Typing tool
|
Complete norovirus genomes
KF429768 | GII.4 New Orleans | ||
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GII.P4 Hunter |
ORF1: 1..5100 ORF2: 5081..6697 ORF3: 6697..7503LOCUS KF429768 7503 bp ss-RNA linear VRL 24-OCT-2013 DEFINITION Norovirus Hu/GII.4/NIHIC1.13/2012/USA, complete sequence. ACCESSION KF429768 VERSION KF429768.1 DBLINK BioProject: PRJNA70471 KEYWORDS . SOURCE Norovirus Hu/GII.4/NIHIC1.13/2012/USA ORGANISM Norovirus Hu/GII.4/NIHIC1.13/2012/USA Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7503) AUTHORS Madupu,R., Halpin,R.A., Ransier,A., Fedorova,N., Tsitrin,T., McLellan,M., Stockwell,T., Amedeo,P., Appalla,L., Bishop,B., Edworthy,P., Gupta,N., Hoover,J., Katzel,D., Li,K., Schobel,S., Shrivastava,S., Thovarai,V., Wang,S., Kim,M., Bok,K., Sosnovtsev,S.V., Wentworth,D.E. and Green,K.Y. TITLE Direct Submission JOURNAL Submitted (28-JUN-2013) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA COMMENT This work was supported by the National Institute of Allergy and Infectious Diseases (NIAID), Genome Sequencing Centers for Infectious Diseases (GSCID) program. The genome sequence was generated using overlapping PCR amplicons spanning the genome. The amplicons were pooled by sample and then barcoded and sequenced using Next Generation Sequencing platforms. The consensus sequences of the internal PCR primer hybridization sites were manually verified using reads from amplicons that spanned across the sites. Genome sequence lacks part of non-coding region. ##Genome-Assembly-Data-START## Current Finishing Status :: Finished Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Genome Coverage :: 984.1x Sequencing Technology :: Sanger; Illumina ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7503 /organism="Norovirus Hu/GII.4/NIHIC1.13/2012/USA" /mol_type="genomic RNA" /strain="Hu/GII.4/NIHIC1.13/2012/USA" /host="Homo sapiens" /db_xref="taxon:1383602" /country="USA: Maryland" /collection_date="20-Oct-2012" /PCR_primers="fwd_name: 1_Forward, fwd_seq: gtgaatgawgatggcgt, rev_name: 1_Reverse, rev_seq: ttggttgagagyttyctg" /PCR_primers="fwd_name: 4_Forward, fwd_seq: ggcaagaagcacacagcctt, rev_name: 4_Reverse, rev_seq: crrctctytgttgtgttgaatccc" /PCR_primers="fwd_name: 7_Forward, fwd_seq: gtgaatgawgatggcgt, rev_name: 7_Reverse, rev_seq: ccagrctrtctttrtctt" /PCR_primers="fwd_name: 8_Forward, fwd_seq: ygactcgtggctgagyagga, rev_name: 8_Reverse, rev_seq: gytgggccctgyagttcawa" /PCR_primers="fwd_name: 9_Forward, fwd_seq: tcaaccaartctgcttcacctg, rev_name: 9_Reverse, rev_seq: aagtcytcctcrgtcgccct" /PCR_primers="fwd_name: 10_Forward, fwd_seq: gggaaraacaagrctggycg, rev_name: 10_Reverse, rev_seq: crrctctytgttgtgttgaatccc" /PCR_primers="fwd_name: 12_Forward, fwd_seq: cagtytcttgtcgrgtyctca, rev_name: 12_Reverse, rev_seq: atcaatyttgtcttttcaca" gene 1..5100 /gene="POL" /locus_tag="H649_43655gpPOL" CDS 1..5100 /gene="POL" /locus_tag="H649_43655gpPOL" /note="genome polyprotein" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AGT17797.1" /translation="MKMASNDASAAAVADSNNDTVKSSSDGVLSSMAVTFKRALGARP KQPPPREIPQRPPRPPTPELIKNIPPPPPNGEDDVVVSYSVKDGISGLPDLSTVRQPE ESNTAFSIPPLNQRESREAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS LARVELTPLSLYWRPVYTPQYLISPDALKRLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK LRPLNILNILASCDWSFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLAVKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKSSLAAYMKTLDLEEEKARKLST KSASPDIVGTVNALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTYLAREV AKRIAASLTGDQRVGLVPRNGVDHWDAYKGERVVLWDDYGMSNPIQDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLAYAEAPEVEK AKRDFPGQPDMWKNAFSPDFTHIKLTLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVRTM PELKQALKNISIKKCQIVYSGSTYTLESDGKGNVKVDRVQSASVQTNNELAGALHHLR TARMRYYVRCVQEALYSIIQIAGAAFVTTRIVKRMNIQSLWSKPQVENTEETTSRDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRADVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKNMTPVYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFERHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLAISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGS NHEDPSETMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 1..990 /gene="POL" /locus_tag="H649_43655gpPOL" /product="protein p48" mat_peptide 991..2088 /gene="POL" /locus_tag="H649_43655gpPOL" /product="NTPase" /note="p41" mat_peptide 2089..2625 /gene="POL" /locus_tag="H649_43655gpPOL" /product="protein p22" mat_peptide 2626..3024 /gene="POL" /locus_tag="H649_43655gpPOL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3025..3567 /gene="POL" /locus_tag="H649_43655gpPOL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3568..5097 /gene="POL" /locus_tag="H649_43655gpPOL" /product="RNA-directed RNA polymerase" primer_bind 1..13 gene 5081..6697 /gene="VP1" /locus_tag="H649_43655gpVP1" CDS 5081..6697 /gene="VP1" /locus_tag="H649_43655gpVP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AGT17798.1" /translation="MKMASSDANPSDGSTANLVPEANNEVMALEPVVGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEVLWSAPLGPDLNPYLSHLARMYNGYAGG FEVQVILAGNAFAAGKIIFAAVPPNFSTEGLSPSQVTMFPHLIVDVRQLEPVMIPLPD IRNNFYHYNQSNDPTIKLIAMLYTPLRANNVGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESKTNPFSVPILTIEEMTNSRFPIPLEKLFTGPSSALVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTHTTKTHTYQMNLAAQNWNSYDPTEETPAPLGTPDFVGKIQGVL TQTTKGNGSTRAHKATVYTGTVEFTPKLGRIQLFTDTDNDLEANQNTKFTPVGVIQDG DHQNEPQQWVLPSYSGRNNHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCL LPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGHHDLVIP PNGYFRFDSWVSPFYTLAPMGNGTGRRRAL" gene 6697..7503 /gene="VP2" /locus_tag="H649_43655gpVP2" CDS 6697..7503 /gene="VP2" /locus_tag="H649_43655gpVP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AGT17799.1" /translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQD SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMRVKQAMLLEGGFSETDAARGAIN APMTKVLDWSGTRYWAPGARTTTYNAGYFSTPQHSGALPGRANLRAVVPARGSSRVSS NSSTATSVYSNQTASTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLNSQAGVFNTRRQPLFAHIRRRGESRA" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctgacagcaa caacgacacc 61 gttaaatctt caagtgacgg agtgctttct agcatggctg tcactttcaa acgagccctc 121 ggggcgcggc ctaaacagcc tcccccgagg gaaataccac aaagaccccc gcgaccaccc 181 actccagaac tgatcaaaaa tatcccccct cccccaccca atggagagga tgatgtagtg 241 gtttcttata gcgtcaaaga tggtatctct ggtttacctg atctttccac cgtcaggcaa 301 ccggaagaat ctaatacggc cttcagtatc cctccactca atcagaggga gagtagagaa 361 gctaaggaac cactgactgg aacaattttg gaaatgtggg atggagaaat ctatcattat 421 ggcctgtacg tagagcgagg tcttgtacta ggtgtgcaca aaccaccagc tgccatcagt 481 ctcgctaggg tcgaactaac accactttcc ttgtactgga gacctgtgta cactccccag 541 tacctcatct ctccagacgc tctcaagaga ctacacggag agacgttccc ctacacagcc 601 tttgacaaca actgctatgc cttttgttgt tgggtcctgg acctaaacga ctcgtggctg 661 agtaggagaa tgatccagag aacaactggc ttcttcagac cctaccaaga ttggaatagg 721 aaacccctcc ccactatgga tgactccaaa ttaaagaagg tggctaacat attcctgtgt 781 gcattgtctt cgctattcac caggcctata aaagatataa tagggaagct aaggcctctt 841 aacatcctta acatcttggc ttcatgtgat tggtcttttg caggcatagt ggagtccttg 901 atactcttgg cagaactctt tggagttttc tggacgcccc cagatgtgtc tgcgatgatt 961 gcccccttac tcggtgacta cgaactgcag ggacctgagg accttgcagt ggagctcgtc 1021 cctgtagtga tggggggaat tggtttggtg ctaggattca ccaaagagaa gattggaaaa 1081 atgttgtcat ctgctgcatc caccctgaga gcttgtaaag atcttggtgc atatgggcta 1141 gagatcctaa agttggctgt gaagtggttc ttcccgaaga aagaggaagc aaatgaactg 1201 gctatagtga gatccatcga ggatgcagtc ctggatctcg aagcaattga aaacaaccat 1261 atgaccacct tgctcaaaga caaaagcagt ctggcagcct acatgaaaac ccttgacctt 1321 gaggaggaga aagccaggaa actctcaacc aagtctgctt cacctgacat tgtgggcaca 1381 gtcaacgccc ttctggcgag aatcgctgct gcacgttctc tggtgcatcg agcgaaggag 1441 gaactttcta gcagaccaag acctgtagtg ttgatgatat caggcagacc aggaataggg 1501 aagacctacc ttgccagaga agtggctaag agaatcgcag cctcccttac aggagaccag 1561 cgtgtaggcc tcgtcccacg caatggcgtc gaccactggg atgcgtacaa gggggagagg 1621 gtcgttctat gggatgacta tggaatgagc aatcccatcc aagatgccct cagattgcaa 1681 gaactcgctg acacttgtcc cctcaccctg aactgtgaca ggattgagaa caaaggaaag 1741 gtctttgaca gcgatgtcat cattatcacc actaacctgg ctaacccagc accactggac 1801 tatgtcaact tcgaagcatg ctcgaggcgc atcgacttcc tcgcgtatgc agaagcccct 1861 gaggtcgaaa aggcgaagcg tgacttccca ggccaacccg atatgtggaa gaacgccttc 1921 agtcctgatt tcacacacat aaaactaaca ttggctccac agggtggttt cgacaagaac 1981 gggaacaccc cacacgggaa gggcgtcatg aagactctca ccaccggctc cctcattgcc 2041 cgggcatcag ggctactcca tgagaggcta gatgaatttg aactacaggg cccaactctc 2101 accactttca actttgaccg caataaagtg cttgccttta gacaacttgc tgctgaaaac 2161 aaatatgggt tgatggacac aatgaaagtt gggaggcagc tcaaggatgt cagaacaatg 2221 ccagagctca agcaagcact caagaatatt tcaatcaaga agtgccagat agtgtacagt 2281 ggtagcacct acacacttga gtctgatggc aagggtaatg tgaaggttga cagagtccaa 2341 agcgcctccg tgcagaccaa caatgagctg gctggcgccc tacaccatct aaggacagcc 2401 agaatgagat actatgtcag gtgtgtccag gaggccctgt attccatcat ccagattgct 2461 ggggctgcat ttgtcaccac gcgcatcgtc aagcgcatga acatacaaag cctatggtct 2521 aaaccacaag tggaaaacac agaggagact accagcaggg acgggtgtcc aaaacccaaa 2581 gatgatgagg agttcgtcat ttcatccgac gacatcaaga ctgaaggcaa gaaagggaaa 2641 aacaagactg gccgcggtaa gaagcacaca gccttctcaa gcaaaggtct cagtgatgaa 2701 gagtacgatg agtacaagag gattagagaa gaaaggaatg gtaagtactc catagaagag 2761 taccttcaag acagggacaa atactatgag gaggtggcca ttgccagggc gaccgaggaa 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tcttcaggcc aacaaggaaa 2881 caacgcaagg aggaaagagc ttctctcggt ttagtcacag gttctgaaat taggaaaaga 2941 aatccagatg atttcaaacc caaggggaaa ttgtgggctg acgatgacag aagtgtggac 3001 tacaatgaga aactcagttt tgaagcccca ccaagcatct ggtcgaggat agtcaacttt 3061 ggttcaggtt ggggattctg ggtttccccc agtttgttca taacatcaac ccatgtcata 3121 ccccagggag caaaggagtt ctttggagtc cccatcaaac aaattcaggt acataagtca 3181 ggcgaattct gtcgcttgag attcccaaaa ccaatcaggg ctgatgtgac gggcatgatc 3241 ttagaagaag gtgcacccga gggcaccgtg gttacactac tcatcaaaag gtccactggg 3301 gaactcatgc ccctagcagc taggatgggg acccatgcaa ccatgaaaat ccaaggacgc 3361 actgttggag gtcaaatggg catgcttctg acaggatcca acgccaaaag catggacctg 3421 ggtaccacac caggtgattg tggctgtccc tacatctaca agagaggaaa tgactatgta 3481 gtcattggag tccacacggc tgccgctcgt gggggcaaca ctgtcatctg tgccacccag 3541 gggagtgagg gagaggctac acttgaaggt ggtgacaaca aagggacata ctgtggtgca 3601 ccaatcctag gcccagggag tgccccaaaa cttagcacca agaccaaatt ctggagatcg 3661 tccacagcac cactcccacc tggcacctat gaaccagcct atcttggtgg tagggatccc 3721 agagtcaagg gtgggccttc actacagcag gtcatgaggg atcagctgaa gccattcaca 3781 gagcccaggg gcaagccacc aaagccaagt gtgttggaag ctgctaagaa aaccatcatc 3841 aatgtccttg agcaaacaat tgatccacct gagaaatggt cgttcgcaca agcttgcgcg 3901 tcacttgata agaccacctc cagtggtcac ccgcaccaca tgcggaaaaa cgactgctgg 3961 aacggggagt ccttcacagg caagctggca gaccaggctt ccaaggccaa cctgatgttt 4021 gaagagggga agaacatgac gccagtctat acagctgcgc ttaaggatga attagttaaa 4081 actgacaaga tttatggtaa gatcaagaaa aggcttctct ggggctcgga tttggcgacc 4141 atgatccggt gtgctcgagc attcggaggc ctaatggatg aactcaaagc gcactgtgtc 4201 acacttccca tcagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagagg 4261 cactccaggt acacgtacca ctatgatgct gattactctc gatgggattc aacacaacag 4321 agagccgtgt tggcagcagc tctagaaatt atggttaagt tctccccaga accacatttg 4381 gcccaggtag tcgcagaaga ccttctttcc cctagcgtgg tggacgtggg tgactttaca 4441 atatcaatta acgagggtct tccctctgga gtgccctgca cctcccaatg gaactccata 4501 gcccactggc ttctcaccct ctgtgcgctc tctgaagtta caaacttgtc tcctgacacc 4561 atacaagcta attccctctt ctctttttat ggtgatgatg aaattgttag cacagacata 4621 aaattggacc cagaaaagtt gacagcaaag ctcagggaat atgggttaaa accaacccgc 4681 cccgacaaaa ctgaaggacc ccttgccatc tctgaagact tggatggcct gactttcttg 4741 cgaagaactg tgacccgcga cccagctggt tggtttggaa aactggagca gagctcaata 4801 ctcaggcaaa tgtactggac taggggttcc aaccatgaag acccatctga aacaatgatt 4861 ccacactccc aaaggcccat acaactgatg tccctactgg gggaggccgc actccacggc 4921 ccaacattct acagcaaaat cagcaagtta gtcattgcag agctaaaaga aggtggcatg 4981 gatttttacg tgcccagaca agagccaatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgagtga 5101 cgccaaccca tctgatgggt ccacagccaa cctcgtccca gaggccaaca atgaggttat 5161 ggctttggag cccgttgttg gtgccgccat tgcggcgcct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa acaattttgt gcaagcccct ggtggagagt ttacagtatc 5281 ccctagaaac gctccaggtg aagtactatg gagcgcgccc ttaggccctg atttgaatcc 5341 ctacctttcc catttggcca gaatgtacaa tggttatgca ggtggttttg aagtgcaggt 5401 aatcctcgcg gggaacgcgt tcgccgccgg aaaaatcata ttcgcagcag tcccaccaaa 5461 tttctcaact gaaggcttga gccccagcca ggtcactatg ttcccccact taatagtaga 5521 tgttaggcaa ctggaacctg tgatgatccc cttacccgat attaggaata atttctatca 5581 ttacaatcaa tcaaatgatc ccaccatcaa attgatagca atgttgtata cacctcttag 5641 ggctaataat gttggtgacg atgtcttcac agtttcttgt cgggtactca cgagaccatc 5701 ccccgatttt gatttcatat ttctagtgcc acccacagtt gaatcaaaaa ccaacccatt 5761 ctctgttcca attctaacta ttgaggagat gaccaattca agattcccca ttcctttgga 5821 aaagttgttc acgggcccca gcagtgccct tgttgttcaa ccacaaaacg gcaggtgcac 5881 gactgatggc gtgctcctgg gtaccaccca actgtctcct gtcaacatct gcaccttcag 5941 aggggatgtc acccatacta caaaaactca tacctaccaa atgaatttgg ctgctcaaaa 6001 ttggaacagt tatgacccaa cagaagaaac cccagccccc ctaggaactc cagatttcgt 6061 gggaaagatc caaggtgtgc tcacccaaac cacgaaggga aatggctcaa cccgtgccca 6121 caaagctaca gtgtacactg ggaccgtcga gttcactcca aaactgggta gaatccaact 6181 tttcactgac acagacaacg atcttgaagc taaccaaaac acaaagttca ccccagtcgg 6241 tgtcatccag gatggtgacc accaaaatga accccaacaa tgggtactcc caagttactc 6301 aggtagaaat aatcacaatg tgcacctggc ccccgctgta gcccccactt ttccgggcga 6361 gcaacttctc ttcttcagat ccactatgcc cggatgcagc gggtacccca acatgaattt 6421 ggactgtctg cttccccagg aatgggtgca atatttctat caagaggcag ccccagcaca 6481 atctgatgtg gctttgctaa gatttgtgaa tccagataca ggtagggttt tgtttgagtg 6541 caagcttcat aaatcaggtt atgtcacagt ggcccacacc ggccaccatg atttggttat 6601 cccccctaat ggttatttca gatttgattc ctgggtcagc cccttctaca cgcttgcccc 6661 catgggaaat ggaacggggc gtagacgtgc attataatgg ctggagcttt ctttgctgga 6721 ttggcatctg acgtccttgg atccggactt ggttctctga tcaatgccgg ggctggggcc 6781 atcaaccaaa aagttgaatt tgaaaacaac agaaaattgc aacaagattc cttccaattt 6841 agtagcaatc tgcaacaggc ttcctttcaa catgataaag agatgctcca agcacaaatt 6901 gaggccacca aaaagttgca acaggaaatg atgagagtta aacaggcaat gctcctagag 6961 ggtgggttct ctgagacaga tgcagcccgt ggggcaatca acgcccccat gacaaaggtt 7021 ttggactgga gtgggacaag gtactgggct cccggtgcta ggactacaac atacaatgca 7081 ggctactttt ccactcccca acactcgggg gcactgccag gaagagctaa tcttagggct 7141 gttgtccccg ctcggggctc ctctagagta tcttctaatt cttctactgc tacctctgtg 7201 tattcaaatc aaactgcttc aacgagactt ggttctacag ctggttctgg taccagtgtc 7261 tcgagcctcc cgtcaactgc aaggactagg agttgggttg aggatcaaaa taggaatttg 7321 tcacctttca tgaggggggc ccacaacata tcgtttgtca ccccaccatc tagcagatcc 7381 tctagtcaag gcacagtctc aaccgtgccc aaagaagttt tgaactccca ggctggcgtt 7441 ttcaatacgc gcaggcagcc tctctttgct cacattcgta ggcgagggga gtcacgggcg 7501 taa //