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Plasmid Files

pcDNA™5/TO

Mammalian vector with a hygromycin resistance gene for tetracycline-inducible expression of proteins.

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pcDNA5 TO.dna
Map and Sequence File:    Download    Open   
Sequence Author:  Thermo Fisher (Invitrogen)
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SspI (5548) FspI (4966) BsaI (4805) AhdI (4744) PciI (3851) BspQI - SapI (3735) BstZ17I (3472) BsmI (3420) PfoI (3275) SacII (2965) MfeI (161) Bpu10I (180) NruI (208) MluI (228) SnaBI (590) AflII (975) HindIII (978) Acc65I (984) KpnI (988) BamHI (996) EcoRV (1031) NotI (1046) PaeR7I - PspXI - XhoI (1052) XbaI (1058) EcoO109I - PspOMI (1064) ApaI (1068) SexAI * (1888) BseRI (2117) StuI (2120) AvrII (2121) TspMI - XmaI (2142) SmaI (2144) PshAI (2212) BfuAI - BspMI (2498) AsiSI (2549) RsrII (2593) pcDNA™5/TO 5667 bp
SspI  (5548)
1 site
A A T A T T T T A T A A
FspI  (4966)
1 site
T G C G C A A C G C G T
BsaI  (4805)
1 site
G G T C T C N C C A G A G N ( N ) 4

Sticky ends from different BsaI sites may not be compatible.
BsaI can be used between 37°C and 50°C.
AhdI  (4744)
1 site
G A C N N N N N G T C C T G N N N N N C A G

The 1-base overhangs produced by AhdI may be hard to ligate.
Sticky ends from different AhdI sites may not be compatible.
PciI  (3851)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
BspQI  (3735)
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  (3735)
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.
BstZ17I  (3472)
1 site
G T A T A C C A T A T G
BsmI  (3420)
1 site
G A A T G C N C T T A C G N

Sticky ends from different BsmI sites may not be compatible.
PfoI  (3275)
1 site
T C C N G G A A G G N C C T

Sticky ends from different PfoI sites may not be compatible.
SacII  (2965)
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.
MfeI  (161)
1 site
C A A T T G G T T A A C
Bpu10I  (180)
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.
NruI  (208)
1 site
T C G C G A A G C G C T
MluI  (228)
1 site
A C G C G T T G C G C A
SnaBI  (590)
1 site
T A C G T A A T G C A T
AflII  (975)
1 site
C T T A A G G A A T T C
HindIII  (978)
1 site
A A G C T T T T C G A A
Acc65I  (984)
1 site
G G T A C C C C A T G G
KpnI  (988)
1 site
G G T A C C C C A T G G
BamHI  (996)
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.
EcoRV  (1031)
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.
NotI  (1046)
1 site
G C G G C C G C C G C C G G C G
PaeR7I  (1052)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (1052)
1 site
V C T C G A G B B G A G C T C V
XhoI  (1052)
1 site
C T C G A G G A G C T C
XbaI  (1058)
1 site
T C T A G A A G A T C T
EcoO109I  (1064)
1 site
R G G N C C Y Y C C N G G R

Sticky ends from different EcoO109I sites may not be compatible.
PspOMI  (1064)
1 site
G G G C C C C C C G G G
ApaI  (1068)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
SexAI  (1888)
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.
BseRI  (2117)
1 site
G A G G A G ( N ) 8 N N C T C C T C ( N ) 8

Sticky ends from different BseRI sites may not be compatible.
BseRI quickly loses activity at 37°C.
Prolonged incubation with BseRI may lead to degradation of the DNA.
StuI  (2120)
1 site
A G G C C T T C C G G A
AvrII  (2121)
1 site
C C T A G G G G A T C C
TspMI  (2142)
1 site
C C C G G G G G G C C C
XmaI  (2142)
1 site
C C C G G G G G G C C C

Efficient cleavage requires at least two copies of the XmaI recognition sequence.
Full cleavage with XmaI may require a long incubation.
SmaI  (2144)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
PshAI  (2212)
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.
BfuAI  (2498)
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  (2498)
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.
AsiSI  (2549)
1 site
G C G A T C G C C G C T A G C G
RsrII  (2593)
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.
HygR
2185 .. 3210  =  1026 bp
341 amino acids  =  38.0 kDa
Product: aminoglycoside phosphotransferase from E. coli
confers resistance to hygromycin
HygR
2185 .. 3210  =  1026 bp
341 amino acids  =  38.0 kDa
Product: aminoglycoside phosphotransferase from E. coli
confers resistance to hygromycin
AmpR
4671 .. 5531  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   4671 .. 5462  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
4671 .. 5531  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   5463 .. 5531  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
4671 .. 5531  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
ori
3912 .. 4500  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
3912 .. 4500  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
f1 ori
1365 .. 1793  =  429 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
f1 ori
1365 .. 1793  =  429 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
CMV enhancer
235 .. 614  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
235 .. 614  =  380 bp
human cytomegalovirus immediate early enhancer
SV40 promoter
1807 .. 2136  =  330 bp
SV40 enhancer and early promoter
SV40 promoter
1807 .. 2136  =  330 bp
SV40 enhancer and early promoter
bGH poly(A) signal
1095 .. 1319  =  225 bp
bovine growth hormone polyadenylation signal
bGH poly(A) signal
1095 .. 1319  =  225 bp
bovine growth hormone polyadenylation signal
CMV promoter
615 .. 818  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
615 .. 818  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
SV40 poly(A) signal
3340 .. 3461  =  122 bp
SV40 polyadenylation signal
SV40 poly(A) signal
3340 .. 3461  =  122 bp
SV40 polyadenylation signal
MCS
968 .. 1077  =  110 bp
multiple cloning site
MCS
968 .. 1077  =  110 bp
multiple cloning site
AmpR promoter
5532 .. 5636  =  105 bp
AmpR promoter
5532 .. 5636  =  105 bp
tet operator
820 .. 838  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
820 .. 838  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
841 .. 859  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
841 .. 859  =  19 bp
bacterial operator O2 for the tetR and tetA genes
SV40 ori
1987 .. 2122  =  136 bp
SV40 origin of replication
SV40 ori
1987 .. 2122  =  136 bp
SV40 origin of replication
TATA box
804 .. 810  =  7 bp
TATA box
804 .. 810  =  7 bp
ORF:  2185 .. 3210  =  1026 bp
ORF:  341 amino acids  =  38.0 kDa
ORF:  4801 .. 5067  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  1316 .. 1582  =  267 bp
ORF:  88 amino acids  =  9.3 kDa
ORF:  774 .. 1151  =  378 bp
ORF:  125 amino acids  =  14.5 kDa
ORF:  2122 .. 2943  =  822 bp
ORF:  273 amino acids  =  30.8 kDa
ORF:  4671 .. 5531  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
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