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Plasmid Files

pIX 3.0

Prokaryotic in vitro translation vector for cloning PCR products generated with the EasyXpress Linear Template Kit.

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pIX 3.0 Sequence and MappIX 3.0.dna
Map and Sequence File   
Sequence Author:  Qiagen
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 EcoO109I (2686) AatII (2632) ZraI (2630) SspI (2514) XmnI (2309) ScaI (2190) TsoI (2109) NmeAIII (1858) BpmI (1780) BsaI (1771) AhdI (1710) PfoI (46) NdeI (184) BstAPI (185) KasI (235) NarI (236) SfoI (237) PluTI (239) HindIII (399) AvaI - BsoBI - PaeR7I - XhoI (406) BmeT110I (407) EagI - NotI (412) NheI (417) BmtI (421) SphI (425) BtgI - NcoI - StyI (426) EcoRV (433) StuI * (439) BamHI (443) ApoI - EcoRI (449) AgeI - SgrAI (455) lac operator BspQI - SapI (701) AflIII - PciI (817) BseYI (1121) PspFI (1125) AlwNI (1233) pIX 3.0 2697 bp
EcoO109I  (2686)
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.
AatII  (2632)
1 site
G A C G T C C T G C A G
ZraI  (2630)
1 site
G A C G T C C T G C A G
SspI  (2514)
1 site
A A T A T T T T A T A A
XmnI  (2309)
1 site
G A A N N N N T T C C T T N N N N A A G
ScaI  (2190)
1 site
A G T A C T T C A T G A
TsoI  (2109)
1 site
T A R C C A ( N ) 9 N N A T Y G G T ( N ) 9

Sticky ends from different TsoI sites may not be compatible.
After cleavage, TsoI can remain bound to DNA and alter its
electrophoretic mobility.
For full activity, add fresh S-adenosylmethionine (SAM).
NmeAIII  (1858)
1 site
G C C G A G ( N ) 18-19 N N C G G C T C ( N ) 18-19

Efficient cleavage requires at least two copies of the NmeAIII
recognition sequence.
Sticky ends from different NmeAIII sites may not be compatible.
For full activity, add fresh S-adenosylmethionine (SAM).
BpmI  (1780)
1 site
C T G G A G ( N ) 14 N N G A C C T C ( N ) 14

Efficient cleavage requires at least two copies of the BpmI
recognition sequence.
Sticky ends from different BpmI sites may not be compatible.
After cleavage, BpmI can remain bound to DNA and alter its
electrophoretic mobility.
BpmI quickly loses activity at 37°C.
BsaI  (1771)
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  (1710)
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.
PfoI  (46)
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.
NdeI  (184)
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.
BstAPI  (185)
1 site
G C A N N N N N T G C C G T N N N N N A C G

Sticky ends from different BstAPI sites may not be compatible.
KasI  (235)
1 site
G G C G C C C C G C G G
NarI  (236)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the NarI
recognition sequence.
SfoI  (237)
1 site
G G C G C C C C G C G G
PluTI  (239)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the PluTI
recognition sequence.
HindIII  (399)
1 site
A A G C T T T T C G A A
AvaI  (406)
1 site
C Y C G R G G R G C Y C

Sticky ends from different AvaI sites may not be compatible.
BsoBI  (406)
1 site
C Y C G R G G R G C Y C

Sticky ends from different BsoBI sites may not be compatible.
BsoBI is typically used at 37°C, but can be used at temperatures
up to 65°C.
PaeR7I  (406)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
XhoI  (406)
1 site
C T C G A G G A G C T C
BmeT110I  (407)
1 site
C Y C G R G G R G C Y C
EagI  (412)
1 site
C G G C C G G C C G G C
NotI  (412)
1 site
G C G G C C G C C G C C G G C G
NheI  (417)
1 site
G C T A G C C G A T C G
BmtI  (421)
1 site
G C T A G C C G A T C G
SphI  (425)
1 site
G C A T G C C G T A C G
BtgI  (426)
1 site
C C R Y G G G G Y R C C

Sticky ends from different BtgI sites may not be compatible.
NcoI  (426)
1 site
C C A T G G G G T A C C
StyI  (426)
1 site
C C W W G G G G W W C C

Sticky ends from different StyI sites may not be compatible.
EcoRV  (433)
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.
StuI  (439)
1 site
A G G C C T T C C G G A
* Blocked by Dcm methylation.
BamHI  (443)
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.
ApoI  (449)
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.
EcoRI  (449)
1 site
G A A T T C C T T A A G
AgeI  (455)
1 site
A C C G G T T G G C C A

AgeI quickly loses activity at 37°C, but can be used at 25°C for
long incubations.
SgrAI  (455)
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.
BspQI  (701)
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  (701)
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  (817)
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  (817)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
BseYI  (1121)
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.
PspFI  (1125)
1 site
C C C A G C G G G T C G
AlwNI  (1233)
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.
AmpR
1637 .. 2497  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   1637 .. 2428  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
1637 .. 2497  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   2429 .. 2497  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
1637 .. 2497  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
ori
878 .. 1466  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
878 .. 1466  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
AmpR promoter
2498 .. 2602  =  105 bp
AmpR promoter
2498 .. 2602  =  105 bp
MCS
406 .. 461  =  56 bp
multiple cloning site
MCS
406 .. 461  =  56 bp
multiple cloning site
lac promoter
524 .. 554  =  31 bp
   Segment 3:  -10  
   524 .. 530  =  7 bp
promoter for the E. coli lac operon
lac promoter
524 .. 554  =  31 bp
   Segment 2:  
   531 .. 548  =  18 bp
promoter for the E. coli lac operon
lac promoter
524 .. 554  =  31 bp
   Segment 1:  -35  
   549 .. 554  =  6 bp
promoter for the E. coli lac operon
lac promoter
524 .. 554  =  31 bp
3 segments
promoter for the E. coli lac operon
M13 fwd
379 .. 395  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 fwd
379 .. 395  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
476 .. 492  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
476 .. 492  =  17 bp
common sequencing primer, one of multiple similar
variants
lac operator
500 .. 516  =  17 bp
The lac repressor binds to the lac operator to inhibit
transcription in E. coli. This inhibition can be
relieved by adding lactose or
isopropyl-β-D-thiogalactopyranoside (IPTG).
lac operator
500 .. 516  =  17 bp
The lac repressor binds to the lac operator to inhibit
transcription in E. coli. This inhibition can be
relieved by adding lactose or
isopropyl-β-D-thiogalactopyranoside (IPTG).
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