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Plasmid Files

YEplac112

Yeast episomal plasmid with a TRP1 marker.

 
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YEplac112.dna
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BspQI - SapI (4980) AflIII - PciI (4863) DrdI (4761) AlwNI (4454) AhdI (3975) BsaI (3909) BsrFI (3890) NmeAIII (3828) TsoI (3577) ScaI (3494) TatI (3492) AatII (3056) ZraI (3054) EcoO109I (2995) PmlI (2915) BstZ17I (2908) Bsu36I (2630) EcoRV (2590) BstXI (2581) HindIII (233) SphI (243) PstI - SbfI (249) SalI (251) XbaI (257) BamHI (263) TspMI - XmaI (268) SmaI (270) Acc65I (272) KpnI (276) Eco53kI (280) SacI (282) EcoRI (284) KasI (445) NarI (446) SfoI (447) PluTI (449) PfoI * (640) HpaI (742) NsiI (1032) SnaBI (1384) BseRI (2024) XcmI (2037) BspDI * - ClaI * (2088) AarI (2438) BsgI (2464) YEplac112 4989 bp
BspQI  (4980)
1 site
G C T C T T C N C G A G A A G N N N N

Sticky ends from different BspQI sites may not be compatible.
SapI  (4980)
1 site
G C T C T T C N C G A G A A G N N N N

Sticky ends from different SapI sites may not be compatible.
SapI gradually settles in solution, so a tube of SapI should be mixed before removing an aliquot.
AflIII  (4863)
1 site
A C R Y G T T G Y R C A

Sticky ends from different AflIII sites may not be compatible.
PciI  (4863)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
DrdI  (4761)
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.
AlwNI  (4454)
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.
AhdI  (3975)
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.
BsaI  (3909)
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.
BsrFI  (3890)
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.
NmeAIII  (3828)
1 site
G C C G A G ( N ) 18-19 N N C G G C T C ( N ) 18-19

Efficient cleavage requires at least two copies of the NmeAIII recognition sequence.
Sticky ends from different NmeAIII sites may not be compatible.
For full activity, add fresh S-adenosylmethionine (SAM).
TsoI  (3577)
1 site
T A R C C A ( N ) 9 N N A T Y G G T ( N ) 9

Sticky ends from different TsoI sites may not be compatible.
After cleavage, TsoI can remain bound to DNA and alter its electrophoretic mobility.
For full activity, add fresh S-adenosylmethionine (SAM).
ScaI  (3494)
1 site
A G T A C T T C A T G A
TatI  (3492)
1 site
W G T A C W W C A T G W
AatII  (3056)
1 site
G A C G T C C T G C A G
ZraI  (3054)
1 site
G A C G T C C T G C A G
EcoO109I  (2995)
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.
PmlI  (2915)
1 site
C A C G T G G T G C A C

PmlI gradually loses activity when stored at -20°C.
BstZ17I  (2908)
1 site
G T A T A C C A T A T G
Bsu36I  (2630)
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.
EcoRV  (2590)
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.
BstXI  (2581)
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.
HindIII  (233)
1 site
A A G C T T T T C G A A
SphI  (243)
1 site
G C A T G C C G T A C G
PstI  (249)
1 site
C T G C A G G A C G T C
SbfI  (249)
1 site
C C T G C A G G G G A C G T C C
SalI  (251)
1 site
G T C G A C C A G C T G
XbaI  (257)
1 site
T C T A G A A G A T C T
BamHI  (263)
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  (268)
1 site
C C C G G G G G G C C C
XmaI  (268)
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  (270)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
Acc65I  (272)
1 site
G G T A C C C C A T G G
KpnI  (276)
1 site
G G T A C C C C A T G G
Eco53kI  (280)
1 site
G A G C T C C T C G A G
SacI  (282)
1 site
G A G C T C C T C G A G
EcoRI  (284)
1 site
G A A T T C C T T A A G
KasI  (445)
1 site
G G C G C C C C G C G G
NarI  (446)
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  (447)
1 site
G G C G C C C C G C G G
PluTI  (449)
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.
PfoI  (640)
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.
HpaI  (742)
1 site
G T T A A C C A A T T G
NsiI  (1032)
1 site
A T G C A T T A C G T A
SnaBI  (1384)
1 site
T A C G T A A T G C A T
BseRI  (2024)
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.
XcmI  (2037)
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.
BspDI  (2088)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
ClaI  (2088)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
AarI  (2438)
1 site
C A C C T G C ( N ) 4 G T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the AarI recognition sequence.
Sticky ends from different AarI sites may not be compatible.
After cleavage, AarI can remain bound to DNA and alter its electrophoretic mobility.
BsgI  (2464)
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).
2μ ori
745 .. 2091  =  1347 bp
yeast 2μ plasmid origin of replication
2μ ori
745 .. 2091  =  1347 bp
yeast 2μ plasmid origin of replication
AmpR
3188 .. 4048  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   3188 .. 3256  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3188 .. 4048  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   3257 .. 4048  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3188 .. 4048  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
TRP1
2201 .. 2875  =  675 bp
224 amino acids  =  24.1 kDa
Product: phosphoribosylanthranilate isomerase, required for tryptophan biosynthesis
yeast auxotrophic marker
TRP1
2201 .. 2875  =  675 bp
224 amino acids  =  24.1 kDa
Product: phosphoribosylanthranilate isomerase, required for tryptophan biosynthesis
yeast auxotrophic marker
ori
4219 .. 4807  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
ori
4219 .. 4807  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
lacZα
216 .. 500  =  285 bp
95 amino acids  =  11.0 kDa
Product: LacZα fragment of β-galactosidase
lacZα
216 .. 500  =  285 bp
95 amino acids  =  11.0 kDa
Product: LacZα fragment of β-galactosidase
AmpR promoter
3083 .. 3187  =  105 bp
AmpR promoter
3083 .. 3187  =  105 bp
TRP1 promoter
2876 .. 2977  =  102 bp
TRP1 promoter
2876 .. 2977  =  102 bp
lac promoter
142 .. 172  =  31 bp
   Segment 1:  -35  
   142 .. 147  =  6 bp
promoter for the E. coli lac operon
lac promoter
142 .. 172  =  31 bp
   Segment 2:  
   148 .. 165  =  18 bp
promoter for the E. coli lac operon
lac promoter
142 .. 172  =  31 bp
   Segment 3:  -10  
   166 .. 172  =  7 bp
promoter for the E. coli lac operon
lac promoter
142 .. 172  =  31 bp
3 segments
promoter for the E. coli lac operon
lac operator
180 .. 196  =  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
180 .. 196  =  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).
MCS
233 .. 289  =  57 bp
pUC19 multiple cloning site
MCS
233 .. 289  =  57 bp
pUC19 multiple cloning site
M13 rev
204 .. 220  =  17 bp
common sequencing primer, one of multiple similar variants
M13 rev
204 .. 220  =  17 bp
common sequencing primer, one of multiple similar variants
M13 fwd
290 .. 306  =  17 bp
common sequencing primer, one of multiple similar variants
M13 fwd
290 .. 306  =  17 bp
common sequencing primer, one of multiple similar variants
ORF:  778 .. 1068  =  291 bp
ORF:  96 amino acids  =  11.5 kDa
ORF:  3188 .. 4048  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  216 .. 530  =  315 bp
ORF:  104 amino acids  =  12.1 kDa
ORF:  2130 .. 2465  =  336 bp
ORF:  111 amino acids  =  12.2 kDa
ORF:  2344 .. 2625  =  282 bp
ORF:  93 amino acids  =  10.8 kDa
ORF:  3652 .. 3918  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  143 .. 499  =  357 bp
ORF:  118 amino acids  =  13.5 kDa
ORF:  524 .. 763  =  240 bp
ORF:  79 amino acids  =  9.8 kDa
ORF:  1544 .. 1810  =  267 bp
ORF:  88 amino acids  =  10.3 kDa
ORF:  2201 .. 2875  =  675 bp
ORF:  224 amino acids  =  24.1 kDa
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