An Integrated Tool of Bioinformatics-Vector nTl 成功大學生物資部中心 Speaker:Shih-Chieh Lin
Speaker: Shih-Chieh Lin An Integrated Tool of Bioinformatics-Vector NTI 成功大學生物資訊中心
358 531 1060 GATC mst3 RNAi TCGA The pSUPER vectors A AGCTT RSUPER H1 prompter TCTAG A Mst3 RNAi plasmid 358 531 1060
BglI(1) si RNA for P53 pBluescriptSK primer(2969) HindIII (51) T7 promoter pBluescriptKS primer(59) M13 forward20(2892) T3 promoter M13 pUC Forward(2877) M13 reverse(139) Lac Z a (2751) M13 pUC reverse(156 lac promoter f1 origin psuper0p53 3220bp pBR322 origin AmpR promoter Ampicilin (1304)
ps uper0 p5 3 3220 bp M13 pUC Forward (2877) M13 forward20 (2892) pBluescriptSK primer (2969) pBluescriptKS primer (59) M13 reverse (139) M13 pUC reverse (156) T7 promoter T3 promoter lac promoter AmpR promoter f1 origin pBR322 origin Lac Z a (2751) Ampicilin (1304) si RNA for P53 B glII (1) HindIII (51)
Why should I use Vector NTI User friendly Consistent multi-Interface pane Interface in All applications 。Easy to understand ·Easy to manage Powerful Illustration Tools for Publication Quality Graphics
Why should I use Vector NTI ? • User friendly • Consistent Multi-Interface Pane Interface in All Applications • Easy to understand • Easy to manage • Powerful Illustration Tools for Publication Quality Graphics
What can Vector NTI help you 。Sequence annotation Compare sequence results Help you design primer Verify your original sequence result 。Map construction Help you determine what kind of expression vector you can use
What can Vector NTI help you ? • Sequence annotation • Compare sequence results • Help you design primer • Verify your original sequence result • Map construction • Help you determine what kind of expression vector you can use
Sequence Annotation CHIP Forward HRE-117-100 CHIP Reverse Sma1(19o3) NheI(926) Saa1(1964) Promoter Forward TindIlΠ(15o) Promoter Reverse KpnI(760) Sma I(1262) BglII (2001) DUSP2 Promoter ENSG00000158050 ENST00000288943.3 2019bp AA->CC GAS2 T->C AA->CC GAS1 SacI(g1）T->C SIE C0X2-918-762-701 mutation2 965bp
DUSP2 Promote r ENSG00000158050 ENST00000288943.3 2019 bp HRE -117~-100 Promoter Forw ard Promoter Rev erse CHIP Forw ard CHIP Rev erse BglII (2001) HindIII (1150) KpnI (760) Nhe I (926) Sma I (1262) Sma I (1903) Sma I (1964) COX2-918 -762 -701 muta tion2 965 bp GAS1 SIE GAS2 T-->C AA-->CC T-->C AA-->CC Sac I (91) Sequence Annotation
Exon 3 Forward 1 Exon 2 Intron 3 Intron 1 Reverse 1 Forward 2 Reverse 2 Exon1 Intron 2 Exon 4 DUSP2 Exon Iptron 2663bp 2 4 4一Exons 一PAC1(L11329) -【ntrons PAC-1 variant I (AF331843) PAC.I variant 2 Forward1 Reverse 1:amplify Wild type Variant 1 (113 229 bp) Forward2 Reverse 2:amplify Wild type Variant 2 (504 162 bp
DUSP2 Exon & Intron 2663 bp Intron 1 Intron 2 Intron 3 Forward 1 Reverse 1 Forward 2 Reverse 2 Exon1 Exon 2 Exon 3 Exon 4 Forward 1 & Reverse 1: amplify Wild type & Variant 1 (113 & 229 bp) Forward 2 & Reverse 2: amplify Wild type & Variant 2 (504 & 162 bp )
Application ofAlignX (430)430 440 450 460 470 480 490 500 5 COX2-918(428)CCTTTCCCGCCTCTCTTTCCAAGAAACAAGGAGGGGGTGAAGGTACGGAGAACAGTATTTCTTCTGTTGAAAGCAACTTAG COX2-918-m1_-740(125)CCTTTCCCGCCTCTCTCTCCAAGCCACAAGGAGGGGGTGAAGGTACGGAGAACAGTATTTCTTCTGTTGAAAGCAACTTAG C0X2-918-m1-701 75)CCTTTCCCGCCTCTCTTTCCAAGAAACAAGGAGGGGGTGAAGGTACGGAGAACAGTATTTCCTCTGTTGCCAGCAACTTAG C0X2-918-m2 (75)CCTTTCCCGCCTCTCTCTCCAAGCCACAAGGAGGGGGTGAAGGTACGGAGAACAGTATTTCCTCTGTTGCCAGCAACTTAG Consensus (430)CCTTTCCCGCCTCTCTTTCCAAGCCACAAGGAGGGGGTGAAGGTACGGAGAACAGTATTTCTTCTGTTGCCAGCAACTTAG (46)46 60 70 80 90 100 110 AF_095289 PTTG3 (1)ATGGCTACTCTGATCTATGTTGATAAGGAAAACGAAGAACCAGGCATCCTTGTGGCTACAAAGGATGGGCTGAA NM_004219_PTTG1 (46)ATGGCTACTCTGATCTATGTTGATAAGGAAAATGGAGAACCAGGCACCCGTGTGGTTGCTAAGGATGGGCTGAA NM 006607 PTTG2 (1)ATGGCTACTCTGATCTACGTTGATAAGGAAATTGGAGAACCAGGCACCCGTGTGGCTGCCAAGGATGTGCTGAA Consensus (46)ATGGCTACTCTGATCTATGTTGATAAGGAAAATGGAGAACCAGGCACCCGTGTGGCTGC AAGGATGGGCTGAA (120)120 130 140 150 160 170 180 190 AF_095289_PTTG3 (75)GCTGGGGTCTGGACCTTCAATCAAAGCCTTAGATGGGA GATCTCAAGTTTCAATATCATGTTTTGGCAAAACAT NM 004219 PTTG1(120)GCTGGGGTCTGGACCTTCAATCAAAGCCTTAGATGGGA NM_006607_PTTG2 (75)GCTGGAGTCTAGACCTTCAATCAAAGCATTAGATGGGATATCTCAAGTTTTAACACCACGTTTTGGCAAAACAT Consensus(120)GCTGGGGTCTGGACCTTCAATCAAAGCCTTAGATGGGAGATCTCAAGTTTCAACACCACGTTTTGGCAAAACAT (193)193 200 210 220 230 240 250 260 AF 095289 PTTG3(148)TTCGATGCTCCCACATCCTTACCTAAAGCTACCAGAAAGGCTTTGGGAACTGTCAACAGAGCTACAGAAAAGTC NM004219PTTG1(193) TT CGATGCCCCACCAGCCTTACCTAAAGCTACTAGAAAGGCTTTGGGAACTGTCAACAGAGCTACAGAAAAGTC NM_006607_PTTG2(148)TACGATGCTCCATCAGCCTTACCTAAAGCTACCAGAAAGGCTTTGGGCACTGTCAACAGAGCTACAGAAAAGTC Consensus(193)TTCGATGCTCCA CAGCCTTACCTAAAGCTACCAGAAAGGCTTTGGGAACTGTCAACAGAGCTACAGAAAAGTC (268)268 280 290 300 310 320 330 340 AF 095289 PTTG3(223)GTAAAGACCAAT GGACCCCTCAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACTGAGAAGACTGTTAAZ NM 004219 PTTG1 (268)GTAAAGACCAAGGGACCCCTCAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACTGAGAAGACTGTTAAZ NM_006607_PTTG2 (223)GTAAAGACCAATGGACCCAGAAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACCGAGAAGACTGTTAAZ Consensus(268)GTAAAGACCAATGGACCCCTCAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACTGAGAAGACTGTTAAZ
(430) 430 440 450 460 470 480 490 500 510 520 537 COX2-918 (428) CCTTTCCCGCCTCTCTTTCCAAGAAACAAGGAGGGGGTGAAGGTACGGAGAACAGTATTTCTTCTGTTGAAAGCAACTTAGCTACAAAGATAAATTACAGCTATGTAC COX2-918-m1_-740 (125) CCTTTCCCGCCTCTCTCTCCAAGCCACAAGGAGGGGGTGAAGGTACGGAGAACAGTATTTCTTCTGTTGAAAGCAACTTAGCTACAAAGATAAATTACAGCTATGTAC COX2-918-m1-701 (75) CCTTTCCCGCCTCTCTTTCCAAGAAACAAGGAGGGGGTGAAGGTACGGAGAACAGTATTTCCTCTGTTGCCAGCAACTTAGCTACAAAGATAAATTACAGCTATGTAC COX2-918-m2 (75) CCTTTCCCGCCTCTCTCTCCAAGCCACAAGGAGGGGGTGAAGGTACGGAGAACAGTATTTCCTCTGTTGCCAGCAACTTAGCTACAAAGATAAATTACAGCTATGTAC Consensus (430) CCTTTCCCGCCTCTCTTTCCAAGCCACAAGGAGGGGGTGAAGGTACGGAGAACAGTATTTCTTCTGTTGCCAGCAACTTAGCTACAAAGATAAATTACAGCTATGTAC Application of AlignX (46) 46 60 70 80 90 100 110 120 130 140 153 AF_095289_PTTG3 (1) ATGGCTACTCTGATCTATGTTGATAAGGAAAACGAAGAACCAGGCATCCTTGTGGCTACAAAGGATGGGCTGAAGCTGGGGTCTGGACCTTCAATCAAAGCCTTAGAT NM_004219_PTTG1 (46) ATGGCTACTCTGATCTATGTTGATAAGGAAAATGGAGAACCAGGCACCCGTGTGGTTGCTAAGGATGGGCTGAAGCTGGGGTCTGGACCTTCAATCAAAGCCTTAGAT NM_006607_PTTG2 (1) ATGGCTACTCTGATCTACGTTGATAAGGAAATTGGAGAACCAGGCACCCGTGTGGCTGCCAAGGATGTGCTGAAGCTGGAGTCTAGACCTTCAATCAAAGCATTAGAT Consensus (46) ATGGCTACTCTGATCTATGTTGATAAGGAAAATGGAGAACCAGGCACCCGTGTGGCTGC AAGGATGGGCTGAAGCTGGGGTCTGGACCTTCAATCAAAGCCTTAGAT (120) 120 130 140 150 160 170 180 190 200 210 227 AF_095289_PTTG3 (75) GCTGGGGTCTGGACCTTCAATCAAAGCCTTAGATGGGAGATCTCAAGTTTCAATATCATGTTTTGGCAAAACATTCGATGCTCCCACATCCTTACCTAAAGCTACCAG NM_004219_PTTG1 (120) GCTGGGGTCTGGACCTTCAATCAAAGCCTTAGATGGGAGATCTCAAGTTTCAACACCACGTTTTGGCAAAACGTTCGATGCCCCACCAGCCTTACCTAAAGCTACTAG NM_006607_PTTG2 (75) GCTGGAGTCTAGACCTTCAATCAAAGCATTAGATGGGATATCTCAAGTTTTAACACCACGTTTTGGCAAAACATACGATGCTCCATCAGCCTTACCTAAAGCTACCAG Consensus (120) GCTGGGGTCTGGACCTTCAATCAAAGCCTTAGATGGGAGATCTCAAGTTTCAACACCACGTTTTGGCAAAACATTCGATGCTCCA CAGCCTTACCTAAAGCTACCAG (193) 193 200 210 220 230 240 250 260 270 280 290 300 AF_095289_PTTG3 (148) TTCGATGCTCCCACATCCTTACCTAAAGCTACCAGAAAGGCTTTGGGAACTGTCAACAGAGCTACAGAAAAGTCAGTAAAGACCAATGGACCCCTCAAACAAAAACAG NM_004219_PTTG1 (193) TTCGATGCCCCACCAGCCTTACCTAAAGCTACTAGAAAGGCTTTGGGAACTGTCAACAGAGCTACAGAAAAGTCTGTAAAGACCAAGGGACCCCTCAAACAAAAACAG NM_006607_PTTG2 (148) TACGATGCTCCATCAGCCTTACCTAAAGCTACCAGAAAGGCTTTGGGCACTGTCAACAGAGCTACAGAAAAGTCAGTAAAGACCAATGGACCCAGAAAACAAAAACAG Consensus (193) TTCGATGCTCCA CAGCCTTACCTAAAGCTACCAGAAAGGCTTTGGGAACTGTCAACAGAGCTACAGAAAAGTCAGTAAAGACCAATGGACCCCTCAAACAAAAACAG (268) 268 280 290 300 310 320 330 340 350 360 375 AF_095289_PTTG3 (223) GTAAAGACCAATGGACCCCTCAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACTGAGAAGACTGTTAAAGCAAAAAACTCTGTTCCTGCCTCAGATGATGGC NM_004219_PTTG1 (268) GTAAAGACCAAGGGACCCCTCAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACTGAGAAGACTGTTAAAGCAAAAAGCTCTGTTCCTGCCTCAGATGATGCC NM_006607_PTTG2 (223) GTAAAGACCAATGGACCCAGAAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACCGAGAAGACTGTTAAAACAAAAAGTTCTGTTCCTGCCTCAGATGACGCC Consensus (268) GTAAAGACCAATGGACCCCTCAAACAAAAACAGCCAAGCTTTTCTGCCAAAAAGATGACTGAGAAGACTGTTAAAGCAAAAAGCTCTGTTCCTGCCTCAGATGATGCC
ContigExpress -[OBP489-1-m2-2] ▣☒ 白Eragment Edit View Align Analyses Assemble Tools Window Help -日X 包%鱼色团际马汉 回国因筲药药QQ“越越器 sh0BP489-1-m2-2948 1 AGTCC AGANA TTTCT CTATC GATAG GTACC GAGCT CGGTA TCCAC TAGTA 图白General Description 51 ACGGC CGCCA GTGTG CTGGA ATTCG GCTTC GGGGT ACCCC TCTAA CCCTG Chromatogram Data 101 GGCTT CCCTG GCGTC CAGGG CCGTC GGGGC CGAGT CCCGA TTCGC TCCCA 151 CCCCG AAGCC GCGCC AGGAC CAACG AGGGC GCAGC CGTAT GCCCC AGCCC 201 GCTCC GCGGA GCCCC TCACA GCCAC cCCCG cCCcG ACCGC GCCCC GCGCG G T CC A TTT C T C T A T C G A T A GG T A CC G A G C T C 223 Fragment 08P489-1 m22 Original position:T (35 bp) Trace values under cursor: A-trace:0 C-trace:0 G-trace:0 T-trace:655 ☑ A G TC G A T AG G T A CC GA G C T C 67 156 789202122232425262728293031323334353 n
Map Construction KpnI(287) Promoter Forward RVprimer3 SacI(293) KpnI(1) Synthetic poly(A)signal NheI(167) nl344) f1 ori HhndΠ39) KpnI(622) SmaI(508) HRE1 CHIP Forward CG->TT HRE.117--100 obp B-lactamase gene (Ampr) CHIP Reverse DUSP2 promoter pGL3-Bac XhoI(664) Smal(1144) 6028bp Nhel(00) Smal (1205) PGL3 OBP489 HRE1-mutation HRE 2 PRomoter Reverse 5446bp g(24p tata fndΠ0259) BglⅢ(g46 GLprimer2 ind皿(g63) Luciferase gene SV40 late poly(A)signal
DUSP2 promoter pGL3-Basic 6028 bp HRE -117~-100 SV40 late poly(A)signal Synthetic poly(A) signal CHIP Forward CHIP Reverse GLprimer2 RVprimer3 Promoter Forward PRomoter Reverse f1 ori Luciferase gene B-lactamase gene (Ampr) BglII (1242) KpnI (1) NheI (167) HindIII (391) HindIII (1259) SmaI (503) SmaI (1144) SmaI (1205) PGL3 OBP489 HRE1-mutation 5446 bp HRE 2 HRE 1 obp tata CG-->TT BglII (946) HindIII (963) NheI (700) SacI (293) XhoI (664) KpnI (287) KpnI (344) KpnI (622) Map Construction