pLKO.1

Stuffer-containing lentiviral vector for expression of shRNA. This plasmid is the official TRC cloning vector.

Sequence Author: The RNAi Consortium

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HomePlasmidsViral Expression & Packaging VectorspLKO.1
EcoRI (8691) BsaBI (8379) SwaI (8210) BstBI (7427) AgeI - SgrAI (6816) NdeI (6748) KflI - PpuMI (6441) BbvCI (5931) EcoNI (5677) NruI * (5344) PspFI (4025) XcmI (25) SpeI (253) BlpI (333) AscI (342) HincII (480) BamHI (510) PflFI - Tth111I (571) BsiWI (585) RsrII (645) BstEII (663) CsiI - SexAI * (1096) Acc65I (1185) KpnI (1189) NcoI (1763) SfiI (1809) AvrII (1856) NgoMIV (2189) NaeI (2191) ScaI (2956) BseYI (4021) pLKO.1 8901 bp
EcoRI  (8691)
1 site		 G A A T T C C T T A A G
BsaBI  (8379)
1 site		 G A T N N N N A T C C T A N N N N T A G
SwaI  (8210)
1 site		 A T T T A A A T T A A A T T T A
SwaI is typically used at 25°C, but is 50% active at 37°C.
BstBI  (7427)
1 site		 T T C G A A A A G C T T
AgeI  (6816)
1 site		 A C C G G T T G G C C A
SgrAI  (6816)
1 site		 C R C C G G Y G G Y G G C C R C
Efficient cleavage requires at least two copies of the SgrAI recognition sequence.
NdeI  (6748)
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.
KflI  (6441)
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  (6441)
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.
BbvCI  (5931)
1 site		 C C T C A G C G G A G T C G
EcoNI  (5677)
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  (5344)
1 site		 T C G C G A A G C G C T
* Blocked by Dam methylation.
PspFI  (4025)
1 site		 C C C A G C G G G T C G
XcmI  (25)
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.
SpeI  (253)
1 site		 A C T A G T T G A T C A
BlpI  (333)
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.
AscI  (342)
1 site		 G G C G C G C C C C G C G C G G
HincII  (480)
1 site		 G T Y R A C C A R Y T G
BamHI  (510)
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  (571)
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  (571)
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  (585)
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  (645)
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  (663)
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  (1096)
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  (1096)
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.
Acc65I  (1185)
1 site		 G G T A C C C C A T G G
KpnI  (1189)
1 site		 G G T A C C C C A T G G
NcoI  (1763)
1 site		 C C A T G G G G T A C C
SfiI  (1809)
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  (1856)
1 site		 C C T A G G G G A T C C
NgoMIV  (2189)
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  (2191)
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  (2956)
1 site		 A G T A C T T C A T G A
BseYI  (4021)
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.
Stuffer
6816 .. 8696  =  1881 bp
can be removed with AgeI + EcoRI and replaced with an shRNA
Stuffer
6816 .. 8696  =  1881 bp
can be removed with AgeI + EcoRI and replaced with an shRNA
AmpR
2650 .. 3510  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 1:  signal sequence  
   2650 .. 2718  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
2650 .. 3510  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 2:  
   2719 .. 3510  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
2650 .. 3510  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
PuroR
529 .. 1128  =  600 bp
199 amino acids  =  21.5 kDa
Product: puromycin N-acetyltransferase
confers resistance to puromycin
PuroR
529 .. 1128  =  600 bp
199 amino acids  =  21.5 kDa
Product: puromycin N-acetyltransferase
confers resistance to puromycin
ori
3681 .. 4269  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
3681 .. 4269  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
hPGK promoter
8898 .. 507  =  511 bp
human phosphoglycerate kinase 1 promoter
hPGK promoter
8898 .. 507  =  511 bp
human phosphoglycerate kinase 1 promoter
f1 ori
2064 .. 2519  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
f1 ori
2064 .. 2519  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
U6 promoter
6570 .. 6810  =  241 bp
RNA polymerase III promoter for human U6 snRNA
U6 promoter
6570 .. 6810  =  241 bp
RNA polymerase III promoter for human U6 snRNA
3' LTR (ΔU3)
1256 .. 1489  =  234 bp
self-inactivating 3' long terminal repeat (LTR) from HIV-1
3' LTR (ΔU3)
1256 .. 1489  =  234 bp
self-inactivating 3' long terminal repeat (LTR) from HIV-1
RRE
5810 .. 6043  =  234 bp
The Rev response element (RRE) of HIV-1 allows for Rev-dependent mRNA export from the nucleus to the cytoplasm.
RRE
5810 .. 6043  =  234 bp
The Rev response element (RRE) of HIV-1 allows for Rev-dependent mRNA export from the nucleus to the cytoplasm.
5' LTR
4965 .. 5145  =  181 bp
truncated 5' long terminal repeat (LTR) from HIV-1
5' LTR
4965 .. 5145  =  181 bp
truncated 5' long terminal repeat (LTR) from HIV-1
SV40 ori
1722 .. 1857  =  136 bp
SV40 origin of replication
SV40 ori
1722 .. 1857  =  136 bp
SV40 origin of replication
HIV-1 ψ
5192 .. 5317  =  126 bp
packaging signal of human immunodeficiency virus type 1
HIV-1 ψ
5192 .. 5317  =  126 bp
packaging signal of human immunodeficiency virus type 1
SV40 poly(A) signal
1561 .. 1682  =  122 bp
SV40 polyadenylation signal
SV40 poly(A) signal
1561 .. 1682  =  122 bp
SV40 polyadenylation signal
cPPT/CTS
8732 .. 8849  =  118 bp
central polypurine tract and central termination sequence of HIV-1
cPPT/CTS
8732 .. 8849  =  118 bp
central polypurine tract and central termination sequence of HIV-1
AmpR promoter
2545 .. 2649  =  105 bp
AmpR promoter
2545 .. 2649  =  105 bp
ORF:  289 .. 1128  =  840 bp
ORF:  279 amino acids  =  29.8 kDa
ORF:  2650 .. 3510  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  1583 .. 1819  =  237 bp
ORF:  78 amino acids  =  8.6 kDa
ORF:  4667 .. 4912  =  246 bp
ORF:  81 amino acids  =  8.9 kDa
ORF:  5688 .. 6545  =  858 bp
ORF:  285 amino acids  =  32.9 kDa
ORF:  8712 .. 257  =  447 bp
ORF:  148 amino acids  =  17.0 kDa
ORF:  334 .. 1179  =  846 bp
ORF:  281 amino acids  =  29.2 kDa
ORF:  4594 .. 4893  =  300 bp
ORF:  99 amino acids  =  10.9 kDa
ORF:  6991 .. 7386  =  396 bp
ORF:  131 amino acids  =  14.0 kDa
ORF:  8817 .. 530  =  615 bp
ORF:  204 amino acids  =  22.2 kDa
ORF:  3114 .. 3380  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  5603 .. 5983  =  381 bp
ORF:  126 amino acids  =  13.3 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

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Fluorescent Protein Genes & Plasmids
Lucigen Vectors
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Structural Genomics Vectors

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