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Plasmid Files

pBI121

Binary Agrobacterium vector with a GUS reporter gene for plant transformation.

 
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 NotI (14,662) PasI (14,110) BstEII (13,001) BstXI (12,671) SfiI (11,038) PflMI * (10,709) NdeI (10,475) FspAI (9695) KflI (9097) BbvCI (9007) AhdI (8953) DraIII (8290) M13 fwd EcoRI (7982) SacI (7715) EcoNI (1627) RB T-DNA repeat PmeI (2492) Bsu36I (2700) NheI (2715) BmtI (2719) PspOMI (3899) ApaI (3903) BspDI - ClaI (4537) lac operator M13 rev HindIII (4950) SbfI (4966) BsaI (5045) ScaI (5179) XbaI (5815) BamHI (5821) TspMI - XmaI (5826) SmaI (5828) SnaBI (6229) Eco53kI (7713) pBI121 14,758 bp
NotI  (14,662)
1 site
G C G G C C G C C G C C G G C G
PasI  (14,110)
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.
BstEII  (13,001)
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.
BstXI  (12,671)
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.
SfiI  (11,038)
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.
PflMI  (10,709)
1 site
C C A N N N N N T G G G G T N N N N N A C C
* Blocked by Dcm methylation.
Sticky ends from different PflMI sites may not be compatible.
NdeI  (10,475)
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.
FspAI  (9695)
1 site
R T G C G C A Y Y A C G C G T R
KflI  (9097)
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.
BbvCI  (9007)
1 site
C C T C A G C G G A G T C G
AhdI  (8953)
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.
DraIII  (8290)
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.
EcoRI  (7982)
1 site
G A A T T C C T T A A G
SacI  (7715)
1 site
G A G C T C C T C G A G
EcoNI  (1627)
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.
PmeI  (2492)
1 site
G T T T A A A C C A A A T T T G
Bsu36I  (2700)
1 site
C C T N A G G G G A N T C C

Sticky ends from different Bsu36I sites may not be compatible.
NheI  (2715)
1 site
G C T A G C C G A T C G
BmtI  (2719)
1 site
G C T A G C C G A T C G
PspOMI  (3899)
1 site
G G G C C C C C C G G G
ApaI  (3903)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
BspDI  (4537)
1 site
A T C G A T T A G C T A
ClaI  (4537)
1 site
A T C G A T T A G C T A
HindIII  (4950)
1 site
A A G C T T T T C G A A
SbfI  (4966)
1 site
C C T G C A G G G G A C G T C C
BsaI  (5045)
1 site
G G T C T C N C C A G A G N ( N ) 4

Sticky ends from different BsaI sites may not be compatible.
BsaI can be used between 37°C and 50°C.
ScaI  (5179)
1 site
A G T A C T T C A T G A
XbaI  (5815)
1 site
T C T A G A A G A T C T
BamHI  (5821)
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.
TspMI  (5826)
1 site
C C C G G G G G G C C C
XmaI  (5826)
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.
SmaI  (5828)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
SnaBI  (6229)
1 site
T A C G T A A T G C A T
Eco53kI  (7713)
1 site
G A G C T C C T C G A G
GUS
5845 .. 7656  =  1812 bp
603 amino acids  =  68.4 kDa
Product: β-glucuronidase
GUS
5845 .. 7656  =  1812 bp
603 amino acids  =  68.4 kDa
Product: β-glucuronidase
trfA
10,242 .. 11,390  =  1149 bp
382 amino acids  =  43.8 kDa
Product: trans-acting replication protein that binds
to and activates oriV
trfA
10,242 .. 11,390  =  1149 bp
382 amino acids  =  43.8 kDa
Product: trans-acting replication protein that binds
to and activates oriV
NeoR/KanR
2838 .. 3632  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from
Tn5
confers resistance to neomycin, kanamycin, and
G418 (Geneticin®)
NeoR/KanR
2838 .. 3632  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from
Tn5
confers resistance to neomycin, kanamycin, and
G418 (Geneticin®)
KanR
11,689 .. 12,483  =  795 bp
264 amino acids  =  31.0 kDa
Product: aminoglycoside phosphotransferase
confers resistance to kanamycin
KanR
11,689 .. 12,483  =  795 bp
264 amino acids  =  31.0 kDa
Product: aminoglycoside phosphotransferase
confers resistance to kanamycin
IS1
12,675 .. 13,442  =  768 bp
prokaryotic transposable element
IS1
12,675 .. 13,442  =  768 bp
prokaryotic transposable element
oriV
14,065 .. 18  =  712 bp
incP origin of replication
oriV
14,065 .. 18  =  712 bp
incP origin of replication
TetR
1339 .. 1989  =  651 bp
216 amino acids  =  23.3 kDa
Product: tetracycline resistance regulatory protein
TetR
1339 .. 1989  =  651 bp
216 amino acids  =  23.3 kDa
Product: tetracycline resistance regulatory protein
traJ
145 .. 516  =  372 bp
123 amino acids  =  13.5 kDa
Product: oriT-recognizing protein
traJ
145 .. 516  =  372 bp
123 amino acids  =  13.5 kDa
Product: oriT-recognizing protein
CaMV 35S promoter
5461 .. 5806  =  346 bp
strong constitutive promoter from cauliflower
mosaic virus
CaMV 35S promoter
5461 .. 5806  =  346 bp
strong constitutive promoter from cauliflower
mosaic virus
NOS terminator
4022 .. 4274  =  253 bp
nopaline synthase terminator and poly(A) signal
NOS terminator
4022 .. 4274  =  253 bp
nopaline synthase terminator and poly(A) signal
NOS terminator
7727 .. 7979  =  253 bp
nopaline synthase terminator and poly(A) signal
NOS terminator
7727 .. 7979  =  253 bp
nopaline synthase terminator and poly(A) signal
NOS promoter
2602 .. 2781  =  180 bp
nopaline synthase promoter
NOS promoter
2602 .. 2781  =  180 bp
nopaline synthase promoter
oriT
549 .. 658  =  110 bp
incP origin of transfer
oriT
549 .. 658  =  110 bp
incP origin of transfer
lac promoter
4859 .. 4889  =  31 bp
   Segment 1:  -35  
   4859 .. 4864  =  6 bp
promoter for the E. coli lac operon
lac promoter
4859 .. 4889  =  31 bp
   Segment 2:  
   4865 .. 4882  =  18 bp
promoter for the E. coli lac operon
lac promoter
4859 .. 4889  =  31 bp
   Segment 3:  -10  
   4883 .. 4889  =  7 bp
promoter for the E. coli lac operon
lac promoter
4859 .. 4889  =  31 bp
3 segments
promoter for the E. coli lac operon
RB T-DNA repeat
2454 .. 2478  =  25 bp
right border repeat from nopaline C58 T-DNA
RB T-DNA repeat
2454 .. 2478  =  25 bp
right border repeat from nopaline C58 T-DNA
LB T-DNA repeat
8622 .. 8646  =  25 bp
left border repeat from nopaline C58 T-DNA
LB T-DNA repeat
8622 .. 8646  =  25 bp
left border repeat from nopaline C58 T-DNA
lac operator
4897 .. 4913  =  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
4897 .. 4913  =  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).
M13 rev
4921 .. 4937  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
4921 .. 4937  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 fwd
7988 .. 8004  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 fwd
7988 .. 8004  =  17 bp
common sequencing primer, one of multiple similar
variants
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