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Plasmid Files

YIp5

Yeast integrating plasmid with a URA3 marker.

 
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YIp5.dna
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AatII (5471) ZraI (5469) SspI (5353) PvuI (4919) AseI (4721) AhdI (4549) BsaAI (3410) PflFI - Tth111I (3403) PfoI (3300) PvuII (3249) BsaBI * (2853) EcoRI (1) BspDI - ClaI (27) HindIII (32) NheI (232) BmtI (236) BamHI (378) SgrAI (413) SphI (569) EcoNI (629) SalI (654) PshAI (719) EagI (942) NruI (977) SbfI (1643) XcmI (1789) NcoI (1866) BstBI (1926) PspOMI * (2035) ApaI * (2039) StuI (2097) NsiI (2488) AvaI - BsoBI - TspMI - XmaI (2540) BmeT110I (2541) SmaI (2542) MscI * (2627) BspEI * (2845) YIp5 5541 bp
AatII  (5471)
1 site
G A C G T C C T G C A G
ZraI  (5469)
1 site
G A C G T C C T G C A G
SspI  (5353)
1 site
A A T A T T T T A T A A
PvuI  (4919)
1 site
C G A T C G G C T A G C
AseI  (4721)
1 site
A T T A A T T A A T T A
AhdI  (4549)
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.
BsaAI  (3410)
1 site
Y A C G T R R T G C A Y
PflFI  (3403)
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  (3403)
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.
PfoI  (3300)
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.
PvuII  (3249)
1 site
C A G C T G G T C G A C
BsaBI  (2853)
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.
EcoRI  (1)
1 site
G A A T T C C T T A A G
BspDI  (27)
1 site
A T C G A T T A G C T A
ClaI  (27)
1 site
A T C G A T T A G C T A
HindIII  (32)
1 site
A A G C T T T T C G A A
NheI  (232)
1 site
G C T A G C C G A T C G
BmtI  (236)
1 site
G C T A G C C G A T C G
BamHI  (378)
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.
SgrAI  (413)
1 site
C R C C G G Y G G Y G G C C R C

Efficient cleavage requires at least two copies of the SgrAI recognition sequence.
SphI  (569)
1 site
G C A T G C C G T A C G
EcoNI  (629)
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.
SalI  (654)
1 site
G T C G A C C A G C T G
PshAI  (719)
1 site
G A C N N N N G T C C T G N N N N C A G

PshAI quickly loses activity at 37°C, but can be used at 25°C for long incubations.
EagI  (942)
1 site
C G G C C G G C C G G C
NruI  (977)
1 site
T C G C G A A G C G C T
SbfI  (1643)
1 site
C C T G C A G G G G A C G T C C
XcmI  (1789)
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.
NcoI  (1866)
1 site
C C A T G G G G T A C C
BstBI  (1926)
1 site
T T C G A A A A G C T T
PspOMI  (2035)
1 site
G G G C C C C C C G G G
* Blocked by Dcm methylation.
ApaI  (2039)
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.
StuI  (2097)
1 site
A G G C C T T C C G G A
NsiI  (2488)
1 site
A T G C A T T A C G T A
AvaI  (2540)
1 site
C Y C G R G G R G C Y C

Sticky ends from different AvaI sites may not be compatible.
BsoBI  (2540)
1 site
C Y C G R G G R G C Y C

Sticky ends from different BsoBI sites may not be compatible.
BsoBI is typically used at 37°C, but can be used at temperatures up to 65°C.
TspMI  (2540)
1 site
C C C G G G G G G C C C
XmaI  (2540)
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.
BmeT110I  (2541)
1 site
C Y C G R G G R G C Y C
SmaI  (2542)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
MscI  (2627)
1 site
T G G C C A A C C G G T
* Blocked by Dcm methylation.
BspEI  (2845)
1 site
T C C G G A A G G C C T
* Blocked by Dam methylation.
TcR
89 .. 1279  =  1191 bp
396 amino acids  =  41.5 kDa
Product: tetracycline efflux protein
confers resistance to tetracycline
TcR
89 .. 1279  =  1191 bp
396 amino acids  =  41.5 kDa
Product: tetracycline efflux protein
confers resistance to tetracycline
AmpR
4476 .. 5336  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 2:  
   4476 .. 5267  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
4476 .. 5336  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 1:  signal sequence  
   5268 .. 5336  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
4476 .. 5336  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
URA3
1661 .. 2464  =  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
1661 .. 2464  =  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
3717 .. 4305  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
ori
3717 .. 4305  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
URA3 promoter
1445 .. 1660  =  216 bp
URA3 promoter
1445 .. 1660  =  216 bp
rop
3098 .. 3289  =  192 bp
63 amino acids  =  7.2 kDa
Product: Rop protein
rop
3098 .. 3289  =  192 bp
63 amino acids  =  7.2 kDa
Product: Rop protein
AmpR promoter
5337 .. 5441  =  105 bp
AmpR promoter
5337 .. 5441  =  105 bp
tet promoter
13 .. 41  =  29 bp
   Segment 1:  -35  
   13 .. 18  =  6 bp
E. coli promoter for tetracycline efflux protein gene
tet promoter
13 .. 41  =  29 bp
   Segment 2:  
   19 .. 35  =  17 bp
E. coli promoter for tetracycline efflux protein gene
tet promoter
13 .. 41  =  29 bp
   Segment 3:  -10  
   36 .. 41  =  6 bp
E. coli promoter for tetracycline efflux protein gene
tet promoter
13 .. 41  =  29 bp
3 segments
E. coli promoter for tetracycline efflux protein gene
ORF:  262 .. 645  =  384 bp
ORF:  127 amino acids  =  14.7 kDa
ORF:  1183 .. 1506  =  324 bp
ORF:  107 amino acids  =  12.3 kDa
ORF:  4606 .. 4872  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  89 .. 1279  =  1191 bp
ORF:  396 amino acids  =  41.5 kDa
ORF:  1661 .. 2464  =  804 bp
ORF:  267 amino acids  =  29.3 kDa
ORF:  2999 .. 3289  =  291 bp
ORF:  96 amino acids  =  11.4 kDa
ORF:  442 .. 792  =  351 bp
ORF:  116 amino acids  =  12.2 kDa
ORF:  1696 .. 2172  =  477 bp
ORF:  158 amino acids  =  16.8 kDa
ORF:  4476 .. 5336  =  861 bp
ORF:  286 amino acids  =  31.5 kDa
ORF:  326 .. 568  =  243 bp
ORF:  80 amino acids  =  8.0 kDa
ORF:  626 .. 1084  =  459 bp
ORF:  152 amino acids  =  16.7 kDa
ORF:  2696 .. 3094  =  399 bp
ORF:  132 amino acids  =  15.3 kDa
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