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Plasmid Files

pOTB7-3

cDNA cloning vector with an f1 origin derived from pOTB7.

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pOTB7-3 Sequence and MappOTB7-3.dna
Map and Sequence File   
Sequence Author:  I.M.A.G.E. Consortium
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 SalI - SgrDI (2812) ScaI (2775) BtgI - NcoI - StyI (2659) MscI (2625) PasI - PflMI * (2590) BsmBI (2582) BpmI (2480) AclI (2445) BsrDI (2377) BspEI (2354) Bpu10I (2131) BspDI - ClaI (2080) BciVI (1862) BaeGI - Bme1580I (1750) ApaLI (1746) AlwNI (1651) AcuI (1518) AccI (2813) M13 fwd Bsu36I (141) StuI * (154) BglI (160) XhoI (185) BstXI (204) NspI (216) BspQI - EarI - SapI (329) SP6 promoter NsiI (610) HindIII (613) Acc65I (619) KpnI (623) Eco53kI (627) SacI (629) BstXI (658) EcoRV (674) BsaBI (676) BstXI (684) XhoI (695) PI-SceI (717) M13 rev BglII (788) AscI - BssHII (797) BsaI (819) HpaI (855) BfuAI - BspMI (866) AanI - AanI - AanI - PsiI (986) BsaAI - DraIII (1114) NgoMIV (1215) NaeI (1217) pOTB7-3 2816 bp
SalI  (2812)
1 site
G T C G A C C A G C T G
SgrDI  (2812)
1 site
C G T C G A C G G C A G C T G C
ScaI  (2775)
1 site
A G T A C T T C A T G A
BtgI  (2659)
1 site
C C R Y G G G G Y R C C

Sticky ends from different BtgI sites may not be compatible.
NcoI  (2659)
1 site
C C A T G G G G T A C C
StyI  (2659)
1 site
C C W W G G G G W W C C

Sticky ends from different StyI sites may not be compatible.
MscI  (2625)
1 site
T G G C C A A C C G G T
PasI  (2590)
1 site
C C C W G G G G G G W C C C

Sticky ends from different PasI sites may not be compatible.
PflMI  (2590)
1 site
C C A N N N N N T G G G G T N N N N N A C C
* Blocked by Dcm methylation.
Sticky ends from different PflMI sites may not be compatible.
BsmBI  (2582)
1 site
C G T C T C N G C A G A G N ( N ) 4

Sticky ends from different BsmBI sites may not be compatible.
BpmI  (2480)
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.
AclI  (2445)
1 site
A A C G T T T T G C A A
BsrDI  (2377)
1 site
G C A A T G N N C G T T A C

Sticky ends from different BsrDI sites may not be compatible.
BspEI  (2354)
1 site
T C C G G A A G G C C T
Bpu10I  (2131)
1 site
C C T N A G C G G A N T C G

Efficient cleavage requires at least two copies of the Bpu10I
recognition sequence.
This recognition sequence is asymmetric, so ligating sticky ends
generated by Bpu10I will not always regenerate a Bpu10I site.
Sticky ends from different Bpu10I sites may not be compatible.
BspDI  (2080)
1 site
A T C G A T T A G C T A
ClaI  (2080)
1 site
A T C G A T T A G C T A
BciVI  (1862)
1 site
G T A T C C ( N ) 5 N C A T A G G ( N ) 5

The 1-base overhangs produced by BciVI may be hard to ligate.
Sticky ends from different BciVI sites may not be compatible.
BaeGI  (1750)
1 site
G K G C M C C M C G K G

Sticky ends from different BaeGI sites may not be compatible.
Bme1580I  (1750)
1 site
G K G C M C C M C G K G

Sticky ends from different Bme1580I sites may not be compatible.
ApaLI  (1746)
1 site
G T G C A C C A C G T G
AlwNI  (1651)
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.
AcuI  (1518)
1 site
C T G A A G ( N ) 14 N N G A C T T C ( N ) 14

Efficient cleavage requires at least two copies of the AcuI
recognition sequence.
Sticky ends from different AcuI sites may not be compatible.
After cleavage, AcuI can remain bound to DNA and alter its
electrophoretic mobility.
For full activity, add fresh S-adenosylmethionine (SAM).
AccI  (2813)
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.
Bsu36I  (141)
1 site
C C T N A G G G G A N T C C

Sticky ends from different Bsu36I sites may not be compatible.
StuI  (154)
1 site
A G G C C T T C C G G A
* Blocked by Dcm methylation.
BglI  (160)
1 site
G C C N N N N N G G C C G G N N N N N C C G

Sticky ends from different BglI sites may not be compatible.
XhoI  (185)
2 sites
C T C G A G G A G C T C
BstXI  (204)
3 sites
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.
NspI  (216)
1 site
R C A T G Y Y G T A C R
BspQI  (329)
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.
EarI  (329)
1 site
C T C T T C N G A G A A G N N N N

Efficient cleavage requires at least two copies of the EarI
recognition sequence.
Sticky ends from different EarI sites may not be compatible.
SapI  (329)
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.
NsiI  (610)
1 site
A T G C A T T A C G T A
HindIII  (613)
1 site
A A G C T T T T C G A A
Acc65I  (619)
1 site
G G T A C C C C A T G G
KpnI  (623)
1 site
G G T A C C C C A T G G
Eco53kI  (627)
1 site
G A G C T C C T C G A G
SacI  (629)
1 site
G A G C T C C T C G A G
BstXI  (658)
3 sites
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.
EcoRV  (674)
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.
BsaBI  (676)
1 site
G A T N N N N A T C C T A N N N N T A G
BstXI  (684)
3 sites
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.
XhoI  (695)
2 sites
C T C G A G G A G C T C
PI-SceI  (717)
1 site
A T C T A T G T C G G G T G C G G A G A A A G A G G T A A T G A A A T G G T A G A T A C A G C C C A C G C C T C T T T C T C C A T T A C T T T A C C

PI-SceI  is a homing endonuclease that can recognize a variety of
similar recognition sequences.
BglII  (788)
1 site
A G A T C T T C T A G A
AscI  (797)
1 site
G G C G C G C C C C G C G C G G
BssHII  (797)
1 site
G C G C G C C G C G C G

BssHII is typically used at 50°C, but is 75% active at 37°C.
BsaI  (819)
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.
HpaI  (855)
1 site
G T T A A C C A A T T G
BfuAI  (866)
1 site
A C C T G C ( N ) 4 T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the BfuAI
recognition sequence.
Sticky ends from different BfuAI sites may not be compatible.
BfuAI is typically used at 50°C, but is 50% active at 37°C.
BspMI  (866)
1 site
A C C T G C ( N ) 4 T G G A C G ( N ) 4 ( N ) 4

Efficient cleavage requires at least two copies of the BspMI
recognition sequence.
Sticky ends from different BspMI sites may not be compatible.
AanI  (986)
1 site
T T A T A A A A T A T T
AanI  (986)
1 site
T T A T A A A A T A T T
AanI  (986)
1 site
T T A T A A A A T A T T
PsiI  (986)
1 site
T T A T A A A A T A T T
BsaAI  (1114)
1 site
Y A C G T R R T G C A Y
DraIII  (1114)
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.
NgoMIV  (1215)
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  (1217)
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.
CmR
2145 .. 2804  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
CmR
2145 .. 2804  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
ori
1416 .. 2004  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
1416 .. 2004  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
f1 ori
890 .. 1345  =  456 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
f1 ori
890 .. 1345  =  456 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
lac promoter
480 .. 510  =  31 bp
   Segment 1:  -35  
   480 .. 485  =  6 bp
promoter for the E. coli lac operon
lac promoter
480 .. 510  =  31 bp
   Segment 2:  
   486 .. 503  =  18 bp
promoter for the E. coli lac operon
lac promoter
480 .. 510  =  31 bp
   Segment 3:  -10  
   504 .. 510  =  7 bp
promoter for the E. coli lac operon
lac promoter
480 .. 510  =  31 bp
3 segments
promoter for the E. coli lac operon
attB1
85 .. 109  =  25 bp
recombination site for the Gateway® BP reaction
attB1
85 .. 109  =  25 bp
recombination site for the Gateway® BP reaction
attB2
763 .. 787  =  25 bp
recombination site for the Gateway® BP reaction
attB2
763 .. 787  =  25 bp
recombination site for the Gateway® BP reaction
SP6 promoter
53 .. 71  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
SP6 promoter
53 .. 71  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
SP6 promoter
576 .. 594  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
SP6 promoter
576 .. 594  =  19 bp
promoter for bacteriophage SP6 RNA polymerase
T7 promoter
819 .. 837  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
819 .. 837  =  19 bp
promoter for bacteriophage T7 RNA polymerase
M13 fwd
111 .. 127  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 fwd
111 .. 127  =  17 bp
common sequencing primer, one of multiple similar
variants
lac operator
518 .. 534  =  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
518 .. 534  =  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).
M13 rev
542 .. 558  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
542 .. 558  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
746 .. 762  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
746 .. 762  =  17 bp
common sequencing primer, one of multiple similar
variants
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