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Plasmid Files

pF3A WG (BYDV)

Flexi® vector with an ampicillin resistance marker, for cell-free translation in a wheat germ extract.

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pF3A WG (BYDV) Sequence and MappF3A WG (BYDV).dna
Map and Sequence File   
Sequence Author:  Promega
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 SP6 promoter BglII (3241) MluI (3122) BspEI (2909) DrdI (2253) PciI (2145) AgeI (2077) BstBI (2050) AhdI (1975) BglI (1857) T7 promoter BYDV 5' UTR BbvCI - Bpu10I (174) AsiSI - PvuI - SgfI (206) BtgI - NcoI (209) DraI - PmeI (573) EcoRI (578) Eco53kI (586) BanII - SacI (588) Acc65I (590) KpnI (594) BbsI (606) BamHI (624) AvaI - BsoBI (660) BmeT110I (661) XbaI (703) NruI (717) SalI (721) AccI (722) PstI - SbfI (731) SphI (737) BlpI (796) EcoO109I (823) SspI (1170) EarI (1176) XmnI (1375) FspI (1752) pF3A WG (BYDV) 3689 bp
BglII  (3241)
1 site
A G A T C T T C T A G A
MluI  (3122)
1 site
A C G C G T T G C G C A
BspEI  (2909)
1 site
T C C G G A A G G C C T
DrdI  (2253)
1 site
G A C N N N N N N G T C C T G N N N N N N C A G

Sticky ends from different DrdI sites may not be compatible.
PciI  (2145)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
AgeI  (2077)
1 site
A C C G G T T G G C C A

AgeI quickly loses activity at 37°C, but can be used at 25°C for
long incubations.
BstBI  (2050)
1 site
T T C G A A A A G C T T
AhdI  (1975)
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.
BglI  (1857)
1 site
G C C N N N N N G G C C G G N N N N N C C G

Sticky ends from different BglI sites may not be compatible.
BbvCI  (174)
1 site
C C T C A G C G G A G T C G
Bpu10I  (174)
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.
AsiSI  (206)
1 site
G C G A T C G C C G C T A G C G
PvuI  (206)
1 site
C G A T C G G C T A G C
SgfI  (206)
1 site
G C G A T C G C C G C T A G C G
BtgI  (209)
1 site
C C R Y G G G G Y R C C

Sticky ends from different BtgI sites may not be compatible.
NcoI  (209)
1 site
C C A T G G G G T A C C
DraI  (573)
1 site
T T T A A A A A A T T T
PmeI  (573)
1 site
G T T T A A A C C A A A T T T G
EcoRI  (578)
1 site
G A A T T C C T T A A G
Eco53kI  (586)
1 site
G A G C T C C T C G A G
BanII  (588)
1 site
G R G C Y C C Y C G R G

Sticky ends from different BanII sites may not be compatible.
SacI  (588)
1 site
G A G C T C C T C G A G
Acc65I  (590)
1 site
G G T A C C C C A T G G
KpnI  (594)
1 site
G G T A C C C C A T G G
BbsI  (606)
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.
BamHI  (624)
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.
AvaI  (660)
1 site
C Y C G R G G R G C Y C

Sticky ends from different AvaI sites may not be compatible.
BsoBI  (660)
1 site
C Y C G R G G R G C Y C

Sticky ends from different BsoBI sites may not be compatible.
BsoBI is typically used at 37°C, but can be used at temperatures
up to 65°C.
BmeT110I  (661)
1 site
C Y C G R G G R G C Y C
XbaI  (703)
1 site
T C T A G A A G A T C T
NruI  (717)
1 site
T C G C G A A G C G C T
SalI  (721)
1 site
G T C G A C C A G C T G
AccI  (722)
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.
PstI  (731)
1 site
C T G C A G G A C G T C
SbfI  (731)
1 site
C C T G C A G G G G A C G T C C
SphI  (737)
1 site
G C A T G C C G T A C G
BlpI  (796)
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.
EcoO109I  (823)
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.
SspI  (1170)
1 site
A A T A T T T T A T A A
EarI  (1176)
1 site
C T C T T C N G A G A A G N N N N

Efficient cleavage requires at least two copies of the EarI
recognition sequence.
Sticky ends from different EarI sites may not be compatible.
XmnI  (1375)
1 site
G A A N N N N T T C C T T N N N N A A G
FspI  (1752)
1 site
T G C G C A A C G C G T
AmpR
1188 .. 2048  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   1188 .. 1256  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
1188 .. 2048  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   1257 .. 2048  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
1188 .. 2048  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
ori
2206 .. 2794  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
2206 .. 2794  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
barnase
233 .. 568  =  336 bp
111 amino acids  =  12.5 kDa
Product: ribonuclease from Bacillus
amyloliquefaciens

The barnase gene is lethal in standard bacterial
transformation strains.
barnase
233 .. 568  =  336 bp
111 amino acids  =  12.5 kDa
Product: ribonuclease from Bacillus
amyloliquefaciens

The barnase gene is lethal in standard bacterial
transformation strains.
cer region
2910 .. 3193  =  284 bp
ColE1-derived recombination site that helps to
maintain plasmids as monomers
cer region
2910 .. 3193  =  284 bp
ColE1-derived recombination site that helps to
maintain plasmids as monomers
BYDV 5' UTR
65 .. 201  =  137 bp
barley yellow dwarf virus 5' untranslated region;
required for function of the cap-independent 3'
translation enhancer (Guo et al., 2001)
BYDV 5' UTR
65 .. 201  =  137 bp
barley yellow dwarf virus 5' untranslated region;
required for function of the cap-independent 3'
translation enhancer (Guo et al., 2001)
BYDV 3' TE
596 .. 702  =  107 bp
cap-independent 3' translation enhancer from barley
yellow dwarf virus (Wang et al., 1997)
BYDV 3' TE
596 .. 702  =  107 bp
cap-independent 3' translation enhancer from barley
yellow dwarf virus (Wang et al., 1997)
AmpR promoter
1083 .. 1187  =  105 bp
AmpR promoter
1083 .. 1187  =  105 bp
rrnB T1 terminator
3423 .. 3509  =  87 bp
transcription terminator T1 from the E. coli rrnB
gene
rrnB T1 terminator
3423 .. 3509  =  87 bp
transcription terminator T1 from the E. coli rrnB
gene
T7 terminator
807 .. 854  =  48 bp
transcription terminator for bacteriophage T7 RNA
polymerase
T7 terminator
807 .. 854  =  48 bp
transcription terminator for bacteriophage T7 RNA
polymerase
rrnB T2 terminator
3601 .. 3628  =  28 bp
transcription terminator T2 from the E. coli rrnB
gene
rrnB T2 terminator
3601 .. 3628  =  28 bp
transcription terminator T2 from the E. coli rrnB
gene
SP6 promoter
23 .. 41  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
SP6 promoter
23 .. 41  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
T7 promoter
46 .. 63  =  18 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
46 .. 63  =  18 bp
promoter for bacteriophage T7 RNA polymerase
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