Addgene pLKO.1 Puro shRNA PIK3C2A KD5 Sequencing Result - Sequence Analyzer Skip to main content
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Sequence Analyzer: pLKO.1 Puro shRNA PIK3C2A KD5 Sequencing Result


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AleI (7001) BbvCI - Bpu10I (6848) MfeI (6613) EcoNI (6594) NruI * (6261) SphI (5745) T3 promoter T3 (5607 .. 5627) M13 rev M13 Reverse (5572 .. 5588) lac operator M13/pUC Reverse (5553 .. 5575) lac promoter CAP binding site L4440 (5340 .. 5357) AflIII - PciI (5242) pBR322ori-F (5087 .. 5106) PspFI (4942) BseYI (4938) ScaI (3873) Amp-R (3785 .. 3804) KflI - PpuMI (274) BspDI * - ClaI * (363) hU6-F (403 .. 423) LKO.1 5' (574 .. 593) NdeI (581) EcoRI (707) XcmI (942) SpeI (1170) BlpI (1250) AscI (1259) hPGK-F (1343 .. 1361) HincII (1397) BamHI (1427) Puro-R (1446 .. 1465) PflFI - Tth111I (1488) BsiWI (1502) RsrII (1562) BstEII (1580) Puro-F (1942 .. 1962) CsiI - SexAI * (2013) NsiI (2099) Acc65I (2102) KpnI (2106) BbsI (2204) SV40pA-R (2515 .. 2534) EBV-rev (2569 .. 2588) NcoI (2680) SfiI (2726) AvrII (2773) T7 promoter T7 (2794 .. 2813) M13 fwd M13 Forward (2823 .. 2840) M13/pUC Forward (2832 .. 2854) F1ori-R (3068 .. 3087) NgoMIV (3106) NaeI (3108) F1ori-F (3278 .. 3299) pLKO.1 Puro shRNA PIK3C2A KD5 7084 bp

Sequence View

60 INNYTSLIHSLIEESQNQQE a t t a a c a a t t a c a c a a g c t t a a t a c a c t c c t t a a t t g a a g a a t c g c a a a a c c a g c a a g a a t a a t t g t t a a t g t g t t c g a a t t a t g t g a g g a a t t a a c t t c t t a g c g t t t t g g t c g t t c t t

120 1 5 10 15 KNEQELLELDKWASL WNWFN gp41 peptide KNEQELLELDKWASLWNWFN a a g a a t g a a c a a g a a t t a t t g g a a t t a g a t a a a t g g g c a a g t t t g t g g a a t t g g t t t a a c t t c t t a c t t g t t c t t a a t a a c c t t a a t c t a t t t a c c c g t t c a a a c a c c t t a a c c a a a t t g

180 (in frame with gp41 peptide) ITNWLWYIKLFIMIVGGLVG ITNWLWYIKLFIMIVGGLVG a t a a c a a a t t g g c t g t g g t a t a t a a a a t t a t t c a t a a t g a t a g t a g g a g g c t t g g t a g g t t a t t g t t t a a c c g a c a c c a t a t a t t t t a a t a a g t a t t a c t a t c a t c c t c c g a a c c a t c c a

240 (in frame with gp41 peptide) LRIVFAVLSIVNRVRQGYSP LRIVFAVLSIVNRVRQGYSP t t a a g a a t a g t t t t t g c t g t a c t t t c t a t a g t g a a t a g a g t t a g g c a g g g a t a t t c a c c a a a t t c t t a t c a a a a a c g a c a t g a a a g a t a t c a c t t a t c t c a a t c c g t c c c t a t a a g t g g t

PpuMIKflI 300 (in frame with gp41 peptide) LSFQTHLPTPRGPDRPEGIE LSFQTHLPTPRGPDRPEGIE t t a t c g t t t c a g a c c c a c c t c c c a a c c c c g a g g g g a c c c g a c a g g c c c g a a g g a a t a g a a a a t a g c a a a g t c t g g g t g g a g g g t t g g g g c t c c c c t g g g c t g t c c g g g c t t c c t t a t c t t

360 (in frame with gp41 peptide) EEGGERDRDRSIRLVNGSRR EEGGERDRDRSIRLVNGSRR g a a g a a g g t g g a g a g a g a g a c a g a g a c a g a t c c a t t c g a t t a g t g a a c g g a t c t c g a c g g c t t c t t c c a c c t c t c t c t c t g t c t c t g t c t a g g t a a g c t a a t c a c t t g c c t a g a g c t g c c

BspDI*ClaI* 420 (in frame with gp41 peptide) YRSRD* U6 promoter G A G G G C C T A T T T C C C A T G hU6-F YRSRD* t a t c g a t c a c g a g a c t a g c c t c g a g c g g c c g c c c c c t t c a c c g a g g g c c t a t t t c c c a t g a t a g c t a g t g c t c t g a t c g g a g c t c g c c g g c g g g g g a a g t g g c t c c c g g a t a a a g g g t a c

480 U6 promoter A T T hU6-F a t t c c t t c a t a t t t g c a t a t a c g a t a c a a g g c t g t t a g a g a g a t a a t t g g a a t t a a t t t g t a a g g a a g t a t a a a c g t a t a t g c t a t g t t c c g a c a a t c t c t c t a t t a a c c t t a a t t a a a c

540 U6 promoter a c t g t a a a c a c a a a g a t a t t a g t a c a a a a t a c g t g a c g t a g a a a g t a a t a a t t t c t t g g g t g a c a t t t g t g t t t c t a t a a t c a t g t t t t a t g c a c t g c a t c t t t c a t t a t t a a a g a a c c c

NdeI 600 U6 promoter G A C T A T C A T A T G C T T A C C G T LKO.1 5' t a g t t t g c a g t t t t a a a a t t a t g t t t t a a a a t g g a c t a t c a t a t g c t t a c c g t a a c t t g a a t c a a a c g t c a a a a t t t t a a t a c a a a a t t t t a c c t g a t a g t a t a c g a a t g g c a t t g a a c t

660 U6 promoter a a g t a t t t c g a t t t c t t g g c t t t a t a t a t c t t g t g g a a a g g a c g a a a c a c c g g g c t c a g a t t c a t a a a g c t a a a g a a c c g a a a t a t a t a g a a c a c c t t t c c t g c t t t g t g g c c c g a g t c t

EcoRI 720 t a t c c a g c a a t a a t c t c g a g a t t a t t g c t g g a t a t c t g a g c t t t t t g a a t t c t c g a c c t c a t a g g t c g t t a t t a g a g c t c t a a t a a c g a c c t a t a g a c t c g a a a a a c t t a a g a g c t g g a g

780 cPPT/CTS g a g a c a a a t g g c a g t a t t c a t c c a c a a t t t t a a a a g a a a a g g g g g g a t t g g g g g g t a c a g c t c t g t t t a c c g t c a t a a g t a g g t g t t a a a a t t t t c t t t t c c c c c c t a a c c c c c c a t g t c

840 cPPT/CTS *LF t g c a g g g g a a a g a a t a g t a g a c a t a a t a g c a a c a g a c a t a c a a a c t a a a g a a t t a c a a a a a c g t c c c c t t t c t t a t c a t c t g t a t t a t c g t t g t c t g t a t g t t t g a t t t c t t a a t g t t t t

900 cPPT/CTS LNCFNLIKPNIVPVASIWKP a c a a a t t a c a a a a a t t c a a a a t t t t c g g g t t t a t t a c a g g g a c a g c a g a g a t c c a c t t t g t g t t t a a t g t t t t t a a g t t t t a a a a g c c c a a a t a a t g t c c c t g t c g t c t c t a g g t g a a a c

XcmI 960 hPGK promoter RPELPNPNRRKWPLGPNACP g c c g c g g c t c g a g g g g g t t g g g g t t g c g c c t t t t c c a a g g c a g c c c t g g g t t t g c g c a g g c g g c g c c g a g c t c c c c c a a c c c c a a c g c g g a a a a g g t t c c g t c g g g a c c c a a a c g c g t c c

1020 hPGK promoter RPQEPRPEPFRLPASGPDRV g a c g c g g c t g c t c t g g g c g t g g t t c c g g g a a a c g c a g c g g c g c c g a c c c t g g g t c t c g c a c t g c g c c g a c g a g a c c c g c a c c a a g g c c c t t t g c g t c g c c g c g g c t g g g a c c c a g a g c g t

1080 hPGK promoter NKVDTRLTVRIKAAVRTPGG c a t t c t t c a c g t c c g t t c g c a g c g t c a c c c g g a t c t t c g c c g c t a c c c t t g t g g g c c c c c g t a a g a a g t g c a g g c a a g c g t c g c a g t g g g c c t a g a a g c g g c g a t g g g a a c a c c c g g g g g

1140 hPGK promoter AVSGAGGRLRSPEKRNAAHR c g g c g a c g c t t c c t g c t c c g c c c c t a a g t c g g g a a g g t t c c t t g c g g t t c g c g g c g t g c c g c c g c t g c g a a g g a c g a g g c g g g g a t t c a g c c c t t c c a a g g a a c g c c a a g c g c c g c a c g g

SpeI 1200 hPGK promoter VHCVSAARRVLVRASPCRWP g g a c g t g a c a a a c g g a a g c c g c a c g t c t c a c t a g t a c c c t c g c a g a c g g a c a g c g c c a g g c c t g c a c t g t t t g c c t t c g g c g t g c a g a g t g a t c a t g g g a g c g t c t g c c t g t c g c g g t c c

AscIBlpI 1260 hPGK promoter MAARRPRWAVANSGCSAG *CP AIAARRGRHATALLPQEAPR g a g c a a t g g c a g c g c g c c g a c c g c g a t g g g c t g t g g c c a a t a g c g g c t g c t c a g c a g g g c c t c g t t a c c g t c g c g c g g c t g g c g c t a c c c g a c a c c g g t t a t c g c c g a c g a g t c g t c c c g

1320 hPGK promoter RAESSGREGAVREAGCGAVV AGLAAAPFPRHPLRPTPRYH ASLLPRSPATRSAPHPATTH g c g c c g a g a g c a g c g g c c g g g a a g g g g c g g t g c g g g a g g c g g g g t g t g g g g c g g t a g t g t c g c g g c t c t c g t c g c c g g c c c t t c c c c g c c a c g c c c t c c g c c c c a c a c c c c g c c a t c a c a

1380 hPGK promoter G T G T T C C G C A T T C T G C A A G hPGK-F WALFLPARCSAFCKPPERTS PGQEQGRPTGCEALRRLARR ARNRGARHEANQLGGSRVDA g g g c c c t g t t c c t g c c c g c g c g g t g t t c c g c a t t c t g c a a g c c t c c g g a g c g c a c g t c g g c c c g g g a c a a g g a c g g g c g c g c c a c a a g g c g t a a g a c g t t c g g a g g c c t c g c g t g c a g c c

BamHIHincII 1440 hPGK promoter AVGSLVDRITDLSPQGDPPE CDAGENVSDGVERGLPIWRL TPERTSRIVSREGWPSGGSS c a g t c g g c t c c c t c g t t g a c c g a a t c a c c g a c c t c t c t c c c c a g g g g g a t c c a c c g g a g c g t c a g c c g a g g g a g c a a c t g g c t t a g t g g c t g g a g a g a g g g g t c c c c c t a g g t g g c c t c g

Tth111IPflFI 1500 1 5 10 15 MTEYKPTVRLATRDDVPR PuroR T A C T G G C T C A T G T T C G G G T G Puro-R LTMTEYKPTVRLATRDDVPR KGHGLVLGRHAEGGAVVDGP VM t t a c c a t g a c c g a g t a c a a g c c c a c g g t g c g c c t c g c c a c c c g c g a c g a c g t c c c c a g g g a a t g g t a c t g g c t c a t g t t c g g g t g c c a c g c g g a g c g g t g g g c g c t g c t g c a g g g g t c c c

BsiWI 1560 20 25 30 35 AVRTLAAAFADYPATRHTVD PuroR AVRTLAAAFADYPATRHTVD GYAGEGGREGVVGGRAVGDI c c g t a c g c a c c c t c g c c g c c g c g t t c g c c g a c t a c c c c g c c a c g c g c c a c a c c g t c g a t c g g c a t g c g t g g g a g c g g c g g c g c a a g c g g c t g a t g g g g c g g t g c g c g g t g t g g c a g c t a g

BstEIIRsrII 1620 40 45 50 55 PDRHIERVTELQELFLTRVG PuroR PDRHIERVTELQELFLTRVG RVAVDLPDGLQLFEEERADP c g g a c c g c c a c a t c g a g c g g g t c a c c g a g c t g c a a g a a c t c t t c c t c a c g c g c g t c g g g c g c c t g g c g g t g t a g c t c g c c c a g t g g c t c g a c g t t c t t g a g a a g g a g t g c g c g c a g c c c g

1680 60 65 70 75 LDIGKVWVADDGAAVAVWTT PuroR LDIGKVWVADDGAAVAVWTT EVDALHPDRVVAGRHRDPGR t c g a c a t c g g c a a g g t g t g g g t c g c g g a c g a c g g c g c c g c g g t g g c g g t c t g g a c c a c g c a g c t g t a g c c g t t c c a c a c c c a g c g c c t g c t g c c g c g g c g c c a c c g c c a g a c c t g g t g c g

1740 80 85 90 95 PESVEAGAVFAEIGPRMAEL PuroR PESVEAGAVFAEIGPRMAEL RLADFRPRHEGLDARAHGLQ c g g a g a g c g t c g a a g c g g g g g c g g t g t t c g c c g a g a t c g g c c c g c g c a t g g c c g a g t t g a g c c t c t c g c a g c t t c g c c c c c g c c a c a a g c g g c t c t a g c c g g g c g c g t a c c g g c t c a a c t

1800 100 105 110 115 SGSRLAAQQQMEGLLAPHRP PuroR SGSRLAAQQQMEGLLAPHRP ATGPQGRLLLHFAEQRRVPG g c g g t t c c c g g c t g g c c g c g c a g c a a c a g a t g g a a g g c c t c c t g g c g c c g c a c c g g c c c a c g c c a a g g g c c g a c c g g c g c g t c g t t g t c t a c c t t c c g g a g g a c c g c g g c g t g g c c g g g t

1860 120 125 130 135 KEPAWFLATVGVSPDHQGKG PuroR KEPAWFLATVGVSPDHQGKG LLGRPEQGGDADRGVVLALT a g g a g c c c g c g t g g t t c c t g g c c a c c g t c g g c g t c t c g c c c g a c c a c c a g g g c a a g g g t c t c c t c g g g c g c a c c a a g g a c c g g t g g c a g c c g c a g a g c g g g c t g g t g g t c c c g t t c c c a g

1920 140 145 150 155 LGSAVVLPGVEAAERAGVPA PuroR LGSAVVLPGVEAAERAGVPA QAAGDHEGSHLRGLAGPHGG t g g g c a g c g c c g t c g t g c t c c c c g g a g t g g a g g c g g c c g a g c g c g c c g g g g t g c c c g c c t a c c c g t c g c g g c a g c a c g a g g g g c c t c a c c t c c g c c g g c t c g c g c g g c c c c a c g g g c g g a

1980 160 165 170 175 FLETSAPRNLPFYERLGFTV PuroR G C A A C C T C C C C T T C T A C G A G C Puro-F FLETSAPRNLPFYERLGFTV EQLGGRGAVEGEVLPEAEGD t c c t g g a g a c c t c c g c g c c c c g c a a c c t c c c c t t c t a c g a g c g g c t c g g c t t c a c c g t c a a g g a c c t c t g g a g g c g c g g g g c g t t g g a g g g g a a g a t g c t c g c c g a g c c g a a g t g g c a g t

SexAI*CsiI 2040 180 185 190 195 TADVEVPEGPRTWCMTRKPG PuroR TADVEVPEGPRTWCMTRKPG GGVDLHGFSRAGPAHGALGT c c g c c g a c g t c g a g g t g c c c g a a g g a c c g c g c a c c t g g t g c a t g a c c c g c a a g c c c g g t g g g c g g c t g c a g c t c c a c g g g c t t c c t g g c g c g t g g a c c a c g t a c t g g g c g t t c g g g c c a c

NsiI 2100 200 A* PuroR A* GSARGVVRLARGFPACSGM c c t g a c g c c c g c c c c a c g a c c c g c a g c g c c c g a c c g a a a g g a g c g c a c g a c c c c a t g c a t g g a c t g c g g g c g g g g t g c t g g g c g t c g c g g g c t g g c t t t c c t c g c g t g c t g g g g t a c g t a

Acc65IKpnI 2160 c g g t a c c t t t a a g a c c a a t g a c t t a c a a g g c a g c t g t a g a t c t t a g c c a c t t t t t a a a a g g c c a t g g a a a t t c t g g t t a c t g a a t g t t c c g t c g a c a t c t a g a a t c g g t g a a a a a t t t t c

BbsI 2220 3' LTR ( Δ U3) a a a a g g g g g g a c t g g a a g g g c t a a t t c a c t c c c a a c g a a g a c a a g a t c t g c t t t t t g c t t t t t t c c c c c c t g a c c t t c c c g a t t a a g t g a g g g t t g c t t c t g t t c t a g a c g a a a a a c g a a

2280 3' LTR ( Δ U3) g t a c t g g g t c t c t c t g g t t a g a c c a g a t c t g a g c c t g g g a g c t c t c t g g c t a a c t a g g g a c a t g a c c c a g a g a g a c c a a t c t g g t c t a g a c t c g g a c c c t c g a g a g a c c g a t t g a t c c c t

2340 3' LTR ( Δ U3) a c c c a c t g c t t a a g c c t c a a t a a a g c t t g c c t t g a g t g c t t c a a g t a g t g t g t g c c c g t c t g g g t g a c g a a t t c g g a g t t a t t t c g a a c g g a a c t c a c g a a g t t c a t c a c a c a c g g g c a g

2400 3' LTR ( Δ U3) t g t t g t g t g a c t c t g g t a a c t a g a g a t c c c t c a g a c c c t t t t a g t c a g t g t g g a a a a t c t a c a a c a c a c t g a g a c c a t t g a t c t c t a g g g a g t c t g g g a a a a t c a g t c a c a c c t t t t a g a

2460 3' LTR ( Δ U3) c t a g c a g t a g t a g t t c a t g t c a t c t t a t t a t t c a g t a t t t a t a a c t t g c a a a g a a a t g a a g a t c g t c a t c a t c a a g t a c a g t a g a a t a a t a a g t c a t a a a t a t t g a a c g t t t c t t t a c t t

2520 SV40 poly(A) signal C G T T A T SV40pA-R t a t c a g a g a g t g a g a g g a a c t t g t t t a t t g c a g c t t a t a a t g g t t a c a a a t a a a g c a a t a a t a g t c t c t c a c t c t c c t t g a a c a a a t a a c g t c g a a t a t t a c c a a t g t t t a t t t c g t t a t

2580 SV40 poly(A) signal G T G G T T T G T C C A EBV-rev C G T A G T G T T T A A A G SV40pA-R g c a t c a c a a a t t t c a c a a a t a a a g c a t t t t t t t c a c t g c a t t c t a g t t g t g g t t t g t c c a c g t a g t g t t t a a a g t g t t t a t t t c g t a a a a a a a g t g a c g t a a g a t c a a c a c c a a a c a g g t

2640 SV40 poly(A) signal SV40 ori A A C T C A T C EBV-rev a a c t c a t c a a t g t a t c t t a t c a t g t c t g g c t c t a g c t a t c c c g c c c c t a a c t c c g c c c a t t t g a g t a g t t a c a t a g a a t a g t a c a g a c c g a g a t c g a t a g g g c g g g g a t t g a g g c g g g t a

NcoI 2700 SV40 ori c c c g c c c c t a a c t c c g c c c a g t t c c g c c c a t t c t c c g c c c c a t g g c t g a c t a a t t t t t t t g g g c g g g g a t t g a g g c g g g t c a a g g c g g g t a a g a g g c g g g g t a c c g a c t g a t t a a a a a a a

SfiI 2760 SV40 ori t a t t t a t g c a g a g g c c g a g g c c g c c t c g g c c t c t g a g c t a t t c c a g a a g t a g t g a g g a g g a t a a a t a c g t c t c c g g c t c c g g c g g a g c c g g a g a c t c g a t a a g g t c t t c a t c a c t c c t c c

AvrII 2820 SV40 ori T7 promoter G G G A T A T C A C T C A G C A T A A T T7 c t t t t t t g g a g g c c t a g g g a c g t a c c c a a t t c g c c c t a t a g t g a g t c g t a t t a c g c g c g c g a a a a a a c c t c c g g a t c c c t g c a t g g g t t a a g c g g g a t a t c a c t c a g c a t a a t g c g c g c g

2880 M13 fwd T G A C C G G C A G C A A A A T G T M13 Forward G C A A A A T G T T G C A G C A C T G A C C C M13/pUC Forward t c a c t g g c c g t c g t t t t a c a a c g t c g t g a c t g g g a a a a c c c t g g c g t t a c c c a a c t t a a t a g t g a c c g g c a g c a a a a t g t t g c a g c a c t g a c c c t t t t g g g a c c g c a a t g g g t t g a a t t a

2940 c g c c t t g c a g c a c a t c c c c c t t t c g c c a g c t g g c g t a a t a g c g a a g a g g c c c g c a c c g a t g c g g a a c g t c g t g t a g g g g g a a a g c g g t c g a c c g c a t t a t c g c t t c t c c g g g c g t g g c t a

3000 f1 ori c g c c c t t c c c a a c a g t t g c g c a g c c t g a a t g g c g a a t g g g a c g c g c c c t g t a g c g g c g c a g c g g g a a g g g t t g t c a a c g c g t c g g a c t t a c c g c t t a c c c t g c g c g g g a c a t c g c c g c g t

3060 f1 ori t t a a g c g c g g c g g g t g t g g t g g t t a c g c g c a g c g t g a c c g c t a c a c t t g c c a g c g c c c t a a a t t c g c g c c g c c c a c a c c a c c a a t g c g c g t c g c a c t g g c g a t g t g a a c g g t c g c g g g a t

NgoMIVNaeI 3120 f1 ori G A G G A A A G C G A A A G A A G G G A F1ori-R g c g c c c g c t c c t t t c g c t t t c t t c c c t t c c t t t c t c g c c a c g t t c g c c g g c t t t c c c c g t c g c g g g c g a g g a a a g c g a a a g a a g g g a a g g a a a g a g c g g t g c a a g c g g c c g a a a g g g g c a

3180 f1 ori c a a g c t c t a a a t c g g g g g c t c c c t t t a g g g t t c c g a t t t a g t g c t t t a c g g c a c c t c g a c g t t c g a g a t t t a g c c c c c g a g g g a a a t c c c a a g g c t a a a t c a c g a a a t g c c g t g g a g c t g

3240 f1 ori c c c a a a a a a c t t g a t t a g g g t g a t g g t t c a c g t a g t g g g c c a t c g c c c t g a t a g a c g g t t g g g t t t t t t g a a c t a a t c c c a c t a c c a a g t g c a t c a c c c g g t a g c g g g a c t a t c t g c c a a

3300 f1 ori G T G G A C T C T T G T T C C A A A C T G G F1ori-F t t t c g c c c t t t g a c g t t g g a g t c c a c g t t c t t t a a t a g t g g a c t c t t g t t c c a a a c t g g a a a a g c g g g a a a c t g c a a c c t c a g g t g c a a g a a a t t a t c a c c t g a g a a c a a g g t t t g a c c t

3360 f1 ori a c a a c a c t c a a c c c t a t c t c g g t c t a t t c t t t t g a t t t a t a a g g g a t t t t g c c g a t t t c g t g t t g t g a g t t g g g a t a g a g c c a g a t a a g a a a a c t a a a t a t t c c c t a a a a c g g c t a a a g c

3420 f1 ori g c c t a t t g g t t a a a a a a t g a g c t g a t t t a a c a a a a a t t t a a c g c g a a t t t t a a c a a a a t a c g g a t a a c c a a t t t t t t a c t c g a c t a a a t t g t t t t t a a a t t g c g c t t a a a a t t g t t t t a t

3480 f1 ori AmpR promoter t t a a c g c t t a c a a t t t a g g t g g c a c t t t t c g g g g a a a t g t g c g c g g a a c c c c t a t t t g t t a a t t g c g a a t g t t a a a t c c a c c g t g a a a a g c c c c t t t a c a c g c g c c t t g g g g a t a a a c a a

3540 AmpR promoter t a t t t t t c t a a a t a c a t t c a a a t a t g t a t c c g c t c a t g a g a c a a t a a c c c t g a t a a a t g c a t a a a a a g a t t t a t g t a a g t t t a t a c a t a g g c g a g t a c t c t g t t a t t g g g a c t a t t t a c g

3600 1 5 10 signal sequence MSIQHFRVALI AmpR promoter AmpR MSIQHFRVALI t t c a a t a a t a t t g a a a a a g g a a g a g t a t g a g t a t t c a a c a t t t c c g t g t c g c c c t t a t t c a a g t t a t t a t a a c t t t t t c c t t c t c a t a c t c a t a a g t t g t a a a g g c a c a g c g g g a a t a a g

3660 15 20 signal sequence PFFAAFCLPVFA 25 30 HPETLVKV AmpR PFFAAFCLPVFAHPETLVKV c c t t t t t t g c g g c a t t t t g c c t t c c t g t t t t t g c t c a c c c a g a a a c g c t g g t g a a a g t a a g g a a a a a a c g c c g t a a a a c g g a a g g a c a a a a a c g a g t g g g t c t t t g c g a c c a c t t t c a t t

3720 35 40 45 50 KDAEDQLGARVGYIELDLNS AmpR KDAEDQLGARVGYIELDLNS a a g a t g c t g a a g a t c a g t t g g g t g c a c g a g t g g g t t a c a t c g a a c t g g a t c t c a a c a g c g t t c t a c g a c t t c t a g t c a a c c c a c g t g c t c a c c c a a t g t a g c t t g a c c t a g a g t t g t c g c

3780 55 60 65 70 GKILESFRPEERFPMMSTFK AmpR GKILESFRPEERFPMMSTFK g t a a g a t c c t t g a g a g t t t t c g c c c c g a a g a a c g t t t t c c a a t g a t g a g c a c t t t t a a a g c a t t c t a g g a a c t c t c a a a a g c g g g g c t t c t t g c a a a a g g t t a c t a c t c g t g a a a a t t t c

3840 75 80 85 90 VLLCGAVLSRIDAGQEQLGR AmpR C G A T A C A C C G C G C C A T A A T A Amp-R VLLCGAVLSRIDAGQEQLGR t t c t g c t a t g t g g c g c g g t a t t a t c c c g t a t t g a c g c c g g g c a a g a g c a a c t c g g t c g c c a a g a c g a t a c a c c g c g c c a t a a t a g g g c a t a a c t g c g g c c c g t t c t c g t t g a g c c a g c g g

ScaI 3900 95 100 105 110 RIHYSQNDLVEYSPVTEKHL AmpR RIHYSQNDLVEYSPVTEKHL g c a t a c a c t a t t c t c a g a a t g a c t t g g t t g a g t a c t c a c c a g t c a c a g a a a a g c a t c t t a c g t a t g t g a t a a g a g t c t t a c t g a a c c a a c t c a t g a g t g g t c a g t g t c t t t t c g t a g a a t

3960 115 120 125 130 TDGMTVRELCSAAITMSDNT AmpR TDGMTVRELCSAAITMSDNT c g g a t g g c a t g a c a g t a a g a g a a t t a t g c a g t g c t g c c a t a a c c a t g a g t g a t a a c a c t g g c c t a c c g t a c t g t c a t t c t c t t a a t a c g t c a c g a c g g t a t t g g t a c t c a c t a t t g t g a c

4020 135 140 145 150 AANLLLTTIGGPKELTAFLH AmpR AANLLLTTIGGPKELTAFLH c g g c c a a c t t a c t t c t g a c a a c g a t c g g a g g a c c g a a g g a g c t a a c c g c t t t t t t g c a c a g c c g g t t g a a t g a a g a c t g t t g c t a g c c t c c t g g c t t c c t c g a t t g g c g a a a a a a c g t g t

4080 155 160 165 170 NMGDHVTRLDRWEPELNEAI AmpR NMGDHVTRLDRWEPELNEAI a c a t g g g g g a t c a t g t a a c t c g c c t t g a t c g t t g g g a a c c g g a g c t g a a t g a a g c c a t a c t g t a c c c c c t a g t a c a t t g a g c g g a a c t a g c a a c c c t t g g c c t c g a c t t a c t t c g g t a t g

4140 175 180 185 190 PNDERDTTMPVAMATTLRKL AmpR PNDERDTTMPVAMATTLRKL c a a a c g a c g a g c g t g a c a c c a c g a t g c c t g t a g c a a t g g c a a c a a c g t t g c g c a a a c t a t g t t t g c t g c t c g c a c t g t g g t g c t a c g g a c a t c g t t a c c g t t g t t g c a a c g c g t t t g a t a

4200 195 200 205 210 LTGELLTLASRQQLIDWMEA AmpR LTGELLTLASRQQLIDWMEA t a a c t g g c g a a c t a c t t a c t c t a g c t t c c c g g c a a c a a t t a a t a g a c t g g a t g g a g g c g g a t t g a c c g c t t g a t g a a t g a g a t c g a a g g g c c g t t g t t a a t t a t c t g a c c t a c c t c c g c c

4260 215 220 225 230 DKVAGPLLRSALPAGWFIAD AmpR DKVAGPLLRSALPAGWFIAD a t a a a g t t g c a g g a c c a c t t c t g c g c t c g g c c c t t c c g g c t g g c t g g t t t a t t g c t g a t a t a t t t c a a c g t c c t g g t g a a g a c g c g a g c c g g g a a g g c c g a c c g a c c a a a t a a c g a c t a t

4320 235 240 245 250 KSGAGERGSRGIIAALGPDG AmpR KSGAGERGSRGIIAALGPDG a a t c t g g a g c c g g t g a g c g t g g g t c t c g c g g t a t c a t t g c a g c a c t g g g g c c a g a t g g t a t t a g a c c t c g g c c a c t c g c a c c c a g a g c g c c a t a g t a a c g t c g t g a c c c c g g t c t a c c a t

4380 255 260 265 270 KPSRIVVIYTTGSQATMDER AmpR KPSRIVVIYTTGSQATMDER a g c c c t c c c g t a t c g t a g t t a t c t a c a c g a c g g g g a g t c a g g c a a c t a t g g a t g a a c g a a t c g g g a g g g c a t a g c a t c a a t a g a t g t g c t g c c c c t c a g t c c g t t g a t a c c t a c t t g c t t

4440 275 280 285 NRQIAEIGASLIKHW* AmpR NRQIAEIGASLIKHW* a t a g a c a g a t c g c t g a g a t a g g t g c c t c a c t g a t t a a g c a t t g g t a a c t g t c a g a c c a a g t a t c t g t c t a g c g a c t c t a t c c a c g g a g t g a c t a a t t c g t a a c c a t t g a c a g t c t g g t t c

4500 t t t a c t c a t a t a t a c t t t a g a t t g a t t t a a a a c t t c a t t t t t a a t t t a a a a g g a t c t a g g a a a t g a g t a t a t a t g a a a t c t a a c t a a a t t t t g a a g t a a a a a t t a a a t t t t c c t a g a t c c

4560 t g a a g a t c c t t t t t g a t a a t c t c a t g a c c a a a a t c c c t t a a c g t g a g t t t t c g t t c c a c t a c t t c t a g g a a a a a c t a t t a g a g t a c t g g t t t t a g g g a a t t g c a c t c a a a a g c a a g g t g a

4620 ori g a g c g t c a g a c c c c g t a g a a a a g a t c a a a g g a t c t t c t t g a g a t c c t t t t t t t c t g c g c g c t c g c a g t c t g g g g c a t c t t t t c t a g t t t c c t a g a a g a a c t c t a g g a a a a a a a g a c g c g c

4680 ori t a a t c t g c t g c t t g c a a a c a a a a a a a c c a c c g c t a c c a g c g g t g g t t t g t t t g c c g g a t c a t t a g a c g a c g a a c g t t t g t t t t t t t g g t g g c g a t g g t c g c c a c c a a a c a a a c g g c c t a g

4740 ori a a g a g c t a c c a a c t c t t t t t c c g a a g g t a a c t g g c t t c a g c a g a g c g c a g a t a c c a a a t a t t c t c g a t g g t t g a g a a a a a g g c t t c c a t t g a c c g a a g t c g t c t c g c g t c t a t g g t t t a t

4800 ori c t g t t c t t c t a g t g t a g c c g t a g t t a g g c c a c c a c t t c a a g a a c t c t g t a g c a c c g c c t a g a c a a g a a g a t c a c a t c g g c a t c a a t c c g g t g g t g a a g t t c t t g a g a c a t c g t g g c g g a t

4860 ori c a t a c c t c g c t c t g c t a a t c c t g t t a c c a g t g g c t g c t g c c a g t g g c g a t a a g t c g t g t c g t a t g g a g c g a g a c g a t t a g g a c a a t g g t c a c c g a c g a c g g t c a c c g c t a t t c a g c a c a g

4920 ori t t a c c g g g t t g g a c t c a a g a c g a t a g t t a c c g g a t a a g g c g c a g c g g t c g g g c t g a a c g g a a t g g c c c a a c c t g a g t t c t g c t a t c a a t g g c c t a t t c c g c g t c g c c a g c c c g a c t t g c c

BseYIPspFI 4980 ori g g g g t t c g t g c a c a c a g c c c a g c t t g g a g c g a a c g a c c t a c a c c g a a c t g a g a t a c c t a c c c c c a a g c a c g t g t g t c g g g t c g a a c c t c g c t t g c t g g a t g t g g c t t g a c t c t a t g g a t g

5040 ori a g c g t g a g c t a t g a g a a a g c g c c a c g c t t c c c g a a g g g a g a a a g g c g g a c a g g t a t c c g g t c g c a c t c g a t a c t c t t t c g c g g t g c g a a g g g c t t c c c t c t t t c c g c c t g t c c a t a g g c c

5100 ori G G G A A A C G C C T G G T pBR322ori-F t a a g c g g c a g g g t c g g a a c a g g a g a g c g c a c g a g g g a g c t t c c a g g g g g a a a c g c c t g g t a t t c g c c g t c c c a g c c t t g t c c t c t c g c g t g c t c c c t c g a a g g t c c c c c t t t g c g g a c c a

5160 ori A T C T T T pBR322ori-F a t c t t t a t a g t c c t g t c g g g t t t c g c c a c c t c t g a c t t g a g c g t c g a t t t t t g t g a t g c t t a g a a a t a t c a g g a c a g c c c a a a g c g g t g g a g a c t g a a c t c g c a g c t a a a a a c a c t a c g a

5220 ori c g t c a g g g g g g c g g a g c c t a t g g a a a a a c g c c a g c a a c g c g g c c t t t t t a c g g t t c c t g g g c a g t c c c c c c g c c t c g g a t a c c t t t t t g c g g t c g t t g c g c c g g a a a a a t g c c a a g g a c c

AflIIIPciI 5280 c c t t t t g c t g g c c t t t t g c t c a c a t g t t c t t t c c t g c g t t a t c c c c t g a t t c t g t g g a t a g g a a a a c g a c c g g a a a a c g a g t g t a c a a g a a a g g a c g c a a t a g g g g a c t a a g a c a c c t a t

5340 A L4440 a c c g t a t t a c c g c c t t t g a g t g a g c t g a t a c c g c t c g c c g c a g c c g a a c g a c c g a g c g c a t g g c a t a a t g g c g g a a a c t c a c t c g a c t a t g g c g a g c g g c g t c g g c t t g c t g g c t c g c g t

5400 G C G A G T C A G T G A G C G A G L4440 g c g a g t c a g t g a g c g a g g a a g c g g a a g a g c g c c c a a t a c g c a a a c c g c c t c t c c c c g c g c c g c t c a g t c a c t c g c t c c t t c g c c t t c t c g c g g g t t a t g c g t t t g g c g g a g a g g g g c g c g

5460 g t t g g c c g a t t c a t t a a t g c a g c t g g c a c g a c a g g t t t c c c g a c t g g a a a g c g g g c a g t g c a a c c g g c t a a g t a a t t a c g t c g a c c g t g c t g t c c a a a g g g c t g a c c t t t c g c c c g t c a c

5520 -35 CAP binding site lac promoter a g c g c a a c g c a a t t a a t g t g a g t t a g c t c a c t c a t t a g g c a c c c c a g g c t t t a c a c t t t a t c g c g t t g c g t t a a t t a c a c t c a a t c g a g t g a g t a a t c c g t g g g g t c c g a a a t g t g a a a t

5580 -10 lac promoter lac operator M13 rev A G C G G A T A A C A A T T T C A C A C A G G M13/pUC Reverse C A G G A A A C A M13 Reverse t g c t t c c g g c t c g t a t g t t g t g t g g a a t t g t g a g c g g a t a a c a a t t t c a c a c a g g a a a c a a c g a a g g c c g a g c a t a c a a c a c a c c t t a a c a c t c g c c t a t t g t t a a a g t g t g t c c t t t g t

5640 M13 rev T3 promoter G C T A T G A C M13 Reverse G C A A T T A A C C C T C A C T A A A G G T3 g c t a t g a c c a t g a t t a c g c c a a g c g c g c a a t t a a c c c t c a c t a a a g g g a a c a a a a g c t g g c g a t a c t g g t a c t a a t g c g g t t c g c g c g t t a a t t g g g a g t g a t t t c c c t t g t t t t c g a c c

5700 RSV promoter a g c t g c a a g c t t a a t g t a g t c t t a t g c a a t a c t c t t g t a g t c t t g c a a c a t g g t a a c g a t t c g a c g t t c g a a t t a c a t c a g a a t a c g t t a t g a g a a c a t c a g a a c g t t g t a c c a t t g c t a

SphI 5760 RSV promoter g a g t t a g c a a c a t g c c t t a c a a g g a g a g a a a a a g c a c c g t g c a t g c c g a t t g g t g g a a g t c t c a a t c g t t g t a c g g a a t g t t c c t c t c t t t t t c g t g g c a c g t a c g g c t a a c c a c c t t c a

5820 RSV promoter a a g g t g g t a c g a t c g t g c c t t a t t a g g a a g g c a a c a g a c g g g t c t g a c a t g g a t t g g a c g t t c c a c c a t g c t a g c a c g g a a t a a t c c t t c c g t t g t c t g c c c a g a c t g t a c c t a a c c t g c

5880 RSV promoter a a c c a c t g a a t t g c c g c a t t g c a g a g a t a t t g t a t t t a a g t g c c t a g c t c g a t a c a t a a a t t g g t g a c t t a a c g g c g t a a c g t c t c t a t a a c a t a a a t t c a c g g a t c g a g c t a t g t a t t t

5940 RSV promoter 5' LTR (truncated) c g g g t c t c t c t g g t t a g a c c a g a t c t g a g c c t g g g a g c t c t c t g g c t a a c t a g g g a a c c c g c c c a g a g a g a c c a a t c t g g t c t a g a c t c g g a c c c t c g a g a g a c c g a t t g a t c c c t t g g g

6000 5' LTR (truncated) a c t g c t t a a g c c t c a a t a a a g c t t g c c t t g a g t g c t t c a a g t a g t g t g t g c c c g t c t g t t t g a c g a a t t c g g a g t t a t t t c g a a c g g a a c t c a c g a a g t t c a t c a c a c a c g g g c a g a c a a

6060 5' LTR (truncated) g t g t g a c t c t g g t a a c t a g a g a t c c c t c a g a c c c t t t t a g t c a g t g t g g a a a a t c t c t a g c a c a c t g a g a c c a t t g a t c t c t a g g g a g t c t g g g a a a a t c a g t c a c a c c t t t t a g a g a t c

6120 5' LTR (truncated) HIV-1 Ψ c a g t g g c g c c c g a a c a g g g a c t t g a a a g c g a a a g g g a a a c c a g a g g a g c t c t c t c g a c g c g t c a c c g c g g g c t t g t c c c t g a a c t t t c g c t t t c c c t t t g g t c t c c t c g a g a g a g c t g c g

6180 HIV-1 Ψ a g g a c t c g g c t t g c t g a a g c g c g c a c g g c a a g a g g c g a g g g g c g g c g a c t g g t g a g t a c g t c c t g a g c c g a a c g a c t t c g c g c g t g c c g t t c t c c g c t c c c c g c c g c t g a c c a c t c a t g c

6240 HIV-1 Ψ c c a a a a a t t t t g a c t a g c g g a g g c t a g a a g g a g a g a g a t g g g t g c g a g a g c g t c a g t a t t g g t t t t t a a a a c t g a t c g c c t c c g a t c t t c c t c t c t c t a c c c a c g c t c t c g c a g t c a t a a

NruI* 6300 a a g c g g g g g a g a a t t a g a t c g c g a t g g g a a a a a a t t c g g t t a a g g c c a g g g g g a a a g a a a t t c g c c c c c t c t t a a t c t a g c g c t a c c c t t t t t t a a g c c a a t t c c g g t c c c c c t t t c t t t

6360 a a a t a t a a a t t a a a a c a t a t a g t a t g g g c a a g c a g g g a g c t a g a a c g a t t c g c a g t t a a t t t t a t a t t t a a t t t t g t a t a t c a t a c c c g t t c g t c c c t c g a t c t t g c t a a g c g t c a a t t a

6420 c c t g g c c t g t t a g a a a c a t c a g a a g g c t g t a g a c a a a t a c t g g g a c a g c t a c a a c c a t c c g g a c c g g a c a a t c t t t g t a g t c t t c c g a c a t c t g t t t a t g a c c c t g t c g a t g t t g g t a g g

6480 c t t c a g a c a g g a t c a g a a g a a c t t a g a t c a t t a t a t a a t a c a g t a g c a a c c c t c t a t t g t g a a g t c t g t c c t a g t c t t c t t g a a t c t a g t a a t a t a t t a t g t c a t c g t t g g g a g a t a a c a

6540 g t g c a t c a a a g g a t a g a g a t a a a a g a c a c c a a g g a a g c t t t a g a c a a g a t a g a g g a a g a g c a c g t a g t t t c c t a t c t c t a t t t t c t g t g g t t c c t t c g a a a t c t g t t c t a t c t c c t t c t c

EcoNI 6600 c a a a a c a a a a g t a a g a c c a c c g c a c a g c a a g c g g c c g c t g a t c t t c a g a c c t g g a g g a g g g t t t t g t t t t c a t t c t g g t g g c g t g t c g t t c g c c g g c g a c t a g a a g t c t g g a c c t c c t c c

MfeI 6660 MRDNWRSELYKYKVVKIEP a g a t a t g a g g g a c a a t t g g a g a a g t g a a t t a t a t a a a t a t a a a g t a g t a a a a a t t g a a c c t c t a t a c t c c c t g t t a a c c t c t t c a c t t a a t a t a t t t a t a t t t c a t c a t t t t t a a c t t g g

6720 LGVAPTKAKRRVVQREKRAV a t t a g g a g t a g c a c c c a c c a a g g c a a a g a g a a g a g t g g t g c a g a g a g a a a a a a g a g c a g t t a a t c c t c a t c g t g g g t g g t t c c g t t t c t c t t c t c a c c a c g t c t c t c t t t t t t c t c g t c a

6780 RRE GIGALFLGFLGAAGSTMGAA g g g a a t a g g a g c t t t g t t c c t t g g g t t c t t g g g a g c a g c a g g a a g c a c t a t g g g c g c a g c c c c t t a t c c t c g a a a c a a g g a a c c c a a g a a c c c t c g t c g t c c t t c g t g a t a c c c g c g t c g

6840 RRE SMTLTVQARQLLSGIVQQQN g t c a a t g a c g c t g a c g g t a c a g g c c a g a c a a t t a t t g t c t g g t a t a g t g c a g c a g c a g a a c a g t t a c t g c g a c t g c c a t g t c c g g t c t g t t a a t a a c a g a c c a t a t c a c g t c g t c g t c t t

Bpu10IBbvCI 6900 RRE NLLRAIEAQQHLLQLTVWGI c a a t t t g c t g a g g g c t a t t g a g g c g c a a c a g c a t c t g t t g c a a c t c a c a g t c t g g g g c a t g t t a a a c g a c t c c c g a t a a c t c c g c g t t g t c g t a g a c a a c g t t g a g t g t c a g a c c c c g t a

6960 RRE KQLQARILAVERYLKDQQLL c a a g c a g c t c c a g g c a a g a a t c c t g g c t g t g g a a a g a t a c c t a a a g g a t c a a c a g c t c c t g t t c g t c g a g g t c c g t t c t t a g g a c c g a c a c c t t t c t a t g g a t t t c c t a g t t g t c g a g g a

AleI 7020 GIWGCSGKLICTTAVPWNAS g g g g a t t t g g g g t t g c t c t g g a a a a c t c a t t t g c a c c a c t g c t g t g c c t t g g a a t g c t a g c c c c t a a a c c c c a a c g a g a c c t t t t g a g t a a a c g t g g t g a c g a c a c g g a a c c t t a c g a t c

7080 WSNKSLEQIWNHTTWMEWDR t t g g a g t a a t a a a t c t c t g g a a c a g a t t t g g a a t c a c a c g a c c t g g a t g g a g t g g g a c a g a a c c t c a t t a t t t a g a g a c c t t g t c t a a a c c t t a g t g t g c t g g a c c t a c c t c a c c c t g t c

7084 E a g a a t c t t

Restriction Enzymes

Instructions: By default, all cutters are shown. Filter on number of cut sites or search by enzyme name.

Filter

Features

Primers

BLAST

BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. Click on the buttons below to submit a BLAST search to NCBI. The results will appear in a new window. See your recent BLAST results on NCBI's website.

  • Nucleotide-Nucleotide BLAST (BLASTN)

  • Translated Nucleotide-Protein BLAST (BLASTX)

  • Sequence alignment using BLAST (BLAST2)

Sequence Analyzer Guide

Map

Displays a graphical map based on nucleotide sequence data labeled with restriction enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. Hovering over data labels will display additional information (e.g. cut site)

To select a portion of sequence, click one location on the plasmid and then a second location to display the sequence between the two locations.

Sequence

Displays both strands of base paired nucleotide sequences with annotated enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. Hovering over data labels will display additional information (e.g. cut site).

To select a portion of sequence, click one location on the sequence and then a second location to display the sequence between the two locations.

Enzymes

List of restriction enzymes that can cut a given nucleotide sequence. Table lists enzyme name and the sequence location of the cut.

Features

List of common features detected in a given nucleotide sequence. Table lists feature name, location, size, color used to indicate its position on the map, and direction (if relevant).

Primers

List of commonly used primers detected in a given nucleotide sequence. Table lists primer name, sequence, length, binding site location, and direction.

BLAST

Use Basic Local Alignment Search Tool (BLAST) via the NCBI website to determine similarity between a given sequence and nucleotide (BLASTN) or protein (BLASTX) sequence databases. Additionally, align a custom nucleotide sequence against a given sequence using BLAST2.

File Downloads

GenBank

File contains the nucleotide sequence and annotated features in GenBank flat file format. Open the file with a text editor or plasmid mapping software to view the sequence.

SnapGene

File contains the nucleotide sequence and enhanced annotations from SnapGene Server. Open the file with SnapGene software or the free Viewer to view the plasmid map, sequence, and perform additional sequence analysis.