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YCp50-poly

Derivative of yeast centromeric vector YCp50 containing the pUC19 polylinker.

 
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YCp50-poly.dna
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AatII (6990) ZraI (6988) PvuI (6438) AhdI (6068) BsaAI (4929) PfoI (4819) BglII (4527) BmtI (4346) NheI (4342) PaeR7I - XhoI (3812) MfeI (3745) EcoRI (1) Eco53kI (9) SacI (11) Acc65I (13) KpnI (17) BamHI (22) XbaI (28) SphI (50) HindIII (52) PshAI (300) EagI (523) NruI (558) KasI (789) NarI (790) SfoI (791) PluTI (793) XcmI (1370) EcoRV (1430) NcoI (1447) BstBI (1507) PspOMI * (1616) ApaI * (1620) NsiI (2069) MscI * (2208) FspAI (2218) BspEI * (2426) AarI (2818) SpeI (2875) HpaI (3682) YCp50-poly 7060 bp
AatII  (6990)
1 site
G A C G T C C T G C A G
ZraI  (6988)
1 site
G A C G T C C T G C A G
PvuI  (6438)
1 site
C G A T C G G C T A G C
AhdI  (6068)
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  (4929)
1 site
Y A C G T R R T G C A Y
PfoI  (4819)
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.
BglII  (4527)
1 site
A G A T C T T C T A G A
BmtI  (4346)
1 site
G C T A G C C G A T C G
NheI  (4342)
1 site
G C T A G C C G A T C G
PaeR7I  (3812)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
XhoI  (3812)
1 site
C T C G A G G A G C T C
MfeI  (3745)
1 site
C A A T T G G T T A A C
EcoRI  (1)
1 site
G A A T T C C T T A A G
Eco53kI  (9)
1 site
G A G C T C C T C G A G
SacI  (11)
1 site
G A G C T C C T C G A G
Acc65I  (13)
1 site
G G T A C C C C A T G G
KpnI  (17)
1 site
G G T A C C C C A T G G
BamHI  (22)
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.
XbaI  (28)
1 site
T C T A G A A G A T C T
SphI  (50)
1 site
G C A T G C C G T A C G
HindIII  (52)
1 site
A A G C T T T T C G A A
PshAI  (300)
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  (523)
1 site
C G G C C G G C C G G C
NruI  (558)
1 site
T C G C G A A G C G C T
KasI  (789)
1 site
G G C G C C C C G C G G
NarI  (790)
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  (791)
1 site
G G C G C C C C G C G G
PluTI  (793)
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.
XcmI  (1370)
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.
EcoRV  (1430)
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  (1447)
1 site
C C A T G G G G T A C C
BstBI  (1507)
1 site
T T C G A A A A G C T T
PspOMI  (1616)
1 site
G G G C C C C C C G G G
* Blocked by Dcm methylation.
ApaI  (1620)
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.
NsiI  (2069)
1 site
A T G C A T T A C G T A
MscI  (2208)
1 site
T G G C C A A C C G G T
* Blocked by Dcm methylation.
FspAI  (2218)
1 site
R T G C G C A Y Y A C G C G T R
BspEI  (2426)
1 site
T C C G G A A G G C C T
* Blocked by Dam methylation.
AarI  (2818)
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.
SpeI  (2875)
1 site
A C T A G T T G A T C A
HpaI  (3682)
1 site
G T T A A C C A A T T G
CEN/ARS
3390 .. 4768  =  1379 bp
S. cerevisiae CEN4 centromere fused to the autonomously replicating sequence ARS1/ARS416
CEN/ARS
3390 .. 4768  =  1379 bp
S. cerevisiae CEN4 centromere fused to the autonomously replicating sequence ARS1/ARS416
AmpR
5995 .. 6855  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 2:  
   5995 .. 6786  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
5995 .. 6855  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 1:  signal sequence  
   6787 .. 6855  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
5995 .. 6855  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
URA3
1242 .. 2045  =  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
1242 .. 2045  =  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
5236 .. 5824  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
ori
5236 .. 5824  =  589 bp
high-copy-number colE1/pMB1/pBR322/pUC origin of replication
URA3 promoter
1026 .. 1241  =  216 bp
URA3 promoter
1026 .. 1241  =  216 bp
AmpR promoter
6856 .. 6960  =  105 bp
AmpR promoter
6856 .. 6960  =  105 bp
MCS
1 .. 57  =  57 bp
pUC19 multiple cloning site
MCS
1 .. 57  =  57 bp
pUC19 multiple cloning site
lac promoter
118 .. 148  =  31 bp
   Segment 3:  -10  
   118 .. 124  =  7 bp
promoter for the E. coli lac operon
lac promoter
118 .. 148  =  31 bp
   Segment 2:  
   125 .. 142  =  18 bp
promoter for the E. coli lac operon
lac promoter
118 .. 148  =  31 bp
   Segment 1:  -35  
   143 .. 148  =  6 bp
promoter for the E. coli lac operon
lac promoter
118 .. 148  =  31 bp
3 segments
promoter for the E. coli lac operon
M13 rev
70 .. 86  =  17 bp
common sequencing primer, one of multiple similar variants
M13 rev
70 .. 86  =  17 bp
common sequencing primer, one of multiple similar variants
lac operator
94 .. 110  =  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
94 .. 110  =  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).
ORF:  3754 .. 3978  =  225 bp
ORF:  74 amino acids  =  8.0 kDa
ORF:  764 .. 1087  =  324 bp
ORF:  107 amino acids  =  12.1 kDa
ORF:  6125 .. 6391  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  243 .. 860  =  618 bp
ORF:  205 amino acids  =  21.8 kDa
ORF:  1242 .. 2045  =  804 bp
ORF:  267 amino acids  =  29.3 kDa
ORF:  2580 .. 2879  =  300 bp
ORF:  99 amino acids  =  12.1 kDa
ORF:  4521 .. 4808  =  288 bp
ORF:  95 amino acids  =  10.7 kDa
ORF:  1277 .. 1753  =  477 bp
ORF:  158 amino acids  =  16.8 kDa
ORF:  5995 .. 6855  =  861 bp
ORF:  286 amino acids  =  31.5 kDa
ORF:  177 .. 665  =  489 bp
ORF:  162 amino acids  =  17.6 kDa
ORF:  2277 .. 2675  =  399 bp
ORF:  132 amino acids  =  15.3 kDa
ORF:  3717 .. 4049  =  333 bp
ORF:  110 amino acids  =  12.7 kDa
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