pcDNA3

Mammalian expression vector with the CMV promoter and a neomycin-resistance marker.

Sequence Author: Thermo Fisher (Invitrogen)

Try SnapGene for Free
|Download SnapGene Viewer
Explore Over 2.7k Plasmids: I.M.A.G.E. Consortium Plasmids | More Plasmid Sets
No matches
HomePlasmidsI.M.A.G.E. Consortium PlasmidspcDNA3
SgrDI (5444) SspI (5327) ScaI (5003) PvuI (4893) AhdI (4523) PciI (3630) BstZ17I (3251) BsmI (3199) PfoI (3054) BstBI (2961) RsrII (2795) BglII (12) MfeI (161) Bpu10I (180) NruI (208) MluI (228) NdeI (484) SnaBI (590) HindIII (889) Acc65I (895) KpnI (899) BamHI (907) EcoRI (938) EcoRV (950) NotI (965) PaeR7I - PspXI - XhoI (971) XbaI (983) PspOMI (989) ApaI (993) SP6 promoter BbsI (1231) DraIII (1545) CsiI - SexAI * (1836) BseRI (2065) StuI (2068) AvrII (2069) TspMI - XmaI (2090) SmaI (2092) KasI (2278) NarI (2279) SfoI (2280) PluTI (2282) MscI (2361) PflFI - Tth111I (2397) BssHII (2676) pcDNA3 5446 bp
SgrDI  (5444)
1 site		 C G T C G A C G G C A G C T G C
SspI  (5327)
1 site		 A A T A T T T T A T A A
ScaI  (5003)
1 site		 A G T A C T T C A T G A
PvuI  (4893)
1 site		 C G A T C G G C T A G C
AhdI  (4523)
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.
PciI  (3630)
1 site		 A C A T G T T G T A C A
PciI is inhibited by nonionic detergents.
BstZ17I  (3251)
1 site		 G T A T A C C A T A T G
BsmI  (3199)
1 site		 G A A T G C N C T T A C G N
Sticky ends from different BsmI sites may not be compatible.
PfoI  (3054)
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.
BstBI  (2961)
1 site		 T T C G A A A A G C T T
RsrII  (2795)
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.
BglII  (12)
1 site		 A G A T C T T C T A G A
MfeI  (161)
1 site		 C A A T T G G T T A A C
Bpu10I  (180)
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  (208)
1 site		 T C G C G A A G C G C T
MluI  (228)
1 site		 A C G C G T T G C G C A
NdeI  (484)
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  (590)
1 site		 T A C G T A A T G C A T
HindIII  (889)
1 site		 A A G C T T T T C G A A
Acc65I  (895)
1 site		 G G T A C C C C A T G G
KpnI  (899)
1 site		 G G T A C C C C A T G G
BamHI  (907)
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.
EcoRI  (938)
1 site		 G A A T T C C T T A A G
EcoRV  (950)
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.
NotI  (965)
1 site		 G C G G C C G C C G C C G G C G
PaeR7I  (971)
1 site		 C T C G A G G A G C T C
PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (971)
1 site		 V C T C G A G B B G A G C T C V
XhoI  (971)
1 site		 C T C G A G G A G C T C
XbaI  (983)
1 site		 T C T A G A A G A T C T
PspOMI  (989)
1 site		 G G G C C C C C C G G G
ApaI  (993)
1 site		 G G G C C C C C C G G G
ApaI can be used between 25°C and 37°C.
BbsI  (1231)
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.
DraIII  (1545)
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.
CsiI  (1836)
1 site		 A C C W G G T T G G W C C A
Sticky ends from different CsiI sites may not be compatible.
SexAI  (1836)
1 site		 A C C W G G T T G G W C C A
* Blocked by Dcm methylation.
Sticky ends from different SexAI sites may not be compatible.
BseRI  (2065)
1 site		 G A G G A G ( N ) 8 N N C T C C T C ( N ) 8
Sticky ends from different BseRI sites may not be compatible.
BseRI quickly loses activity at 37°C.
Prolonged incubation with BseRI may lead to degradation of the DNA.
StuI  (2068)
1 site		 A G G C C T T C C G G A
AvrII  (2069)
1 site		 C C T A G G G G A T C C
TspMI  (2090)
1 site		 C C C G G G G G G C C C
XmaI  (2090)
1 site		 C C C G G G G G G C C C
Cleavage may be enhanced when more than one copy of the XmaI recognition sequence is present.
SmaI  (2092)
1 site		 C C C G G G G G G C C C
SmaI can be used at 37°C for brief incubations.
KasI  (2278)
1 site		 G G C G C C C C G C G G
NarI  (2279)
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.
SfoI  (2280)
1 site		 G G C G C C C C G C G G
PluTI  (2282)
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.
MscI  (2361)
1 site		 T G G C C A A C C G G T
PflFI  (2397)
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  (2397)
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.
BssHII  (2676)
1 site		 G C G C G C C G C G C G
BssHII is typically used at 50°C, but is 75% active at 37°C.
AmpR
4450 .. 5310  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 2:  
   4450 .. 5241  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
4450 .. 5310  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 1:  signal sequence  
   5242 .. 5310  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
4450 .. 5310  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
NeoR/KanR
2151 .. 2945  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from Tn5
confers resistance to neomycin, kanamycin, and G418 (Geneticin)
NeoR/KanR
2151 .. 2945  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from Tn5
confers resistance to neomycin, kanamycin, and G418 (Geneticin)
ori
3691 .. 4279  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
3691 .. 4279  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
f1 ori
1312 .. 1740  =  429 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
f1 ori
1312 .. 1740  =  429 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
CMV enhancer
235 .. 614  =  380 bp
human cytomegalovirus immediate early enhancer
CMV enhancer
235 .. 614  =  380 bp
human cytomegalovirus immediate early enhancer
SV40 promoter
1754 .. 2084  =  331 bp
SV40 enhancer and early promoter
SV40 promoter
1754 .. 2084  =  331 bp
SV40 enhancer and early promoter
bGH poly(A) signal
1042 .. 1266  =  225 bp
bovine growth hormone polyadenylation signal
bGH poly(A) signal
1042 .. 1266  =  225 bp
bovine growth hormone polyadenylation signal
CMV promoter
615 .. 818  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
CMV promoter
615 .. 818  =  204 bp
human cytomegalovirus (CMV) immediate early promoter
SV40 poly(A) signal
3119 .. 3240  =  122 bp
SV40 polyadenylation signal
SV40 poly(A) signal
3119 .. 3240  =  122 bp
SV40 polyadenylation signal
MCS
889 .. 994  =  106 bp
multiple cloning site
MCS
889 .. 994  =  106 bp
multiple cloning site
AmpR promoter
5311 .. 5415  =  105 bp
AmpR promoter
5311 .. 5415  =  105 bp
T7 promoter
863 .. 881  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
863 .. 881  =  19 bp
promoter for bacteriophage T7 RNA polymerase
SP6 promoter
998 .. 1016  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
SP6 promoter
998 .. 1016  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
SV40 ori
1935 .. 2070  =  136 bp
SV40 origin of replication
SV40 ori
1935 .. 2070  =  136 bp
SV40 origin of replication
ORF:  2323 .. 2709  =  387 bp
ORF:  128 amino acids  =  14.6 kDa
ORF:  4580 .. 4846  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  1263 .. 1529  =  267 bp
ORF:  88 amino acids  =  9.3 kDa
ORF:  2151 .. 2945  =  795 bp
ORF:  264 amino acids  =  29.0 kDa
ORF:  4450 .. 5310  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  2460 .. 2996  =  537 bp
ORF:  178 amino acids  =  19.8 kDa
Click here to try SnapGene

Download pcDNA3.dna file

SnapGene

SnapGene is the easiest way to plan, visualize and document your everyday molecular biology procedures

  • Fast accurate construct design for all major molecular cloning techniques
  • Validate sequenced constructs using powerful alignment tools
  • Customize plasmid maps with flexible annotation and visualization controls
  • Automatically generate a rich graphical history of every edit and procedure
Download SnapGene

SnapGene Viewer

SnapGene Viewer is free software that allows molecular biologists to create, browse, and share richly annotated sequence files.

  • Gain unparalleled visibility of your plasmids, DNA and protein sequences
  • Annotate features on your plasmids using the curated feature database
  • Store, search, and share your sequences, files and maps
Download SnapGene Viewer

Individual Sequences & Maps

Lafmid BA
pcDNAII
pCR2.1-TOPO (linearized)
pExpress-1
pAD-GAL4
pcDNA3.1(+)
pCR3.1
pME18S-FL3
pAMP1
pcDNA3.1(-)
pCR3.1 (linearized)
pOTB7
pAMP10
pcDNA3.1 Zeo(+)
pCR4-TOPO
pOTB7-3
pBK-CMV
pCMV SPORT
pCR4-TOPO (linearized)
pOTB7a
pBluescribe (modified)
pCMV SPORT2
pCS105
pPCR-Script Amp SK(+)
pBluescript II SK(+)
pCMV SPORT4
pCS107
pRKW2
pBluescript KS(+)
pCMV SPORT6
pCS108
pSPORT 1
pBluescript SK(+)
pCMV SPORT6.1
pCS2+
pSPORT 2
pBluescript SK(-)
pCMV SPORT6ccdB
pCS22+
pT7T3D-PacI
pBluescript-FL
pCR-Blunt II-TOPO
pCS2G
pUC19
pBluescript II KS(+)
pCR-Blunt II-TOPO (linearized)
pDNR-Dual
pYX-Asc
pBluescriptR
pCR-XL-TOPO
pDNR-LIB
pZErO-2
pcDNA3
pCR-XL-TOPO (linearized)
pDONR201
pZL1
pcDNAI
pCR2.1-TOPO
pDONR223

Plasmid Sets

Basic Cloning Vectors
I.M.A.G.E. Consortium Plasmids
pET & Duet Vectors (Novagen)
TA and GC Cloning Vectors
Coronavirus Resources
Insect Cell Vectors
pGEX Vectors (GE Healthcare)
TOPO Cloning Vectors
CRISPR Plasmids
Luciferase Vectors
Plant Vectors
Viral Expression & Packaging Vectors
Fluorescent Protein Genes & Plasmids
Lucigen Vectors
Qiagen Vectors
Yeast Plasmids
Gateway® Cloning Vectors
Mammalian Expression Vectors
Structural Genomics Vectors

The maps, notes, and annotations in the zip file on this page are copyrighted material. This material may be used without restriction by academic, nonprofit, and governmental entities, except that the source must be cited as ’’www.snapgene.com/resources’’. Commercial entities must contact GSL Biotech LLC for permission and terms of use.

Discover the most user-friendly molecular biology experience.
Try for Free