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Plasmid Files

pPhi-Yellow-B

Vector for expressing PhiYFP in bacteria.

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pPhi-Yellow-B.dna
Map and Sequence File:    Download    Open   
Sequence Author:  Evrogen
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BbsI (4092) EcoO109I (4090) AatII (4036) ZraI (4034) PvuI (3484) FspI (3336) AseI (3286) BglI (3234) AhdI (3114) AlwNI (2637) AflIII - PciI (2221) BstAPI (2045) NdeI (2044) PaeR7I - XhoI (1) PsiI (49) MfeI (59) BseRI (115) BsaBI * (126) BamHI (127) SacII (216) SgrAI (274) AleI (304) SphI (384) BglII (617) BssHII (798) HindIII (831) NheI (951) BmtI (955) Bpu10I (976) PvuII (1103) BspEI (1199) PasI (1435) NcoI - StyI (1504) XbaI (1808) PfoI (1865) PflFI - Tth111I (1968) AccI (1993) BstZ17I (1994) pPhi-Yellow-B 4106 bp
BbsI  (4092)
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  (4090)
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  (4036)
1 site
G A C G T C C T G C A G
ZraI  (4034)
1 site
G A C G T C C T G C A G
PvuI  (3484)
1 site
C G A T C G G C T A G C
FspI  (3336)
1 site
T G C G C A A C G C G T
AseI  (3286)
1 site
A T T A A T T A A T T A
BglI  (3234)
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.
AhdI  (3114)
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  (2637)
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.
AflIII  (2221)
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  (2221)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
BstAPI  (2045)
1 site
G C A N N N N N T G C C G T N N N N N A C G

Sticky ends from different BstAPI sites may not be compatible.
NdeI  (2044)
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.
PaeR7I  (1)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
XhoI  (1)
1 site
C T C G A G G A G C T C
PsiI  (49)
1 site
T T A T A A A A T A T T
MfeI  (59)
1 site
C A A T T G G T T A A C
BseRI  (115)
1 site
G A G G A G ( N ) 8 N N C T C C T C ( N ) 8

Sticky ends from different BseRI sites may not be compatible.
BseRI quickly loses activity at 37°C.
Prolonged incubation with BseRI may lead to degradation of the DNA.
BsaBI  (126)
1 site
G A T N N N N A T C C T A N N N N T A G
* Blocked by Dam methylation.
BamHI  (127)
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.
SacII  (216)
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.
SgrAI  (274)
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.
AleI  (304)
1 site
C A C N N N N G T G G T G N N N N C A C
SphI  (384)
1 site
G C A T G C C G T A C G
BglII  (617)
1 site
A G A T C T T C T A G A
BssHII  (798)
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.
HindIII  (831)
1 site
A A G C T T T T C G A A
NheI  (951)
1 site
G C T A G C C G A T C G
BmtI  (955)
1 site
G C T A G C C G A T C G
Bpu10I  (976)
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.
PvuII  (1103)
1 site
C A G C T G G T C G A C
BspEI  (1199)
1 site
T C C G G A A G G C C T
PasI  (1435)
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.
NcoI  (1504)
1 site
C C A T G G G G T A C C
StyI  (1504)
1 site
C C W W G G G G W W C C

Sticky ends from different StyI sites may not be compatible.
XbaI  (1808)
1 site
T C T A G A A G A T C T
PfoI  (1865)
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.
PflFI  (1968)
1 site
G A C N N N G T C C T G N N N C A G

The 1-base overhangs produced by PflFI may be hard to ligate.
Sticky ends from different PflFI sites may not be compatible.
Tth111I  (1968)
1 site
G A C N N N G T C C T G N N N C A G

The 1-base overhangs produced by Tth111I may be hard to ligate.
Sticky ends from different Tth111I sites may not be compatible.
AccI  (1993)
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.
BstZ17I  (1994)
1 site
G T A T A C C A T A T G
AmpR
3041 .. 3901  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 2:  
   3041 .. 3832  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3041 .. 3901  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 1:  signal sequence  
   3833 .. 3901  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
AmpR
3041 .. 3901  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and related antibiotics
PhiYFP
130 .. 831  =  702 bp
233 amino acids  =  25.9 kDa
Product: Phialidium yellow fluorescent proteim
mammalian codon-optimized
PhiYFP
130 .. 831  =  702 bp
233 amino acids  =  25.9 kDa
Product: Phialidium yellow fluorescent proteim
mammalian codon-optimized
CmR
990 .. 1649  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
CmR
990 .. 1649  =  660 bp
219 amino acids  =  25.7 kDa
Product: chloramphenicol acetyltransferase
confers resistance to chloramphenicol
ori
2282 .. 2870  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
ori
2282 .. 2870  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin of replication
AmpR promoter
3902 .. 4006  =  105 bp
AmpR promoter
3902 .. 4006  =  105 bp
lambda t0 terminator
852 .. 946  =  95 bp
transcription terminator from phage lambda
lambda t0 terminator
852 .. 946  =  95 bp
transcription terminator from phage lambda
rrnB T1 terminator
1714 .. 1800  =  87 bp
transcription terminator T1 from the E. coli rrnB gene
rrnB T1 terminator
1714 .. 1800  =  87 bp
transcription terminator T1 from the E. coli rrnB gene
T5 promoter
10 .. 54  =  45 bp
   Segment 1:  
   10 .. 24  =  15 bp
bacteriophage T5 promoter for E. coli RNA polymerase, with embedded lac operator
T5 promoter
10 .. 54  =  45 bp
   Segment 2:  -35  
   25 .. 30  =  6 bp
bacteriophage T5 promoter for E. coli RNA polymerase, with embedded lac operator
T5 promoter
10 .. 54  =  45 bp
   Segment 3:  
   31 .. 47  =  17 bp
bacteriophage T5 promoter for E. coli RNA polymerase, with embedded lac operator
T5 promoter
10 .. 54  =  45 bp
   Segment 4:  -10  
   48 .. 54  =  7 bp
bacteriophage T5 promoter for E. coli RNA polymerase, with embedded lac operator
T5 promoter
10 .. 54  =  45 bp
4 segments
bacteriophage T5 promoter for E. coli RNA polymerase, with embedded lac operator
lac operator
62 .. 78  =  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
62 .. 78  =  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).
ATG
115 .. 117  =  3 bp
1 amino acid  =  149.2 Da
Product: start codon
ATG
115 .. 117  =  3 bp
1 amino acid  =  149.2 Da
Product: start codon
lac operator
30 .. 46  =  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
30 .. 46  =  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).
ORF:  115 .. 831  =  717 bp
ORF:  238 amino acids  =  26.4 kDa
ORF:  990 .. 1649  =  660 bp
ORF:  219 amino acids  =  25.7 kDa
ORF:  3171 .. 3437  =  267 bp
ORF:  88 amino acids  =  9.2 kDa
ORF:  3041 .. 3901  =  861 bp
ORF:  286 amino acids  =  31.5 kDa
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