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Plasmid Files

YCp50-poly

Derivative of yeast centromeric vector YCp50 containing the pUC19 polylinker.

 
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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) HpaI (3682) EcoRI (1) Eco53kI (9) SacI (11) Acc65I (13) KpnI (17) BamHI (22) XbaI (28) MCS SphI (50) HindIII (52) M13 rev lac operator lac promoter 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) 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
HpaI  (3682)
1 site
G T T A A C C A A T T G
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
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).
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