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Plasmid Files

YCplac111

Yeast centromeric plasmid with a LEU2 marker.

 
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YCplac111.dna
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BspQI - SapI (6094) DrdI (5875) AlwNI (5568) AhdI (5089) BsaI (5023) AatII (4170) ZraI (4168) SacII (3881) PpuMI (3791) PflMI (3775) BstEII (3644) AflII (3364) XcmI (3127) HindIII (233) SphI (243) PstI - SbfI (249) SalI (251) AccI (252) 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) DraIII (1428) BsaBI (1516) NgoMIV (1771) NaeI (1773) NheI (1801) BmtI (1805) BtgZI (1913) BglII (1986) AarI (2303) BsgI (2329) EcoRV (2933) YCplac111 6103 bp
BspQI  (6094)
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  (6094)
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.
DrdI  (5875)
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  (5568)
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  (5089)
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  (5023)
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.
AatII  (4170)
1 site
G A C G T C C T G C A G
ZraI  (4168)
1 site
G A C G T C C T G C A G
SacII  (3881)
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.
PpuMI  (3791)
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.
PflMI  (3775)
1 site
C C A N N N N N T G G G G T N N N N N A C C

Sticky ends from different PflMI sites may not be compatible.
BstEII  (3644)
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.
AflII  (3364)
1 site
C T T A A G G A A T T C
XcmI  (3127)
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.
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
AccI  (252)
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.
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.
DraIII  (1428)
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.
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.
BsgI  (2329)
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).
EcoRV  (2933)
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.
CEN/ARS
1066 .. 2229  =  1164 bp
S. cerevisiae CEN4 centromere fused to the autonomously replicating sequence ARS1/ARS416
CEN/ARS
1066 .. 2229  =  1164 bp
S. cerevisiae CEN4 centromere fused to the autonomously replicating sequence ARS1/ARS416
LEU2
2589 .. 3683  =  1095 bp
364 amino acids  =  39.0 kDa
Product: 3-isopropylmalate dehydrogenase, required for leucine biosynthesis
yeast auxotrophic marker
LEU2
2589 .. 3683  =  1095 bp
364 amino acids  =  39.0 kDa
Product: 3-isopropylmalate dehydrogenase, required for leucine biosynthesis
yeast auxotrophic marker
AmpR
4302 .. 5162  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   4302 .. 4370  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
4302 .. 5162  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   4371 .. 5162  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
4302 .. 5162  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
ori
5333 .. 5921  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
ori
5333 .. 5921  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
LEU2 promoter
3684 .. 4091  =  408 bp
LEU2 promoter
3684 .. 4091  =  408 bp
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
4197 .. 4301  =  105 bp
AmpR promoter
4197 .. 4301  =  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:  2710 .. 3021  =  312 bp
ORF:  103 amino acids  =  11.1 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:  4302 .. 5162  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  143 .. 520  =  378 bp
ORF:  125 amino acids  =  14.4 kDa
ORF:  2066 .. 2545  =  480 bp
ORF:  159 amino acids  =  17.7 kDa
ORF:  4766 .. 5032  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  2209 .. 2442  =  234 bp
ORF:  77 amino acids  =  8.9 kDa
ORF:  2589 .. 3683  =  1095 bp
ORF:  364 amino acids  =  39.0 kDa
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