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Plasmid Files

pLP1

Lentiviral packaging plasmid containing the HIV-1 gag and pol genes.

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pLP1.dna
Map and Sequence File:    Download    Open   
Sequence Author:  Thermo Fisher (Invitrogen)
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Bsu36I (8815) PvuI (8256) FspI (8108) PspFI (7301) BseYI (7297) HaeII (7241) SacII (6067) AleI (5960) BbvCI - Bpu10I (5807) BspEI (5672) AarI - BfuAI - BspMI (5611) AflII (5308) NdeI (328) SnaBI (434) BsmBI (683) PmlI (1323) BspDI * - ClaI * (1396) SphI (2012) MfeI (2533) AvrII (2576) BclI * (2994) SbfI (3408) BstZ17I (3494) EcoRV (3544) PflFI - Tth111I (3646) AgeI (4050) pLP1 8889 bp
Bsu36I  (8815)
1 site
C C T N A G G G G A N T C C

Sticky ends from different Bsu36I sites may not be compatible.
PvuI  (8256)
1 site
C G A T C G G C T A G C
FspI  (8108)
1 site
T G C G C A A C G C G T
PspFI  (7301)
1 site
C C C A G C G G G T C G
BseYI  (7297)
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.
HaeII  (7241)
1 site
R G C G C Y Y C G C G R
SacII  (6067)
1 site
C C G C G G G G C G C C

Efficient cleavage requires at least two copies of the SacII recognition sequence.
AleI  (5960)
1 site
C A C N N N N G T G G T G N N N N C A C
BbvCI  (5807)
1 site
C C T C A G C G G A G T C G
Bpu10I  (5807)
1 site
C C T N A G C G G A N T C G

Efficient cleavage requires at least two copies of the Bpu10I recognition sequence.
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.
BspEI  (5672)
1 site
T C C G G A A G G C C T
AarI  (5611)
1 site
C A C C T G C ( N ) 4 G T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the AarI recognition sequence.
Sticky ends from different AarI sites may not be compatible.
After cleavage, AarI can remain bound to DNA and alter its electrophoretic mobility.
BfuAI  (5611)
1 site
A C C T G C ( N ) 4 T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the BfuAI recognition sequence.
Sticky ends from different BfuAI sites may not be compatible.
BfuAI is typically used at 50°C, but is 50% active at 37°C.
BspMI  (5611)
1 site
A C C T G C ( N ) 4 T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the BspMI recognition sequence.
Sticky ends from different BspMI sites may not be compatible.
AflII  (5308)
1 site
C T T A A G G A A T T C
NdeI  (328)
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.
SnaBI  (434)
1 site
T A C G T A A T G C A T
BsmBI  (683)
1 site
C G T C T C N G C A G A G N ( N ) 4

Sticky ends from different BsmBI sites may not be compatible.
PmlI  (1323)
1 site
C A C G T G G T G C A C

PmlI gradually loses activity when stored at -20°C.
BspDI  (1396)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
ClaI  (1396)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
SphI  (2012)
1 site
G C A T G C C G T A C G
MfeI  (2533)
1 site
C A A T T G G T T A A C
AvrII  (2576)
1 site
C C T A G G G G A T C C
BclI  (2994)
1 site
T G A T C A A C T A G T
* Blocked by Dam methylation.
BclI is typically used at 50-55°C, but is 50% active at 37°C.
SbfI  (3408)
1 site
C C T G C A G G G G A C G T C C
BstZ17I  (3494)
1 site
G T A T A C C A T A T G
EcoRV  (3544)
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.
PflFI  (3646)
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  (3646)
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.
AgeI  (4050)
1 site
A C C G G T T G G C C A
pol
2650 .. 5661  =  3012 bp
1003 amino acids  =  113.7 kDa
Product: HIV-1 Pol polyprotein
pol
2650 .. 5661  =  3012 bp
1003 amino acids  =  113.7 kDa
Product: HIV-1 Pol polyprotein
AmpR
7813 .. 8673  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   7813 .. 8604  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
7813 .. 8673  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   8605 .. 8673  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
7813 .. 8673  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
ori
7054 .. 7642  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
7054 .. 7642  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
β-globin intron
796 .. 1271  =  476 bp
internally truncated intron from human β-globin
β-globin intron
796 .. 1271  =  476 bp
internally truncated intron from human β-globin
β-globin poly(A)
6150 .. 6544  =  395 bp
human β-globin polyadenylation signal
β-globin poly(A)
6150 .. 6544  =  395 bp
human β-globin polyadenylation signal
CMV enhancer
79 .. 458  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
79 .. 458  =  380 bp
human cytomegalovirus immediate early enhancer
RRE
5686 .. 5919  =  234 bp
The Rev response element (RRE) of HIV-1 allows for Rev-dependent mRNA export from the nucleus to the cytoplasm.
RRE
5686 .. 5919  =  234 bp
The Rev response element (RRE) of HIV-1 allows for Rev-dependent mRNA export from the nucleus to the cytoplasm.
CMV promoter
459 .. 662  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
459 .. 662  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
AmpR promoter
8674 .. 8778  =  105 bp
AmpR promoter
8674 .. 8778  =  105 bp
gag
1355 .. 2857  =  1503 bp
500 amino acids  =  55.9 kDa
Product: HIV-1 Gag polyprotein
gag
1355 .. 2857  =  1503 bp
500 amino acids  =  55.9 kDa
Product: HIV-1 Gag polyprotein
cPPT/CTS
5346 .. 5463  =  118 bp
central polypurine tract and central termination sequence of HIV-1
cPPT/CTS
5346 .. 5463  =  118 bp
central polypurine tract and central termination sequence of HIV-1
ORF:  2923 .. 5661  =  2739 bp
ORF:  912 amino acids  =  103.5 kDa
ORF:  1355 .. 2857  =  1503 bp
ORF:  500 amino acids  =  55.9 kDa
ORF:  5606 .. 6124  =  519 bp
ORF:  172 amino acids  =  19.3 kDa
ORF:  7943 .. 8209  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  5431 .. 5859  =  429 bp
ORF:  142 amino acids  =  15.9 kDa
ORF:  7813 .. 8673  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  4140 .. 4415  =  276 bp
ORF:  91 amino acids  =  10.0 kDa
ORF:  8570 .. 8830  =  261 bp
ORF:  86 amino acids  =  9.8 kDa
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