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Plasmid Files

pSIREN-RetroQ

Linearized retroviral vector for inserting an shRNA cassette that will be co-expressed with a puromycin resistance gene.

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pSIREN-RetroQ.dna
Map and Sequence File:    Download    Open   
Sequence Author:  Clontech (TaKaRa)
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< BamHI > (6438) BglII (6180) U6 forward sequencing primer (6103 .. 6130) AfeI (5692) ApoI (5641) PshAI (5280) AscI (5146) SnaBI (4888) BtgZI (4882) SspI (4259) XmnI (4054) ScaI (3935) PvuI (3825) FspI (3677) < EcoRI > (0) AgeI (120) BlpI (283) BsmI (441) BfuAI - BspMI (519) BsiWI (586) RsrII (646) SacII (744) DraIII (1101) PaeR7I - XhoI (1191) EcoRV (1198) PvuII (1241) NheI (1340) BmtI (1344) SalI (1433) AccI (1434) SfiI (2268) AvrII (2315) BspQI - SapI (2446) AflIII - PciI (2562) pSIREN-RetroQ 6438 bp
End  (6438)
0 sites
BglII  (6180)
1 site
A G A T C T T C T A G A
AfeI  (5692)
1 site
A G C G C T T C G C G A
ApoI  (5641)
1 site
R A A T T Y Y T T A A R

ApoI is typically used at 50°C, but is 50% active at 37°C.
PshAI  (5280)
1 site
G A C N N N N G T C C T G N N N N C A G

PshAI quickly loses activity at 37°C, but can be used at 25°C for long incubations.
AscI  (5146)
1 site
G G C G C G C C C C G C G C G G
SnaBI  (4888)
1 site
T A C G T A A T G C A T
BtgZI  (4882)
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.
SspI  (4259)
1 site
A A T A T T T T A T A A
XmnI  (4054)
1 site
G A A N N N N T T C C T T N N N N A A G
ScaI  (3935)
1 site
A G T A C T T C A T G A
PvuI  (3825)
1 site
C G A T C G G C T A G C
FspI  (3677)
1 site
T G C G C A A C G C G T
Start  (0)
0 sites
AgeI  (120)
1 site
A C C G G T T G G C C A
BlpI  (283)
1 site
G C T N A G C C G A N T C G

Sticky ends from different BlpI sites may not be compatible.
BsmI  (441)
1 site
G A A T G C N C T T A C G N

Sticky ends from different BsmI sites may not be compatible.
BfuAI  (519)
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  (519)
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.
BsiWI  (586)
1 site
C G T A C G G C A T G C

BsiWI is typically used at 55°C, but is 50% active at 37°C.
RsrII  (646)
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.
SacII  (744)
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.
DraIII  (1101)
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.
PaeR7I  (1191)
1 site
C T C G A G G A G C T C

PaeR7I does not recognize the sequence CTCTCGAG.
XhoI  (1191)
1 site
C T C G A G G A G C T C
EcoRV  (1198)
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.
PvuII  (1241)
1 site
C A G C T G G T C G A C
NheI  (1340)
1 site
G C T A G C C G A T C G
BmtI  (1344)
1 site
G C T A G C C G A T C G
SalI  (1433)
1 site
G T C G A C C A G C T G
AccI  (1434)
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.
SfiI  (2268)
1 site
G G C C N N N N N G G C C C C G G N N N N N C C G G

Efficient cleavage requires at least two copies of the SfiI recognition sequence.
Sticky ends from different SfiI sites may not be compatible.
AvrII  (2315)
1 site
C C T A G G G G A T C C
BspQI  (2446)
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  (2446)
1 site
G C T C T T C N C G A G A A G N N N N