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Plasmid Files

pSC-A-amp/kan (linearized)

Linearized vector with modified 3'-U overhangs and bound topoisomerase, for efficient TA cloning of PCR products.

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pSC-A-amp kan (linearized) Sequence and MappSC-A-amp kan (linearized).dna
Map and Sequence File   
Sequence Author:  Agilent Technologies
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 Acc65I (4204) lac operator BspQI - SapI (3923) AflIII - PciI (3806) AlwNI (3397) BclI * (3046) Bsu36I (2982) AgeI (2932) BstBI (2858) DraIII (2408) SspI (2017) KpnI (4208) PspOMI (4210) EcoO109I (4211) ApaI (4214) AbsI - PaeR7I - PspXI - XhoI (4219) SalI (4225) AccI (4226) HincII (4227) BspDI - ClaI (4235) HindIII (4240) EcoRV (4248) EcoRI (4259) End (4270) Start (1) EcoRI (7) PstI (26) TspMI - XmaI (28) SmaI (30) BamHI (34) SpeI (40) XbaI (46) NotI (53) SacII (64) Eco53kI (69) SacI (71) RsrII (483) NcoI - StyI (566) SphI (601) MscI (920) KasI (999) NarI (1000) SfoI (1001) PluTI (1003) AhdI (1213) BsaI (1274) BpmI (1283) PvuI (1583) XmnI (1812) pSC-A-amp/kan 4269 bp
Acc65I  (4204)
1 site
G G T A C C C C A T G G
BspQI  (3923)
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  (3923)
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.
AflIII  (3806)
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  (3806)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
AlwNI  (3397)
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.
BclI  (3046)
1 site
T G A T C A A C T A G T
* Blocked by Dam methylation.
BclI is typically used at 50-55°C, but is 50% active at 37°C.
Bsu36I  (2982)
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.
AgeI  (2932)
1 site
A C C G G T T G G C C A

AgeI quickly loses activity at 37°C, but can be used at 25°C for
long incubations.
BstBI  (2858)
1 site
T T C G A A A A G C T T
DraIII  (2408)
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.
SspI  (2017)
1 site
A A T A T T T T A T A A
KpnI  (4208)
1 site
G G T A C C C C A T G G
PspOMI  (4210)
1 site
G G G C C C C C C G G G
EcoO109I  (4211)
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.
ApaI  (4214)
1 site
G G G C C C C C C G G G

ApaI can be used between 25°C and 37°C.
AbsI  (4219)
1 site
C C T C G A G G G G A G C T C C
PaeR7I  (4219)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
PspXI  (4219)
1 site
V C T C G A G B B G A G C T C V
XhoI  (4219)
1 site
C T C G A G G A G C T C
SalI  (4225)
1 site
G T C G A C C A G C T G
AccI  (4226)
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.
HincII  (4227)
1 site
G T Y R A C C A R Y T G
BspDI  (4235)
1 site
A T C G A T T A G C T A
ClaI  (4235)
1 site
A T C G A T T A G C T A
HindIII  (4240)
1 site
A A G C T T T T C G A A
EcoRV  (4248)
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.
EcoRI  (4259)
2 sites
G A A T T C C T T A A G
End  (4270)
0 sites
Start  (1)
0 sites
EcoRI  (7)
2 sites
G A A T T C C T T A A G
PstI  (26)
1 site
C T G C A G G A C G T C
TspMI  (28)
1 site
C C C G G G G G G C C C
XmaI  (28)
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  (30)
1 site
C C C G G G G G G C C C

SmaI can be used at 37°C for brief incubations.
BamHI  (34)
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.
SpeI  (40)
1 site
A C T A G T T G A T C A
XbaI  (46)
1 site
T C T A G A A G A T C T
NotI  (53)
1 site
G C G G C C G C C G C C G G C G
SacII  (64)
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.
Eco53kI  (69)
1 site
G A G C T C C T C G A G
SacI  (71)
1 site
G A G C T C C T C G A G
RsrII  (483)
1 site
C G G W C C G G C C W G G C

Efficient cleavage requires at least two copies of the RsrII
recognition sequence.
Sticky ends from different RsrII sites may not be compatible.
For full activity, add fresh DTT.
NcoI  (566)
1 site
C C A T G G G G T A C C
StyI  (566)
1 site
C C W W G G G G W W C C

Sticky ends from different StyI sites may not be compatible.
SphI  (601)
1 site
G C A T G C C G T A C G
MscI  (920)
1 site
T G G C C A A C C G G T
KasI  (999)
1 site
G G C G C C C C G C G G
NarI  (1000)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the NarI
recognition sequence.
SfoI  (1001)
1 site
G G C G C C C C G C G G
PluTI  (1003)
1 site
G G C G C C C C G C G G

Efficient cleavage requires at least two copies of the PluTI
recognition sequence.
AhdI  (1213)
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.
BsaI  (1274)
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.
BpmI  (1283)
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.
PvuI  (1583)
1 site
C G A T C G G C T A G C
XmnI  (1812)
1 site
G A A N N N N T T C C T T N N N N A A G
AmpR
1140 .. 2000  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 2:  
   1140 .. 1931  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
1140 .. 2000  =  861 bp
286 amino acids  =  31.6 kDa
   Segment 1:  signal sequence  
   1932 .. 2000  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
1140 .. 2000  =  861 bp
286 amino acids  =  31.6 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
NeoR/KanR
337 .. 1131  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from
Tn5
confers resistance to neomycin, kanamycin, and
G418 (Geneticin®)
NeoR/KanR
337 .. 1131  =  795 bp
264 amino acids  =  29.0 kDa
Product: aminoglycoside phosphotransferase from
Tn5
confers resistance to neomycin, kanamycin, and
G418 (Geneticin®)
ori
3162 .. 3750  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
3162 .. 3750  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
f1 ori
2175 .. 2533  =  359 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
f1 ori
2175 .. 2533  =  359 bp
f1 bacteriophage origin of replication; arrow
indicates direction of (+) strand synthesis
LacZα
2 .. 229  =  228 bp
75 amino acids  =  8.4 kDa
Product: LacZα fragment of β-galactosidase
LacZα
2 .. 229  =  228 bp
75 amino acids  =  8.4 kDa
Product: LacZα fragment of β-galactosidase
LacZα
4148 .. 4269  =  122 bp
40 amino acids  =  4.2 kDa
Product: LacZα fragment of β-galactosidase
LacZα
4148 .. 4269  =  122 bp
40 amino acids  =  4.2 kDa
Product: LacZα fragment of β-galactosidase
AmpR promoter
2001 .. 2105  =  105 bp
AmpR promoter
2001 .. 2105  =  105 bp
lox66/71
2565 .. 2598  =  34 bp
loxP double mutant with a very low affinity for Cre
recombinase
lox66/71
2565 .. 2598  =  34 bp
loxP double mutant with a very low affinity for Cre
recombinase
lac promoter
4074 .. 4104  =  31 bp
   Segment 1:  -35  
   4074 .. 4079  =  6 bp
promoter for the E. coli lac operon
lac promoter
4074 .. 4104  =  31 bp
   Segment 2:  
   4080 .. 4097  =  18 bp
promoter for the E. coli lac operon
lac promoter
4074 .. 4104  =  31 bp
   Segment 3:  -10  
   4098 .. 4104  =  7 bp
promoter for the E. coli lac operon
lac promoter
4074 .. 4104  =  31 bp
3 segments
promoter for the E. coli lac operon
lac operator
4112 .. 4128  =  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
4112 .. 4128  =  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).
MCS
2 .. 72  =  71 bp
multiple cloning site
MCS
2 .. 72  =  71 bp
multiple cloning site
MCS
4204 .. 4269  =  66 bp
multiple cloning site
MCS
4204 .. 4269  =  66 bp
multiple cloning site
T7 promoter
81 .. 99  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T7 promoter
81 .. 99  =  19 bp
promoter for bacteriophage T7 RNA polymerase
T3 promoter
4173 .. 4191  =  19 bp
promoter for bacteriophage T3 RNA polymerase
T3 promoter
4173 .. 4191  =  19 bp
promoter for bacteriophage T3 RNA polymerase
M13 fwd
109 .. 125  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 fwd
109 .. 125  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
4136 .. 4152  =  17 bp
common sequencing primer, one of multiple similar
variants
M13 rev
4136 .. 4152  =  17 bp
common sequencing primer, one of multiple similar
variants
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