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Plasmid Files

ptdTomato

Vector for expressing tdTomato in bacteria.

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ptdTomato Sequence and MapptdTomato.dna
Map and Sequence File   
Sequence Author:  Clontech
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 BspQI - SapI (4057) AflIII - PciI (3940) BsaI (2986) BpmI (2983) NmeAIII (2905) PvuI (2683) TsoI (2654) ScaI (2571) XmnI (2452) SspI (2247) AatII (2133) ZraI (2131) AflII (2067) BstAPI (2011) PvuII (55) HindIII (234) BfuAI - BspMI (239) SphI (244) SalI (252) AccI (253) HincII (254) BamHI (264) TspMI - XmaI (269) SmaI (271) Acc65I (273) AgeI (276) KpnI (277) BsrGI (1709) NotI (1721) ApoI - EcoRI (1735) SpeI (1799) PspOMI (1814) ApaI (1818) PfoI (1872) NdeI (2010) ptdTomato 4065 bp
BspQI  (4057)
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  (4057)
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  (3940)
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  (3940)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
BsaI  (2986)
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.
BpmI  (2983)
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.
NmeAIII  (2905)
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).
PvuI  (2683)
1 site
C G A T C G G C T A G C
TsoI  (2654)
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).
ScaI  (2571)
1 site
A G T A C T T C A T G A
XmnI  (2452)
1 site
G A A N N N N T T C C T T N N N N A A G
SspI  (2247)
1 site
A A T A T T T T A T A A
AatII  (2133)
1 site
G A C G T C C T G C A G
ZraI  (2131)
1 site
G A C G T C C T G C A G
AflII  (2067)
1 site
C T T A A G G A A T T C

The sticky ends produced by AflII are hard to ligate.
BstAPI  (2011)
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.
PvuII  (55)
1 site
C A G C T G G T C G A C
HindIII  (234)
1 site
A A G C T T T T C G A A
BfuAI  (239)
1 site
A C C T G C ( N ) 4 T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the BfuAI
recognition sequence.
Sticky ends from different BfuAI sites may not be compatible.
BfuAI is typically used at 50°C, but is 50% active at 37°C.
BspMI  (239)
1 site
A C C T G C ( N ) 4 T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the BspMI
recognition sequence.
Sticky ends from different BspMI sites may not be compatible.
SphI  (244)
1 site
G C A T G C C G T A C G
SalI  (252)
1 site
G T C G A C C A G C T G
AccI  (253)
1 site
G T M K A C C A K M T G

Efficient cleavage with AccI requires ≥13 bp on each side of the
recognition sequence.
Sticky ends from different AccI sites may not be compatible.
HincII  (254)
1 site
G T Y R A C C A R Y T G
BamHI  (264)
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.
TspMI  (269)
1 site
C C C G G G G G G C C C
XmaI  (269)
1 site
C C C G G G G G G C C C

Efficient cleavage requires at least two copies of the XmaI
recognition sequence.
Full cleavage with XmaI may require a long incubation.
SmaI  (271)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
Acc65I  (273)
1 site
G G T A C C C C A T G G
AgeI  (276)
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.
KpnI  (277)
1 site
G G T A C C C C A T G G
BsrGI  (1709)
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  (1721)
1 site
G C G G C C G C C G C C G G C G
ApoI  (1735)
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  (1735)
1 site
G A A T T C C T T A A G
SpeI  (1799)
1 site
A C T A G T T G A T C A
PspOMI  (1814)
1 site
G G G C C C C C C G G G
ApaI  (1818)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
PfoI  (1872)
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  (2010)
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.
tdTomato
289 .. 1719  =  1431 bp
476 amino acids  =  54.2 kDa
Product: tandem dimeric (pseudo-monomeric)
derivative of DsRed
mammalian codon-optimized
tdTomato
289 .. 1719  =  1431 bp
476 amino acids  =  54.2 kDa
Product: tandem dimeric (pseudo-monomeric)
derivative of DsRed
mammalian codon-optimized
AmpR
2265 .. 3125  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   2265 .. 2333  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
2265 .. 3125  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   2334 .. 3125  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
2265 .. 3125  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
ori
3296 .. 3884  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
3296 .. 3884  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
AmpR promoter
2160 .. 2264  =  105 bp
AmpR promoter
2160 .. 2264  =  105 bp
lac promoter
143 .. 173  =  31 bp
   Segment 1:  -35  
   143 .. 148  =  6 bp
promoter for the E. coli lac operon
lac promoter
143 .. 173  =  31 bp
   Segment 2:  
   149 .. 166  =  18 bp
promoter for the E. coli lac operon
lac promoter
143 .. 173  =  31 bp
   Segment 3:  -10  
   167 .. 173  =  7 bp
promoter for the E. coli lac operon
lac promoter
143 .. 173  =  31 bp
3 segments
promoter for the E. coli lac operon
lac operator
181 .. 197  =  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
181 .. 197  =  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).
M13 rev
205 .. 221  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
205 .. 221  =  17 bp
common sequencing primer, one of multiple similar
variants
ATG
217 .. 219  =  3 bp
1 amino acid  =  149.2 Da
Product: lacZ start codon
ATG
217 .. 219  =  3 bp
1 amino acid  =  149.2 Da
Product: lacZ start codon
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