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pQCXIN

Self-inactivating bicistronic retroviral vector for expression of a gene together with a neomycin (G418) resistance marker.

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pQCXIN.dna
Map and Sequence File:    Download    Open   
Sequence Author:  Clontech (TaKaRa)
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SspI (7055) ScaI (6731) PvuI (6621) AlwNI (5774) SfiI (5064) BmtI (4140) NheI (4136) EcoRV (3994) BsgI (3903) PaeR7I - PspXI - XhoI (3853) AscI (542) PshAI (676) BstEII (1252) Bpu10I (1455) BglII (1576) XbaI (1595) 5' pQC Seq/PCR primer (2141 .. 2164) SbfI (2230) NotI (2243) AgeI (2250) BsiWI (2262) PacI (2273) BamHI (2278) BspEI * (2281) EcoRI (2285) 3' pQC Seq/PCR primer (2329 .. 2352) PspOMI (2421) ApaI (2425) PmlI (2624) AarI (2647) PflMI (2761) BmgBI (2851) BstXI (2894) NgoMIV (3523) NaeI (3525) RsrII (3539) pQCXIN 7400 bp
SspI  (7055)
1 site
A A T A T T T T A T A A
ScaI  (6731)
1 site
A G T A C T T C A T G A
PvuI  (6621)
1 site
C G A T C G G C T A G C
AlwNI  (5774)
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.
SfiI  (5064)
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.
BmtI  (4140)
1 site
G C T A G C C G A T C G
NheI  (4136)
1 site
G C T A G C C G A T C G
EcoRV  (3994)
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.
BsgI  (3903)
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).
PaeR7I  (3853)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (3853)
1 site
V C T C G A G B B G A G C T C V
XhoI  (3853)
1 site
C T C G A G G A G C T C
AscI  (542)
1 site
G G C G C G C C C C G C G C G G
PshAI  (676)
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.
BstEII  (1252)
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.
Bpu10I  (1455)
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.
BglII  (1576)
1 site
A G A T C T T C T A G A
XbaI  (1595)
1 site
T C T A G A A G A T C T
SbfI  (2230)
1 site
C C T G C A G G G G A C G T C C
NotI  (2243)
1 site
G C G G C C G C C G C C G G C G
AgeI  (2250)
1 site
A C C G G T T G G C C A
BsiWI  (2262)
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.
PacI  (2273)
1 site
T T A A T T A A A A T T A A T T
BamHI  (2278)
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.
BspEI  (2281)
1 site
T C C G G A A G G C C T
* Blocked by Dam methylation.
EcoRI  (2285)
1 site
G A A T T C C T T A A G
PspOMI  (2421)
1 site
G G G C C C C C C G G G
ApaI  (2425)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
PmlI  (2624)
1 site
C A C G T G G T G C A C

PmlI gradually loses activity when stored at -20°C.
AarI  (2647)
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.
PflMI  (2761)
1 site
C