Addgene pENTR D-TOPO-C3_8 - Sequence Analyzer Skip to main content
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Sequence Analyzer: pENTR D-TOPO-C3_8


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PciI (3413) DrdI (3311) pBR322ori-F (3258 .. 3277) BssSI - BssSαI (3240) BciVI (3215) BsiHKAI (3103) ApaLI (3099) AlwNI (3004) PflMI (2501) BsmBI - Esp3I (2254) AsiSI - PvuI (2238) BsrFI (2192) SspI (2163) EcoNI (2150) Kan-R (1880 .. 1899) NruI (1895) pENTR-R (1802 .. 1821) L4440 (92 .. 109) BspQI - SapI (111) rrnB T2 terminator BsaHI (327) AclI (364) HpaI (501) M13/pUC Forward (522 .. 544) M13 Forward (536 .. 553) AhdI (549) AflII (554) AvaI - BsoBI (560) BtgI (669) EagI - NotI - SacII (672) DraIII (690) BfuAI - BspMI - PaqCI (767) BsgI (809) AccI (836) BstZ17I (837) StyI (846) BbvCI (872) BstAPI (912) BanI (955) PpuMI * (967) NdeI (1357) AscI - BssHII (1536) EcoRV (1656) T7 promoter T7 (1660 .. 1679) M13 Reverse (1684 .. 1700) pENTR D-TOPO-C3_8 3419 bp

Sequence View

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

BspQISapI 120 A G C G A G T C A G T G A G C G A G L4440 t a c c g c t c g c c g c a g c c g a a c g a c c g a g c g c a 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 a t g g c g a g c g g c g t c g g c t t g c t g g c t c g c g t 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

180 g c g c c c a a t a c g c a a a c c g c c t c t c c c c g c g c 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 c g g g t t a t g c g t t t g g c g g a g a g g g g c g c g 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

240 c g a c a g g t t t c c c g a c t g g a a a g c g g g c a g t g a g c g c a a c g c a a t t a a t a c g c g t a c c g c g c t g t c c a a a g g g c t g a c c t t t c g c c c g t c a c t c g c g t t g c g t t a a t t a t g c g c a t g g c g

300 rrnB T2 terminator t a g c c a g g a a g a g t t t g t a g a a a c g c a a a a a g g c c a t c c g t c a g g a t g g c c t t c t g c t t a a t c g g t c c t t c t c a a a c a t c t t t g c g t t t t t c c g g t a g g c a g t c c t a c c g g a a g a c g a a t

BsaHI 360 g t t t g a t g c c t g g c a g t t t a t g g c g g g c g t c c t g c c c g c c a c c c t c c g g g c c g t t g c t t c c a a a c t a c g g a c c g t c a a a t a c c g c c c g c a g g a c g g g c g g t g g g a g g c c c g g c a a c g a a g

AclI 420 rrnB T1 terminator a c a a c g t t c a a a t c c g c t c c c g g c g g a t t t g t c c t a c t c a g g a g a g c g t t c a c c g a c a a a t g t t g c a a g t t t a g g c g a g g g c c g c c t a a a c a g g a t g a g t c c t c t c g c a a g t g g c t g t t t

480 rrnB T1 terminator c a a c a g a t a a a a c g a a a g g c c c a g t c t t c c g a c t g a g c c t t t c g t t t t a t t t g a t g c c t g g t t g t c t a t t t t g c t t t c c g g g t c a g a a g g c t g a c t c g g a a a g c a a a a t a a a c t a c g g a c

HpaI 540 M13 fwd C C C A G T C A C G A C G T T G T A A M13/pUC Forward T G T A A M13 Forward g c a g t t c c c t a c t c t c g c g t t a a c g c t a g c a t g g a t g t t t t c c c a g t c a c g a c g t t g t a a c g t c a a g g g a t g a g a g c g c a a t t g c g a t c g t a c c t a c a a a a g g g t c a g t g c t g c a a c a t t

BsoBIAvaIAflIIAhdI 600 M13 fwd attL1 A A C G M13/pUC Forward A A C G A C G G C C A G T M13 Forward a a c g a c g g c c a g t c t t a a g c t c g g g c c c c a a a t a a t g a t t t t a t t t t g a c t g a t a g t g a c t t g c t g c c g g t c a g a a t t c g a g c c c g g g g t t t a t t a c t a a a a t a a a a c t g a c t a t c a c t g

660 attL1 c t g t t c g t t g c a a c a a a t t g a t g a g c a a t g c t t t t t t a t a a t g c c a a c t t t g t a c a a a a a g a c a a g c a a c g t t g t t t a a c t a c t c g t t a c g a a a a a a t a t t a c g g t t g a a a c a t g t t t t t

DraIIIBtgISacIIEagINotI 720 attL1 a g c a g g c t c c g c g g c c g c c c c c t t c a c c g t g t g g g a g a a a a g t c t t c a g g c t g t g g g g g t t c g t c c g a g g c g c c g g c g g g g g a a g t g g c a c a c c c t c t t t t c a g a a g t c c g a c a c c c c c a

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

AccIBstZ17IBsgI 840 t g g c t g t g t g c a g t g g g a a g c t c a t g a a g g a t g a g a a a c c t a c c g c t a t c c t c t g t a t a c a c c g a c a c a c g t c a c c c t t c g a g t a c t t c c t a c t c t t t g g a t g g c g a t a g g a g a c a t a t g

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

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

PpuMI* 1020 c a g c c a g g t c c c c a c t t a c c g t g t g a a c t g c c t c g c c a a a t g t g c c a g g a g c c t c c t g t a g t c g g t c c a g g g g t g a a t g g c a c a c t t g a c g g a g c g g t t t a c a c g g t c c t c g g a g g a c a t

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

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

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

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

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

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

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

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

BssHIIAscI 1560 attL2 g a g t t c t c c t c t g c c a t t c a c a a g g c a a a g g g t g g g c g c g c c g a c c c a g c t t t c t t g t a c c t c a a g a g g a g a c g g t a a g t g t t c c g t t t c c c a c c c g c g c g g c t g g g t c g a a a g a a c a t g

1620 attL2 a a a g t t g g c a t t a t a a g a a a g c a t t g c t t a t c a a t t t g t t g c a a c g a a c a g g t c a c t a t c t t t c a a c c g t a a t a t t c t t t c g t a a c g a a t a g t t a a a c a a c g t t g c t t g t c c a g t g a t a g

EcoRV 1680 attL2 T7 promoter G G G A T A T C A C T C A G C A T A A T T7 a g t c a a a a t a a a a t c a t t a t t t g c c a t c c a g c t g a t a t c c c c t a t a g t g a g t c g t a t t a c t c a g t t t t a t t t t a g t a a t a a a c g g t a g g t c g a c t a t a g g g g a t a t c a c t c a g c a t a a t g

1740 M13 rev C A G T A T C G A C A A A G G A C M13 Reverse a t g g t c a t a g c t g t t t c c t g g c a g c t c t g g c c c g t g t c t c a a a a t c t c t g a t g t t a c a t t t a c c a g t a t c g a c a a a g g a c c g t c g a g a c c g g g c a c a g a g t t t t a g a g a c t a c a a t g t a a

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

1860 1 5 10 15 MSHIQRETSRPRLNSN KanR G T T C C C C A C A A T A C T C G G T A pENTR-R MSHIQRETSRPRLNSN a c a a g g g g t g t t a t g a g c c a t a t t c a a c g g g a a a c g t c g a g g c c g c g a t t a a a t t c c a a c t g t t c c c c a c a a t a c t c g g t a t a a g t t g c c c t t t g c a g c t c c g g c g c t a a t t t a a g g t t g

NruI 1920 20 25 30 35 MDADLYGYKWARDNVGQSGA KanR C C A T A T T T A C C C G A G C G C T A Kan-R MDADLYGYKWARDNVGQSGA a t g g a t g c t g a t t t a t a t g g g t a t a a a t g g g c t c g c g a t a a t g t c g g g c a a t c a g g t g c g t a c c t a c g a c t a a a t a t a c c c a t a t t t a c c c g a g c g c t a t t a c a g c c c g t t a g t c c a c g c

1980 40 45 50 55 TIYRLYGKPDAPELFLKHGK KanR TIYRLYGKPDAPELFLKHGK a c a a t c t a t c g c t t g t a t g g g a a g c c c g a t g c g c c a g a g t t g t t t c t g a a a c a t g g c a a a t g t t a g a t a g c g a a c a t a c c c t t c g g g c t a c g c g g t c t c a a c a a a g a c t t t g t a c c g t t t

2040 60 65 70 75 GSVANDVTDEMVRLNWLTEF KanR GSVANDVTDEMVRLNWLTEF g g t a g c g t t g c c a a t g a t g t t a c a g a t g a g a t g g t c a g a c t a a a c t g g c t g a c g g a a t t t c c a t c g c a a c g g t t a c t a c a a t g t c t a c t c t a c c a g t c t g a t t t g a c c g a c t g c c t t a a a

2100 80 85 90 95 MPLPTIKHFIRTPDDAWLLT KanR MPLPTIKHFIRTPDDAWLLT a t g c c t c t t c c g a c c a t c a a g c a t t t t a t c c g t a c t c c t g a t g a t g c a t g g t t a c t c a c c t a c g g a g a a g g c t g g t a g t t c g t a a a a t a g g c a t g a g g a c t a c t a c g t a c c a a t g a g t g g

EcoNI 2160 100 105 110 115 TAIPGKTAFQVLEEYPDSGE KanR TAIPGKTAFQVLEEYPDSGE a c t g c g a t c c c c g g a a a a a c a g c a t t c c a g g t a t t a g a a g a a t a t c c t g a t t c a g g t g a a t g a c g c t a g g g g c c t t t t t g t c g t a a g g t c c a t a a t c t t c t t a t a g g a c t a a g t c c a c t t

BsrFISspI 2220 120 125 130 135 NIVDALAVFLRRLHSIPVCN KanR NIVDALAVFLRRLHSIPVCN a a t a t t g t t g a t g c g c t g g c a g t g t t c c t g c g c c g g t t g c a t t c g a t t c c t g t t t g t a a t t t a t a a c a a c t a c g c g a c c g t c a c a a g g a c g c g g c c a a c g t a a g c t a a g g a c a a a c a t t a

BsmBIEsp3IAsiSIPvuI 2280 140 145 150 155 CPFNSDRVFRLAQAQSRMNN KanR CPFNSDRVFRLAQAQSRMNN t g t c c t t t t a a c a g c g a t c g c g t a t t t c g t c t c g c t c a g g c g c a a t c a c g a a t g a a t a a c a c a g g a a a a t t g t c g c t a g c g c a t a a a g c a g a g c g a g t c c g c g t t a g t g c t t a c t t a t t g

2340 160 165 170 175 GLVDASDFDDERNGWPVEQV KanR GLVDASDFDDERNGWPVEQV g g t t t g g t t g a t g c g a g t g a t t t t g a t g a c g a g c g t a a t g g c t g g c c t g t t g a a c a a g t c c c a a a c c a a c t a c g c t c a c t a a a a c t a c t g c t c g c a t t a c c g a c c g g a c a a c t t g t t c a g

2400 180 185 190 195 WKEMHKLLPFSPDSVVTHGD KanR WKEMHKLLPFSPDSVVTHGD t g g a a a g a a a t g c a t a a a c t t t t g c c a t t c t c a c c g g a t t c a g t c g t c a c t c a t g g t g a t a c c t t t c t t t a c g t a t t t g a a a a c g g t a a g a g t g g c c t a a g t c a g c a g t g a g t a c c a c t a

2460 200 205 210 215 FSLDNLIFDEGKLIGCIDVG KanR FSLDNLIFDEGKLIGCIDVG t t c t c a c t t g a t a a c c t t a t t t t t g a c g a g g g g a a a t t a a t a g g t t g t a t t g a t g t t g g a a a g a g t g a a c t a t t g g a a t a a a a a c t g c t c c c c t t t a a t t a t c c a a c a t a a c t a c a a c c t

PflMI 2520 220 225 230 235 RVGIADRYQDLAILWNCLGE KanR RVGIADRYQDLAILWNCLGE c g a g t c g g a a t c g c a g a c c g a t a c c a g g a t c t t g c c a t c c t a t g g a a c t g c c t c g g t g a g g c t c a g c c t t a g c g t c t g g c t a t g g t c c t a g a a c g g t a g g a t a c c t t g a c g g a g c c a c t c

2580 240 245 250 255 FSPSLQKRLFQKYGIDNPDM KanR FSPSLQKRLFQKYGIDNPDM t t t t c t c c t t c a t t a c a g a a a c g g c t t t t t c a a a a a t a t g g t a t t g a t a a t c c t g a t a t g a a a a g a g g a a g t a a t g t c t t t g c c g a a a a a g t t t t t a t a c c a t a a c t a t t a g g a c t a t a c

2640 260 265 270 NKLQFHLMLDEFF* KanR NKLQFHLMLDEFF* a a t a a a t t g c a g t t t c a t t t g a t g c t c g a t g a g t t t t t c t a a t c a g a a t t g g t t a a t t g g t t a t t t a a c g t c a a a g t a a a c t a c g a g c t a c t c a a a a a g a t t a g t c t t a a c c a a t t a a c c

2700 t t g t a a c a c t g g c a g a g c a t t a c g c t g a c t t g a c g g g a c g g c g c a a g c t c a t g a c c a a a a a a c a t t g t g a c c g t c t c g t a a t g c g a c t g a a c t g c c c t g c c g c g t t c g a g t a c t g g t t t t

2760 t c c c t t a a c g t g a g t t a c g c g 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 a g g g a a t t g c a c t c a a t g c g c 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

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

2880 ori c c g c t a c c a g c g g t g g t t t g t t t g c c g g a t c a 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 g g c g a t g g t c g c c a c c a a a c a a a c g g c c t a g 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

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

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

AlwNI 3060 ori g t g g c t g c t g c c a g t g g c g a t a a g t c g t g t c 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 a c c g a c g a c g g t c a c c g c t a t t c a g c a c a g 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

ApaLIBsiHKAI 3120 ori c c g g a t a a g g c g c a g c g g t c g g g c t g a a c g g 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 g g c c t a t t c c g c g t c g c c a g c c c g a c t t g c c 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

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

BciVI 3240 ori c c c g a a g g g a g a a a g g c g g a c a g g t a t c c g g t 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 g g g c t t c c c t c t t t c c g c c t g t c c a t a g g c c 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

BssSαIBssSI 3300 ori G G G A A A C G C C T G G T A T C T T T pBR322ori-F a c g a g g g a g c t t c c a g g g g g a a a c g c c t g g t a t 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 t g c t c c c t c g a a g g t c c c c c t t t g c g g a c c a 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

DrdI 3360 ori c t c t g a c t t g a g c g t c g a t t t t t g t g a t g c t 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 a g a c t g a a c t c g c a g c t a a a a a c a c t a c g a 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

PciI 3419 g c c a g c a a c g c g g c c t t t t t a c g g t t c c t g g 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 g g t c g t t g c g c c g g a a a a a t g c c a a g g a c c 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

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.