Addgene pKM-U6-reRNA-hsRUNX Sequencing Result - Sequence Analyzer Skip to main content
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Sequence Analyzer: pKM-U6-reRNA-hsRUNX Sequencing Result


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XmnI (5591) Amp-R (5542 .. 5561) BsaI (5053) AhdI (4992) AlwNI (4515) pBR322ori-F (4240 .. 4259) AflIII - PciI (4099) L4440 (3989 .. 4006) BspQI - SapI (3983) CAP binding site M13/pUC Reverse (3771 .. 3793) lac operator M13 Reverse (3758 .. 3774) M13 rev T3 (3719 .. 3739) SacI (3705) Eco53kI (3703) AflII (3615) pBABE 3' (3433 .. 3453) SphI (3389) NsiI (3387) SV40pro-F (3259 .. 3278) StuI (3206) AvrII (3201) SmaI (3182) AvaI - BsoBI - TspMI - XmaI (3180) BclI * (3150) AatII (3118) ZraI (3116) F1ori-F (144 .. 165) F1ori-R (356 .. 375) M13/pUC Forward (588 .. 610) M13 Forward (602 .. 619) T7 (629 .. 648) T7 promoter Kozak sequence AleI (883) BstXI (940) FseI (960) hU6-F (1014 .. 1034) EcoO109I (1016) LKO.1 5' (1185 .. 1204) KasI (1541) NarI (1542) SfoI (1543) PluTI (1545) CsiI - SexAI * (1591) HpaI (1742) MfeI (1751) NruI (1839) SalI (1845) BstZ17I (1854) SV40 poly(A) signal PfoI (2046) SacII (2363) RsrII (2730) AsiSI (2779) PstI (2808) pKM-U6-reRNA-hsRUNX 5903 bp

Sequence View

5ʹ 3ʹ 60 f1 ori c c a c c t a a a t t g t a a g c g t t a a t a t t t t g t t a a a a t t c g c g t t a a a t t t t t g t t a a a t c a g g t g g a t t t a a c a t t c g c a a t t a t a a a a c a a t t t t a a g c g c a a t t t a a a a a c a a t t t a g t

120 f1 ori g c t c a t t t t t t a a c c a a t a g g c c g a a a t c g g c a a a a t c c c t t a t a a a t c a a a a g a a t a g a c g a g t a a a a a a t t g g t t a t c c g g c t t t a g c c g t t t t a g g g a a t a t t t a g t t t t c t t a t c t

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

240 f1 ori a c t c c a a c g t c a a a g g g c g a a a a a c c g t c t a t c a g g g c g a t g g c c c a c t a c g t g a a c c a t t g a g g t t g c a g t t t c c c g c t t t t t g g c a g a t a g t c c c g c t a c c g g g t g a t g c a c t t g g t a

300 f1 ori c a c c c t a a t c a a g t t t t t t g g g g t c g a g g t g c c g t a a a g c a c t a a a t c g g a a c c c t a a a g g t g g g a t t a g t t c a a a a a a c c c c a g c t c c a c g g c a t t t c g t g a t t t a g c c t t g g g a t t t c

360 f1 ori A G G G A F1ori-R g g a g c c c c c g a t t t a g a g c t t g a c g g g g a a a g c c g g c g a a c g t g g c g a g a a a g g a a g g g a c c t c g g g g g c t a a a t c t c g a a c t g c c c c t t t c g g c c g c t t g c a c c g c t c t t t c c t t c c c t

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

480 f1 ori c a c c a c a c c c g c c g c g c t t a a t g c g c c g c t a c a g g g c g c g t c c c a t t c g c c a t t c a g g c t g t g g t g t g g g c g g c g c g a a t t a c g c g g c g a t g t c c c g c g c a g g g t a a g c g g t a a g t c c g a

540 g c g c a a c t g t t g g g a a g g g c g a t c g g t g c g g g c c t c t t c g c t a t t a c g c c a g c t g g c g a a c g c g t t g a c a a c c c t t c c c g c t a g c c a c g c c c g g a g a a g c g a t a a t g c g g t c g a c c g c t t

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

660 M13 fwd T7 promoter T T G T A A A A C G M13/pUC Forward T G T A A A A C G A C G G C C A G T M13 Forward T A A T A C G A C T C A C T A T A G G G T7 t t g t a a a a c g a c g g c c a g t g a g c g c g c g t a a t a c g a c t c a c t a t a g g g c g a a t t g g g t a c a a c a t t t t g c t g c c g g t c a c t c g c g c g c a t t a t g c t g a g t g a t a t c c c g c t t a a c c c a t g

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

780 a c a a g t a c t t a g g g a a a a t t t t a c t c a a t t a a a a g t a a a a g t a t c t g g c t a g a a t c t t a c t g t t c a t g a a t c c c t t t t a a a a t g a g t t a a t t t t c a t t t t c a t a g a c c g a t c t t a g a a t g

840 t t g a g t a a a a g t a a a a a a g t a c t c c a t t a a a a t t g t a c t t g a g t a t t a a g g a a g t a a a a g a a c t c a t t t t c a t t t t t t c a t g a g g t a a t t t t a a c a t g a a c t c a t a a t t c c t t c a t t t t c

AleI 900 Kozak sequence loxP t a a a a g c a a g a a a g a t c g a t c t c g a a g g a t c t g g a g g c c a c c a t g g t g t c g a t a a c t t c g a t t t t c g t t c t t t c t a g c t a g a g c t t c c t a g a c c t c c g g t g g t a c c a c a g c t a t t g a a g c

FseIBstXI 960 loxP t a t a g c a t a c a t t a t a c g a a g t t a t c g a t a g t c c a g t g t g g t g g a a t t g c c c t t g g c c g g a t a t c g t a t g t a a t a t g c t t c a a t a g c t a t c a g g t c a c a c c a c c t t a a c g g g a a c c g g c c

EcoO109I 1020 lox2272 U6 promoter G A G G G C C hU6-F c c a t a a c t t c g t a t a g g a t a c t t t a t a c g a a g t t a t g g t a c c g g c g c g c a t g t g a g g g c c g g t a t t g a a g c a t a t c c t a t g a a a t a t g c t t c a a t a c c a t g g c c g c g c g t a c a c t c c c g g

1080 U6 promoter T A T T T C C C A T G A T T hU6-F 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 a t a a t t 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 t a t t a a c

1140 U6 promoter 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 a a g t a a t 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 t t c a t t a

1200 U6 promoter G A C T A T C A T A T G C T T A LKO.1 5' 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 a t g c 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 t a c g a a t

1260 U6 promoter C C G T LKO.1 5' 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 c g a a a c a 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 g c t t t g t

1320 U6 promoter c c g a t t c a a g a a t c c c g a a g t g a a g a a t c t t g c c g t c c g t a c a t g g a c t t g c c c g a a c t g g g c t a a g t t c t t a g g g c t t c a c t t c t t a g a a c g g c a g g c a t g t a c c t g a a c g g g c t t g a c

1380 t g g g g a a a c c c a t g a c c g a g a c g a g a a c g c t g c g c t g a a c a t t c g g c g t g a a g c g t t g g t a c c c c t t t g g g t a c t g g c t c t g c t c t t g c g a c g c g a c t t g t a a g c c g c a c t t c g c a a c c a

1440 g g c t g c g g g a a t c t c a g a c a c c t t a a a c g c t c a t g g a g g c t a t g t c a g a c c t g c t t c g g c c c g a c g c c c t t a g a g t c t g t g g a a t t t g c g a g t a c c t c c g a t a c a g t c t g g a c g a a g c c g

1500 g g g c a a t g g t c t g c g a a g t g a g a a t c a c g c g a c t t t a g t c g t g t g a g g t t c a a a t t g a t g c c c g t t a c c a g a c g c t t c a c t c t t a g t g c g c t g a a a t c a g c a c a c t c c a a g t t t a a c t a c

KasINarISfoIPluTI 1560 HDV ribozyme g c t a c a t a t c a g a g g c c g g c a t g g t c c c a g c c t c c t c g c t g g c g c c g g c t g g g c a a c a t g c g a t g t a t a g t c t c c g g c c g t a c c a g g g t c g g a g g a g c g a c c g c g g c c g a c c c g t t g t a c

SexAI*CsiI 1620 HDV ribozyme c t t c g g c a t g g c g a a t g g g a c t t t t t t g g t a c c a g g t a c g g c c g c t t c g a g c a g a c a t g a g a a g c c g t a c c g c t t a c c c t g a a a a a a c c a t g g t c c a t g c c g g c g a a g c t c g t c t g t a c t

1680 SV40 poly(A) signal t a a g a t a c a t t g a t g a g t t t g g a c a a a c c a c a a c t a g a a t g c a g t g a a a a a a a t g c t t t a a t t c t a t g t a a c t a c t c a a a c c t g t t t g g t g t t g a t c t t a c g t c a c t t t t t t t a c g a a a t

1740 SV40 poly(A) signal t t t g t g a a a t t t g t g a t g c t a t t g c t t t a t t t g t a a c c a t t a t a a g c t g c a a t a a a c a a g a a a c a c t t t a a a c a c t a c g a t a a c g a a a t a a a c a t t g g t a a t a t t c g a c g t t a t t t g t t c

MfeIHpaI 1800 SV40 poly(A) signal t t a a c a a c a a c a a t t g c a t t c a t t t t a t g t t t c a g g t t c a g g g g g a g a t g t g g g a g g t t t a a t t g t t g t t g t t a a c g t a a g t a a a a t a c a a a g t c c a a g t c c c c c t c t a c a c c c t c c a a a

BstZ17ISalINruI 1860 t t t a a a g c a a g t a a a a c c t c t a c a a a t g t g g t a a a a t c g c g a a g g t c g a c g g t a t a c a g a a a a t t t c g t t c a t t t t g g a g a t g t t t a c a c c a t t t t a g c g c t t c c a g c t g c c a t a t g t c t

1920 SV40 poly(A) signal c a t g a t a a g a t a c a t t g a t g a g t t t g g a c a a a c c a c a a c t a g a a t g c a g t g a a a a a a a t g g t a c t a t t c t a t g t a a c t a c t c a a a c c t g t t t g g t g t t g a t c t t a c g t c a c t t t t t t t a c

1980 SV40 poly(A) signal c t t t a t t t g t g a a a t t t g t g a t g c t a t t g c t t t a t t t g t a a c c a t t a t a a g c t g c a a t a a g a a a t a a a c a c t t t a a a c a c t a c g a t a a c g a a a t a a a c a t t g g t a a t a t t c g a c g t t a t t

2040 SV40 poly(A) signal a c a a g t t g g g g t g g g c g a a g a a c t c c a g c a t g a g a t c c c c g c g c t g g a g g a t c a t c c a g c t g t t c a a c c c c a c c c g c t t c t t g a g g t c g t a c t c t a g g g g c g c g a c c t c c t a g t a g g t c g

PfoI 2100 c g g c g t c c c g g a a a a c g a t t c c g a a g c c c a a c c t t t c a t a g a a g g c g g c g g t g g a a t c g a g c c g c a g g g c c t t t t g c t a a g g c t t c g g g t t g g a a a g t a t c t t c c g c c g c c a c c t t a g c t

2160 340 335 330 *EKARPRTSPRRNGS HygR 340 335 330 *EKARPRTSPRRNGS HygR *EKARPRTSPRRNGS a a t c t c g t a g c a c g t g c t a t t c c t t t g c c c t c g g a c g a g t g c t g g g g c g t c g g t t t c c a c t t a g a g c a t c g t g c a c g a t a a g g a a a c g g g a g c c t g c t c a c g a c c c c g c a g c c a a a g g t g

2220 325 320 315 310 DALVEVCGDTWVAASRRAIQ HygR 325 320 315 310 DALVEVCGDTWVAASRRAIQ HygR DALVEVCGDTWVAASRRAIQ t a t c g g c g a g t a c t t c t a c a c a g c c a t c g g t c c a g a c g g c c g c g c t t c t g c g g g c g a t t t a t a g c c g c t c a t g a a g a t g t g t c g g t a g c c a g g t c t g c c g g c g c g a a g a c g c c c g c t a a a

2280 305 300 295 290 TRGVTGAGSRVIADCRGQAW HygR 305 300 295 290 TRGVTGAGSRVIADCRGQAW HygR TRGVTGAGSRVIADCRGQAW g t g t a c g c c c g a c a g t c c c g g c t c c g g a t c g g a c g a t t g c g t c g c a t c g a c c c t g c g c c c c a c a t g c g g g c t g t c a g g g c c g a g g c c t a g c c t g c t a a c g c a g c g t a g c t g g g a c g c g g g

2340 285 280 275 270 AADDFNGDVLSQYLQDLGIR HygR 285 280 275 270 AADDFNGDVLSQYLQDLGIR HygR AADDFNGDVLSQYLQDLGIR a a g c t g c a t c a t c g a a a t t g c c g t c a a c c a a g c t c t g a t a g a g t t g g t c a a g a c c a a t g c t t c g a c g t a g t a g c t t t a a c g g c a g t t g g t t c g a g a c t a t c t c a a c c a g t t c t g g t t a c g

SacII 2400 265 260 255 250 LMYARLRPSGALEPHRREFY HygR 265 260 255 250 LMYARLRPSGALEPHRREFY HygR MPPLEV LMYARLRPSGALEPHRREFY g g a g c a t a t a c g c c c g g a g c c g c g g c g a t c c t g c a a g c t c c g g a t g c c t c c g c t c g a a g t c c t c g t a t a t g c g g g c c t c g g c g c c g c t a g g a c g t t c g a g g c c t a c g g a g g c g a g c t t c a

2460 245 240 235 230 RTQQEMCALWPRWFFINAVE HygR 245 240 235 230 RTQQEMCALWPRWFFINAVE HygR ARLLLHTSQPRPPEEDVGDL RTQQEMCALWPRWFFINAVE a g c g c g t c t g c t g c t c c a t a c a a g c c a a c c a c g g c c t c c a g a a g a a g a t g t t g g c g a c c t t c g c g c a g a c g a c g a g g t a t g t t c g g t t g g t g c c g g a g g t c t t c t t c t a c a a c c g c t g g a

2520 225 220 215 210 YQSDGFMAESWDIVATIRGN HygR 225 220 215 210 YQSDGFMAESWDIVATIRGN HygR VLGIPEHRLAPVNDRCYAAI YQSDGFMAESWDIVATIRGN c g t a t t g g g a a t c c c c g a a c a t c g c c t c g c t c c a g t c a a t g a c c g c t g t t a t g c g g c c a t g c a t a a c c c t t a g g g g c t t g t a g c g g a g c g a g g t c a g t t a c t g g c g a c a a t a c g c c g g t a

2580 205 200 195 190 DTLVNNSGFDAHVLHRVEPC HygR 205 200 195 190 DTLVNNSGFDAHVLHRVEPC HygR VRQDIVGAEIRVHEVPDFGA DTLVNNSGFDAHVLHRVEPC t g t c c g t c a g g a c a t t g t t g g a g c c g a a a t c c g c g t g c a c g a g g t g c c g g a c t t c g g g g c a c a g g c a g t c c t g t a a c a a c c t c g g c t t t a g g c g c a c g t g c t c c a c g g c c t g a a g c c c c g

2640 185 180 175 170 DEAWLMLEDLAQAVSASVTD HygR 185 180 175 170 DEAWLMLEDLAQAVSASVTD HygR VLGPKHQLIESLRDGRTDGV DEAWLMLEDLAQAVSASVTD a g t c c t c g g c c c a a a g c a t c a g c t c a t c g a g a g c c t g c g c g a c g g a c g c a c t g a c g g t g t t c a g g a g c c g g g t t t c g t a g t c g a g t a g c t c t c g g a c g c g c t g c c t g c g t g a c t g c c a c a

2700 165 160 155 150 DMVTQWHYVHPDAIACIFDR HygR 165 160 155 150 DMVTQWHYVHPDAIACIFDR HygR VHHSLPVIHMGISNRAYEIT DMVTQWHYVHPDAIACIFDR c g t c c a t c a c a g t t t g c c a g t g a t a c a c a t g g g g a t c a g c a a t c g c g c a t a t g a a a t c a c g c a g g t a g t g t c a a a c g g t c a c t a t g t g t a c c c c t a g t c g t t a g c g c g t a t a c t t t a g t g

RsrII 2760 145 140 135 130 WTTYQGIGQPGFPGFGSTQS HygR 145 140 135 130 WTTYQGIGQPGFPGFGSTQS HygR PCSVLTDSLRSEWAEPARLA WTTYQGIGQPGFPGFGSTQS g c c a t g t a g t g t a t t g a c c g a t t c c t t g c g g t c c g a a t g g g c c g a a c c c g c t c g t c t g g c c g g t a c a t c a c a t a a c t g g c t a a g g a a c g c c a g g c t t a c c c g g c t t g g g c g a g c a g a c c g

PstIAsiSI 2820 125 120 115 110 LDAAAIADMAEAVPQLVAPL HygR 125 120 115 110 LDAAAIADMAEAVPQLVAPL HygR KIGRSDRIHGLRDRLQNSGQ LDAAAIADMAEAVPQLVAPL t a a g a t c g g c c g c a g c g a t c g c a t c c a t g g c c t c c g c g a c c g g c t g c a g a a c a g c g g g c a a t t c t a g c c g g c g t c g c t a g c g t a g g t a c c g g a g g c g c t g g c c g a c g t c t t g t c g c c c g t

2880 105 100 95 90 ETEPLDQLTVGQARRSICYT HygR 105 100 95 90 ETEPLDQLTVGQARRSICYT HygR FGFRQVLQRDTLCTAGDAIG ETEPLDQLTVGQARRSICYT g t t c g g t t t c a g g c a g g t c t t g c a a c g t g a c a c c c t g t g c a c g g c g g g a g a t g c a a t a g g c a a g c c a a a g t c c g t c c a g a a c g t t g c a c t g t g g g a c a c g t g c c g c c c t c t a c g t t a t c c

2940 85 80 75 70 LSESFEGIDLVEPIPLAASA HygR 85 80 75 70 LSESFEGIDLVEPIPLAASA HygR QALAEFPNVKHFRNRERGRC LSESFEGIDLVEPIPLAASA t c a g g c t c t c g c t g a a t t c c c c a a t g t c a a g c a c t t c c g g a a t c g g g a g c g c g g c c g a t g a g t c c g a g a g c g a c t t a a g g g g t t a c a g t t c g t g a a g g c c t t a g c c c t c g c g c c g g c t a c

3000 65 60 55 50 FHRYVYRDKYFGDACSNVRL HygR 65 60 55 50 FHRYVYRDKYFGDACSNVRL HygR KVPINITIFVETIGAAIYPQ FHRYVYRDKYFGDACSNVRL c a a a g t g c c g a t a a a c a t a a c g a t c t t t g t a g a a a c c a t c g g c g c a g c t a t t t a c c c g c a g t t t c a c g g c t a t t t g t a t t g c t a g a a a c a t c t t t g g t a g c c g c g t c g a t a a a t g g g c g t

3060 45 40 35 30 VYGRGGVDFSFARSEEGESL HygR 45 40 35 30 VYGRGGVDFSFARSEEGESL HygR DISTPSYIEAESTRFFALRE VYGRGGVDFSFARSEEGESL g g a c a t a t c c a c g c c c t c c t a c a t c g a a g c t g a a a g c a c g a g a t t c t t c g c c c t c c g a g a c c t g t a t a g g t g c g g g a g g a t g t a g c t t c g a c t t t c g t g c t c t a a g a a g c g g g a g g c t c t

ZraIAatII 3120 25 20 15 10 QMLDSVSDFKEILFKEVSTA HygR 25 20 15 10 QMLDSVSDFKEILFKEVSTA HygR LHQVGDAVELFDQKLLDRRR QMLDSVSDFKEILFKEVSTA g c t g c a t c a g g t c g g a g a c g c t g t c g a a c t t t t c g a t c a g a a a c t t c t c g a c a g a c g t c g c g a c g t a g t c c a g c c t c t g c g a c a g c t t g a a a a g c t a g t c t t t g a a g a g c t g t c t g c a g c

BclI* 3180 5 1 TLEPKKM HygR 5 1 TLEPKKM HygR GEFRLFHHVLIRSENGYTSS TLEPKKM c g g t g a g t t c a g g c t t t t t c a t c a c g t g c t g a t c a g a t c c g a a a a t g g a t a t a c a a g c t c g c c a c t c a a g t c c g a a a a a g t a g t g c a c g a c t a g t c t a g g c t t t t a c c t a t a t g t t c g a g

StuIAvrIITspMIBsoBIXmaIAvaISmaI 3240 SV40 promoter SV40 promoter SV40 ori RELFAKA* c c g g g a g c t t t t t g c a a a a g c c t a g g c c t c c a a a a a a g c c t c c t c a c t a c t t c t g g a a t a g g c c c t c g a a a a a c g t t t t c g g a t c c g g a g g t t t t t t c g g a g g a g t g a t g a a g a c c t t a t

3300 SV40 promoter SV40 promoter SV40 ori G G A G C C G G A G A C G T A T T T A T SV40pro-F g c t c a g a g g c a g a g g c g g c c t c g g c c t c t g c a t a a a t a a a a a a a a t t a g t c a g c c a t g g g c g a g t c t c c g t c t c c g c c g g a g c c g g a g a c g t a t t t a t t t t t t t t a a t c a g t c g g t a c c c

3360 SV40 promoter SV40 promoter SV40 ori g c g g a g a a t g g g c g g a a c t g g g c g g a g t t a g g g g c g g g a t g g g c g g a g t t a g g g g c g g g a c g c c t c t t a c c c g c c t t g a c c c g c c t c a a t c c c c g c c c t a c c c g c c t c a a t c c c c g c c c t

NsiISphI 3420 SV40 promoter SV40 promoter c t a t g g t t g c t g a c t a a t t g a g a t g c a t g c t t t g c a t a c t t c t g c c t g c t g g g g a g c c t g g a t a c c a a c g a c t g a t t a a c t c t a c g t a c g a a a c g t a t g a a g a c g g a c g a c c c c t c g g a c

3480 A C C C T A A C T G A C A C A C A T T C C pBABE 3' g g g a c t t t c c a c a c c c t a a c t g a c a c a c a t t c c a c a g a a t t c a a g t g a t c t c c a a a a a a t c c c t g a a a g g t g t g g g a t t g a c t g t g t g t a a g g t g t c t t a a g t t c a c t a g a g g t t t t t t a

3540 a a g t a c t t t t t g a c t g t a a a t a a a a t t g t a a g g a g t a a a a a g t a c t t t t t t t t c t a a a a a t t c a t g a a a a a c t g a c a t t t a t t t t a a c a t t c c t c a t t t t t c a t g a a a a a a a a g a t t t t t

3600 a a t g t a a t t a a g t a a a a g t a a a a g t a t t g a t t t t t a a t t g t a c t c a a g t a a a g t a a a a a t t t a c a t t a a t t c a t t t t c a t t t t c a t a a c t a a a a a t t a a c a t g a g t t c a t t t c a t t t t t a

AflII 3660 c c c c a a a a a t a a t a c t t a a g t a c a g t a a t c a a g t a a a a t t a c t c a a g t a c t t t a c a c c t c g g g g t t t t t a t t a t g a a t t c a t g t c a t t a g t t c a t t t t a a t g a g t t c a t g a a a t g t g g a g

Eco53kISacI 3720 T3 promoter G G T3 t g g t t c t t g a c c c c c t a c c t t c a g c a a g c c c a g c a g a t c c g a g c t c c a g c t t t t g t t c c c a c c a a g a a c t g g g g g a t g g a a g t c g t t c g g g t c g t c t a g g c t c g a g g t c g a a a a c a a g g g

3780 T3 promoter M13 rev A A A T C A C T C C C A A T T A A C G T3 C A G T A T C G A C A A A G G A C M13 Reverse G G A C A C A C T T M13/pUC Reverse t t t a g t g a g g g t t a a t t g c g c g c t t g g c g t a a t c a t g g t c a t a g c t g t t t c c t g t g t g a a a a a t c a c t c c c a a t t a a c g c g c g a a c c g c a t t a g t a c c a g t a t c g a c a a a g g a c a c a c t t

3840 -10 -35 lac operator lac promoter T A A C A A T A G G C G A M13/pUC Reverse a t t g t t a t c c g c t c a c a a t t c c a c a c a a c a t a c g a g c c g g a a g c a t a a a g t g t a a a g c c t t a a c a a t a g g c g a g t g t t a a g g t g t g t t g t a t g c t c g g c c t t c g t a t t t c a c a t t t c g g a

3900 CAP binding site g g g g t g c c t a a t g a g t g a g c t a a c t c a c a t t a a t t g c g t t g c g c t c a c t g c c c g c t t t c c c c c c a c g g a t t a c t c a c t c g a t t g a g t g t a a t t a a c g c a a c g c g a g t g a c g g g c g a a a g g

3960 a g t c g g g a a a c c t g t c g t g c c a g c t g c a t t a a t g a a t c g g c c a a c g c g c g g g g a g a g g c g t c a g c c c t t t g g a c a g c a c g g t c g a c g t a a t t a c t t a g c c g g t t g c g c g c c c c t c t c c g c

BspQISapI 4020 G A G C G A G T G A C T G A G C G A L4440 g t t t g c g t a t t g g g c g c t c t t c c g c t t c c t c g c t c a c t g a c t c g c t g c g c t c g g t c g t t c c a a a c g c a t a a c c c g c g a g a a g g c g a a g g a g c g a g t g a c t g a g c g a c g c g a g c c a g c a a g

4080 g g c t g c g g c g a g c g g t a t c a g c t c a c t c a a a g g c g g t a a t a c g g t t a t c c a c a g a a t c a g c c g a c g c c g c t c g c c a t a g t c g a g t g a g t t t c c g c c a t t a t g c c a a t a g g t g t c t t a g t c

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

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

4260 ori T T T C T A T G G T C C G C A A A G G G pBR322ori-F g a c g c t c a a g t c a g a g g t g g c g a a a c c c g a c a g g a c t a t a a a g a t a c c a g g c g t t t c c c c c t g c g a g t t c a g t c t c c a c c g c t t t g g g c t g t c c t g a t a t t t c t a t g g t c c g c a a a g g g g

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

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

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

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

AlwNI 4560 ori c a c t g g c a g c a g c c a c t g g t a a c a g g a t t a g c a g a g c g a g g t a t g t a g g c g g t g c t a c a g g t g a c c g t c g t c g g t g a c c a t t g t c c t a a t c g t c t c g c t c c a t a c a t c c g c c a c g a t g t c

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

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

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

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

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

4920 * AmpR * a t t a a a a a t g a a g t t t t a a a t c a a t c t a a a g t a t a t a t g a g t a a a c t t g g t c t g a c a g t t t a a t t t t t a c t t c a a a a t t t a g t t a g a t t t c a t a t a t a c t c a t t t g a a c c a g a c t g t c a a

4980 285 280 275 270 WHKILSAGIEAIQRNREDMT AmpR WHKILSAGIEAIQRNREDMT a c c a a t g c t t a a t c a g t g a g g c a c c t a t c t c a g c g a t c t g t c t a t t t c g t t c a t c c a t a g t g g t t a c g a a t t a g t c a c t c c g t g g a t a g a g t c g c t a g a c a g a t a a a g c a a g t a g g t a t c

AhdI 5040 265 260 255 250 AQSGTTYIVVIRSPKGDPGL AmpR AQSGTTYIVVIRSPKGDPGL t t g c c t g a c t c c c c g t c g t g t a g a t a a c t a c g a t a c g g g a g g g c t t a c c a t c t g g c c c c a a a c g g a c t g a g g g g c a g c a c a t c t a t t g a t g c t a t g c c c t c c c g a a t g g t a g a c c g g g g t

BsaI 5100 245 240 235 230 AAIIGRSGREGAGSKDAIFW AmpR AAIIGRSGREGAGSKDAIFW g t g c t g c a a t g a t a c c g c g a g a c c c a c g c t c a c c g g c t c c a g a t t t a t c a g c a a t a a a c c c a c g a c g t t a c t a t g g c g c t c t g g g t g c g a g t g g c c g a g g t c t a a a t a g t c g t t a t t t g g

5160 225 220 215 210 GAPLASRLLPGAVKDAEMWD AmpR GAPLASRLLPGAVKDAEMWD a g c c a g c c g g a a g g g c c g a g c g c a g a a g t g g t c c t g c a a c t t t a t c c g c c t c c a t c c a g t t c g g t c g g c c t t c c c g g c t c g c g t c t t c a c c a g g a c g t t g a a a t a g g c g g a g g t a g g t c a

5220 205 200 195 190 ILQQRSALTLLEGTLLKRLT AmpR ILQQRSALTLLEGTLLKRLT c t a t t a a t t g t t g c c g g g a a g c t a g a g t a a g t a g t t c g c c a g t t a a t a g t t t g c g c a a c g g a t a a t t a a c a a c g g c c c t t c g a t c t c a t t c a t c a a g c g g t c a a t t a t c a a a c g c g t t g c

5280 185 180 175 170 TAMAVPMTTDREDNPIAENL AmpR TAMAVPMTTDREDNPIAENL t t g t t g c c a t t g c t a c a g g c a t c g t g g t g t c a c g c t c g t c g t t t g g t a t g g c t t c a t t c a a a c a a c g g t a a c g a t g t c c g t a g c a c c a c a g t g c g a g c a g c a a a c c a t a c c g a a g t a a g t

5340 165 160 155 150 EPEWRDLRTVHDGMNHLFAT AmpR EPEWRDLRTVHDGMNHLFAT g c t c c g g t t c c c a a c g a t c a a g g c g a g t t a c a t g a t c c c c c a t g t t g t g c a a a a a a g c g g c g a g g c c a a g g g t t g c t a g t t c c g c t c a a t g t a c t a g g g g g t a c a a c a c g t t t t t t c g c c

5400 145 140 135 130 LEKPGGITTLLLNAATNDSM AmpR LEKPGGITTLLLNAATNDSM t t a g c t c c t t c g g t c c t c c g a t c g t t g t c a g a a g t a a g t t g g c c g c a g t g t t a t c a c t c a a a t c g a g g a a g c c a g g a g g c t a g c a a c a g t c t t c a t t c a a c c g g c g t c a c a a t a g t g a g t

5460 125 120 115 110 TIAASCLERVTMGDTLHKET AmpR TIAASCLERVTMGDTLHKET t g g t t a t g g c a g c a c t g c a t a a t t c t c t t a c t g t c a t g c c a t c c g t a a g a t g c t t t t c t g a c c a a t a c c g t c g t g a c g t a t t a a g a g a a t g a c a g t a c g g t a g g c a t t c t a c g a a a a g a c

5520 105 100 95 90 VPSYEVLDNQSYHIRRGLQE AmpR VPSYEVLDNQSYHIRRGLQE t g a c t g g t g a g t a c t c a a c c a a g t c a t t c t g a g a a t a g t g t a t g c g g c g a c c g a g t t g c t a c t g a c c a c t c a t g a g t t g g t t c a g t a a g a c t c t t a t c a c a t a c g c c g c t g g c t c a a c g a

5580 85 80 75 70 QGADIRSLVAGCLLVKFTSM AmpR A T A A T A C C G C G C C A C A T A G C Amp-R QGADIRSLVAGCLLVKFTSM c t t g c c c g g c g t c a a t a c g g g a t a a t a c c g c g c c a c a t a g c a g a a c t t t a a a a g t g c t c a g a a c g g g c c g c a g t t a t g c c c t a t t a t g g c g c g g t g t a t c g t c t t g a a a t t t t c a c g a g t

XmnI 5640 65 60 55 50 MPFREEPRFSELIKGSNLDL AmpR MPFREEPRFSELIKGSNLDL t c a t t g g a a a a c g t t c t t c g g g g c g a a a a c t c t c a a g g a t c t t a c c g c t g t t g a g a t c c a a g t a a c c t t t t g c a a g a a g c c c c g c t t t t g a g a g t t c c t a g a a t g g c g a c a a c t c t a g g t

5700 45 40 35 30 EIYGVRAGLQDEADKVKVLT AmpR EIYGVRAGLQDEADKVKVLT g t t c g a t g t a a c c c a c t c g t g c a c c c a a c t g a t c t t c a g c a t c t t t t a c t t t c a c c a g c g c a a g c t a c a t t g g g t g a g c a c g t g g g t t g a c t a g a a g t c g t a g a a a a t g a a a g t g g t c g c

5760 25 EPH 20 15 10 signal sequence AFVPLCFAAFFPILAVR AmpR EPHAFVPLCFAAFFPILAVR t t t c t g g g t g a g c a a a a a c a g g a a g g c a a a a t g c c g c a a a a a a g g g a a t a a g g g c g a c a c a a a g a c c c a c t c g t t t t t g t c c t t c c g t t t t a c g g c g t t t t t t c c c t t a t t c c c g c t g t g

5820 5 1 signal sequence FHQISM AmpR AmpR promoter FHQISM g g a a a t g t t g a a t a c t c a t a c t c t t c c t t t t t c a a t a t t a t t g a a g c a t t t a t c a g g g t t c c t t t a c a a c t t a t g a g t a t g a g a a g g a a a a a g t t a t a a t a a c t t c g t a a a t a g t c c c a a

5880 AmpR promoter a t t g t c t c a t g a g c g g a t a c a t a t t t g a a t g t a t t t a g a a a a a t a a a c a a a t a g g g g t t c t a a c a g a g t a c t c g c c t a t g t a t a a a c t t a c a t a a a t c t t t t t a t t t g t t t a t c c c c a a g

3ʹ 5ʹ 5903 AmpR promoter c g c g c a c a t t t c c c c g a a a a g t g g c g c g t g t a a a g g g g c t t t t c a c

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.