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Plasmid Files

YCplac33

Yeast centromeric plasmid with a URA3 marker.

 
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YCplac33.dna
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DrdI (5375) AhdI (4589) AatII (3670) ZraI (3668) NdeI (3449) XcmI (3237) PpuMI (3208) EcoRV (3176) NcoI (3155) BstBI (3097) BsmI (3004) ApaI * (2990) PspOMI * (2986) StuI (2928) 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) SpeI (550) PflFI - Tth111I (942) BsaBI (1516) NgoMIV (1771) NaeI (1773) NheI (1801) BmtI (1805) BtgZI (1913) BglII (1986) AarI (2303) BstXI (2446) BspDI * - ClaI * (2455) NsiI (2541) Bpu10I (2631) BsmBI (2738) YCplac33 5603 bp
DrdI  (5375)
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.
AhdI  (4589)
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.
AatII  (3670)
1 site
G A C G T C C T G C A G
ZraI  (3668)
1 site
G A C G T C C T G C A G
NdeI  (3449)
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.
XcmI  (3237)
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.
PpuMI  (3208)
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.
EcoRV  (3176)
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.
NcoI  (3155)
1 site
C C A T G G G G T A C C
BstBI  (3097)
1 site
T T C G A A A A G C T T
BsmI  (3004)
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.
ApaI  (2990)
1 site
G G G C C C C C C G G G
* Blocked by Dcm methylation.
ApaI can be used between 25°C and 37°C.
PspOMI  (2986)
1 site
G G G C C C C C C G G G
* Blocked by Dcm methylation.
StuI  (2928)
1 site
A G G C C T T C C G G A
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.
SpeI  (550)
1 site
A C T A G T T G A T C A
PflFI  (942)
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  (942)
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.
BsaBI  (1516)
1 site
G A T N N N N A T C C T A N N N N T A G
NgoMIV  (1771)
1 site
G C C G G C C G G C C G

Efficient cleavage requires at least two copies of the NgoMIV recognition sequence.
NaeI  (1773)
1 site
G C C G G C C G G C C G

Efficient cleavage requires at least two copies of the NaeI recognition sequence.
NheI  (1801)
1 site
G C T A G C C G A T C G
BmtI  (1805)
1 site
G C T A G C C G A T C G
BtgZI  (1913)
1 site
G C G A T G ( N ) 10 C G C T A C ( N ) 10 ( N ) 4

Sticky ends from different BtgZI sites may not be compatible.
After cleavage, BtgZI can remain bound to DNA and alter its electrophoretic mobility.
BtgZI is typically used at 60°C, but is 75% active at 37°C.
BglII  (1986)
1 site
A G A T C T T C T A G A
AarI  (2303)
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.
BstXI  (2446)
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.
BspDI  (2455)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
ClaI  (2455)
1 site
A T C G A T T A G C T A
* Blocked by Dam methylation.
NsiI  (2541)
1 site
A T G C A T T A C G T A
Bpu10I  (2631)
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.
BsmBI  (2738)
1 site
C G T C T C N G C A G A G N ( N ) 4

Sticky ends from different BsmBI sites may not be compatible.
CEN/ARS
1064 .. 2227  =  1164 bp
S. cerevisiae CEN4 centromere fused to the autonomously replicating sequence ARS1/ARS416
CEN/ARS
1064 .. 2227  =  1164 bp
S. cerevisiae CEN4 centromere fused to the autonomously replicating sequence ARS1/ARS416
AmpR
3802 .. 4662  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   3802 .. 3870  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3802 .. 4662  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   3871 .. 4662  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3802 .. 4662  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
URA3
2562 .. 3365  =  804 bp
267 amino acids  =  29.3 kDa
Product: orotidine-5'-phosphate decarboxylase, required for uracil biosynthesis
yeast auxotrophic marker, counterselectable with 5-fluoroorotic acid (5-FOA)
URA3
2562 .. 3365  =  804 bp
267 amino acids  =  29.3 kDa
Product: orotidine-5'-phosphate decarboxylase, required for uracil biosynthesis
yeast auxotrophic marker, counterselectable with 5-fluoroorotic acid (5-FOA)
ori
4833 .. 5421  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
ori
4833 .. 5421  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
lacZα
216 .. 554  =  339 bp
112 amino acids  =  13.1 kDa
Product: LacZα fragment of β-galactosidase
lacZα
216 .. 554  =  339 bp
112 amino acids  =  13.1 kDa
Product: LacZα fragment of β-galactosidase
URA3 promoter
3366 .. 3586  =  221 bp
URA3 promoter
3366 .. 3586  =  221 bp
AmpR promoter
3697 .. 3801  =  105 bp
AmpR promoter
3697 .. 3801  =  105 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:  2854 .. 3330  =  477 bp
ORF:  158 amino acids  =  16.8 kDa
ORF:  3802 .. 4662  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  216 .. 554  =  339 bp
ORF:  112 amino acids  =  13.1 kDa
ORF:  1980 .. 2330  =  351 bp
ORF:  116 amino acids  =  12.8 kDa
ORF:  2562 .. 3365  =  804 bp
ORF:  267 amino acids  =  29.3 kDa
ORF:  4266 .. 4532  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  143 .. 520  =  378 bp
ORF:  125 amino acids  =  14.4 kDa
ORF:  2066 .. 2476  =  411 bp
ORF:  136 amino acids  =  14.8 kDa
ORF:  2209 .. 2442  =  234 bp
ORF:  77 amino acids  =  8.9 kDa
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