Addgene rAAV-U6-MeCP2shRNA-CamKIIa-mCherry Sequencing Result - Sequence Analyzer Skip to main content
Addgene

Sequence Analyzer: rAAV-U6-MeCP2shRNA-CamKIIa-mCherry Sequencing Result


Map View

pBRrevBam (6636 .. 6655) AfeI (6596) pRS-marker (6403 .. 6422) pGEX 3' (6281 .. 6303) pBRforEco (6225 .. 6243) SspI (6069) Amp-R (5815 .. 5834) ScaI (5745) PvuI (5635) FspI (5487) pBR322ori-F (4513 .. 4532) AflIII - PciI (4372) pBABE 3' (4172 .. 4192) CsiI - SexAI * (4100) SfiI (3922) AvrII (3868) BGH-rev (3418 .. 3435) AccI (3402) SP6 (112 .. 129) Acc65I (332) KpnI (336) AbsI (338) EcoRI (356) DraIII - PmlI (395) hU6-F (445 .. 465) LKO.1 5' (616 .. 635) NdeI (623) BamHI (689) BsaBI * (728) BglII (757) HindIII (763) Bsu36I (1161) PflFI - Tth111I (1214) BsmI (1229) PaqCI (1804) PpuMI * (1878) NruI (1902) mCherry-R (2190 .. 2208) SbfI (2400) mCherry-F (2458 .. 2477) BbvCI (2583) AleI (2687) WPRE-R (2856 .. 2876) SacII (3306) SalI (3401) rAAV-U6-MeCP2shRNA-CamKIIa-mCherry 6833 bp

Sequence View

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

120 SP6 promoter A T T T A G G T G SP6 g t t a g a a c g c g g c t a c a a t t a a t a c a t a a c c t t a t g t a t c a t a c a c a t a c g a t t t a g g t g c a a t c t t g c g c c g a t g t t a a t t a t g t a t t g g a a t a c a t a g t a t g t g t a t g c t a a a t c c a c

180 SP6 promoter AAV2 ITR A C A C T A T A G SP6 a c a c t a t a g a a t a c a c g g a a t t a a t t c t a g c t g c g c g c t c g c t c g c t c a c t g a g g c c g c c t g t g a t a t c t t a t g t g c c t t a a t t a a g a t c g a c g c g c g a g c g a g c g a g t g a c t c c g g c g g

240 AAV2 ITR c g g g c a a a g c c c g g g c g t c g g g c g a c c t t t g g t c g c c c g g c c t c a g t g a g c g a g c g a g c g g c c c g t t t c g g g c c c g c a g c c c g c t g g a a a c c a g c g g g c c g g a g t c a c t c g c t c g c t c g c

300 AAV2 ITR c g c a g a g a g g g a g t g g c c a a c t c c a t c a c t a g g g g t t c c t t g t a g t t a a t g a t t a a c c c g g c g t c t c t c c c t c a c c g g t t g a g g t a g t g a t c c c c a a g g a a c a t c a a t t a c t a a t t g g g c

EcoRIAcc65IKpnIAbsI 360 c c a t g c t a c t t a t c t a c g t a g c c a t g c t c t a g g t a c c c t c g a g g a g g a g a a g c a t g a a t t g g t a c g a t g a a t a g a t g c a t c g g t a c g a g a t c c a t g g g a g c t c c t c c t c t t c g t a c t t a a

DraIIIPmlI 420 c c c c a g t g g a a a g a c g c g c a g g c a a a a c g c a c c a c g t g a c g g a g c g t g a c c g c g c g c c g a g g g g t c a c c t t t c t g c g c g t c c g t t t t g c g t g g t g c a c t g c c t c g c a c t g g c g c g c g g c t

480 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 c g c g c g c c a a g g t c g g g c a g g a a 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 c g c g c g c g g t t c c a g c c c g t c c t t 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

540 U6 promoter 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 a 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 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 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

600 U6 promoter 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 a g t t t g c a g t t t t a a a a 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 a t c a a a c g t c a a a a t t t t

NdeI 660 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 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 a g t a t t t c g a t t t c t t g 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 t t c a t a a a g c t a a a g a a c

BamHI 720 U6 promoter g g t t t a t a t a t c t t g t g g a a a g g a c g c g g g a t c c c g t c a g a a g a c c a g g a t c t c c a t t c a c c a a a t a t a t a g a a c a c c t t t c c t g c g c c c t a g g g c a g t c t t c t g g t c c t a g a g g t a a g t

HindIIIBglIIBsaBI* 780 a g a g a t g g a g a t c c t g g t c t t c t g a c t t t t t t g g a a a g a t c t a a g c t t g g c a c t g g c c g t t c t c t a c c t c t a g g a c c a g a a g a c t g a a a a a a c c t t t c t a g a t t c g a a c c g t g a c c g g c a

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

900 g a a a t g t c a g a g c t a g a a c t t g a a c t c a g a t t a c t a a t c t t a a a t t c c a t g c c t t g g g g g c t t t a c a g t c t c g a t c t t g a a c t t g a g t c t a a t g a t t a g a a t t t a a g g t a c g g a a c c c c c

960 c a t g c a a g t a c g a t a t a c a g a a g g a g t g a a c t c a t t a g g g c a g a t g a c c a a t g a g t t t a g g t a c g t t c a t g c t a t a t g t c t t c c t c a c t t g a g t a a t c c c g t c t a c t g g t t a c t c a a a t c

1020 g a a a g a a g a g t c c a g g g c a g g g t a c a t c t a c a c c a c c c g c c c a g c c c t g g g t g a g t c c a g c t t t c t t c t c a g g t c c c g t c c c a t g t a g a t g t g g t g g g c g g g t c g g g a c c c a c t c a g g t c

1080 c c a c g t t c a c c t c a t t a t a g t t g c c t c t c t c c a g t c c t a c c t t g a c g g g a a g c a c a a g c a g g t g c a a g t g g a g t a a t a t c a a c g g a g a g a g g t c a g g a t g g a a c t g c c c t t c g t g t t c g t

1140 g a a a c t g g g a c a g g a g c c c c a g g a g a c c a a a t c t t c a t g g t c c c t c t g g g a g g a t g g g t g c t t t g a c c c t g t c c t c g g g g t c c t c t g g t t t a g a a g t a c c a g g g a g a c c c t c c t a c c c a c

Bsu36I 1200 g g g a g a g c t g t g g c a g a g g c c t c a g g a g g g g c c c t g c t g c t c a g t g g t g a c a g a t a g g g g c c c t c t c g a c a c c g t c t c c g g a g t c c t c c c c g g g a c g a c g a g t c a c c a c t g t c t a t c c c c

BsmITth111IPflFI 1260 t g a g a a a g c a g a c a g a g t c a t t c c g t c a g c a t t c t g g g t c t g t t t g g t a c t t c t t c t c a c a c t c t t t c g t c t g t c t c a g t a a g g c a g t c g t a a g a c c c a g a c a a a c c a t g a a g a a g a g t g

1320 g c t a a g g t g g c g g t g t g a t a t g c a c a a t g g c t a a a a a g c a g g g a g a g c t g g a a a g a a a c a c g a t t c c a c c g c c a c a c t a t a c g t g t t a c c g a t t t t t c g t c c c t c t c g a c c t t t c t t t g t

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

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

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

1560 a g g g t a a c t a c a t c c t g t c t t t c t c a a g g a c c a t c c c a g a a t g t g g c a c c c a c t a g c c g t t c c c a t t g a t g t a g g a c a g a a a g a g t t c c t g g t a g g g t c t t a c a c c g t g g g t g a t c g g c a

1620 t a c c a t a g c a a c t g c c t c t t t g c c c c a c t t a a t c c c a t c c c g t c t g t t a a a a g g g c c c t a a t g g t a t c g t t g a c g g a g a a a c g g g g t g a a t t a g g g t a g g g c a g a c a a t t t t c c c g g g a t

1680 t a g t t g g a g g t g g g g g a g g t a g g a a g a g c g a t g a t c a c t t g t g g a c t a a g t t t g t t c g c a a t c a a c c t c c a c c c c c t c c a t c c t t c t c g c t a c t a g t g a a c a c c t g a t t c a a a c a a g c g t

1740 t c c c c t t c t c c a a c c c c c t c a g t a c a t c a c c c t g g g g g a a c a g g g t c c a c t t g c t c c t g g a g g g g a a g a g g t t g g g g g a g t c a t g t a g t g g g a c c c c c t t g t c c c a g g t g a a c g a g g a c c

1800 g c c c a c a c a g t c c t g c a g t a t t g t g t a t a t a a g g c c a g g g c a a a g a g g a g c a g g t t t t a a c g g g t g t g t c a g g a c g t c a t a a c a c a t a t a t t c c g g t c c c g t t t c t c c t c g t c c a a a a t t

PaqCI 1860 a g t g a a a g g c a g g c a g g t g t t g g g g a g g c a g t t a c c g g g g c a a c g g g a a c a g g g c g t t t c t c a c t t t c c g t c c g t c c a c a a c c c c t c c g t c a a t g g c c c c g t t g c c c t t g t c c c g c a a a g

NruIPpuMI* 1920 MGTWMLTKAREAVSSH g g a g g t g g t t g c c a t g g g g a c c t g g a t g c t g a c g a a g g c t c g c g a g g c t g t g a g c a g c c a c c t c c a c c a a c g g t a c c c c t g g a c c t a c g a c t g c t t c c g a g c g c t c c g a c a c t c g t c g g t

1980 SALLRSPKLVSQAGSPFALR c a g t g c c c t g c t c a g a a g c c c c a a g c t c g t c a g t c a a g c c g g t t c t c c g t t t g c a c t c a g g t c a c g g g a c g a g t c t t c g g g g t t c g a g c a g t c a g t t c g g c c a a g a g g c a a a c g t g a g t c

2040 STGRRVAPSSGGSGGSGGSG g a g c a c g g g c a g g c g a g t g g c c c c t a g t t c t g g g g g c a g c g g g g g a t c a g g t g g c a g c g g c t c g t g c c c g t c c g c t c a c c g g g g a t c a a g a c c c c c g t c g c c c c c t a g t c c a c c g t c g c c

2100 1 5 10 15 MVSKGEEDNMAIIKEFMRF mCherry GMVSKGEEDNMAIIKEFMRF t g g c a t g g t g a g c a a g g g c g a g g a g g a t a a c a t g g c c a t c a t c a a g g a g t t c a t g c g c t t a c c g t a c c a c t c g t t c c c g c t c c t c c t a t t g t a c c g g t a g t a g t t c c t c a a g t a c g c g a a

2160 20 25 30 35 KVHMEGSVNGHEFEIEGEGE mCherry KVHMEGSVNGHEFEIEGEGE c a a g g t g c a c a t g g a g g g c t c c g t g a a c g g c c a c g a g t t c g a g a t c g a g g g c g a g g g c g a g t t c c a c g t g t a c c t c c c g a g g c a c t t g c c g g t g c t c a a g c t c t a g c t c c c g c t c c c g c t

2220 40 45 50 55 GRPYEGTQTAKLKVTKGGPL mCherry G G T T C G A C T T C C A C T G G T T mCherry-R GRPYEGTQTAKLKVTKGGPL g g g c c g c c c c t a c g a g g g c a c c c a g a c c g c c a a g c t g a a g g t g a c c a a g g g t g g c c c c c t c c c g g c g g g g a t g c t c c c g t g g g t c t g g c g g t t c g a c t t c c a c t g g t t c c c a c c g g g g g a

2280 60 65 70 75 PFAWDILSPQFMYGSKAYVK mCherry PFAWDILSPQFMYGSKAYVK g c c c t t c g c c t g g g a c a t c c t g t c c c c t c a g t t c a t g t a c g g c t c c a a g g c c t a c g t g a a c g g g a a g c g g a c c c t g t a g g a c a g g g g a g t c a a g t a c a t g c c g a g g t t c c g g a t g c a c t t

2340 80 85 90 95 HPADIPDYLKLSFPEGFKWE mCherry HPADIPDYLKLSFPEGFKWE g c a c c c c g c c g a c a t c c c c g a c t a c t t g a a g c t g t c c t t c c c c g a g g g c t t c a a g t g g g a c g t g g g g c g g c t g t a g g g g c t g a t g a a c t t c g a c a g g a a g g g g c t c c c g a a g t t c a c c c t

SbfI 2400 100 105 110 115 RVMNFEDGGVVTVTQDSSLQ mCherry RVMNFEDGGVVTVTQDSSLQ g c g c g t g a t g a a c t t c g a g g a c g g c g g c g t g g t g a c c g t g a c c c a g g a c t c c t c c c t g c a c g c g c a c t a c t t g a a g c t c c t g c c g c c g c a c c a c t g g c a c t g g g t c c t g a g g a g g g a c g t

2460 120 125 130 135 DGEFIYKVKLRGTNFPSDGP mCherry C C C mCherry-F DGEFIYKVKLRGTNFPSDGP g g a c g g c g a g t t c a t c t a c a a g g t g a a g c t g c g c g g c a c c a a c t t c c c c t c c g a c g g c c c c c t g c c g c t c a a g t a g a t g t t c c a c t t c g a c g c g c c g t g g t t g a a g g g g a g g c t g c c g g g

2520 140 145 150 155 VMQKKTMGWEASSERMYPED mCherry C G T A A T G C A G A A G A A G A mCherry-F VMQKKTMGWEASSERMYPED c g t a a t g c a g a a g a a g a c c a t g g g c t g g g a g g c c t c c t c c g a g c g g a t g t a c c c c g a g g a g c a t t a c g t c t t c t t c t g g t a c c c g a c c c t c c g g a g g a g g c t c g c c t a c a t g g g g c t c c t

2580 160 165 170 175 GALKGEIKQRLKLKDGGHYD mCherry GALKGEIKQRLKLKDGGHYD c g g c g c c c t g a a g g g c g a g a t c a a g c a g a g g c t g a a g c t g a a g g a c g g c g g c c a c t a c g a g c c g c g g g a c t t c c c g c t c t a g t t c g t c t c c g a c t t c g a c t t c c t g c c g c c g g t g a t g c t

BbvCI 2640 180 185 190 195 AEVKTTYKAKKPVQLPGAYN mCherry AEVKTTYKAKKPVQLPGAYN c g c t g a g g t c a a g a c c a c c t a c a a g g c c a a g a a g c c c g t g c a g c t g c c c g g c g c c t a c a a g c g a c t c c a g t t c t g g t g g a t g t t c c g g t t c t t c g g g c a c g t c g a c g g g c c g c g g a t g t t

AleI 2700 200 205 210 215 VNIKLDITSHNEDYTIVEQY mCherry VNIKLDITSHNEDYTIVEQY c g t c a a c a t c a a g t t g g a c a t c a c c t c c c a c a a c g a g g a c t a c a c c a t c g t g g a a c a g t a g c a g t t g t a g t t c a a c c t g t a g t g g a g g g t g t t g c t c c t g a t g t g g t a g c a c c t t g t c a t

2760 220 225 230 235 ERAEGRHSTGGMDELYK* mCherry ERAEGRHSTGGMDELYK* c g a a c g c g c c g a g g g c c g c c a c t c c a c c g g c g g c a t g g a c g a g c t g t a c a a g t a g g g t g g g c t t g c g c g g c t c c c g g c g g t g a g g t g g c c g c c g t a c c t g c t c g a c a t g t t c a t c c c a c c

2820 WPRE c a g c g g t g g c a c t c g a g t a a g c t a t c a a g c t a g c t t a t c g a t a a t c a a c c t c t g g a t t a c g t c g c c a c c g t g a g c t c a t t c g a t a g t t c g a t c g a a t a g c t a t t a g t t g g a g a c c t a a t g

2880 WPRE A C A A C G A G G A A A A T G C G A T A C WPRE-R a a a a t t t g t g a a a g a t t g a c t g g t a t t c t t a a c t a t g t t g c t c c t t t t a c g c t a t g t g g a t t t t a a a c a c t t t c t a a c t g a c c a t a a g a a t t g a t a c a a c g a g g a a a a t g c g a t a c a c c t

2940 WPRE MPLYHAIASRMAFIFS MLLLPVWLSFSP t a c g c t g c t t t a a t g c c t t t g t a t c a t g c t a t t g c t t c c c g t a t g g c t t t c a t t t t c t c c a t g c g a c g a a a t t a c g g a a a c a t a g t a c g a t a a c g a a g g g c a t a c c g a a a g t a a a a g a g g

3000 WPRE SLYKSWLLSLYEELWPVVRQ PCINPGCCLFMRSCGPLSGN t c c t t g t a t a a a t c c t g g t t g c t g t c t c t t t a t g a g g a g t t g t g g c c c g t t g t c a g g c a a a g g a a c a t a t t t a g g a c c a a c g a c a g a g a a a t a c t c c t c a a c a c c g g g c a a c a g t c c g t t

3060 WPRE RGVVCTVFADATPTGWGIAT VAWCALCLLTQPPLVGALPP c g t g g c g t g g t g t g c a c t g t g t t t g c t g a c g c a a c c c c c a c t g g t t g g g g c a t t g c c a c c g c a c c g c a c c a c a c g t g a c a c a a a c g a c t g c g t t g g g g g t g a c c a a c c c c g t a a c g g t g g

3120 WPRE TCQLLSGTFAFPLPIATAEL PVSSFPGLSLSPSLLPRRNS a c c t g t c a g c t c c t t t c c g g g a c t t t c g c t t t c c c c c t c c c t a t t g c c a c g g c g g a a c t c t g g a c a g t c g a g g a a a g g c c c t g a a a g c g a a a g g g g g a g g g a t a a c g g t g c c g c c t t g a g

3180 WPRE IAACLARCWTGARLLGTDNS SPPALPAAGQGLGCWALTIP a t c g c c g c c t g c c t t g c c c g c t g c t g g a c a g g g g c t c g g c t g t t g g g c a c t g a c a a t t c c t a g c g g c g g a c g g a a c g g g c g a c g a c c t g t c c c c g a g c c g a c a a c c c g t g a c t g t t a a g g

3240 WPRE (in frame with Factor Xa site) *RGKRPQEGTNGGP VVLSGKSSSFPWLLACVATW WCCRGNHRPFLGCSPVLPPG g t g g t g t t g t c g g g g a a a t c a t c g t c c t t t c c t t g g c t g c t c g c c t g t g t t g c c a c c t g g c a c c a c a a c a g c c c c t t t a g t a g c a g g a a a g g a a c c g a c g a g c g g a c a c a a c g g t g g a c c

3300 WPRE (in frame with Factor Xa site) NQAPRGEAVDR 1 RGEI Factor Xa site ILRGTSFCYVPSALNPADLP FCAGRPSATSLRPSIQRTFL a t t c t g c g c g g g a c g t c c t t c t g c t a c g t c c c t t c g g c c c t c a a t c c a g c g g a c c t t c c t t a a g a c g c g c c c t g c a g g a a g a c g a t g c a g g g a a g c c g g g a g t t a g g t c g c c t g g a a g g a

SacII 3360 WPRE SRGLLPALRPLPRLRLRPQT PAACCRLCGLFRVFAFALRR t c c c g c g g c c t g c t g c c g g c t c t g c g g c c t c t t c c g c g t c t t c g c c t t c g c c c t c a g a c g a g g g c g c c g g a c g a c g g c c g a g a c g c c g g a g a a g g c g c a g a a g c g g a a g c g g g a g t c t g c

SalIAccI 3420 WPRE G G A BGH-rev SRISLWAASPHRYRRLADQP VGSPFGPPPRIDTVDSLISL a g t c g g a t c t c c c t t t g g g c c g c c t c c c c g c a t c g a t a c c g t c g a c t c g c t g a t c a g c c t t c a g c c t a g a g g g a a a c c c g g c g g a g g g g c g t a g c t a t g g c a g c t g a g c g a c t a g t c g g a

3480 bGH poly(A) signal G C T G A C A C G G A A G A T BGH-rev RLCLLVASHLLFAPPPCLP* DCAF* c g a c t g t g c c t t c t a g t t g c c a g c c a t c t g t t g t t t g c c c c t c c c c c g t g c c t t c c t t g a g c t g a c a c g g a a g a t c a a c g g t c g g t a g a c a a c a a a c g g g g a g g g g g c a c g g a a g g a a c t

3540 bGH poly(A) signal c c c t g g a a g g t g c c a c t c c c a c t g t c c t t t c c t a a t a a a a t g a g g a a a t t g c a t c g c a t t g g g a c c t t c c a c g g t g a g g g t g a c a g g a a a g g a t t a t t t t a c t c c t t t a a c g t a g c g t a a

3600 bGH poly(A) signal g t c t g a g t a g g t g t c a t t c t a t t c t g g g g g g t g g g g t g g g g c a g g a c a g c a a g g g g g a g g c a g a c t c a t c c a c a g t a a g a t a a g a c c c c c c a c c c c a c c c c g t c c t g t c g t t c c c c c t c c

3660 bGH poly(A) signal a t t g g g a a g a c a a t a g c a g g c a t g c t g g g g a t g c g g t g g g c t c t a t g g c t t c t g a g g c g g t a a c c c t t c t g t t a t c g t c c g t a c g a c c c c t a c g c c a c c c g a g a t a c c g a a g a c t c c g c c

3720 a a a g a a c c a g c t g g g g c t c g a c t a g a g c a t g g c t a c g t a g a t a a g t a g c a t g g c g g g t t a t t t c t t g g t c g a c c c c g a g c t g a t c t c g t a c c g a t g c a t c t a t t c a t c g t a c c g c c c a a t

3780 a t c a t t a a c t a c a a g g a a c c c c t a g t g a t g g a g t t g g c c a c t c c c t c t c t g c g c g c t c g c t a g t a a t t g a t g t t c c t t g g g g a t c a c t a c c t c a a c c g g t g a g g g a g a g a c g c g c g a g c g

3840 t c g c t c a c t g a g g c c g g g c g a c c a a a g g t c g c c c g a c g c c c g g g c g g c c t c a g t g a g c g a a g c g a g t g a c t c c g g c c c g c t g g t t t c c a g c g g g c t g c g g g c c c g c c g g a g t c a c t c g c t

AvrII 3900 SV40 promoter SV40 ori g c g a g c g c g c a 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 c g c t c g c g c g t 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

SfiI 3960 SV40 promoter SV40 ori t g g a a t a g c t c a g a g g c c 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 a c c t t a t c g a g t c t c c g g 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

4020 SV40 promoter SV40 ori c c a t g g g 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 t a c c c 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

4080 SV40 promoter g g c g g g a 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 c c g c c c t 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

SexAI*CsiI 4140 SV40 promoter g a g c c t g g g g a c t t t c c a c a c c 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 c g g a c c c c t g a a a g g t g t g g 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

4200 SV40 promoter A C C C T A A C T G A C A C A C A T T C C pBABE 3' c t g c c t g c t g g g g a g c c t g 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 c t g c g a c g g a c g a c c c c t c g g a c 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 g a c g

4260 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 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 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 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

4320 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 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 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 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

AflIIIPciI 4380 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 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 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 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

4440 ori 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 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 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 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

4500 ori 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 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 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 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

4560 ori T T T C T A T G G T C C G C A A A G G G pBR322ori-F 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 g a a g c t c c c t c g t g c g c t c t c c t 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 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

4620 ori 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 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 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 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

4680 ori 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 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 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 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

4740 ori 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 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 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 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

4800 ori 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 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 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 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

4860 ori 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 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 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 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

4920 ori 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 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 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 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

4980 ori 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 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 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 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

5040 ori 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 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 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 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

5100 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 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 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 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

5160 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 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 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 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

5220 285 280 *WHKILSAGI AmpR *WHKILSAGI 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 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 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 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

5280 275 270 265 260 EAIQRNREDMTAQSGTTYIV AmpR EAIQRNREDMTAQSGTTYIV 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 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 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 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

5340 255 250 245 240 VIRSPKGDPGLAAIIGRSGR AmpR VIRSPKGDPGLAAIIGRSGR 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 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 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 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

5400 235 230 225 220 EGAGSKDAIFWGAPLASRLL AmpR EGAGSKDAIFWGAPLASRLL 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 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 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 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

5460 215 210 205 200 PGAVKDAEMWDILQQRSALT AmpR PGAVKDAEMWDILQQRSALT 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 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 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 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

FspI 5520 195 190 185 180 LLEGTLLKRLTTAMAVPMTT AmpR LLEGTLLKRLTTAMAVPMTT 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 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 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 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

5580 175 170 165 160 DREDNPIAENLEPEWRDLRT AmpR DREDNPIAENLEPEWRDLRT 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 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 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 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

PvuI 5640 155 150 145 140 VHDGMNHLFATLEKPGGITT AmpR VHDGMNHLFATLEKPGGITT 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 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 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 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

5700 135 130 125 120 LLLNAATNDSMTIAASCLER AmpR LLLNAATNDSMTIAASCLER 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 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 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 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

ScaI 5760 115 110 105 100 VTMGDTLHKETVPSYEVLDN AmpR VTMGDTLHKETVPSYEVLDN 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 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 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 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

5820 95 90 85 80 QSYHIRRGLQEQGADIRSLV AmpR A T A A T A Amp-R QSYHIRRGLQEQGADIRSLV 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 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 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 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

5880 75 70 65 60 AGCLLVKFTSMMPFREEPRF AmpR C C G C G C C A C A T A G C Amp-R AGCLLVKFTSMMPFREEPRF 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 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 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 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

5940 55 50 45 40 SELIKGSNLDLEIYGVRAGL AmpR SELIKGSNLDLEIYGVRAGL 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 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 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 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

6000 35 30 25 QDEADKVKVLTEPH 20 signal sequence AFVPLC AmpR QDEADKVKVLTEPHAFVPLC 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 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 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 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

6060 15 10 5 1 signal sequence FAAFFPILAVRFHQISM AmpR AmpR promoter FAAFFPILAVRFHQISM 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 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 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 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

SspI 6120 AmpR promoter 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 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 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 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

6180 AmpR promoter 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 c g c g c a c a t t t c c c c g a a a a g t g c c 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 g c g c g t g t a a a g g g g c t t t t c a c g g t g

6240 A A T A G G C G T A T C A C G A pBRforEco c t g a c g t c t a a g a a a c c a t t a t t a t c a t g a c a t t a a c c t a t a a a a a t a g g c g t a t c a c g a g a c t g c a g a t t c t t t g g t a a t a a t a g t a c t g t a a t t g g a t a t t t t t a t c c g c a t a g t g c t

6300 G G C pBRforEco G G A G A C T G T G T A C G T C G A G G pGEX 3' g g c c c t t t c g t c t c g c g c g t t t c g g t g a t g a c g g t g a a a a c c t c t g a c a c a t g c a g c t c c c c g g g a a a g c a g a g c g c g c a a a g c c a c t a c t g c c a c t t t t g g a g a c t g t g t a c g t c g a g g

6360 G C C pGEX 3' c g g a g a c g g t c a c a g c t t g t c t g t a a g c g g a t g c c g g g a g c a g a c a a g c c c g t c a g g g c g g c c t c t g c c a g t g t c g a a c a g a c a t t c g c c t a c g g c c c t c g t c t g t t c g g g c a g t c c c g c

6420 C G G C A T C A G A G C A G A T T G pRS-marker c g t c a g c g g g t g t t g g c g g g t g t c g g g g c t g g c t t a a c t a t g c g g c a t c a g a g c a g a t t g g c a g t c g c c c a c a a c c g c c c a c a g c c c c g a c c g a a t t g a t a c g c c g t a g t c t c g t c t a a c

6480 T A pRS-marker t a c t g a g a g t g c a c c a t t c g a c g c t c t c c c t t a t g c g a c t c c t g c a t t a g g a a g c a g c c c a t g a c t c t c a c g t g g t a a g c t g c g a g a g g g a a t a c g c t g a g g a c g t a a t c c t t c g t c g g g

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

AfeI 6600 g c g c c c a a c a g t c c c c c g g c c a c g g g g c c t g c c a c c a t a c c c a c g c c g a a a c a a g c g c t c c g c g g g t t g t c a g g g g g c c g g t g c c c c g g a c g g t g g t a t g g g t g c g g c t t t g t t c g c g a g

6660 G G T G A T G T C G G C G A T A T A G G pBRrevBam a t g a g c c c g a a g t g g c g a g c c c g a t c t t c c c c a t c g g t g a t g t c g g c g a t a t a g g c g c c a t a c t c g g g c t t c a c c g c t c g g g c t a g a a g g g g t a g c c a c t a c a g c c g c t a t a t c c g c g g t

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

6780 c t a g c g a t g a c c c t g c t g a t t g g t t c g c t g a c c a t t t c c g g g t g c g g g a c g g c g t t a c c a g a t c g c t a c t g g g a c g a c t a a c c a a g c g a c t g g t a a a g g c c c a c g c c c t g c c g c a a t g g t

3ʹ 5ʹ 6833 g a a a c t c a g a a g g t t c g t c c a a c c a a a c c g a c t c t g a c g g c a g t t t a c g a g a g c t t t g a g t c t t c c a a g c a g g t t g g t t t g g c t g a g a c t g c c g t c a a a t g c t c t 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.