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Plasmid Files

pQCXIP

Self-inactivating bicistronic retroviral vector for expression of a gene together with a puromycin resistance marker.

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pQCXIP.dna
Map and Sequence File:    Download    Open   
Sequence Author:  Clontech (TaKaRa)
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SspI (6836) ScaI (6512) PvuI (6402) FspI (6254) AlwNI (5555) BspQI - SapI (5023) SfiI (4845) BmtI (3921) NheI (3917) PvuII (3818) EcoRV (3775) AscI (542) Bpu10I (1455) BglII (1576) XbaI (1595) 5' pQC Seq/PCR primer (2141 .. 2164) SbfI (2230) NotI (2243) AgeI (2250) 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) RsrII (3030) BsgI (3684) pQCXIP 7181 bp
SspI  (6836)
1 site
A A T A T T T T A T A A
ScaI  (6512)
1 site
A G T A C T T C A T G A
PvuI  (6402)
1 site
C G A T C G G C T A G C
FspI  (6254)
1 site
T G C G C A A C G C G T
AlwNI  (5555)
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.
BspQI  (5023)
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  (5023)
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.
SfiI  (4845)
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  (3921)
1 site
G C T A G C C G A T C G
NheI  (3917)
1 site
G C T A G C C G A T C G
PvuII  (3818)
1 site
C A G C T G G T C G A C
EcoRV  (3775)
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.
AscI  (542)
1 site
G G C G C G C C C C G C G C G G
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
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 C A N N N N N T G G G G T N N N N N A C C

Sticky ends from different PflMI sites may not be compatible.
BmgBI  (2851)
1 site
C A C G T C G T G C A G

This recognition sequence is asymmetric, so ligating blunt ends generated by BmgBI will not always regenerate a BmgBI site.
RsrII  (3030)
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.
BsgI  (3684)
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).
5' pQC Seq/PCR primer
24-mer  /  54% GC
1 binding site
2141 .. 2164  =  24 annealed bases
Tm  =  66°C
3' pQC Seq/PCR primer
24-mer  /  54% GC
1 binding site
2329 .. 2352  =  24 annealed bases
Tm  =  64°C
AmpR
5959 .. 6819  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 2:  
   5959 .. 6750  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
5959 .. 6819  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 1:  signal sequence  
   6751 .. 6819  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
5959 .. 6819  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
PuroR
2914 .. 3513  =  600 bp
199 amino acids  =  21.5 kDa
Product: puromycin N-acetyltransferase
confers resistance to puromycin
PuroR
2914 .. 3513  =  600 bp
199 amino acids  =  21.5 kDa
Product: puromycin N-acetyltransferase
confers resistance to puromycin
ori
5200 .. 5788  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
5200 .. 5788  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
IRES
2308 .. 2881  =  574 bp
internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV)
IRES
2308 .. 2881  =  574 bp
internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV)
3' LTR (ΔU3)
3887 .. 4312  =  426 bp
self-inactivating 3' long terminal repeat (LTR) from Moloney murine leukemia virus
3' LTR (ΔU3)
3887 .. 4312  =  426 bp
self-inactivating 3' long terminal repeat (LTR) from Moloney murine leukemia virus
gag (truncated)
1151 .. 1567  =  417 bp
truncated MMLV gag gene lacking the start codon
gag (truncated)
1151 .. 1567  =  417 bp
truncated MMLV gag gene lacking the start codon
CMV enhancer
7110 .. 308  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
7110 .. 308  =  380 bp
human cytomegalovirus immediate early enhancer
SV40 promoter
4578 .. 4907  =  330 bp
SV40 enhancer and early promoter
SV40 promoter
4578 .. 4907  =  330 bp
SV40 enhancer and early promoter
CMV enhancer
1604 .. 1907  =  304 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
1604 .. 1907  =  304 bp
human cytomegalovirus immediate early enhancer
CMV promoter
309 .. 512  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
309 .. 512  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
1908 .. 2111  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
1908 .. 2111  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
MMLV Ψ
751 .. 950  =  200 bp
packaging signal of Moloney murine leukemia virus (MMLV)
MMLV Ψ
751 .. 950  =  200 bp
packaging signal of Moloney murine leukemia virus (MMLV)
5' LTR (truncated)
513 .. 688  =  176 bp
truncated long terminal repeat from Moloney murine sarcoma virus
5' LTR (truncated)
513 .. 688  =  176 bp
truncated long terminal repeat from Moloney murine sarcoma virus
AmpR promoter
6820 .. 6924  =  105 bp
AmpR promoter
6820 .. 6924  =  105 bp
MCS
2225 .. 2290  =  66 bp
multiple cloning site
MCS
2225 .. 2290  =  66 bp
multiple cloning site
SV40 ori
4758 .. 4893  =  136 bp
SV40 origin of replication
SV40 ori
4758 .. 4893  =  136 bp
SV40 origin of replication
ORF:  2791 .. 3513  =  723 bp
ORF:  240 amino acids  =  26.2 kDa
ORF:  6089 .. 6355  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  4136 .. 4426  =  291 bp
ORF:  96 amino acids  =  10.5 kDa
ORF:  838 .. 1098  =  261 bp
ORF:  86 amino acids  =  9.5 kDa
ORF:  2806 .. 3564  =  759 bp
ORF:  252 amino acids  =  26.3 kDa
ORF:  5959 .. 6819  =  861 bp
ORF:  286 amino acids  =  31.5 kDa
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