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Plasmid Files

pEZ™ BAC (HpaI linearized)

HpaI-linearized and dephosphorylated BAC vector with inducible copy number, suitable for cloning toxic inserts.

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pEZ BAC (HpaI linearized) Sequence and MappEZ BAC (HpaI linearized).dna
Map and Sequence File   
Sequence Author:  Lucigen
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 SacII (6780) FseI (6776) BciVI - MreI (6765) XcmI (6575) XbaI (6065) EcoNI (5791) SmaI (5768) TspMI - XmaI (5766) FspAI (5509) BsrGI (5477) SbfI (5240) BlpI (4779) AfeI (4695) MfeI (4270) NdeI (4254) BstXI (4180) KpnI (4054) Acc65I (4050) PflFI - Tth111I (3989) BseRI (3563) BclI * (3459) T3Te terminator AscI (7001) NotI (7029) BEZ-F1 (7119 .. 7142) BsrBI (7159) lac operator HindIII (7236) SphI (7246) < HpaI > (7260) < HpaI > (0) BamHI (7) PmlI (19) EcoRI (24) BEZ-R1 (109 .. 132) KasI (211) NarI (212) SfoI (213) BbeI (215) NotI (241) PmeI (290) EcoO109I - PpuMI (604) DraIII (645) ScaI (1539) BstAPI (1619) BstEII (1652) SexAI * (1656) PciI (1775) AhdI (1776) PspOMI (2289) ApaI - BanII (2293) AccI (2365) PfoI * (2505) SpeI (2535) AleI (2718) pEZ™ BAC 7260 bp
SacII  (6780)
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.
FseI  (6776)
1 site
G G C C G G C C C C G G C C G G

FseI gradually loses activity when stored at -20°C.
BciVI  (6765)
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.
MreI  (6765)
1 site
C G C C G G C G G C G G C C G C
XcmI  (6575)
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.
XbaI  (6065)
1 site
T C T A G A A G A T C T
EcoNI  (5791)
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.
SmaI  (5768)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
TspMI  (5766)
1 site
C C C G G G G G G C C C
XmaI  (5766)
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.
FspAI  (5509)
1 site
R T G C G C A Y Y A C G C G T R
BsrGI  (5477)
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.
SbfI  (5240)
1 site
C C T G C A G G G G A C G T C C
BlpI  (4779)
1 site
G C T N A G C C G A N T C G

Sticky ends from different BlpI sites may not be compatible.
AfeI  (4695)
1 site
A G C G C T T C G C G A
MfeI  (4270)
1 site
C A A T T G G T T A A C
NdeI  (4254)
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.
BstXI  (4180)
1 site
C C A N N N N N N T G G G G T N N N N N N A C C

Sticky ends from different BstXI sites may not be compatible.
KpnI  (4054)
1 site
G G T A C C C C A T G G
Acc65I  (4050)
1 site
G G T A C C C C A T G G
PflFI  (3989)
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  (3989)
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.
BseRI  (3563)
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.
BclI  (3459)
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.
AscI  (7001)
1 site
G G C G C G C C C C G C G C G G
NotI  (7029)
2 sites
G C G G C C G C C G C C G G C G
BsrBI  (7159)
1 site
C C G C T C G G C G A G

This recognition sequence is asymmetric, so ligating blunt ends
generated by BsrBI will not always regenerate a BsrBI site.
BsrBI is typically used at 37°C, but can be used at temperatures
up to 50°C.
HindIII  (7236)
1 site
A A G C T T T T C G A A
SphI  (7246)
1 site
G C A T G C C G T A C G
End  (7260)
0 sites
Start  (0)
0 sites
BamHI  (7)
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.
PmlI  (19)
1 site
C A C G T G G T G C A C

PmlI gradually loses activity when stored at -20°C.
EcoRI  (24)
1 site
G A A T T C C T T A A G
KasI  (211)
1 site
G G C G C C C C G C G G
NarI  (212)
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  (213)
1 site
G G C G C C C C G C G G
BbeI  (215)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the BbeI
recognition sequence.
NotI  (241)
2 sites
G C G G C C G C C G C C G G C G
PmeI  (290)
1 site
G T T T A A A C C A A A T T T G
EcoO109I  (604)
1 site
R G G N C C Y Y C C N G G R

Sticky ends from different EcoO109I sites may not be compatible.
PpuMI  (604)
1 site
R G G W C C Y Y C C W G G R

Sticky ends from different PpuMI sites may not be compatible.
DraIII  (645)
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.
ScaI  (1539)
1 site
A G T A C T T C A T G A
BstAPI  (1619)
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.
BstEII  (1652)
1 site
G G T N A C C C C A N T G G

Sticky ends from different BstEII sites may not be compatible.
BstEII is typically used at 60°C, but is 50% active at 37°C.
SexAI  (1656)
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.
PciI  (1775)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
AhdI  (1776)
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.
PspOMI  (2289)
1 site
G G G C C C C C C G G G
ApaI  (2293)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
BanII  (2293)
1 site
G R G C Y C C Y C G R G

Sticky ends from different BanII sites may not be compatible.
AccI  (2365)
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.
PfoI  (2505)
1 site
T C C N G G A A G G N C C T
* Blocked by Dcm methylation.
Sticky ends from different PfoI sites may not be compatible.
SpeI  (2535)
1 site
A C T A G T T G A T C A
AleI  (2718)
1 site
C A C N N N N G T G G T G N N N N C A C
BEZ-F1
24-mer  /  50% GC
1 binding site
7119 .. 7142  =  24 annealed bases
Tm  =  60°C
BEZ-R1
24-mer  /  54% GC
1 binding site
109 .. 132  =  24 annealed bases
Tm  =  62°C
sopA
3356 .. 4531  =  1176 bp
391 amino acids  =  44.1 kDa
Product: partitioning protein for the bacterial F
plasmid
sopA
3356 .. 4531  =  1176 bp
391 amino acids  =  44.1 kDa
Product: partitioning protein for the bacterial F
plasmid
repE
5110 .. 5865  =  756 bp
251 amino acids  =  29.4 kDa
Product: replication initiation protein for the
bacterial F plasmid
repE
5110 .. 5865  =  756 bp
251 amino acids  =  29.4 kDa
Product: replication initiation protein for the
bacterial F plasmid
CmR
909 .. 1568  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
CmR
909 .. 1568  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
oriV
6251 .. 6865  =  615 bp
origin of replication for the bacterial F plasmid
oriV
6251 .. 6865  =  615 bp
origin of replication for the bacterial F plasmid
sopC
1839 .. 2312  =  474 bp
centromere-like partitioning region of the bacterial F
plasmid
sopC
1839 .. 2312  =  474 bp
centromere-like partitioning region of the bacterial F
plasmid
cos
385 .. 783  =  399 bp
lambda cos site; allows packaging into phage
lambda particles
cos
385 .. 783  =  399 bp
lambda cos site; allows packaging into phage
lambda particles
incC
4857 .. 5107  =  251 bp
incompatibility region of the bacterial F plasmid
incC
4857 .. 5107  =  251 bp
incompatibility region of the bacterial F plasmid
ori2
5956 .. 6175  =  220 bp
secondary origin of replication for the bacterial F
plasmid; also known as oriS
ori2
5956 .. 6175  =  220 bp
secondary origin of replication for the bacterial F
plasmid; also known as oriS
lacZα
1 .. 201  =  201 bp
66 amino acids  =  7.5 kDa
Product: LacZα fragment of β-galactosidase
lacZα
1 .. 201  =  201 bp
66 amino acids  =  7.5 kDa
Product: LacZα fragment of β-galactosidase
lacZα
7189 .. 7260  =  72 bp
24 amino acids  =  2.7 kDa
Product: LacZα fragment of β-galactosidase
lacZα
7189 .. 7260  =  72 bp
24 amino acids  =  2.7 kDa
Product: LacZα fragment of β-galactosidase
loxP
253 .. 286  =  34 bp
Cre-mediated recombination occurs in the 8-bp core
sequence (GCATACAT).
loxP
253 .. 286  =  34 bp
Cre-mediated recombination occurs in the 8-bp core
sequence (GCATACAT).
loxP
6960 .. 6993  =  34 bp
Cre-mediated recombination occurs in the 8-bp core
sequence (GCATACAT).
loxP
6960 .. 6993  =  34 bp
Cre-mediated recombination occurs in the 8-bp core
sequence (GCATACAT).
tonB terminator
305 .. 336  =  32 bp
bidirectional E. coli tonB-P14 transcription
terminator
tonB terminator
305 .. 336  =  32 bp
bidirectional E. coli tonB-P14 transcription
terminator
lac promoter
7115 .. 7145  =  31 bp
   Segment 1:  -35  
   7115 .. 7120  =  6 bp
promoter for the E. coli lac operon
lac promoter
7115 .. 7145  =  31 bp
   Segment 2:  
   7121 .. 7138  =  18 bp
promoter for the E. coli lac operon
lac promoter
7115 .. 7145  =  31 bp
   Segment 3:  -10  
   7139 .. 7145  =  7 bp
promoter for the E. coli lac operon
lac promoter
7115 .. 7145  =  31 bp
3 segments
promoter for the E. coli lac operon
T3Te terminator
6909 .. 6938  =  30 bp
phage T3 early transcription terminator
T3Te terminator
6909 .. 6938  =  30 bp
phage T3 early transcription terminator
T7Te terminator
1583 .. 1606  =  24 bp
phage T7 early transcription terminator
T7Te terminator
1583 .. 1606  =  24 bp
phage T7 early transcription terminator
lac operator
7153 .. 7169  =  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
7153 .. 7169  =  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).
sopB
2385 .. 3356  =  972 bp
323 amino acids  =  35.4 kDa
Product: partitioning protein for the bacterial F
plasmid
sopB
2385 .. 3356  =  972 bp
323 amino acids  =  35.4 kDa
Product: partitioning protein for the bacterial F
plasmid
T7 promoter
32 .. 50  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
32 .. 50  =  19 bp
promoter for bacteriophage T7 RNA polymerase
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