pcDNAI

Vector for high-level expression of a cloned cDNA in mammalian cells.

Sequence Author: Thermo Fisher (Invitrogen)

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SfiI (3961) PasI (3695) KflI (3690) XcmI (3579) BclI * (3416) EcoNI (3362) ScaI (3184) HpaI (2893) BsgI (2714) BbsI (2630) PflMI (2482) SP6 promoter XbaI (2290) NsiI (2289) NspI - SphI (2287) PaeR7I - PspXI - XhoI (2278) NotI (2272) EcoRV (2257) PstI (2254) EcoRI (2245) BamHI (2214) HindIII (2196) AlwNI (217) ApaLI (312) BseYI (322) PspFI (326) BciVI (428) BssSI - BssSαI (453) NheI (587) BmtI (591) AclI (612) DraIII (830) BsrFI - NgoMIV (931) NaeI (933) SacII (1182) TaqII (1478) Bpu10I (1487) NruI (1515) AflIII - MluI (1535) CMV enhancer NdeI (1791) SnaBI (1897) T7 promoter pcDNAI 4033 bp
SfiI  (3961)
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.
PasI  (3695)
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.
KflI  (3690)
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.
XcmI  (3579)
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.
BclI  (3416)
1 site
T G A T C A A C T A G T
* Blocked by Dam methylation.
BclI is typically used at 50-55°C, but is 50% active at 37°C.
EcoNI  (3362)
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.
ScaI  (3184)
1 site
A G T A C T T C A T G A
HpaI  (2893)
1 site
G T T A A C C A A T T G
BsgI  (2714)
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).
BbsI  (2630)
1 site
G A A G A C N N C T T C T G N N ( N ) 4

Sticky ends from different BbsI sites may not be compatible.
BbsI gradually loses activity when stored at -20°C.
PflMI  (2482)
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.
XbaI  (2290)
1 site
T C T A G A A G A T C T
NsiI  (2289)
1 site
A T G C A T T A C G T A
NspI  (2287)
1 site
R C A T G Y Y G T A C R
SphI  (2287)
1 site
G C A T G C C G T A C G
PaeR7I  (2278)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (2278)
1 site
V C T C G A G B B G A G C T C V
XhoI  (2278)
1 site
C T C G A G G A G C T C
NotI  (2272)
1 site
G C G G C C G C C G C C G G C G
EcoRV  (2257)
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.
PstI  (2254)
1 site
C T G C A G G A C G T C
EcoRI  (2245)
1 site
G A A T T C C T T A A G
BamHI  (2214)
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.
HindIII  (2196)
1 site
A A G C T T T T C G A A
AlwNI  (217)
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.
ApaLI  (312)
1 site
G T G C A C C A C G T G
BseYI  (322)
1 site
C C C A G C G G G T C G

After cleavage, BseYI can remain bound to DNA and alter its electrophoretic mobility.
PspFI  (326)
1 site
C C C A G C G G G T C G
BciVI  (428)
1 site
G T A T C C ( N ) 5 N C A T A G G ( N ) 5

The 1-base overhangs produced by BciVI may be hard to ligate.
Sticky ends from different BciVI sites may not be compatible.
BssSI  (453)
1 site
C A C G A G G T G C T C
BssSαI  (453)
1 site
C A C G A G G T G C T C
NheI  (587)
1 site
G C T A G C C G A T C G
BmtI  (591)
1 site
G C T A G C C G A T C G
AclI  (612)
1 site
A A C G T T T T G C A A
DraIII  (830)
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.
BsrFI  (931)
1 site
R C C G G Y Y G G C C R

Cleavage may be enhanced when more than one copy of the BsrFI recognition sequence is present.
After cleavage, BsrFI can remain bound to DNA and alter its electrophoretic mobility.
NgoMIV  (931)
1 site
G C C G G C C G G C C G

Efficient cleavage requires at least two copies of the NgoMIV recognition sequence.
NaeI  (933)
1 site
G C C G G C C G G C C G

Efficient cleavage requires at least two copies of the NaeI recognition sequence.
SacII  (1182)
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.
TaqII  (1478)
1 site
G A C C G A ( N ) 9 N N C T G G C T ( N ) 9

Sticky ends from different TaqII sites may not be compatible.
Bpu10I  (1487)
1 site
C C T N A G C G G A N T C G

Cleavage may be enhanced when more than one copy of the Bpu10I recognition sequence is present.
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.
NruI  (1515)
1 site
T C G C G A A G C G C T
AflIII  (1535)
1 site
A C R Y G T T G Y R C A

Sticky ends from different AflIII sites may not be compatible.
MluI  (1535)
1 site
A C G C G T T G C G C A
NdeI  (1791)
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  (1897)
1 site
T A C G T A A T G C A T
ori
2 .. 570  =  569 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
2 .. 570  =  569 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
f1 ori
603 .. 1061  =  459 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
f1 ori
603 .. 1061  =  459 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
CMV enhancer
1542 .. 1921  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
1542 .. 1921  =  380 bp
human cytomegalovirus immediate early enhancer
CMV promoter
1922 .. 2125  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
1922 .. 2125  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
supF
1204 .. 1383  =  180 bp
3 segments
   Segment 1:  
   1204 .. 1278  =  75 bp
Product: E. coli amber-suppressor tyrosine tRNA
supF
1204 .. 1383  =  180 bp
3 segments
   Segment 2:  mature tRNA  
   1279 .. 1363  =  85 bp
Product: E. coli amber-suppressor tyrosine tRNA
supF
1204 .. 1383  =  180 bp
3 segments
   Segment 3:  
   1364 .. 1383  =  20 bp
Product: E. coli amber-suppressor tyrosine tRNA
supF
1204 .. 1383  =  180 bp
3 segments
Product: E. coli amber-suppressor tyrosine tRNA
SV40 ori
3874 .. 4009  =  136 bp
SV40 origin of replication
SV40 ori
3874 .. 4009  =  136 bp
SV40 origin of replication
SV40 poly(A) signal
2894 .. 3028  =  135 bp
SV40 polyadenylation signal
SV40 poly(A) signal
2894 .. 3028  =  135 bp
SV40 polyadenylation signal
MCS
2196 .. 2295  =  100 bp
multiple cloning site
MCS
2196 .. 2295  =  100 bp
multiple cloning site
small t intron
2407 .. 2472  =  66 bp
simian virus 40 (SV40) small t antigen intron
small t intron
2407 .. 2472  =  66 bp
simian virus 40 (SV40) small t antigen intron
T7 promoter
2170 .. 2188  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
2170 .. 2188  =  19 bp
promoter for bacteriophage T7 RNA polymerase
SP6 promoter
2305 .. 2323  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
SP6 promoter
2305 .. 2323  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
ORF:  2551 .. 2871  =  321 bp
ORF:  106 amino acids  =  12.1 kDa
ORF:  2877 .. 3128  =  252 bp
ORF:  83 amino acids  =  9.3 kDa
ORF:  2969 .. 3397  =  429 bp
ORF:  142 amino acids  =  15.2 kDa
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