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Plasmid Files

pBluescriptR

pBluescript derivative modified at RIKEN for cDNA cloning.

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pBluescriptR Sequence and MappBluescriptR.dna
Map and Sequence File   
Sequence Author:  I.M.A.G.E. Consortium
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 NgoMIV (129) XmnI (2682) BsaHI (2620) ScaI (2563) TatI (2561) BpmI (2153) BsaI (2144) AhdI (2083) AlwNI (1606) PspFI (1498) NaeI (131) BtgZI (229) BsaAI (234) DraIII (237) PsiI (362) M13 fwd BtgI (658) AleI (660) SacII (661) BstXI (662) NotI (667) EcoRI (733) SalI (739) AccI (740) HincII (741) AvaI - BsoBI - PaeR7I - PspXI - XhoI (744) BmeT110I (745) BamHI (753) PspOMI (787) ApaI (791) Acc65I (793) KpnI (797) M13 rev lac operator BspQI - SapI (1074) AflIII - PciI (1190) NspI (1194) BseYI (1494) pBluescriptR 2998 bp
NgoMIV  (129)
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.
XmnI  (2682)
1 site
G A A N N N N T T C C T T N N N N A A G
BsaHI  (2620)
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  (2563)
1 site
A G T A C T T C A T G A
TatI  (2561)
1 site
W G T A C W W C A T G W
BpmI  (2153)
1 site
C T G G A G ( N ) 14 N N G A C C T C ( N ) 14

Efficient cleavage requires at least two copies of the BpmI
recognition sequence.
Sticky ends from different BpmI sites may not be compatible.
After cleavage, BpmI can remain bound to DNA and alter its
electrophoretic mobility.
BpmI quickly loses activity at 37°C.
BsaI  (2144)
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  (2083)
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  (1606)
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  (1498)
1 site
C C C A G C G G G T C G
NaeI  (131)
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.
BtgZI  (229)
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.
BsaAI  (234)
1 site
Y A C G T R R T G C A Y
DraIII  (237)
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.
PsiI  (362)
1 site
T T A T A A A A T A T T
BtgI  (658)
1 site
C C R Y G G G G Y R C C

Sticky ends from different BtgI sites may not be compatible.
AleI  (660)
1 site
C A C N N N N G T G G T G N N N N C A C
SacII  (661)
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.
BstXI  (662)
1 site
C C A N N N N N N T G G G G T N N N N N N A C C

Sticky ends from different BstXI sites may not be compatible.
NotI  (667)
1 site
G C G G C C G C C G C C G G C G
EcoRI  (733)
1 site
G A A T T C C T T A A G
SalI  (739)
1 site
G T C G A C C A G C T G
AccI  (740)
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.
HincII  (741)
1 site
G T Y R A C C A R Y T G
AvaI  (744)
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  (744)
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.
PaeR7I  (744)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (744)
1 site
V C T C G A G B B G A G C T C V
XhoI  (744)
1 site
C T C G A G G A G C T C
BmeT110I  (745)
1 site
C Y C G R G G R G C Y C
BamHI  (753)
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.
PspOMI  (787)
1 site
G G G C C C C C C G G G
ApaI  (791)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
Acc65I  (793)
1 site
G G T A C C C C A T G G
KpnI  (797)
1 site
G G T A C C C C A T G G
BspQI  (1074)
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  (1074)
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.
AflIII  (1190)
1 site
A C R Y G T T G Y R C A

Sticky ends from different AflIII sites may not be compatible.
PciI  (1190)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
NspI  (1194)
1 site
R C A T G Y Y G T A C R
BseYI  (1494)
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.
AmpR
2010 .. 2870  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   2010 .. 2801  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
2010 .. 2870  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   2802 .. 2870  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
2010 .. 2870  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
ori
1251 .. 1839  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
1251 .. 1839  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
f1 ori
4 .. 459  =  456 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
f1 ori
4 .. 459  =  456 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
AmpR promoter
2871 .. 2975  =  105 bp
AmpR promoter
2871 .. 2975  =  105 bp
MCS
733 .. 798  =  66 bp
multiple cloning site
MCS
733 .. 798  =  66 bp
multiple cloning site
loxP
674 .. 707  =  34 bp
Cre-mediated recombination occurs in the 8-bp core
sequence (GCATACAT).
loxP
674 .. 707  =  34 bp
Cre-mediated recombination occurs in the 8-bp core
sequence (GCATACAT).
lac promoter
897 .. 927  =  31 bp
   Segment 3:  -10  
   897 .. 903  =  7 bp
promoter for the E. coli lac operon
lac promoter
897 .. 927  =  31 bp
   Segment 2:  
   904 .. 921  =  18 bp
promoter for the E. coli lac operon
lac promoter
897 .. 927  =  31 bp
   Segment 1:  -35  
   922 .. 927  =  6 bp
promoter for the E. coli lac operon
lac promoter
897 .. 927  =  31 bp
3 segments
promoter for the E. coli lac operon
T7 promoter
623 .. 641  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
623 .. 641  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T3 promoter
810 .. 828  =  19 bp
promoter for bacteriophage T3 RNA polymerase
T3 promoter
810 .. 828  =  19 bp
promoter for bacteriophage T3 RNA polymerase
M13 fwd
600 .. 616  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 fwd
600 .. 616  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
849 .. 865  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
849 .. 865  =  17 bp
common sequencing primer, one of multiple similar
variants
lac operator
873 .. 889  =  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
873 .. 889  =  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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