pRHA-109

pBR322-derived high copy number plasmid encoding the rhaB promoter plus rhaR and rhaS genes, for rhamnose-inducible protein expression in E. coli.

Sequence Author: Xbrane Bioscience

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BbsI (4176) EcoO109I (4174) AatII (4120) ZraI (4118) XmnI (3797) ScaI (3678) PstI (3443) BsaI (3259) BmrI (3238) DrdI (2413) PciI (2305) BspQI - SapI (2189) NdeI (2128) KpnI (2126) Acc65I (2122) HindIII (29) PacI (37) PflMI (70) AvaI - BsoBI - TspMI - XmaI (90) SmaI (92) BstXI (240) BsgI (257) NheI (322) BmtI (326) PfoI (568) XcmI (979) BstEII - DraIII (999) BtgZI (1083) BbvCI (1145) AflII (1169) BmgBI (1281) BglII (1351) PvuII (1417) PaqCI (1434) AgeI - SgrAI (1619) MluI (1750) BsaAI (1877) SalI (2077) AccI (2078) XbaI (2083) BamHI (2089) pRHA-109 4193 bp
BbsI  (4176)
1 site
G A A G A C N N C T T C T G N N ( N ) 4

Sticky ends from different BbsI sites may not be compatible.
BbsI gradually loses activity when stored at -20°C.
EcoO109I  (4174)
1 site
R G G N C C Y Y C C N G G R

Sticky ends from different EcoO109I sites may not be compatible.
AatII  (4120)
1 site
G A C G T C C T G C A G
ZraI  (4118)
1 site
G A C G T C C T G C A G
XmnI  (3797)
1 site
G A A N N N N T T C C T T N N N N A A G
ScaI  (3678)
1 site
A G T A C T T C A T G A
PstI  (3443)
1 site
C T G C A G G A C G T C
BsaI  (3259)
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.
BmrI  (3238)
1 site
A C T G G G ( N ) 4 N T G A C C C ( N ) 4

The 1-base overhangs produced by BmrI may be hard to ligate.
Sticky ends from different BmrI sites may not be compatible.
Unlike most restriction enzymes, BmrI can cleave DNA in the absence of magnesium.
DrdI  (2413)
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.
PciI  (2305)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
BspQI  (2189)
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  (2189)
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.
NdeI  (2128)
1 site
C A T A T G G T A T A C

Prolonged incubation with NdeI may lead to removal of additional nucleotides.
KpnI  (2126)
1 site
G G T A C C C C A T G G
Acc65I  (2122)
1 site
G G T A C C C C A T G G
HindIII  (29)
1 site
A A G C T T T T C G A A
PacI  (37)
1 site
T T A A T T A A A A T T A A T T
PflMI  (70)
1 site
C C A N N N N N T G G G G T N N N N N A C C

Sticky ends from different PflMI sites may not be compatible.
AvaI  (90)
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  (90)
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.
TspMI  (90)
1 site
C C C G G G G G G C C C
XmaI  (90)
1 site
C C C G G G G G G C C C

Cleavage may be enhanced when more than one copy of the XmaI recognition sequence is present.
SmaI  (92)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
BstXI  (240)
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.
BsgI  (257)
1 site
G T G C A G ( N ) 14 N N C A C G T C ( N ) 14

Efficient cleavage requires at least two copies of the BsgI recognition sequence.
Sticky ends from different BsgI sites may not be compatible.
For full activity, add fresh S-adenosylmethionine (SAM).
NheI  (322)
1 site
G C T A G C C G A T C G
BmtI  (326)
1 site
G C T A G C C G A T C G
PfoI  (568)
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.
XcmI  (979)
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.
BstEII  (999)
1 site
G G T N A C C C C A N T G G

Sticky ends from different BstEII sites may not be compatible.
BstEII is typically used at 60°C, but is 50% active at 37°C.
DraIII  (999)
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.
BtgZI  (1083)
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.
BbvCI  (1145)
1 site
C C T C A G C G G A G T C G
AflII  (1169)
1 site
C T T A A G G A A T T C
BmgBI  (1281)
1 site
C A C G T C G T G C A G

This recognition sequence is asymmetric, so ligating blunt ends generated by BmgBI will not always regenerate a BmgBI site.
BglII  (1351)
1 site
A G A T C T T C T A G A
PvuII  (1417)
1 site
C A G C T G G T C G A C
PaqCI  (1434)
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 PaqCI recognition sequence.
Sticky ends from different PaqCI sites may not be compatible.
Cleavage can be improved with PaqCI Activator.
AgeI  (1619)
1 site
A C C G G T T G G C C A
SgrAI  (1619)
1 site
C R C C G G Y G G Y G G C C R C

Efficient cleavage requires at least two copies of the SgrAI recognition sequence.
MluI  (1750)
1 site
A C G C G T T G C G C A
BsaAI  (1877)
1 site
Y A C G T R R T G C A Y
SalI  (2077)
1 site
G T C G A C C A G C T G
AccI  (2078)
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.
XbaI  (2083)
1 site
T C T A G A A G A T C T
BamHI  (2089)
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.
AmpR
3125 .. 3985  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
   Segment 2:  
   3125 .. 3916  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3125 .. 3985  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
   Segment 1:  signal sequence  
   3917 .. 3985  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3125 .. 3985  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
rhaR
37 .. 885  =  849 bp
282 amino acids  =  32.3 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: transcriptional activator of rhaSR
Function: regulator; Degradation of small molecules: Carbon compounds
positive regulator for rhaRS operon
rhaR
37 .. 885  =  849 bp
282 amino acids  =  32.3 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: transcriptional activator of rhaSR
Function: regulator; Degradation of small molecules: Carbon compounds
positive regulator for rhaRS operon
rhaS
959 .. 1795  =  837 bp
278 amino acids  =  32.3 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: transcriptional activator of rhaBAD and rhaT
Function: regulator; Degradation of small molecules: Carbon compounds
positive regulator for rhaBAD operon
rhaS
959 .. 1795  =  837 bp
278 amino acids  =  32.3 kDa
Genetic Code:  Bacterial, Archaeal and Plant Plastid
Product: transcriptional activator of rhaBAD and rhaT
Function: regulator; Degradation of small molecules: Carbon compounds
positive regulator for rhaBAD operon
ori
2366 .. 2954  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
2366 .. 2954  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
rhaB promoter
1941 .. 2059  =  119 bp
promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)
rhaB promoter
1941 .. 2059  =  119 bp
promoter of the E. coli rhaBAD operon, conferring tight induction with L-rhamnose and repression with D-glucose in the presence of RhaR and RhaS (Giacalone et al., 2006)
AmpR promoter
3986 .. 4090  =  105 bp
AmpR promoter
3986 .. 4090  =  105 bp
MCS
2077 .. 2132  =  56 bp
multiple cloning site
MCS
2077 .. 2132  =  56 bp
multiple cloning site
ORF:  169 .. 534  =  366 bp
ORF:  121 amino acids  =  14.0 kDa
ORF:  3255 .. 3521  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  959 .. 1795  =  837 bp
ORF:  278 amino acids  =  32.3 kDa
ORF:  3125 .. 3985  =  861 bp
ORF:  286 amino acids  =  31.5 kDa
ORF:  37 .. 975  =  939 bp
ORF:  312 amino acids  =  35.7 kDa
ORF:  1231 .. 1476  =  246 bp
ORF:  81 amino acids  =  9.4 kDa
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