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Plasmid Files

pTRIPZ™

Empty lentiviral vector for doxycycline-inducible expression of an shRNAmir together with TurboRFP.

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pTRIPZ Sequence and MappTRIPZ.dna
Map and Sequence File
Sequence Author:  Open Biosystems
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 SgrDI (13,000) SspI (12,883) FspI (12,301) AhdI (12,079) AanI (10,694) AsiSI (9884) AanI (9054) PmeI (8404) AanI (8354) BsiWI (6732) AanI (13,038) HIV-1 ψ BbvCI (1424) AleI (1577) SgrAI (2500) MauBI (2578) XbaI (2707) tet operator tet operator tet operator tet operator tet operator tet operator minimal CMV promoter AgeI (2992) BsrGI (3042) PasI (3223) TurboRFP BspDI - ClaI (3701) HpaI (3790) PaeR7I - PspXI - XhoI (3805) BamHI (3817) BsaBI * (3822) EcoRI (3829) MluI (4064) AfeI (4125) AanI (4935) SpeI (5231) NheI (5282) BmtI (5286) BamHI (5288) XcmI (5339) BamHI (6076) NotI (6083) pTRIPZ™ 13,320 bp
SgrDI  (13,000)
1 site
C G T C G A C G G C A G C T G C
SspI  (12,883)
1 site
A A T A T T T T A T A A
FspI  (12,301)
1 site
T G C G C A A C G C G T
AhdI  (12,079)
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.
AanI  (10,694)
5 sites
T T A T A A A A T A T T
AsiSI  (9884)
1 site
G C G A T C G C C G C T A G C G
AanI  (9054)
5 sites
T T A T A A A A T A T T
PmeI  (8404)
1 site
G T T T A A A C C A A A T T T G
AanI  (8354)
5 sites
T T A T A A A A T A T T
BsiWI  (6732)
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.
AanI  (13,038)
5 sites
T T A T A A A A T A T T
BbvCI  (1424)
1 site
C C T C A G C G G A G T C G
AleI  (1577)
1 site
C A C N N N N G T G G T G N N N N C A C
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
XbaI  (2707)
1 site
T C T A G A A G A T C T
AgeI  (2992)
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.
BsrGI  (3042)
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.
PasI  (3223)
1 site
C C C W G G G G G G W C C C

Sticky ends from different PasI sites may not be compatible.
BspDI  (3701)
1 site
A T C G A T T A G C T A
ClaI  (3701)
1 site
A T C G A T T A G C T A
HpaI  (3790)
1 site
G T T A A C C A A T T G
PaeR7I  (3805)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (3805)
1 site
V C T C G A G B B G A G C T C V
XhoI  (3805)
1 site
C T C G A G G A G C T C
BamHI  (3817)
3 sites
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.
BsaBI  (3822)
1 site
G A T N N N N A T C C T A N N N N T A G
* Blocked by Dam methylation.
EcoRI  (3829)
1 site
G A A T T C C T T A A G
MluI  (4064)
1 site
A C G C G T T G C G C A
AfeI  (4125)
1 site
A G C G C T T C G C G A
AanI  (4935)
5 sites
T T A T A A A A T A T T
SpeI  (5231)
1 site
A C T A G T T G A T C A
NheI  (5282)
1 site
G C T A G C C G A T C G
BmtI  (5286)
1 site
G C T A G C C G A T C G
BamHI  (5288)
3 sites
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.
XcmI  (5339)
1 site
C C A N N N N N N N N N T G G G G T N N N N N N N N N A C C

The 1-base overhangs produced by XcmI may be hard to ligate.
Sticky ends from different XcmI sites may not be compatible.
BamHI  (6076)
3 sites
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.
NotI  (6083)
1 site
G C G G C C G C C G C C G G C G
UbC promoter
4070 .. 5281  =  1212 bp
human ubiquitin C promoter
UbC promoter
4070 .. 5281  =  1212 bp
human ubiquitin C promoter
HygR (inactivated)
9516 .. 10,545  =  1030 bp
The hygromycin resistance gene was inactivated by
destroying an EcoRI site within the coding sequence.
HygR (inactivated)
9516 .. 10,545  =  1030 bp
The hygromycin resistance gene was inactivated by
destroying an EcoRI site within the coding sequence.
AmpR
12,006 .. 12,866  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   12,006 .. 12,797  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
12,006 .. 12,866  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   12,798 .. 12,866  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
12,006 .. 12,866  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
rtTA3
5334 .. 6041  =  708 bp
235 amino acids  =  26.3 kDa
Product: reverse tetracycline transactivator 3
activates expression from Tet-responsive promoters
in the presence of doxycycline
rtTA3
5334 .. 6041  =  708 bp
235 amino acids  =  26.3 kDa
Product: reverse tetracycline transactivator 3
activates expression from Tet-responsive promoters
in the presence of doxycycline
TurboRFP
3005 .. 3700  =  696 bp
231 amino acids  =  26.1 kDa
Product: red fluorescent protein from Entacmaea
quadricolor

mammalian codon-optimized
TurboRFP
3005 .. 3700  =  696 bp
231 amino acids  =  26.1 kDa
Product: red fluorescent protein from Entacmaea
quadricolor

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
6673 .. 7275  =  603 bp
200 amino acids  =  21.6 kDa
Product: puromycin N-acetyltransferase
confers resistance to puromycin
PuroR
6673 .. 7275  =  603 bp
200 amino acids  =  21.6 kDa
Product: puromycin N-acetyltransferase
confers resistance to puromycin
WPRE
7291 .. 7879  =  589 bp
woodchuck hepatitis virus posttranscriptional
regulatory element
WPRE
7291 .. 7879  =  589 bp
woodchuck hepatitis virus posttranscriptional
regulatory element
ori
11,247 .. 11,835  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
11,247 .. 11,835  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
IRES
6098 .. 6666  =  569 bp
internal ribosome entry site (IRES) of the
encephalomyocarditis virus (EMCV)
IRES
6098 .. 6666  =  569 bp
internal ribosome entry site (IRES) of the
encephalomyocarditis virus (EMCV)
f1 ori
8696 .. 9124  =  429 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
f1 ori
8696 .. 9124  =  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
9138 .. 9467  =  330 bp
SV40 enhancer and early promoter
SV40 promoter
9138 .. 9467  =  330 bp
SV40 enhancer and early promoter
shRNAmir insertion site
3806 .. 4064  =  259 bp
A fragment encoding a microRNA-adapted shRNA
can be inserted between the XhoI and MluI sites.
shRNAmir insertion site
3806 .. 4064  =  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)
8086 .. 8319  =  234 bp
self-inactivating 3' long terminal repeat (LTR) from
HIV-1
3' LTR (ΔU3)
8086 .. 8319  =  234 bp
self-inactivating 3' long terminal repeat (LTR) from
HIV-1
bGH poly(A) signal
8426 .. 8650  =  225 bp
bovine growth hormone polyadenylation signal
bGH poly(A) signal
8426 .. 8650  =  225 bp
bovine growth hormone polyadenylation signal
SV40 poly(A) signal
13,019 .. 13,153  =  135 bp
SV40 polyadenylation signal
SV40 poly(A) signal
13,019 .. 13,153  =  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
10,675 .. 10,796  =  122 bp
SV40 polyadenylation signal
SV40 poly(A) signal
10,675 .. 10,796  =  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
12,867 .. 12,971  =  105 bp
AmpR promoter
12,867 .. 12,971  =  105 bp
EM7 promoter
2639 .. 2686  =  48 bp
synthetic bacterial promoter
EM7 promoter
2639 .. 2686  =  48 bp
synthetic bacterial promoter
minimal CMV promoter
2930 .. 2968  =  39 bp
human cytomegalovirus (CMV) immediate early
promoter
minimal CMV promoter
2930 .. 2968  =  39 bp
human cytomegalovirus (CMV) immediate early
promoter
loxP511
5294 .. 5327  =  34 bp
Cre-mediated recombination occurs in the 8-bp core
sequence (GTATACAT). loxP511 sites are compatible
with each other, but incompatible with wild-type
loxP sites.
loxP511
5294 .. 5327  =  34 bp
Cre-mediated recombination occurs in the 8-bp core
sequence (GTATACAT). loxP511 sites are compatible
with each other, but incompatible with wild-type
loxP sites.
loxP511
6042 .. 6075  =  34 bp
Cre-mediated recombination occurs in the 8-bp core
sequence (GTATACAT). loxP511 sites are compatible
with each other, but incompatible with wild-type
loxP sites.
loxP511
6042 .. 6075  =  34 bp
Cre-mediated recombination occurs in the 8-bp core
sequence (GTATACAT). loxP511 sites are compatible
with each other, but incompatible with wild-type
loxP sites.
tet operator
2722 .. 2740  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2722 .. 2740  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2757 .. 2775  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2757 .. 2775  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2793 .. 2811  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2793 .. 2811  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2829 .. 2847  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2829 .. 2847  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2864 .. 2882  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2864 .. 2882  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2900 .. 2918  =  19 bp
bacterial operator O2 for the tetR and tetA genes
tet operator
2900 .. 2918  =  19 bp
bacterial operator O2 for the tetR and tetA genes
SV40 ori
9318 .. 9453  =  136 bp
SV40 origin of replication
SV40 ori
9318 .. 9453  =  136 bp
SV40 origin of replication
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