pSIREN-RetroQ-DsRed-Express

Linearized retroviral vector for inserting an shRNA cassette that will be co-expressed with DsRed-Express.

Sequence Author: Clontech (TaKaRa)

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<BamHI> (6543) U6 forward sequencing primer (6468 .. 6491) BglII (6285) Bpu10I (6164) ApoI (5746) EagI (5598) PshAI (5385) AscI (5251) CMV enhancerSspI (4364) XmnI (4159) ScaI (4040) PvuI (3930) <EcoRI> (0) AgeI (605) FspAI (666) SbfI (958) PflMI* (1136) BstXI (1160) BsgI (1197) AleI (1245) PaeR7I - XhoI (1296) EcoRV (1303) SalI (1538) AccI (1539) SfiI (2373) AvrII (2420) HindIII (2436) BspQI - SapI (2551) AflIII - PciI (2667) AlwNI (3083) pSIREN-RetroQ-DsRed-Express 6543 bp
End  (6543)
0 sites
BglII  (6285)
1 site		 A G A T C T T C T A G A
Bpu10I  (6164)
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.
ApoI  (5746)
1 site		 R A A T T Y Y T T A A R
ApoI is typically used at 50°C, but is 50% active at 37°C.
EagI  (5598)
1 site		 C G G C C G G C C G G C
PshAI  (5385)
1 site		 G A C N N N N G T C C T G N N N N C A G
PshAI quickly loses activity at 37°C, but can be used at 25°C for long incubations.
AscI  (5251)
1 site		 G G C G C G C C C C G C G C G G
SspI  (4364)
1 site		 A A T A T T T T A T A A
XmnI  (4159)
1 site		 G A A N N N N T T C C T T N N N N A A G
ScaI  (4040)
1 site		 A G T A C T T C A T G A
PvuI  (3930)
1 site		 C G A T C G G C T A G C
Start  (0)
0 sites
AgeI  (605)
1 site		 A C C G G T T G G C C A
FspAI  (666)
1 site		 R T G C G C A Y Y A C G C G T R
SbfI  (958)
1 site		 C C T G C A G G G G A C G T C C
PflMI  (1136)
1 site		 C C A N N N N N T G G G G T N N N N N A C C
* Blocked by Dcm methylation.
Sticky ends from different PflMI sites may not be compatible.
BstXI  (1160)
1 site		 C C A N N N N N N T G G G G T N N N N N N A C C
Sticky ends from different BstXI sites may not be compatible.
BsgI  (1197)
1 site		 G T G C A G ( N ) 14 N N C A C G T C ( N ) 14
Efficient cleavage requires at least two copies of the BsgI recognition sequence.
Sticky ends from different BsgI sites may not be compatible.
For full activity, add fresh S-adenosylmethionine (SAM).
AleI  (1245)
1 site		 C A C N N N N G T G G T G N N N N C A C
PaeR7I  (1296)
1 site		 C T C G A G G A G C T C
PaeR7I does not recognize the sequence CTCTCGAG.
XhoI  (1296)
1 site		 C T C G A G G A G C T C
EcoRV  (1303)
1 site		 G A T A T C C T A T A G
EcoRV is reportedly more prone than its isoschizomer Eco32I to delete a base after cleavage.
SalI  (1538)
1 site		 G T C G A C C A G C T G
AccI  (1539)
1 site		 G T M K A C C A K M T G
Efficient cleavage with AccI requires ≥13 bp on each side of the recognition sequence.
Sticky ends from different AccI sites may not be compatible.
SfiI  (2373)
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  (2420)
1 site		 C C T A G G G G A T C C
HindIII  (2436)
1 site		 A A G C T T T T C G A A
BspQI  (2551)
1 site		 G C T C T T C N C G A G A A G N N N N
Sticky ends from different BspQI sites may not be compatible.
SapI  (2551)
1 site		 G C T C T T C N C G A G A A G N N N N
Sticky ends from different SapI sites may not be compatible.
SapI gradually settles in solution, so a tube of SapI should be mixed before removing an aliquot.
AflIII  (2667)
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  (2667)
1 site		 A C A T G T T G T A C A
PciI is inhibited by nonionic detergents.
AlwNI  (3083)
1 site		 C A G N N N C T G G T C N N N G A C
Sticky ends from different AlwNI sites may not be compatible.
U6 forward sequencing primer
24-mer  /  38% GC
1 binding site
6468 .. 6491  =  24 annealed bases
Tm  =  55°C
AmpR
3487 .. 4347  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
   Segment 2:  
   3487 .. 4278  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3487 .. 4347  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
   Segment 1:  signal sequence  
   4279 .. 4347  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3487 .. 4347  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
DsRed-Express
618 .. 1295  =  678 bp
225 amino acids  =  25.7 kDa
Product: rapidly maturing tetrameric variant of DsRed fluorescent protein
mammalian codon-optimized
DsRed-Express
618 .. 1295  =  678 bp
225 amino acids  =  25.7 kDa
Product: rapidly maturing tetrameric variant of DsRed fluorescent protein
mammalian codon-optimized
ori
2728 .. 3316  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
2728 .. 3316  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
3' LTR (ΔU3)
1415 .. 1840  =  426 bp
self-inactivating 3' long terminal repeat (LTR) from Moloney murine leukemia virus
3' LTR (ΔU3)
1415 .. 1840  =  426 bp
self-inactivating 3' long terminal repeat (LTR) from Moloney murine leukemia virus
gag (truncated)
5860 .. 6276  =  417 bp
truncated MMLV gag gene lacking the start codon
gag (truncated)
5860 .. 6276  =  417 bp
truncated MMLV gag gene lacking the start codon
CMV enhancer
4638 .. 5017  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
4638 .. 5017  =  380 bp
human cytomegalovirus immediate early enhancer
SV40 promoter
2106 .. 2435  =  330 bp
SV40 enhancer and early promoter
SV40 promoter
2106 .. 2435  =  330 bp
SV40 enhancer and early promoter
CMV enhancer
66 .. 369  =  304 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
66 .. 369  =  304 bp
human cytomegalovirus immediate early enhancer
U6 promoter
6300 .. 6540  =  241 bp
Truncated RNA polymerase III promoter for human U6 snRNA used in pSIREN vectors such as pSIREN-RetroQ-ZsGreen1. Expected transcription start site is 8bp downstream of this feature.
U6 promoter
6300 .. 6540  =  241 bp
Truncated RNA polymerase III promoter for human U6 snRNA used in pSIREN vectors such as pSIREN-RetroQ-ZsGreen1. Expected transcription start site is 8bp downstream of this feature.
CMV promoter
370 .. 573  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
370 .. 573  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
5018 .. 5221  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
5018 .. 5221  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
MMLV Ψ
5460 .. 5659  =  200 bp
packaging signal of Moloney murine leukemia virus (MMLV)
MMLV Ψ
5460 .. 5659  =  200 bp
packaging signal of Moloney murine leukemia virus (MMLV)
5' LTR (truncated)
5222 .. 5397  =  176 bp
truncated long terminal repeat from Moloney murine sarcoma virus
5' LTR (truncated)
5222 .. 5397  =  176 bp
truncated long terminal repeat from Moloney murine sarcoma virus
AmpR promoter
4348 .. 4452  =  105 bp
AmpR promoter
4348 .. 4452  =  105 bp
SV40 ori
2286 .. 2421  =  136 bp
SV40 origin of replication
SV40 ori
2286 .. 2421  =  136 bp
SV40 origin of replication
ORF:  3617 .. 3883  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  618 .. 1295  =  678 bp
ORF:  225 amino acids  =  25.7 kDa
ORF:  1664 .. 1954  =  291 bp
ORF:  96 amino acids  =  10.5 kDa
ORF:  3487 .. 4347  =  861 bp
ORF:  286 amino acids  =  31.5 kDa
ORF:  5547 .. 5807  =  261 bp
ORF:  86 amino acids  =  9.5 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
pRSI16cb-U6-sh-13kCB18-HTS6-UbiC-TagRFP-2A-Puro
pAdenoX-ZsGreen1 Linear
pLHCX
pLVX-TRE3G-ZsGreen1
pRSI16-U6-sh-HTS6-UbiC-TagRFP-2A-Puro
pB-RS
pLKO.1
pLX301
pRSI17cb-U6-sh-13kCB18-HTS6-UbiC-TagGFP2-2A-Puro
pBABE-Hygro
pLKO.1 puro
pLX302
pRSI17-U6-sh-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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