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Plasmid Files

pcDNAI

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

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pcDNAI Sequence and MappcDNAI.dna
Map and Sequence File   
Sequence Author:  Invitrogen (Life Technologies)
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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) 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) BssS α I (453) NheI (587) BmtI (591) AclI (612) DraIII (830) BsrFI - NgoMIV (931) NaeI (933) SacII (1182) Bpu10I (1487) NruI (1515) AflIII - MluI (1535) NdeI (1791) SnaBI (1897) 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.
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

Efficient cleavage requires at least two copies of the BsrFI
recognition sequence.
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.
Bpu10I  (1487)
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.
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
   Segment 1:  
   1204 .. 1278  =  75 bp
Product: E. coli amber-suppressor tyrosine tRNA
supF
1204 .. 1383  =  180 bp
   Segment 2:  mature tRNA  
   1279 .. 1363  =  85 bp
Product: E. coli amber-suppressor tyrosine tRNA
supF
1204 .. 1383  =  180 bp
   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
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