics Vectors

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