Team:NYMU-Taipei/Sequences/Virus Proteins

/* sequence */ .sequence{ border:1px solid black; font-family:"courier new",courier,helvetica; font-size:90%; max-width:600px; } .sequence .seq{ padding:5px; /*white-space:pre-wrap; white-space:-moz-pre-wrap; wordBreak:break-all; word-wrap:break-word;*/ width:100%; } .bbcut{ background-color:red; } .bbcutmut{ background-color:pink; text-decoration:overline underline; }

/* one primer */ .seq .primer{ background-color:yellow; }

/* overlapping primers */ .seq .primer2{ background-color:gold; text-decoration:overline underline; } .seq .f{	text-decoration:overline; } .seq .r{	text-decoration:underline; }

H1N1 NA
outer primer gaattcgcggccgcttctag ATGAACCCCAACCAGAAGA 55deg, GC:47%, 20+19=39bp ctgcagcggccgctactagta TTACTCGAGTCACTTGTCGATG 55deg, GC:45%, 21+22=43bp inner 1: PstI@pos70, 55deg, GC:50%, 20bp CTGATCCTaCAGATCGGCAA TTGCCGATCTGtAGGATCAG inner 2: PstI@pos369, 56deg, GC:58%, 19bp CTTCATCAGCTGtAGCCCC GGGGCTaCAGCTGATGAAG inner 3: PstI@pos951, 55deg, GC:45%, 20bp TACATCTGtAGCGGCATCTT AAGATGCCGCTaCAGATGTA

H1N1 HA
outer primer: gaattcgcggccgcttctag ATGAAGGCCATCCTGGTG 55deg, GC:56%, 20+18=38bp ctgcagcggccgctactagta TCAGATGCAGATCCTGCAtTGCAGG 63deg, GC:52%, 21+25=46bp

H5N1 NA
outer primer: gaattcgcggccgcttctag ATGAATCCAAATCAGAAGATAATAACCA 55deg, GC:29%, 20+28=48bp ctgcagcggccgctactagta CTACTTGTCAATGGTGAATGGC 55deg, GC:45%, 21+22=43bp inner primer: SpeI@pos1252, 56deg, GC:56%, 18bp ATTTGGACcAGTGGGAGC GCTCCCACTgGTCCAAAT

H5N1 HA
outer primer: gaattcgcggccgcttctag ATGGAGAAAATAGTGCTTCTTTTTG 54deg, GC:32%, 20+25=45bp ctgcagcggccgctactagta TTAAATGCAAATTCTGCATTGTAACG 55deg, GC:31%, 21+26=47bp inner primer1: EcoRI@pos253, 54deg, GC:43%, 21bp TGTGTGACGAgTTCATCAATG CATTGATGAAcTCGTCACACA inner primer2: PstI@pos1142, 55deg, GC:50%, 18bp TACGCTGCcGACAAAGAA TTCTTTGTCgGCAGCGTA inner primer3: XbaI@pos1359, 55deg, GC:43%, 23bp GAGAGAACTCTgGACTTTCATGA TCATGAAAGTCcAGAGTTCTCTC

HIV-1 gp120
outer primer: gaattcgcggccgcttctag ATGAGAGTGACGGGGATC 54deg, GC:56%, 20+18=38bp ctgcagcggccgctactagta TTATTGCAAAGCTGCTTCAAATC 54deg, GC:35%, 21+23=44bp inner primer: EcoRI@pos2500, 54deg, GC:28%, 32bp GATAGGATTATAGAgTTCATACAAAGATTTTG CAAAATCTTTGTATGAAcTCTATAATCCTATC

adenovirus type 13 penton base
1 atgaggcgcg cggtggtgtc ttcctctcct cctccctcgt acgagagcgt gatggcgcag 61 gcgaccctgg aggttccgtt tgtgcctccg cggtatatgg ctcctacgga gggcagaaac 121 agcattcgtt actcggagct ggctccgcag tacgacacca ctcgcgtgta cttggtggac 181 aacaagtcgg cggacatcgc ttccctgaac taccaaaacg accacagcaa cttcctgacc 241 acggtggtgc agaacaacga tttcaccccc gccgaggcca gcacgcagac gataaatttt 301 gacgagcggt cgcggtgggg cggtgatctg aagaccattc tgcacaccaa catgcccaat 361 gtgaacgagt acatgttcac cagcaagttt aaggcgcggg tgatggtggc taggaagcac 421 cccaaagatg tgcaggatcc taatgataga agcaaggata tcttagagta taagtggttt 481 gagtttaccc tgcccgaggg caacttttcc gagaccatga ccatagacct gatgaacaac 541 gccatcttgg aaaactactt gcaagtgggg cggcaaaatg gcgtgctgga gagtgatatc 601 ggagtcaagt ttgacagcag gaatttcaga ctgggctggg acccggagac caagctggta 661 atgccggggg tctacaccta cgaggccttc cacccggacg tggtgctact gccgggctgc 721 ggggtggact tcaccgagag ccgcctgagc aacctcctgg gcattcgcaa gaagcaacct 781 tttcaagagg gcttcagaat catgtatgag gatctagaag ggggcaacat ccctgccctg 841 ctggatgtgg atgcatacct caaaagcaag aatgatctgg aagaggctac caaaaatgca 901 aacagagctg ctgctaatgg aggtggtgaa actaggggag atacttttct caccaccgaa 961 cagctgagag ccgctggcaa ggagctggtt attaagccaa tcaaggaaga tgctagcaaa 1021 aggagctata atgtcataga tgacacccat gacacgctgt accgaagctg gtacctgtcc 1081 tacacatacg gggaccccga gaagggagtg cagtcgtgga cgctgctcac caccccggac 1141 gtcacctgcg gcgcggagca agtctactgg tcgctgccgg acctcatgca agaccccgtc 1201 accttccgct ctacccagca agtcagcaac taccccgtgg tcggcgccga gctcatgcct 1261 ttccgcgcca agagctttta caacgacctc gccgtctact cccagctcat ccgcagctac 1321 acctccctca cccacgtctt caaccgcttc cccgacaacc agatcctctg ccgcccgccc 1381 gcgcccacca tcaccaccgt cagtgaaaac gtgcctgctc tcacagatca cgggacgcta 1441 ccgctgcgca gcagtatccg cggagtccag cgagtgaccg tcactgacgc ccgtcgccgc 1501 acctgtccct acgtctacaa ggccctgggc atagtcgcgc cgcgcgtgct ctctagtcgc 1561 accttt
 * the same as type 3

adenovirus type 13 fiber protein
1 ctttggacaa cacctgatcc atcgcccaat tgtaaagccg aaacagaaaa ggactcaaag 61 cttactttgg ttctaacaaa atgcggaagt caaatcttag ctactgtgtc tattattgtt 121 cttaagggta aatatgaatt tgttaaaaaa gaaacagagc ctaagtcctt tgatgttaaa 181 ttgctgtttg acagcaaagg agtgcttcta ccaacttcaa atctttccaa agaatattgg 241 aactatagaa gttatgataa caacatagga actccttatg aaaatgcagt tccatttatg 301 ccaaatctaa aagcttatcc aaaaccaact aaaactgctt cagataaagc agaaaataaa 361 ataagcagtg ctaaaaacaa aattgtaagc aacttctact ttggagggca agcatatcaa 421 cctgggacaa taataattaa gtttaatgag gaaatagatg agacatgtgc atactctatc 481 acctttaact ttggttgggg caaggtatat gacaatccat ttccatttga taccacctct 541 tttaccttct cttatattgc ccaagaaaat gaagacaaag actaa F:gcttctag atgaggcgcgcgg 55deg,77%GC, 8+13bp R:ctgcagcggccgctactagta ttagtctttgtcttcattttcttggg 55deg, 35%GC 21+26bp
 * primer for adenovirus penton base and fiber protein link