pRS413

Yeast centromere vector with a HIS3 marker and an MCS derived from pBLUESCRIPT II.
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SwaI (4426) PmlI (4402) PpuMI (4388) BsaHI (4006) ScaI (3949) NmeAIII (3617) BsaI (3530) AhdI (3469) AlwNI (2992) PspFI (2884) BseYI (2880) PfoI (46) AfeI (213) BseRI (303) BsaBI * (561) NdeI (694) MscI (711) BsmI (716) BsiWI (916) NheI (1008) BmtI (1012) BclI * (1052) NsiI (1283) DraIII (1647) BtgZI (1648) NgoMIV (1748) NaeI (1750) PspOMI (2082) ApaI (2086) AbsI - PaeR7I - PspXI - XhoI (2091) SalI (2097) HincII (2099) BspDI - ClaI (2107) EcoRV (2120) EcoRI (2124) TspMI - XmaI (2136) SmaI (2138) BamHI (2142) SpeI (2148) XbaI (2154) EagI - NotI (2161) BtgI (2170) SacII (2173) Eco53kI (2180) SacI (2182) lac operator pRS413 4970 bp
SwaI  (4426)
1 site
A T T T A A A T T A A A T T T A

SwaI is typically used at 25°C, but is 50% active at 37°C.
PmlI  (4402)
1 site
C A C G T G G T G C A C
PpuMI  (4388)
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.
BsaHI  (4006)
1 site
G R C G Y C C Y G C R G

BsaHI is typically used at 37°C, but is even more active at 60°C.
ScaI  (3949)
1 site
A G T A C T T C A T G A
NmeAIII  (3617)
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).
BsaI  (3530)
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.
AhdI  (3469)
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.
AlwNI  (2992)
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.
PspFI  (2884)
1 site
C C C A G C G G G T C G
BseYI  (2880)
1 site
C C C A G C G G G T C G

After cleavage, BseYI can remain bound to DNA and alter its electrophoretic mobility.
PfoI  (46)
1 site
T C C N G G A A G G N C C T

Sticky ends from different PfoI sites may not be compatible.
AfeI  (213)
1 site
A G C G C T T C G C G A
BseRI  (303)
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.
BsaBI  (561)
1 site
G A T N N N N A T C C T A N N N N T A G
* Blocked by Dam methylation.
NdeI  (694)
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.
MscI  (711)
1 site
T G G C C A A C C G G T
BsmI  (716)
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.
BsiWI  (916)
1 site
C G T A C G G C A T G C

BsiWI is typically used at 55°C, but is 50% active at 37°C.
NheI  (1008)
1 site
G C T A G C C G A T C G
BmtI  (1012)
1 site
G C T A G C C G A T C G
BclI  (1052)
1 site
T G A T C A A C T A G T
* Blocked by Dam methylation.
BclI is typically used at 50-55°C, but is 50% active at 37°C.
NsiI  (1283)
1 site
A T G C A T T A C G T A
DraIII  (1647)
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.
BtgZI  (1648)
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.
NgoMIV  (1748)
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  (1750)
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.
PspOMI  (2082)
1 site
G G G C C C C C C G G G
ApaI  (2086)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
AbsI  (2091)
1 site
C C T C G A G G G G A G C T C C
PaeR7I  (2091)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (2091)
1 site
V C T C G A G B B G A G C T C V
XhoI  (2091)
1 site
C T C G A G G A G C T C
SalI  (2097)
1 site
G T C G A C C A G C T G
HincII  (2099)
1 site
G T Y R A C C A R Y T G
BspDI  (2107)
1 site
A T C G A T T A G C T A
ClaI  (2107)
1 site
A T C G A T T A G C T A
EcoRV  (2120)
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.
EcoRI  (2124)
1 site
G A A T T C C T T A A G
TspMI  (2136)
1 site
C C C G G G G G G C C C
XmaI  (2136)
1 site
C C C G G G G G G C C C

Cleavage may be enhanced when more than one copy of the XmaI recognition sequence is present.
SmaI  (2138)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
BamHI  (2142)
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.
SpeI  (2148)
1 site
A C T A G T T G A T C A
XbaI  (2154)
1 site
T C T A G A A G A T C T
EagI  (2161)
1 site
C G G C C G G C C G G C
NotI  (2161)
1 site
G C G G C C G C C G C C G G C G
BtgI  (2170)
1 site
C C R Y G G G G Y R C C

Sticky ends from different BtgI sites may not be compatible.
SacII  (2173)
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.
Eco53kI  (2180)
1 site
G A G C T C C T C G A G
SacI  (2182)
1 site
G A G C T C C T C G A G
AmpR
3396 .. 4256  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 2:  
   3396 .. 4187  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3396 .. 4256  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
   Segment 1:  signal sequence  
   4188 .. 4256  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3396 .. 4256  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
HIS3
504 .. 1163  =  660 bp
219 amino acids  =  23.8 kDa
Product: imidazoleglycerol-phosphate dehydratase, required for histidine biosynthesis
yeast auxotrophic marker
HIS3
504 .. 1163  =  660 bp
219 amino acids  =  23.8 kDa
Product: imidazoleglycerol-phosphate dehydratase, required for histidine biosynthesis
yeast auxotrophic marker
ori
2637 .. 3225  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
ori
2637 .. 3225  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
lacZα
1661 .. 2239  =  579 bp
192 amino acids  =  20.6 kDa
Product: LacZα fragment of β-galactosidase
lacZα
1661 .. 2239  =  579 bp
192 amino acids  =  20.6 kDa
Product: LacZα fragment of β-galactosidase
CEN/ARS
4398 .. 4901  =  504 bp
S. cerevisiae CEN6 centromere fused to an autonomously replicating sequence
CEN/ARS
4398 .. 4901  =  504 bp
S. cerevisiae CEN6 centromere fused to an autonomously replicating sequence
HIS3 promoter
317 .. 503  =  187 bp
HIS3 promoter
317 .. 503  =  187 bp
AmpR promoter
4257 .. 4361  =  105 bp
AmpR promoter
4257 .. 4361  =  105 bp
lac promoter
2283 .. 2313  =  31 bp
3 segments
   Segment 3:  -10  
   2283 .. 2289  =  7 bp
promoter for the E. coli lac operon
lac promoter
2283 .. 2313  =  31 bp
3 segments
   Segment 2:  
   2290 .. 2307  =  18 bp
promoter for the E. coli lac operon
lac promoter
2283 .. 2313  =  31 bp
3 segments
   Segment 1:  -35  
   2308 .. 2313  =  6 bp
promoter for the E. coli lac operon
lac promoter
2283 .. 2313  =  31 bp
3 segments
promoter for the E. coli lac operon
lac operator
2259 .. 2275  =  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
2259 .. 2275  =  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).
f1 ori
1423 .. 1878  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
f1 ori
1423 .. 1878  =  456 bp
f1 bacteriophage origin of replication; arrow indicates direction of (+) strand synthesis
MCS
2076 .. 2183  =  108 bp
pBluescript multiple cloning site
MCS
2076 .. 2183  =  108 bp
pBluescript multiple cloning site
T7 promoter
2049 .. 2067  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
2049 .. 2067  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T3 promoter
2196 .. 2214  =  19 bp
promoter for bacteriophage T3 RNA polymerase
T3 promoter
2196 .. 2214  =  19 bp
promoter for bacteriophage T3 RNA polymerase
M13 fwd
2023 .. 2039  =  17 bp
common sequencing primer, one of multiple similar variants
M13 fwd
2023 .. 2039  =  17 bp
common sequencing primer, one of multiple similar variants
M13 rev
2235 .. 2251  =  17 bp
common sequencing primer, one of multiple similar variants
M13 rev
2235 .. 2251  =  17 bp
common sequencing primer, one of multiple similar variants
ORF:  1120 .. 1431  =  312 bp
ORF:  103 amino acids  =  12.6 kDa
ORF:  3526 .. 3792  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  504 .. 1163  =  660 bp
ORF:  219 amino acids  =  23.8 kDa
ORF:  3396 .. 4256  =  861 bp
ORF:  286 amino acids  =  31.6 kDa
ORF:  1661 .. 2239  =  579 bp
ORF:  192 amino acids  =  20.6 kDa
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