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Plasmid Files

pHRed

Red fluorescent protein that serves as a ratiometric pH sensor.

 
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pHRed.dna
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600 400 200 pHRed End (669) EcoP15I (630) BsiEI (579) NspI - SphI (558) BsiHKAI (529) BanII (425) StyI (411) BmrI (385) AclI (353) MmeI (338) HaeII (276) AfeI (274) BmeT110I (218) AvaI - BsoBI (217) BbvCI - Bpu10I (179) EcoRV (168) HincII - HpaI (57) BanI (49) Start (0) pHRed 669 bp
End  (669)
0 sites
EcoP15I  (630)
1 site
C A G C A G ( N ) 25 G T C G T C ( N ) 25 N N

Efficient cleavage requires two inversely oriented copies of the EcoP15I recognition sequence.
Sticky ends from different EcoP15I sites may not be compatible.
EcoP15I requires ATP for activity.
BsiEI  (579)
1 site
C G R Y C G G C Y R G C

Sticky ends from different BsiEI sites may not be compatible.
NspI  (558)
1 site
R C A T G Y Y G T A C R
SphI  (558)
1 site
G C A T G C C G T A C G
BsiHKAI  (529)
1 site
G W G C W C C W C G W G

Sticky ends from different BsiHKAI sites may not be compatible.
BanII  (425)
1 site
G R G C Y C C Y C G R G

Sticky ends from different BanII sites may not be compatible.
StyI  (411)
1 site
C C W W G G G G W W C C

Sticky ends from different StyI sites may not be compatible.
BmrI  (385)
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.
AclI  (353)
1 site
A A C G T T T T G C A A
MmeI  (338)
1 site
T C C R A C ( N ) 18 N N A G G Y T G ( N ) 18

Efficient cleavage requires at least two copies of the MmeI recognition sequence.
Sticky ends from different MmeI sites may not be compatible.
For full activity, add fresh S-adenosylmethionine (SAM).
HaeII  (276)
1 site
R G C G C Y Y C G C G R
AfeI  (274)
1 site
A G C G C T T C G C G A
BmeT110I  (218)
1 site
C Y C G R G G R G C Y C
AvaI  (217)
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  (217)
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.
BbvCI  (179)
1 site
C C T C A G C G G A G T C G
Bpu10I  (179)
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.
EcoRV  (168)
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.
HincII  (57)
1 site
G T Y R A C C A R Y T G
HpaI  (57)
1 site
G T T A A C C A A T T G
BanI  (49)
1 site
G G Y R C C C C R Y G G

Sticky ends from different BanI sites may not be compatible.
Start  (0)
0 sites
pHRed
1 .. 669  =  669 bp
222 amino acids  =  25.1 kDa
   Segment 1:  
   1 .. 3  =  3 bp
   1 amino acid  =  149.2 Da
Product: red fluorescent protein that serves as a ratiometric pH sensor (Tantama et al., 2011)
contains an A213S mutation relative to the parental mKeima protein
pHRed
1 .. 669  =  669 bp
222 amino acids  =  25.1 kDa
   Segment 2:  1a  
   4 .. 6  =  3 bp
   1 amino acid  =  117.2 Da
Product: red fluorescent protein that serves as a ratiometric pH sensor (Tantama et al., 2011)
contains an A213S mutation relative to the parental mKeima protein
pHRed
1 .. 669  =  669 bp
222 amino acids  =  25.1 kDa
   Segment 3:  
   7 .. 669  =  663 bp
   220 amino acids  =  24.8 kDa
Product: red fluorescent protein that serves as a ratiometric pH sensor (Tantama et al., 2011)
contains an A213S mutation relative to the parental mKeima protein
pHRed
1 .. 669  =  669 bp
222 amino acids  =  25.1 kDa
3 segments
Product: red fluorescent protein that serves as a ratiometric pH sensor (Tantama et al., 2011)
contains an A213S mutation relative to the parental mKeima protein
ORF:  1 .. 669  =  669 bp
ORF:  222 amino acids  =  25.1 kDa
ORF:  1 .. 669  =  669 bp
ORF:  223 amino acids  =  23.7 kDa  (no start codon)
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