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Plasmid Files

pOTB7

cDNA cloning vector with a Gateway® recombination cassette.

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pOTB7.dna
Map and Sequence File:    Download    Open   
Sequence Author:  Berkeley Drosophila Genome Project
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SalI - SgrDI (1811) ScaI (1774) SspI (1669) BtgI - NcoI - StyI (1658) MscI (1624) PasI - PflMI * (1589) BsmBI (1581) BpmI (1479) AclI (1444) BsrDI (1376) BspEI (1353) TsoI (1258) PvuII (1257) Bpu10I (1130) EagI - NotI (1091) BspDI - ClaI (1079) DrdI (957) AccI (1812) BamHI (79) Bsu36I (141) I-CeuI (144) StuI * (154) BglI (160) EcoRI (165) SpeI (175) AbsI - PaeR7I - PspXI - XhoI (185) PI-SceI (207) BglII (278) BsrFI (284) BsaI (293) HpaI (329) BfuAI - BspMI (340) PstI (354) TspMI - XmaI (358) SmaI (360) AcuI (517) AlwNI (650) ApaLI (745) BaeGI - Bme1580I - BsiHKAI - Bsp1286I (749) HaeII (819) BciVI (861) BssS α I (886) pOTB7 1815 bp
SalI  (1811)
1 site
G T C G A C C A G C T G
SgrDI  (1811)
1 site
C G T C G A C G G C A G C T G C
ScaI  (1774)
1 site
A G T A C T T C A T G A
SspI  (1669)
1 site
A A T A T T T T A T A A
BtgI  (1658)
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  (1658)
1 site
C C A T G G G G T A C C
StyI  (1658)
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  (1624)
1 site
T G G C C A A C C G G T
PasI  (1589)
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  (1589)
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  (1581)
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  (1479)
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  (1444)
1 site
A A C G T T T T G C A A
BsrDI  (1376)
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  (1353)
1 site
T C C G G A A G G C C T
TsoI  (1258)
1 site
T A R C C A ( N ) 9 N N A T Y G G T ( N ) 9

Sticky ends from different TsoI sites may not be compatible.
After cleavage, TsoI can remain bound to DNA and alter its electrophoretic mobility.
For full activity, add fresh S-adenosylmethionine (SAM).
PvuII  (1257)
1 site
C A G C T G G T C G A C
Bpu10I  (1130)
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.
EagI  (1091)
1 site
C G G C C G G C C G G C
NotI  (1091)
1 site
G C G G C C G C C G C C G G C G
BspDI  (1079)
1 site
A T C G A T T A G C T A
ClaI  (1079)
1 site
A T C G A T T A G C T A
DrdI  (957)
1 site
G A C N N N N N N G T C C T G N N N N N N C A G

Sticky ends from different DrdI sites may not be compatible.
AccI  (1812)
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.
BamHI  (79)
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.
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.
I-CeuI  (144)
1 site
T A A C T A T A A C G G T C C T A A G G T A G C G A A T T G A T A T T G C C A G G A T T C C A T C G C T

I-CeuI is a homing endonuclease that can recognize a variety of similar recognition sequences.
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.
EcoRI  (165)
1 site
G A A T T C C T T A A G
SpeI  (175)
1 site
A C T A G T T G A T C A
AbsI  (185)
1 site
C C T C G A G G G G A G C T C C
PaeR7I  (185)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (185)
1 site
V C T C G A G B B G A G C T C V
XhoI  (185)
1 site
C T C G A G G A G C T C
PI-SceI  (207)
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  (278)
1 site
A G A T C T T C T A G A
BsrFI  (284)
1 site
R C C G G Y Y G G C C R

Efficient cleavage requires at least two copies of the BsrFI recognition sequence.
After cleavage, BsrFI can remain bound to DNA and alter its electrophoretic mobility.
BsaI  (293)
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  (329)
1 site
G T T A A C C A A T T G
BfuAI  (340)
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  (340)
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.
PstI  (354)
1 site
C T G C A G G A C G T C
TspMI  (358)
1 site
C C C G G G G G G C C C
XmaI  (358)
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.
SmaI  (360)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
AcuI  (517)
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).
AlwNI  (650)
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.
ApaLI  (745)
1 site
G T G C A C C A C G T G
BaeGI  (749)
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  (749)
1 site
G K G C M C C M C G K G

Sticky ends from different Bme1580I sites may not be compatible.
BsiHKAI  (749)
1 site
G W G C W C C W C G W G

Sticky ends from different BsiHKAI sites may not be compatible.
Bsp1286I  (749)
1 site
G D G C H C C H C G D G

Sticky ends from different Bsp1286I sites may not be compatible.
HaeII  (819)
1 site
R G C G C Y Y C G C G R
BciVI  (861)
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.
BssSαI  (886)
1 site
C A C G A G G T G C T C
CmR
1144 .. 1803  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
CmR
1144 .. 1803  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
ori
415 .. 1003  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
415 .. 1003  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
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
253 .. 277  =  25 bp
recombination site for the Gateway® BP reaction
attB2
253 .. 277  =  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
T7 promoter
293 .. 311  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
293 .. 311  =  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
M13 rev
236 .. 252  =  17 bp
common sequencing primer, one of multiple similar variants
M13 rev
236 .. 252  =  17 bp
common sequencing primer, one of multiple similar variants
ORF:  379 .. 669  =  291 bp
ORF:  96 amino acids  =  10.5 kDa
ORF:  1144 .. 1803  =  660 bp
ORF:  219 amino acids  =  25.7 kDa
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