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Plasmid Files

pGIPZ

Empty lentiviral vector for constitutive expression of an shRNAmir together with TurboGFP.

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pGIPZ Sequence and MappGIPZ.dna
Map and Sequence File   
Sequence Author:  Open Biosystems
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 SspI (11,251) FspI (10,669) AhdI (10,447) BstZ17I (9175) AsiSI (8252) PshAI (7915) PmeI (6776) Bsu36I (6383) MluI (5650) SgrDI (11,368) NruI * (833) EcoNI (1170) BbvCI - Bpu10I (1424) AleI (1577) KflI - PpuMI (1934) SgrAI (2500) MauBI (2578) SfiI (2621) XbaI (2707) SnaBI (3070) CMV promoter BlpI (3564) BsrGI (4089) NotI (4100) BsiWI (4749) HpaI (5376) PaeR7I - PspXI - XhoI (5391) BamHI (5403) pGIPZ 11,688 bp
SspI  (11,251)
1 site
A A T A T T T T A T A A
FspI  (10,669)
1 site
T G C G C A A C G C G T
AhdI  (10,447)
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.
BstZ17I  (9175)
1 site
G T A T A C C A T A T G
AsiSI  (8252)
1 site
G C G A T C G C C G C T A G C G
PshAI  (7915)
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.
PmeI  (6776)
1 site
G T T T A A A C C A A A T T T G
Bsu36I  (6383)
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.
MluI  (5650)
1 site
A C G C G T T G C G C A
SgrDI  (11,368)
1 site
C G T C G A C G G C A G C T G C
NruI  (833)
1 site
T C G C G A A G C G C T
* Blocked by Dam methylation.
EcoNI  (1170)
1 site
C C T N N N N N A G G G G A N N N N N T C C

The 1-base overhangs produced by EcoNI may be hard to ligate.
Sticky ends from different EcoNI sites may not be compatible.
BbvCI  (1424)
1 site
C C T C A G C G G A G T C G
Bpu10I  (1424)
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.
AleI  (1577)
1 site
C A C N N N N G T G G T G N N N N C A C
KflI  (1934)
1 site
G G G W C C C C C C W G G G

Sticky ends from different KflI sites may not be compatible.
PpuMI  (1934)
1 site
R G G W C C Y Y C C W G G R

Sticky ends from different PpuMI sites may not be compatible.
SgrAI  (2500)
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.
MauBI  (2578)
1 site
C G C G C G C G G C G C G C G C
SfiI  (2621)
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.
XbaI  (2707)
1 site
T C T A G A A G A T C T
SnaBI  (3070)
1 site
T A C G T A A T G C A T
BlpI  (3564)
1 site
G C T N A G C C G A N T C G

Sticky ends from different BlpI sites may not be compatible.
BsrGI  (4089)
1 site
T G T A C A A C A T G T

BsrGI is typically used at 37°C, but is even more active at 60°C.
NotI  (4100)
1 site
G C G G C C G C C G C C G G C G
BsiWI  (4749)
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.
HpaI  (5376)
1 site
G T T A A C C A A T T G
PaeR7I  (5391)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (5391)
1 site
V C T C G A G B B G A G C T C V
XhoI  (5391)
1 site
C T C G A G G A G C T C
BamHI  (5403)
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.
HygR
7888 .. 8913  =  1026 bp
341 amino acids  =  38.0 kDa
Product: aminoglycoside phosphotransferase from E.
coli

confers resistance to hygromycin
HygR
7888 .. 8913  =  1026 bp
341 amino acids  =  38.0 kDa
Product: aminoglycoside phosphotransferase from E.
coli

confers resistance to hygromycin
AmpR
10,374 .. 11,234  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   10,374 .. 11,165  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
10,374 .. 11,234  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   11,166 .. 11,234  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
10,374 .. 11,234  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
TurboGFP
3390 .. 4088  =  699 bp
232 amino acids  =  25.7 kDa
Product: improved green fluorescent protein from
Pontellina plumata
mammalian codon-optimized
TurboGFP
3390 .. 4088  =  699 bp
232 amino acids  =  25.7 kDa
Product: improved green fluorescent protein from
Pontellina plumata
mammalian codon-optimized
5' LTR
1 .. 634  =  634 bp
5' long terminal repeat (LTR) from HIV-1
5' LTR
1 .. 634  =  634 bp
5' long terminal repeat (LTR) from HIV-1
PuroR
4690 .. 5292  =  603 bp
200 amino acids  =  21.6 kDa
Product: puromycin N-acetyltransferase
confers resistance to puromycin
PuroR
4690 .. 5292  =  603 bp
200 amino acids  =  21.6 kDa
Product: puromycin N-acetyltransferase
confers resistance to puromycin
WPRE
5663 .. 6251  =  589 bp
woodchuck hepatitis virus posttranscriptional
regulatory element
WPRE
5663 .. 6251  =  589 bp
woodchuck hepatitis virus posttranscriptional
regulatory element
ori
9615 .. 10,203  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
9615 .. 10,203  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
IRES
4115 .. 4683  =  569 bp
internal ribosome entry site (IRES) of the
encephalomyocarditis virus (EMCV)
IRES
4115 .. 4683  =  569 bp
internal ribosome entry site (IRES) of the
encephalomyocarditis virus (EMCV)
f1 ori
7068 .. 7496  =  429 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
f1 ori
7068 .. 7496  =  429 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
BleoR
2245 .. 2619  =  375 bp
124 amino acids  =  13.8 kDa
Product: antibiotic-binding protein
confers resistance to bleomycin, phleomycin, and
Zeocin™
BleoR
2245 .. 2619  =  375 bp
124 amino acids  =  13.8 kDa
Product: antibiotic-binding protein
confers resistance to bleomycin, phleomycin, and
Zeocin™
SV40 promoter
7510 .. 7839  =  330 bp
SV40 enhancer and early promoter
SV40 promoter
7510 .. 7839  =  330 bp
SV40 enhancer and early promoter
CMV enhancer
2791 .. 3094  =  304 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
2791 .. 3094  =  304 bp
human cytomegalovirus immediate early enhancer
shRNAmir insertion site
5392 .. 5650  =  259 bp
A fragment encoding a microRNA-adapted shRNA
can be inserted between the XhoI and MluI sites.
shRNAmir insertion site
5392 .. 5650  =  259 bp
A fragment encoding a microRNA-adapted shRNA
can be inserted between the XhoI and MluI sites.
RRE
1303 .. 1536  =  234 bp
The Rev response element (RRE) of HIV-1 allows for
Rev-dependent mRNA export from the nucleus to
the cytoplasm.
RRE
1303 .. 1536  =  234 bp
The Rev response element (RRE) of HIV-1 allows for
Rev-dependent mRNA export from the nucleus to
the cytoplasm.
3' LTR (ΔU3)
6458 .. 6691  =  234 bp
self-inactivating 3' long terminal repeat (LTR) from
HIV-1
3' LTR (ΔU3)
6458 .. 6691  =  234 bp
self-inactivating 3' long terminal repeat (LTR) from
HIV-1
bGH poly(A) signal
6798 .. 7022  =  225 bp
bovine growth hormone polyadenylation signal
bGH poly(A) signal
6798 .. 7022  =  225 bp
bovine growth hormone polyadenylation signal
CMV promoter
3095 .. 3298  =  204 bp
human cytomegalovirus (CMV) immediate early
promoter
CMV promoter
3095 .. 3298  =  204 bp
human cytomegalovirus (CMV) immediate early
promoter
SV40 poly(A) signal
11,387 .. 11,521  =  135 bp
SV40 polyadenylation signal
SV40 poly(A) signal
11,387 .. 11,521  =  135 bp
SV40 polyadenylation signal
HIV-1 ψ
681 .. 806  =  126 bp
packaging signal of human immunodeficiency virus
type 1
HIV-1 ψ
681 .. 806  =  126 bp
packaging signal of human immunodeficiency virus
type 1
SV40 poly(A) signal
9043 .. 9164  =  122 bp
SV40 polyadenylation signal
SV40 poly(A) signal
9043 .. 9164  =  122 bp
SV40 polyadenylation signal
cPPT/CTS
2063 .. 2180  =  118 bp
central polypurine tract and central termination
sequence of HIV-1
cPPT/CTS
2063 .. 2180  =  118 bp
central polypurine tract and central termination
sequence of HIV-1
AmpR promoter
11,235 .. 11,339  =  105 bp
AmpR promoter
11,235 .. 11,339  =  105 bp
EM7 promoter
2639 .. 2686  =  48 bp
synthetic bacterial promoter
EM7 promoter
2639 .. 2686  =  48 bp
synthetic bacterial promoter
SV40 ori
7690 .. 7825  =  136 bp
SV40 origin of replication
SV40 ori
7690 .. 7825  =  136 bp
SV40 origin of replication
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