Addgene pLKO.1P ERCC2_2 Sequencing Result - Sequence Analyzer Skip to main content
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Sequence Analyzer: pLKO.1P ERCC2_2 Sequencing Result


Map View

BspDI * - ClaI * (7045) KflI - PpuMI (6956) AleI (6599) BbvCI - Bpu10I (6446) MfeI (6211) EcoNI (6192) NruI * (5859) SphI (5343) T3 promoter T3 (5205 .. 5225) M13 rev M13 Reverse (5170 .. 5186) lac operator M13/pUC Reverse (5151 .. 5173) lac promoter CAP binding site L4440 (4938 .. 4955) AflIII - PciI (4840) pBR322ori-F (4685 .. 4704) PspFI (4540) BseYI (4536) ScaI (3471) hU6-F (1 .. 21) LKO.1 5' (172 .. 191) NdeI (179) EcoRI (305) XcmI (540) SpeI (768) BlpI (848) AscI (857) hPGK-F (941 .. 959) HincII (995) BamHI (1025) Puro-R (1044 .. 1063) PflFI - Tth111I (1086) BsiWI (1100) RsrII (1160) BstEII (1178) Puro-F (1540 .. 1560) CsiI - SexAI * (1611) NsiI (1697) Acc65I (1700) KpnI (1704) BbsI (1802) SV40pA-R (2113 .. 2132) EBV-rev (2167 .. 2186) NcoI (2278) SfiI (2324) AvrII (2371) T7 promoter T7 (2392 .. 2411) M13 fwd M13 Forward (2421 .. 2438) M13/pUC Forward (2430 .. 2452) F1ori-R (2666 .. 2685) NgoMIV (2704) NaeI (2706) F1ori-F (2876 .. 2897) Amp-R (3383 .. 3402) pLKO.1P ERCC2_2 7084 bp

Sequence View

60 U6 promoter G A G G G C C T A T T T C C C A T G A T T hU6-F g a g g g c c t a t t t c c c a t g 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 c t c c c g g a t a a a g g g t a c 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

120 U6 promoter a t a a t t g g a a t t a a t t t g 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 t a t t a a c c t t a a t t a a a c 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

NdeI 180 U6 promoter G A C T A T C A T LKO.1 5' a a g t a a t a a t t t c t t g g g 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 t t c a t t a t t a a a g a a c c c 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

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

300 U6 promoter c g a a a c a c c g g c c a g t t c c a g a t t c g t g a g a a c t c g a g t t c t c a c g a a t c t g g a a c t g g t g c t t t g t g g c c g g t c a a g g t c t a a g c a c t c t t g a g c t c a a g a g t g c t t a g a c c t t g a c c a

EcoRI 360 cPPT/CTS t t t t g a a t t c t c g a c c t c 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 a a a a c t t a a g a g c t g g 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

420 cPPT/CTS g g g g a t t g g g g g g t a c a g 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 c c c c t a a c c c c c c a t g t c 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

480 cPPT/CTS *LFLNCFNLIKPNIVPV a a c t a a a g a a t t a c a a a a 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 t t g a t t t c t t a a t g t t t t 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

XcmI 540 hPGK promoter ASIWKPRPELPNPNRRKWPL c a g c a g a g a t c c a c t t t g 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 t c g t c t c t a g g t g a a a c 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

600 hPGK promoter GPNACPRPQEPRPEPFRLPA g c c c t g g g t t t g c g c a g g 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 g g g a c c c a a a c g c g t c c 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

660 hPGK promoter SGPDRVNKVDTRLTVRIKAA c c g a c c c t g g g t c t c g c a 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 g g c t g g g a c c c a g a g c g t 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

720 hPGK promoter VRTPGGAVSGAGGRLRSPEK c t a c c c t t g t g g g c c c c c 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 g a t g g g a a c a c c c g g g g g 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

SpeI 780 hPGK promoter RNAAHRVHCVSAARRVLVRA t g c g g t t c g c g g c g t g c c 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 a c g c c a a g c g c c g c a c 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

840 hPGK promoter MAARRPRWAVAN SPCRWPAIAARRGRHATALL c a g a c g g a c a g c g c c a g g 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 t c t g c c t g t c g c g g t c 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

AscIBlpI 900 hPGK promoter SGCSAGRAESSGREGAVREA *CPAGLAAAPFPRHPLR PQEAPRASLLPRSPATRSAP g c g g c t g c t c a g c a g g g c 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 c g c c g a c g a g t c g t c c c g 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

960 hPGK promoter G T G T T C C G C A T T C T G C A A G hPGK-F GCGAVVWALFLPARCSAFCK PTPRYHPGQEQGRPTGCEAL HPATTHARNRGARHEANQLG g g t g t g g g g c g g t a g t g t 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 c a c a c c c c g c c a t c a c a 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

HincII 1020 hPGK promoter PPERTSAVGSLVDRITDLSP RRLARRCDAGENVSDGVERG GSRVDATPERTSRIVSREGW c t c c g g a g c g c a c g t c g g 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 g a g g c c t c g c g t g c a g c 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

BamHI 1080 1 5 10 MTEYKPTVRLAT hPGK promoter PuroR T A C T G G C T C A T G T T C G G G T G Puro-R QGDPPELTMTEYKPTVRLAT LPIWRLKGHGLVLGRHAEGG PSGGSSVM a g g g g g a t c c a c c g g a g c 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 t c c c c c t a g g t g g c c t c 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

BsiWITth111IPflFI 1140 15 20 25 30 RDDVPRAVRTLAAAFADYPA PuroR RDDVPRAVRTLAAAFADYPA AVVDGPGYAGEGGREGVVGG g c g a c g a c g t c c c c a g g g 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 t g c t g c a g g g g t c c 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

BstEIIRsrII 1200 35 40 45 50 TRHTVDPDRHIERVTELQEL PuroR TRHTVDPDRHIERVTELQEL RAVGDIRVAVDLPDGLQLFE c g c g c c a c a c c g t c g a t c 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 g c g c g g t g t g g c a g c t a g 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

1260 55 60 65 70 FLTRVGLDIGKVWVADDGAA PuroR FLTRVGLDIGKVWVADDGAA EERADPEVDALHPDRVVAGR t c c t c a c g c g c g t c g g g c 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 a g g a g t g c g c g c a g c c c g 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

1320 75 80 85 90 VAVWTTPESVEAGAVFAEIG PuroR VAVWTTPESVEAGAVFAEIG HRDPGRRLADFRPRHEGLDA t g g c g g t c t g g a c c a c g c 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 a c c g c c a g a c c t g g t g c g 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

1380 95 100 105 110 PRMAELSGSRLAAQQQMEGL PuroR PRMAELSGSRLAAQQQMEGL RAHGLQATGPQGRLLLHFAE c g c g c a t g g c c g a g t t g a 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 g c g c g t a c c g g c t c a a c t 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

1440 115 120 125 130 LAPHRPKEPAWFLATVGVSP PuroR LAPHRPKEPAWFLATVGVSP QRRVPGLLGRPEQGGDADRG t g g c g c c g c a c c g g c c c a 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 g c g g c g t g g c c g g g t 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

1500 135 140 145 150 DHQGKGLGSAVVLPGVEAAE PuroR DHQGKGLGSAVVLPGVEAAE VVLALTQAAGDHEGSHLRGL a c c a c c a g g g c a a g g g t c 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 t g g t g g t c c c g t t c c c a g 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

1560 155 160 165 170 RAGVPAFLETSAPRNLPFYE PuroR G C A A C C T C C C C T T C T A C G A G C Puro-F RAGVPAFLETSAPRNLPFYE AGPHGGEQLGGRGAVEGEVL g c g c c g g g g t g c c c g c c t 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 c g c g g c c c c a c g g g c g g 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

SexAI*CsiI 1620 175 180 185 190 RLGFTVTADVEVPEGPRTWC PuroR RLGFTVTADVEVPEGPRTWC PEAEGDGGVDLHGFSRAGPA g g c t c g g c t t c a c c g t c a 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 c c g a g c c g a a g t g g c a g t 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

1680 195 200 MTRKPGA* PuroR MTRKPGA* HGALGTGSARGVVRLARGFP t g a c c c g c a a g c c c g g t g 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 a c t g g g c g t t c g g g c c a c 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

NsiIAcc65IKpnI 1740 ACSGM g c g c a c g a c c c c a t g c a t 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 c g c g t g c t g g g g t a c g t a 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

1800 3' LTR ( Δ U3) t t a g c c a c t t t t t a a a a g 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 t c g g t g a a a a a t t t t c 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

BbsI 1860 3' LTR ( Δ U3) a a g a t c t g c t t t t t g c t t 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 t c t a g a c g a a a a a c g a 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

1920 3' LTR ( Δ U3) t c t c t g g c t a a c t a g g g a 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 g a g a c c g a t t g a t c c c t 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

1980 3' LTR ( Δ U3) a a g t a g t g t g t g c c c g t c 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 t t c a t c a c a c a c g g g c a g 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

2040 3' LTR ( Δ U3) a g t c a g t g t g g a a a a t c t 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 t c a g t c a c a c c t t t t a g 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

2100 SV40 poly(A) signal a a c t t g c a a a g a a a t g a a 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 t t g a a c g t t t c t t t a c t t 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

2160 SV40 poly(A) signal C G T T A T C G T A G T G T T T A A A G SV40pA-R g t t a c a a a t a a a g c a a t a 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 a a t g t t t a t t t c g t t a t 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

2220 SV40 poly(A) signal G T G G T T T G T C C A A A C T C A T C EBV-rev c t a g t t g t g g t t t g t c c a 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 a t c a a c a c c a a a c a g g 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

NcoI 2280 SV40 ori g c c c c t a a c t c c g c c c a t 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 c g g g g a t t g a g g c g g g t a 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

SfiI 2340 SV40 ori t g g c t g a c t a a t t t t t t t 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 a c c g a c t g a t t a a a a a a a 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

AvrII 2400 SV40 ori T7 promoter G G G A T A T C A T7 c c a g a a g t a g t g a g g a g g 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 g t c t t c a t c a c t c c t c 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

2460 T7 promoter M13 fwd C T C A G C A T A A T T7 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 g a g t c g t a t t a c g c g c g c 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 c t c a g c a t a a t g c g c g c g 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

2520 g g c g t t a c c c a a c t t a a t 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 c c g c a a t g g g t t g a a t t a 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

2580 f1 ori g a a g a g g c c c g c a c c g a t 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 c t t c t c c g g g c g t g g c t 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

2640 f1 ori g c g c c c t g t a g c g g c g c a 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 c g c g g g a c a t c g c c g c g t 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

2700 f1 ori G A G G A A A G C G A A A G A A G G G A F1ori-R a c a c t t g c c a g c g c c c t a 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 g t g a a c g g t c g c g g g a 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

NgoMIVNaeI 2760 f1 ori t t c g c c g g c t t t c c c c g t 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 a a g c g g c c g a a a g g g g c a 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

2820 f1 ori g c t t t a c g g c a c c t c g a c 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 c g a a a t g c c g t g g a g c t g 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

2880 f1 ori G T G G A F1ori-F t c g c c c t g a t a g a c g g t t 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 a g c g g g a c t a t c t g c c a 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

2940 f1 ori C T C T T G T T C C A A A C T G G F1ori-F c t c t t g t t c c a a a c t g g a 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 a g a a c a a g g t t t g a c c t 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

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

3060 f1 ori AmpR promoter g c g a a t t t t a a c a a a a t a 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 c g c t t a a a a t t g t t t t a 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

3120 AmpR promoter g c g g a a c c c c t a t t t g t t 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 c g c c t t g g g g a t a a a c a a 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

3180 1 5 signal sequence MSIQH AmpR promoter AmpR MSIQH a a t a a c c c t g a t a a a t g c 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 t a t t g g g a c t a t t t a c g 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

3240 10 15 20 signal sequence FRVALIPFFAAFCLPVFA 25 HP AmpR FRVALIPFFAAFCLPVFAHP t c c g t g t c g c c c t t a t t c 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 g g c a c a g c g g g a a t a a g 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

3300 30 35 40 45 ETLVKVKDAEDQLGARVGYI AmpR ETLVKVKDAEDQLGARVGYI a a a c g c t g g t g a a a g t a a 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 t t t g c g a c c a c t t t c a t t 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

3360 50 55 60 65 ELDLNSGKILESFRPEERFP AmpR ELDLNSGKILESFRPEERFP a a c t g g a t c t c a a c a g c g 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 t g a c c t a g a g t t g t c g c 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

3420 70 75 80 85 MMSTFKVLLCGAVLSRIDAG AmpR C G A T A C A C C G C G C C A T A A T A Amp-R MMSTFKVLLCGAVLSRIDAG t g a t g a g c a c t t t t a a a g 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 c t a c t c g t g a a a a t t t 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

ScaI 3480 90 95 100 105 QEQLGRRIHYSQNDLVEYSP AmpR QEQLGRRIHYSQNDLVEYSP a a g a g c a a c t c g g t c g c c 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 t c t c g t t g a g c c a g c g g 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

3540 110 115 120 125 VTEKHLTDGMTVRELCSAAI AmpR VTEKHLTDGMTVRELCSAAI t c a c a g a a a a g c a t c t t a 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 a g t g t c t t t t c g t a g a a t 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

3600 130 135 140 145 TMSDNTAANLLLTTIGGPKE AmpR TMSDNTAANLLLTTIGGPKE c c a t g a g t g a t a a c a c t g 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 g g t a c t c a c t a t t g t g a c 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

3660 150 155 160 165 LTAFLHNMGDHVTRLDRWEP AmpR LTAFLHNMGDHVTRLDRWEP t a a c c g c t t t t t t g c a c a 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 t t g g c g a a a a a a c g t g t 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

3720 170 175 180 185 ELNEAIPNDERDTTMPVAMA AmpR ELNEAIPNDERDTTMPVAMA a g c t g a a t g a a g c c a t a c 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 t c g a c t t a c t t c g g t a t g 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

3780 190 195 200 205 TTLRKLLTGELLTLASRQQL AmpR TTLRKLLTGELLTLASRQQL c a a c g t t g c g c a a a c t a t 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 g t t g c a a c g c g t t t g a t a 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

3840 210 215 220 225 IDWMEADKVAGPLLRSALPA AmpR IDWMEADKVAGPLLRSALPA t a g a c t g g a t g g a g g c g g 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 a t c t g a c c t a c c t c c g c c 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

3900 230 235 240 245 GWFIADKSGAGERGSRGIIA AmpR GWFIADKSGAGERGSRGIIA g c t g g t t t a t t g c t g a t a 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 g a c c a a a t a a c g a c t a t 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

3960 250 255 260 265 ALGPDGKPSRIVVIYTTGSQ AmpR ALGPDGKPSRIVVIYTTGSQ c a c t g g g g c c a g a t g g t a 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 g t g a c c c c g g t c t a c c a t 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

4020 270 275 280 285 ATMDERNRQIAEIGASLIKH AmpR ATMDERNRQIAEIGASLIKH c a a c t a t g g a t g a a c g a a 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 t t g a t a c c t a c t t g c t t 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

4080 W* AmpR W* g g t a a c t g t c a g a c c a a g 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 c c a t t g a c a g t c t g g t t c 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

4140 a a t t t a a a a g g a t c t a g g 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 t t a a a t t t t c c t a g a t c c 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

4200 ori g t g a g t t t t c g t t c c a c t 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 c a c t c a a a a g c a a g g t g a 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

4260 ori a t c c t t t t t t t c t g c g c g 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 a g g a a a a a a a g a c g c g 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

4320 ori t g g t t t g t t t g c c g g a t c 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 a c c a a a c a a a c g g c c t a g 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

4380 ori g a g c g c a g a t a c c a a a t a 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 c t c g c g t c t a t g g t t t a t 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

4440 ori a c t c t g t a g c a c c g c c t a 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 t g a g a c a t c g t g g c g g a t 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

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

BseYIPspFI 4560 ori a g c g g t c g g g c t g a a c g g 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 t c g c c a g c c c g a c t t g c 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

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

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

4740 ori G G G A A A C G C C T G G T A T C T T T pBR322ori-F c a g g g g g a a a c g c c t g g t 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 c c c c t t t g c g g a c c a 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

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

AflIIIPciI 4860 c c t t t t t a c g g t t c c t g g 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 g g a a a a a t g c c a a g g a c c 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

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

4980 A G C G A G T C A G T G A G C G A G L4440 g c c g a a c g a c c g a g c g c a 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 c g g c t t g c t g g c t c g c g t 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

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

5100 CAP binding site a c t g g a a a g c g g g c a g t g 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 t g a c c t t t c g c c c g t c a c 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

5160 -35 -10 lac promoter lac operator A G C G G A T A A C M13/pUC Reverse c c c a g g c t t t a c a c t t t a 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 g g g t c c g a a a t g t g a a a t 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

5220 lac operator M13 rev T3 promoter 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 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 T3 a a t t t c a c a c a g g a a a c a 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 t t a a a g t g t g t c c t t t g t 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

5280 T3 promoter RSV promoter A A A G G T3 a a a g g g a a c a a a a g c t g g 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 t c c c t t g t t t t c g a c c 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

5340 RSV promoter t t g c a a c a t g g t a a c g a t 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 a c g t t g t a c c a t t g c t a 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

SphI 5400 RSV promoter a t g c c g a t t g g t g g a a g t 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 a c g g c t a a c c a c c t t c a 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

5460 RSV promoter t c t g a c a t g g a t t g g a c g 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 a g a c t g t a c c t a a c c t g c 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

5520 RSV promoter 5' LTR (truncated) c c t a g c t c g a t a c a t a a a 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 g g a t c g a g c t a t g t a t t t 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

5580 5' LTR (truncated) t g g c t a a c t a g g g a 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 c c g a t t g a t c c c t 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

5640 5' LTR (truncated) a g t g t g t g c c c g t c 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 t c a c a c a c g g g c a g 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

5700 5' LTR (truncated) a g t g t g g a a a a t c t c t a g 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 t c a c a c c t t t t a g a g a t 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

5760 HIV-1 Ψ g a g g a g c t c t c t c g a c g c 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 t c c t c g a g a g a g c t g 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

5820 HIV-1 Ψ c g g c g a c t g g t g a g t a c g 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 g c c g c t g a c c a c t c a t g c 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

NruI* 5880 HIV-1 Ψ t g c g a g a g c g t c a g t a t t 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 c g c t c t c g c a g t c a t 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

5940 a g g c c a g g g g g a a a g a a a 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 t c c g g t c c c c c t t t c t t 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

6000 g a a c g a t t c g c a g t t a a t 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 c t t g c t a a g c g t c a a t t a 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

6060 g g a c a g c t a c a a c c a t c c 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 c c t g t c g a t g t t g g t a g g 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

6120 g t a g c a a c c c t c t a t t g t 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 c a t c g t t g g g a g a t a a c a 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

6180 g a c a a g a t a g a g g a a g a g 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 g t t c t a t c t c c t t c t c 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

MfeIEcoNI 6240 MRDNWRSELYKYK c t t c a g a c c t g g a g g a g g 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 g a a g t c t g g a c c t c c t 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

6300 VVKIEPLGVAPTKAKRRVVQ a g t a g t a a a a a t t g a a c c 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 t c a t c a t t t t t a a c t t g g 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

6360 RRE REKRAVGIGALFLGFLGAAG g a g a g a a a a a a g a g c a g t 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 c t c t c t t t t t t c t c g t c a 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

6420 RRE STMGAASMTLTVQARQLLSG a a g c a c t a t g g g c g c a g c 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 t c g t g a t a c c c g c g t c g 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

Bpu10IBbvCI 6480 RRE IVQQQNNLLRAIEAQQHLLQ t a t a g t g c a g c a g c a g a a 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 t a t c a c g t c g t c g t c t 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

6540 RRE LTVWGIKQLQARILAVERYL a c t c a c a g t c t g g g g c a t 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 t g a g t g t c a g a c c c c g t a 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

AleI 6600 RRE KDQQLLGIWGCSGKLICTTA a a a g g a t c a a c a g c t c c t 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 t t c c t a g t t g t c g a g g a 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

6660 VPWNASWSNKSLEQIWNHTT t g t g c c t t g g a a t g c t a g 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 a c a c g g a a c c t t a c g a t c 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

6720 WMEWDREINNYTSLIHSLIE c t g g a t g g a g t g g g a c a g a g a a 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 g a c c t a c c t c a c c c t g t c t c t t 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

6780 1 5 10 KNEQELLELDKWA gp41 peptide ESQNQQEKNEQELLELDKWA a g a a t c g c a a a a c c a g c a a g a a 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 t c t t a g c g t t t t g g t c g t t c t t 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

6840 15 SL (in frame with gp41 peptide) WNWFNITNWLWYIKLFIM gp41 peptide SLWNWFNITNWLWYIKLFIM a a g t t t g t g g a a t t g g t t t a a c 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 t t c a a a c a c c t t a a c c a a a t t g 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

6900 (in frame with gp41 peptide) IVGGLVGLRIVFAVLSIVNR IVGGLVGLRIVFAVLSIVNR g a t a g t a g g a g g c t t g g t a g g t 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 c t a t c a t c c t c c g a a c c a t 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

PpuMIKflI 6960 (in frame with gp41 peptide) VRQGYSPLSFQTHLPTPRGP VRQGYSPLSFQTHLPTPRGP a g t t a g g c a g g g a t a t t c a c c a 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 t c a a t c c g t c c c t a t a a g t g g t 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

7020 (in frame with gp41 peptide) DRPEGIEEEGGERDRDRSIR DRPEGIEEEGGERDRDRSIR c g a c a g g c c c g a a g g a a t a g a a 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 g c t g t c c g g g c t t c c t t a t c t t 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

BspDI*ClaI* 7080 (in frame with gp41 peptide) LVNGSRRYRSRD* LVNGSRRYRSRD* a t t a g t g a a c g g a t c t c g a c g g 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 t a a t c a c t t g c c t a g a g c t g c c 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

7084 c a c c g t g g

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.