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Plasmid Files

ptd-Tomato-N1

Vector for fusing tdTomato to the C-terminus of a partner protein.

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ptd-Tomato-N1.dna
Map and Sequence File:    Download    Open   
Sequence Author:  Clontech (TaKaRa)
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AflIII - PciI (5385) ApaLI (5071) BsaI (4456) PfoI (4242) RsrII (3983) BsrDI (3700) PflFI - Tth111I (3585) PluTI (3470) SfoI (3468) NarI (3467) KasI (3466) BspDI * - ClaI * (3307) SfiI (3242) AseI (7) NdeI (234) SnaBI (340) NheI (591) BmtI (595) BglII (609) PaeR7I - XhoI (613) Eco53kI (618) SacI (620) HindIII (622) EcoRI (629) SalI (639) AccI (640) Acc65I (645) KpnI (649) SacII (652) PspOMI (653) TspMI - XmaI (656) ApaI (657) SmaI (658) BamHI (660) AgeI (666) BsrGI (2099) NotI (2111) XbaI * (2121) MfeI (2217) HpaI (2230) Bts α I (2306) AflII (2349) DraIII (2583) ptd-Tomato-N1 5443 bp
AflIII  (5385)
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  (5385)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
ApaLI  (5071)
1 site
G T G C A C C A C G T G
BsaI  (4456)
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.
PfoI  (4242)
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.
RsrII  (3983)
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.
BsrDI  (3700)
1 site
G C A A T G N N C G T T A C

Sticky ends from different BsrDI sites may not be compatible.
PflFI  (3585)
1 site
G A C N N N G T C C T G N N N C A G

The 1-base overhangs produced by PflFI may be hard to ligate.
Sticky ends from different PflFI sites may not be compatible.
Tth111I  (3585)
1 site
G A C N N N G T C C T G N N N C A G

The 1-base overhangs produced by Tth111I may be hard to ligate.
Sticky ends from different Tth111I sites may not be compatible.
PluTI  (3470)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the PluTI recognition sequence.
SfoI  (3468)
1 site
G G C G C C C C G C G G
NarI  (3467)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the NarI recognition sequence.
KasI  (3466)
1 site
G G C G C C C C G C G G
BspDI  (3307)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
ClaI  (3307)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
SfiI  (3242)
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.
AseI  (7)
1 site
A T T A A T T A A T T A
NdeI  (234)
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.
SnaBI  (340)
1 site
T A C G T A A T G C A T
NheI  (591)
1 site
G C T A G C C G A T C G
BmtI  (595)
1 site
G C T A G C C G A T C G
BglII  (609)
1 site
A G A T C T T C T A G A
PaeR7I  (613)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
XhoI  (613)
1 site
C T C G A G G A G C T C
Eco53kI  (618)
1 site
G A G C T C C T C G A G
SacI  (620)
1 site
G A G C T C C T C G A G
HindIII  (622)
1 site
A A G C T T T T C G A A
EcoRI  (629)
1 site
G A A T T C C T T A A G
SalI  (639)
1 site
G T C G A C C A G C T G
AccI  (640)
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.
Acc65I  (645)
1 site
G G T A C C C C A T G G
KpnI  (649)
1 site
G G T A C C C C A T G G
SacII  (652)
1 site
C C G C G G G G C G C C

Efficient cleavage requires at least two copies of the SacII recognition sequence.
PspOMI  (653)
1 site
G G G C C C C C C G G G
TspMI  (656)
1 site
C C C G G G G G G C C C
XmaI  (656)
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.
ApaI  (657)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
SmaI  (658)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
BamHI  (660)
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.
AgeI  (666)
1 site
A C C G G T T G G C C A
BsrGI  (2099)
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  (2111)
1 site
G C G G C C G C C G C C G G C G
XbaI  (2121)
1 site
T C T A G A A G A T C T
* Blocked by Dam methylation.
MfeI  (2217)
1 site
C A A T T G G T T A A C
HpaI  (2230)
1 site
G T T A A C C A A T T G
BtsαI  (2306)
1 site
G C A G T G N N C G T C A C

Sticky ends from different BtsαI sites may not be compatible.
AflII  (2349)
1 site
C T T A A G G A A T T C
DraIII  (2583)
1 site
C A C N N N G T G G T G N N N C A C

Sticky ends from different DraIII sites may not be compatible.
tdTomato
679 .. 2109  =  1431 bp
476 amino acids  =  54.2 kDa
Product: tandem dimeric (pseudo-monomeric) derivative of DsRed
mammalian codon-optimized
tdTomato
679 .. 2109  =  1431 bp
476 amino acids  =  54.2 kDa
Product: tandem dimeric (pseudo-monomeric) derivative of DsRed
mammalian codon-optimized
NeoR/KanR
3339 .. 4133  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from Tn5
confers resistance to neomycin, kanamycin, and G418 (Geneticin)
NeoR/KanR
3339 .. 4133  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from Tn5
confers resistance to neomycin, kanamycin, and G418 (Geneticin)
ori
4741 .. 5329  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
4741 .. 5329  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
f1 ori
2359 .. 2814  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
f1 ori
2359 .. 2814  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
SV40 promoter
2947 .. 3304  =  358 bp
SV40 enhancer and early promoter
SV40 promoter
2947 .. 3304  =  358 bp
SV40 enhancer and early promoter
CMV enhancer
61 .. 364  =  304 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
61 .. 364  =  304 bp
human cytomegalovirus immediate early enhancer
CMV promoter
365 .. 568  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
365 .. 568  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
SV40 poly(A) signal
2231 .. 2352  =  122 bp
SV40 polyadenylation signal
SV40 poly(A) signal
2231 .. 2352  =  122 bp
SV40 polyadenylation signal
AmpR promoter
2841 .. 2945  =  105 bp
AmpR promoter
2841 .. 2945  =  105 bp
MCS
591 .. 671  =  81 bp
multiple cloning site of fluorescent protein plasmids
MCS
591 .. 671  =  81 bp
multiple cloning site of fluorescent protein plasmids
HSV TK poly(A) signal
4365 .. 4412  =  48 bp
herpesvirus thymidine kinase polyadenylation signal
HSV TK poly(A) signal
4365 .. 4412  =  48 bp
herpesvirus thymidine kinase polyadenylation signal
SV40 ori
3155 .. 3290  =  136 bp
SV40 origin of replication
SV40 ori
3155 .. 3290  =  136 bp
SV40 origin of replication
ORF:  679 .. 2109  =  1431 bp
ORF:  476 amino acids  =  54.2 kDa
ORF:  3511 .. 3897  =  387 bp
ORF:  128 amino acids  =  14.6 kDa
ORF:  4154 .. 4603  =  450 bp
ORF:  149 amino acids  =  16.3 kDa
ORF:  3339 .. 4133  =  795 bp
ORF:  264 amino acids  =  29.0 kDa
ORF:  607 .. 1362  =  756 bp
ORF:  251 amino acids  =  25.6 kDa
ORF:  447 .. 746  =  300 bp
ORF:  99 amino acids  =  10.7 kDa
ORF:  3648 .. 4184  =  537 bp
ORF:  178 amino acids  =  19.8 kDa
ORF:  4359 .. 4592  =  234 bp
ORF:  77 amino acids  =  8.6 kDa
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