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Plasmid Files

pRetro-Lib

Retroviral vector for delivery and expression of libraries or individual genes.

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pRetro-Lib Sequence and MappRetro-Lib.dna
Map and Sequence File   
Sequence Author:  Clontech
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 SacII (4871) SspI (4529) XmnI (4324) ScaI (4205) PvuI (4095) FspI (3947) AseI (3897) BsrFI (3805) PspFI (3140) BseYI (3136) AflIII - PciI (2832) BspQI - SapI (2716) NdeI (2655) BstZ17I (2605) AccI (2604) AscI (443) PshAI (577) SpeI (726) AfeI (989) BstEII (1153) SexAI * (1281) BsrGI (1348) 5' sequencing primer (1444 .. 1463) EcoRI (1470) SfiI (1487) SbfI (1496) BamHI (1497) HpaI (1564) PsiI (1584) Stuffer fragment BamHI (1695) SfiI (1708) BspDI - ClaI (1719) 3' sequencing primer (1760 .. 1785) XbaI (2060) BsaAI (2586) pRetro-Lib 4891 bp
SacII  (4871)
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.
SspI  (4529)
1 site
A A T A T T T T A T A A
XmnI  (4324)
1 site
G A A N N N N T T C C T T N N N N A A G
ScaI  (4205)
1 site
A G T A C T T C A T G A
PvuI  (4095)
1 site
C G A T C G G C T A G C
FspI  (3947)
1 site
T G C G C A A C G C G T
AseI  (3897)
1 site
A T T A A T T A A T T A
BsrFI  (3805)
1 site
R C C G G Y Y G G C C R

Efficient cleavage requires at least two copies of the BsrFI
recognition sequence.
After cleavage, BsrFI can remain bound to DNA and alter its
electrophoretic mobility.
PspFI  (3140)
1 site
C C C A G C G G G T C G
BseYI  (3136)
1 site
C C C A G C G G G T C G

After cleavage, BseYI can remain bound to DNA and alter its
electrophoretic mobility.
AflIII  (2832)
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  (2832)
1 site
A C A T G T T G T A C A

PciI is inhibited by nonionic detergents.
BspQI  (2716)
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  (2716)
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  (2655)
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.
BstZ17I  (2605)
1 site
G T A T A C C A T A T G
AccI  (2604)
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.
AscI  (443)
1 site
G G C G C G C C C C G C G C G G
PshAI  (577)
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.
SpeI  (726)
1 site
A C T A G T T G A T C A
AfeI  (989)
1 site
A G C G C T T C G C G A
BstEII  (1153)
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.
SexAI  (1281)
1 site
A C C W G G T T G G W C C A
* Blocked by Dcm methylation.
Sticky ends from different SexAI sites may not be compatible.
BsrGI  (1348)
1 site
T G T A C A A C A T G T

BsrGI is typically used at 37°C, but is even more active at 60°C.
EcoRI  (1470)
1 site
G A A T T C C T T A A G
SfiI  (1487)
2 sites
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.
SbfI  (1496)
1 site
C C T G C A G G G G A C G T C C
BamHI  (1497)
2 sites
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.
HpaI  (1564)
1 site
G T T A A C C A A T T G
PsiI  (1584)
1 site
T T A T A A A A T A T T
BamHI  (1695)
2 sites
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.
SfiI  (1708)
2 sites
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.
BspDI  (1719)
1 site
A T C G A T T A G C T A
ClaI  (1719)
1 site
A T C G A T T A G C T A
XbaI  (2060)
1 site
T C T A G A A G A T C T
BsaAI  (2586)
1 site
Y A C G T R R T G C A Y
5' sequencing primer
20-mer  /  55% GC
1 binding site
1444 .. 1463  =  20 annealed bases
Tm  =  56°C
3' sequencing primer
26-mer  /  54% GC
1 binding site
1760 .. 1785  =  26 annealed bases
Tm  =  64°C
AmpR
3652 .. 4512  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 2:  
   3652 .. 4443  =  792 bp
   263 amino acids  =  28.9 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
3652 .. 4512  =  861 bp
286 amino acids  =  31.5 kDa
   Segment 1:  signal sequence  
   4444 .. 4512  =  69 bp
   23 amino acids  =  2.6 kDa
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
AmpR
3652 .. 4512  =  861 bp
286 amino acids  =  31.5 kDa
2 segments
Product: β-lactamase
confers resistance to ampicillin, carbenicillin, and
related antibiotics
3' LTR
1763 .. 2356  =  594 bp
long terminal repeat from Moloney murine leukemia
virus
3' LTR
1763 .. 2356  =  594 bp
long terminal repeat from Moloney murine leukemia
virus
5' LTR
1 .. 589  =  589 bp
long terminal repeat from Moloney murine leukemia
virus
5' LTR
1 .. 589  =  589 bp
long terminal repeat from Moloney murine leukemia
virus
ori
2893 .. 3481  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
ori
2893 .. 3481  =  589 bp
high-copy-number ColE1/pMB1/pBR322/pUC origin
of replication
gag (truncated)
1052 .. 1468  =  417 bp
truncated MMLV gag gene lacking the start codon
gag (truncated)
1052 .. 1468  =  417 bp
truncated MMLV gag gene lacking the start codon
MMLV Ψ
652 .. 851  =  200 bp
packaging signal of Moloney murine leukemia virus
(MMLV)
MMLV Ψ
652 .. 851  =  200 bp
packaging signal of Moloney murine leukemia virus
(MMLV)
Stuffer fragment
1503 .. 1694  =  192 bp
Stuffer fragment
1503 .. 1694  =  192 bp
AmpR promoter
4513 .. 4617  =  105 bp
AmpR promoter
4513 .. 4617  =  105 bp
MCS A
1470 .. 1502  =  33 bp
multiple cloning site
MCS A
1470 .. 1502  =  33 bp
multiple cloning site
MCS B
1695 .. 1723  =  29 bp
multiple cloning site
MCS B
1695 .. 1723  =  29 bp
multiple cloning site
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