Typing tool
|
Complete norovirus genomes
KF429787 | GII.4 Farmington Hills | ||
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GII.P4 New Orleans |
ORF1: 1..5100 ORF2: 5081..6700 ORF3: 6700..7506LOCUS KF429787 7506 bp ss-RNA linear VRL 24-OCT-2013 DEFINITION Norovirus Hu/GII.4/NIHIC28.5/2012/USA, complete sequence. ACCESSION KF429787 VERSION KF429787.1 DBLINK BioProject: PRJNA70471 KEYWORDS STANDARD_DRAFT. SOURCE Norovirus Hu/GII.4/NIHIC28.5/2012/USA ORGANISM Norovirus Hu/GII.4/NIHIC28.5/2012/USA Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Picornavirales; Caliciviridae; Norovirus; Norwalk virus. REFERENCE 1 (bases 1 to 7506) 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 :: Standard Draft Assembly Method :: clc_ref_assemble_long v. 3.22.55705 Genome Coverage :: 1393.1x Sequencing Technology :: Sanger; Illumina ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..7506 /organism="Norovirus Hu/GII.4/NIHIC28.5/2012/USA" /mol_type="genomic RNA" /strain="Hu/GII.4/NIHIC28.5/2012/USA" /host="Homo sapiens" /db_xref="taxon:1383606" /country="USA: Maryland" /collection_date="10-Aug-2012" /PCR_primers="fwd_name: 2_Forward, fwd_seq: ccgcaaaatcttcaagtg, rev_name: 2_Reverse, rev_seq: cwacaggtcttggtctgctrga" /PCR_primers="fwd_name: 3_Forward, fwd_seq: tcaaccaartctgcttcacctg, rev_name: 3_Reverse, rev_seq: ratcctttgccggatcttgg" /PCR_primers="fwd_name: 6_Forward, fwd_seq: gagrccrtccccygattttg, rev_name: 6_Reverse, rev_seq: atcaatyttgtcttttcaca" /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" gene 1..5100 /gene="POL" /locus_tag="H649_43673gpPOL" CDS 1..5100 /gene="POL" /locus_tag="H649_43673gpPOL" /note="genome polyprotein" /codon_start=1 /product="nonstructural polyprotein" /protein_id="AGT17829.1" /translation="MKMASNDASAAAVANSNNDTAKSSSDGVFSNMAVTFKRALGARP KQPPPREIPQRPPRPPTPELVKNIPPPPPNGEDEIVVSYSVKDGVSGLPDLSTVRQPE ESNTAFSVPPLSQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLILGVHKPPAAIS LARIELTPLSLFWRPVYTPQYLISPDTLRKLHGETFPYTAFDNNCYAFCCWVLDLNDS WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANILLCTLSSLFTRPIKDLIGK LRPLNILNILASCDWTFAGIVESLILLGELFGIFWTPPDVSAMIAPLLGDYELQGPED LAVELVPVVMGGIGLVLGFTKEKIGKMLSSAATTLRACKDLGAYGLEILKLVMKWFFP KKEEANELAIVRSIEDAVLDLEAIENNHMTTLLKDKDSLAVYMRTLDLEEEKARKLST KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVMMLSGRPGIGKTHLAREV AKRIAASLTGDQRVGLIPRNGVDHWDSYRGERIVLWDDYGMSNPIHDALRLQELADTC PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK AKRDFPGQPDMWKNAFSSDFSHIKLTLAPQGGFDKNGNTPHGKGVMKTLTIGSLIARA SGLLHERLDEFELQGPTLTTFNFDRNKVLAFRQLAAENKYGLMETMKVGRQLKDVRTM PELKQALKNISIKRCQIVYNGSTYTLESDGKGSVKVDRVQSASVQTNNELAGALHHLR SARIRYYVKCVQEALYSIIQIAGAAFVTTRIVKRMNIQNLWSKPQVENTEETTNKDGC PKPKDDEEFVISSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV TGSEIRKRNPDDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP SLFITSTHVIPQGAKEFFGVSVKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGSEGEATLEGGDNKGTYCGAPILG PGNAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW NGESFTGKLADQASKANLMFEEGKSMTPIYTAALKDELVKTDKIYGKIKKRLLWGSDL ATMIRCARAFGGLMDELKAHCVTLPIRVGMNMNEDGPIIFEKHSRYTYHYDADYSRWD STQQRAVLAAALEIMVKFSPEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT SQWNSIAHWLLTLCALSEVTNLSPDTIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLR EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGS NHEDPSETMIPHSQRPIQLMSLLGEAALHGPAFYSKISKLVIAELKEGGMDFYVPRQE PMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE" mat_peptide 1..990 /gene="POL" /locus_tag="H649_43673gpPOL" /product="protein p48" mat_peptide 991..2088 /gene="POL" /locus_tag="H649_43673gpPOL" /product="NTPase" /note="p41" mat_peptide 2089..2625 /gene="POL" /locus_tag="H649_43673gpPOL" /product="protein p22" mat_peptide 2626..3024 /gene="POL" /locus_tag="H649_43673gpPOL" /product="viral genome-linked protein" /note="VPg" mat_peptide 3025..3567 /gene="POL" /locus_tag="H649_43673gpPOL" /product="3C-like protease" /note="3CLpro; calicivirin" mat_peptide 3568..5097 /gene="POL" /locus_tag="H649_43673gpPOL" /product="RNA-directed RNA polymerase" primer_bind 1..13 gene 5081..6700 /gene="VP1" /locus_tag="H649_43673gpVP1" CDS 5081..6700 /gene="VP1" /locus_tag="H649_43673gpVP1" /codon_start=1 /product="capsid protein VP1" /protein_id="AGT17830.1" /translation="MKMASNDATPSDGSSANLVPEANNEVMALEPVAGAAIAAPVAGQ QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSASLGPDLNPYLSHLSRMYNGYAGS FEVQVILAGNAFTAGKIIFAAVPPNFRTEGLSPSQITMFPHIITDVRQLEPVLIPLPD IRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT QLSPVNICTFRGDVTRIGNSREYRMNLASLNWNNYDPTEEIPAPLGTPDFAGKIQGVL TQTTRHDGSTRGHKATVYTGSAGFTPKLGSVQFSTDTDNDLEANQNTRFTPVGVIQDG NAHQGEPQQWVLPNYAGRDGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDC LLPQEWVQHFYQESAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGPHDLVI PPNGYFRFDSWVNQFYTLAPMGNGAGRRRAL" gene 6700..7506 /gene="VP2" /locus_tag="H649_43673gpVP2" CDS 6700..7506 /gene="VP2" /locus_tag="H649_43673gpVP2" /note="minor capsid protein" /codon_start=1 /product="capsid protein VP2" /protein_id="AGT17831.1" /translation="MAGAIIAGLASDVLSSGLGSLINAGAGVINQKVDFENNKQLQQN SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMGIKQAVLLKGGFSETDAARGAVN APMTKVLDWSGTRYWAPNASTTTYNAGRFSTPQPSGALPGRTNLRTAAPARGSPSISS NASTATSVYSNQTVSTRLGTSAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI SFVTPPSSRSSSQGTVSTVPKEVLDSWTGAFNTRRQPLFAHIRKRGESRV" ORIGIN 1 atgaagatgg cgtctaacga cgcttccgct gccgctgttg ctaacagcaa caacgacacc 61 gcaaaatctt caagtgacgg agtgttttct aacatggctg tcacttttaa acgagccctc 121 ggggcgcggc ctaaacagcc tcccccgagg gaaataccac aaagaccccc acgaccacct 181 actccagagc tggtcaaaaa tatcccccct cccccaccca acggagagga tgaaatagtg 241 gtttcttata gtgttaagga tggcgtttcc ggcttgcctg atctttccac cgtcagacaa 301 ccggaagaat ccaacacggc cttcagtgtc cctccactca gtcagaggga gaacagagac 361 gctaaggagc cactgactgg aactattctg gaaatgtggg atggagagat ctatcattat 421 ggtctgtatg tggagcgagg tctcatatta ggtgtgcaca aaccaccagc cgccattagc 481 ctcgccagaa tagaactaac accactctcc ttgttctgga ggcctgtgta tactcctcag 541 tacctcatct ctccagatac tctcaggaaa ttgcacggag agacgttccc ctacacagcc 601 tttgacaaca attgctatgc cttttgctgc tgggtcctgg acctaaacga ctcgtggctg 661 agtaggagaa tgatccaaag aacaactggc ttcttcagac cctaccagga ttggaatagg 721 aaacccctcc ccactatgga tgactccaag ttaaagaagg tagctaacat actcctgtgt 781 acactgtctt cgctattcac caggcccata aaagatttaa tagggaagct aaggcccctt 841 aacatcctca acatcttggc ctcatgtgat tggactttcg caggcatagt ggaatccttg 901 atactcttgg gagaactctt tggtattttc tggacacccc cagatgtgtc tgcgatgatt 961 gcccccttac tcggtgacta cgagctacaa ggacctgagg accttgcagt ggagctcgtc 1021 cctgtagtaa tggggggaat tggtctggtg ctaggattca ccaaagagaa gatcgggaaa 1081 atgttgtcat ctgctgcaac caccttgaga gcttgtaaag atcttggtgc atatgggtta 1141 gagatcctaa agttggtcat gaagtggttc ttcccgaaga aagaggaggc aaatgagctg 1201 gctatagtga gatccattga ggacgcagtt ctggatctcg aggcaattga gaacaaccat 1261 atgaccacct tgctcaaaga caaagacagt ctggcagtct acatgagaac ccttgacctt 1321 gaggaggaga aagccaggaa gctctcaacc aagtctgcct cacctgacat cgtgggcaca 1381 atcaacgccc ttctggcgag aatcgctgca gcacgctctc tggtgcaccg agcaaaggag 1441 gagctctcca gcagaccaag acctgtggtg atgatgttgt caggcagacc aggaataggg 1501 aagacccacc ttgctaggga agtggctaag agaattgcag cctcccttac aggagatcag 1561 cgtgtgggcc tcatcccacg caacggcgtc gaccactggg attcgtacag gggggagagg 1621 atcgtccttt gggacgacta tggaatgagc aatcccatcc acgatgccct cagactgcaa 1681 gaactcgctg acacctgccc cctcacccta aattgtgata ggattgagaa taaaggaaag 1741 gtctttgaca gcgatgtcat tatcatcacc actaacctgg ctaacccagc accactggac 1801 tatgtcaact ttgaagcatg ttcgaggcgc attgacttcc tcgtgtatgc agaagcccct 1861 gaggtcgaaa aggcgaaacg cgacttccca ggccaacccg acatgtggaa gaacgccttc 1921 agctctgact tctcacacat aaaactgaca ctggctccac agggtggctt cgacaagaac 1981 ggaaacaccc cacacggaaa gggcgtcatg aagactctca ccattggctc ccttattgcc 2041 agggcatcag ggctactcca tgagaggcta gatgaatttg aattacaggg cccaaccctc 2101 accaccttca actttgatcg caacaaagtg cttgccttta gacaacttgc tgcagaaaac 2161 aaatatgggt taatggaaac aatgaaagtc gggagacagc tcaaggacgt caggacaatg 2221 ccagagctta aacaagcact caagaatatc tcaatcaaga ggtgccaaat agtatacaat 2281 ggtagtacct acacacttga gtccgatggc aagggcagtg tgaaagttga cagagttcag 2341 agtgcctccg tacagaccaa caatgagctg gctggcgcac tgcaccatct aagaagcgcc 2401 agaataagat actatgttaa gtgtgtccag gaggccctgt attccataat ccagattgct 2461 ggggctgcat ttgtcaccac gcgcattgtc aagcgcatga acatacaaaa cctatggtcc 2521 aaaccacaag tggaaaacac agaggagact accaacaagg atgggtgccc aaaacccaaa 2581 gatgatgagg agttcgtcat ttcatccgac gacatcaaaa ctgaaggtaa gaaagggaag 2641 aacaagactg gccgcggcaa gaagcacaca gccttctcaa gcaaaggtct cagtgatgaa 2701 gagtacgatg agtacaagag gatcagagaa gagaggaatg gcaagtactc catagaagag 2761 taccttcagg acagggacaa atactatgag gaggtggcta ttgccagagc gaccgaggag 2821 gacttctgtg aagaggagga ggccaagatc cggcaaagga tctttagacc aacaaggaaa 2881 caacgcaagg aggaaagagc ttctctcggc ctagtcacag gttctgagat taggaaaaga 2941 aacccagatg acttcaagcc caaagggaaa ctgtgggctg acgatgacag aagtgtggac 3001 tacaatgaga aactcagttt tgaagccccc ccaagcatct ggtcgaggat agtcaacttt 3061 ggttcaggtt gggggttctg ggtctccccc agtctgttca taacatcaac ccatgtcata 3121 ccccagggcg caaaggaatt ctttggggtc tctgtcaagc aaattcaggt acataaatca 3181 ggtgaatttt gccgcttgag gttcccaaaa ccaatcagaa ctgatgtgac gggcatgatc 3241 ttagaagaag gtgcacccga gggcaccgtg gtcacactac ttattaaaag atccactggt 3301 gaactcatgc ccctagcagc caggatggga acccatgcaa ccatgaaaat tcaagggcgc 3361 actgtcgggg gtcaaatggg catgcttctg acaggatcca acgccaaaag tatggatctg 3421 ggtaccacac caggtgattg tggctgcccc tacatctaca agagaggaaa tgactatgtg 3481 gttataggag tccacacggc tgccgctcgt gggggaaaca ctgtcatatg tgccacccag 3541 gggagtgagg gagaagctac actcgagggt ggtgacaata aaggaacata ctgtggtgca 3601 ccaatcctag gcccagggaa tgccccaaag ctcagtacta agaccaaatt ctggagatcg 3661 tccacagcac cactcccacc tggtacctat gaaccagcct accttggtgg caaggacccc 3721 agagtcaagg gtggcccttc actgcagcaa gtcatgaggg atcagctgaa gccatttaca 3781 gagcccagag gcaaaccacc aaagccaagt gtgttggaag ctgccaagaa aaccatcatc 3841 aatgtccttg agcaaacaat tgatccacct gagaaatggt catttgcaca agcttgcgcg 3901 tcccttgaca aaaccacttc cagtggccat ccacaccaca tgcggaaaaa cgactgctgg 3961 aacggagagt ccttcacagg caagctggcg gaccaagctt ccaaggccaa cctgatgttt 4021 gaagaaggga aaagcatgac cccaatctac acagctgcac ttaaggatga attagttaag 4081 actgacaaaa tttatggtaa gatcaagaag aggcttctct ggggctcgga tctagcaacc 4141 atgattcgat gtgctcgagc attcggaggc ctaatggatg aactcaaagc gcactgtgtc 4201 acacttccca ttagagttgg tatgaatatg aatgaggatg gccccatcat cttcgagaaa 4261 cattccaggt atacatacca ctatgatgct gattactctc gatgggattc aacacaacag 4321 agagccgtgt tggcagcagc tctagagatc atggtgaaat tctccccaga accacatttg 4381 gctcaggtag tcgcagagga cctcctttct cctagcgtgg tggacgtggg tgacttcaca 4441 atatcaatca acgagggcct tccttctggg gtgccctgca cctcccaatg gaactccatc 4501 gcccactggc tcctcactct ctgtgcgctc tctgaagtta caaatttgtc tcctgacacc 4561 atacaggcta attccctctt ctctttctat ggtgatgatg aaattgtcag cacagatata 4621 aaattggacc cggaaaaatt gacagcaaag ctcagggaat atgggctgaa gccaacacgc 4681 cctgacaaaa ccgaaggacc ccttgtcatc tctgaagact tggatggcct gaccttcctg 4741 cggaggactg tgacccgcga cccagcaggt tggtttggga aactggatca gagctcaata 4801 ctcaggcaaa tgtactggac taggggttcc aaccatgaag atccatctga aacaatgatt 4861 ccacactccc aaagacccat acaattgatg tccctactgg gggaggccgc acttcatggc 4921 ccagcatttt acagcaaaat cagcaaatta gtcattgcag agctaaaaga aggtggcatg 4981 gatttttacg tgcccagaca agagccaatg ttcagatgga tgagattctc agatctgagc 5041 acgtgggagg gcgatcgcaa tctggctccc agttttgtga atgaagatgg cgtcgaatga 5101 cgctacccca tctgatgggt cctcggccaa cctcgtccca gaggccaaca atgaggttat 5161 ggctttagaa cccgttgctg gcgccgcgat tgcggcacct gtagcgggcc aacaaaatgt 5221 aattgacccc tggattagaa ataattttgt acaagcccct ggtggagagt ttacagtatc 5281 ccctagaaac gctccaggtg aaatactatg gagcgcgtcc ttgggccctg atttgaaccc 5341 ctacctttcc cacttgtcta gaatgtataa tggttatgca ggtagttttg aagtgcaggt 5401 aatcctcgcg gggaacgcgt tcaccgctgg gaaaatcata tttgcagcag tcccaccaaa 5461 tttccgaact gaaggcttga gccccagcca gatcaccatg ttcccccaca taataacaga 5521 tgttagacaa ttggaacctg tgttgatccc cttgcctgat attaggaaca atttctacca 5581 ttataatcaa tcaaatgacc ccactattaa attgatagca atgctgtata cgccacttag 5641 ggccaataat gctggggatg atgttttcac agtctcttgc cgagttctca caaggccatc 5701 ccccgatttt gatttcatat ttctggtgcc acccacagtt gaatcaagaa ctaaaccatt 5761 ctctgtccca gtcctaactg ttgaggagat gaccaactca agattcccta ttcctttgga 5821 aaagttgttc acgggcccta gcagtgcctt tgttgttcag ccacaaaatg gtagatgcac 5881 gactgatggc gtgctcttag gtaccaccca actgtctcct gtcaacatct gcaccttcag 5941 gggggatgtc acccgcattg gaaattctcg cgagtacaga atgaacctgg cctccctaaa 6001 ttggaacaat tatgacccaa cagaagaaat cccagccccc ctgggaaccc cagattttgc 6061 aggcaagatc caaggtgtgc tcacccagac cacaaggcat gacggttcga cccgcggtca 6121 caaagccacg gtgtacactg gaagtgccgg attcacccca aagctaggca gtgttcaatt 6181 ctccactgac acagacaatg accttgaggc caaccaaaac acgaggttca ccccagtcgg 6241 tgtcatccag gacggcaacg cccaccaagg agaacctcag caatgggtgc tcccaaacta 6301 tgcaggcaga gatggtcaca atgtacacct agcccctgcc gtggccccca ctttcccggg 6361 tgagcaactt ctcttcttta ggtccaccat gcccgggtgt agcgggtatc ccaatatgaa 6421 tttggactgc ctactccccc aggagtgggt gcagcacttc taccaagagt cagccccagc 6481 acaatccgac gtggcattac ttagatttgt gaatccagac acaggtaggg ttttgtttga 6541 gtgcaaactt cataaatcag gctacgtgac agtggctcac actggcccac atgatttggt 6601 catccccccc aatggctatt ttagatttga ttcctgggtc aaccagttct acacacttgc 6661 ccccatggga aatggagcgg ggcgtaggcg tgcattataa tggctggagc tatcattgct 6721 ggattggcat ctgatgtcct tagctctgga cttggttccc taatcaatgc tggggctggg 6781 gtcatcaacc aaaaagtcga ttttgaaaat aataaacaac tgcaacaaaa ctccttccaa 6841 tttagcagca atctacaaca ggcttccttt caacatgata aagagatgct ccaagcacaa 6901 attgaggcca ccaaaaagtt gcaacaggag atgatgggaa tcaaacaggc agtactccta 6961 aagggtgggt tctctgagac agatgcagcc cgtggggcag tcaacgcccc catgacaaag 7021 gttttggact ggagtggaac aaggtactgg gctcccaatg ctagcaccac aacatacaat 7081 gcaggccgct tttccacccc ccagccctcg ggggcgttgc caggaagaac taatctcagg 7141 actgctgccc ccgctcgggg ctcccccagc atatcttcta atgcttctac tgctacttct 7201 gtctattcaa atcaaactgt ttcaacgaga cttggtactt cagctggttc tggtaccagt 7261 gtctcgagcc tcccgtcaac tgcgaggact aggagctggg ttgaggatca aaacaggaat 7321 ttgtcacctt tcatgagagg ggctcacaac atatcgtttg ttaccccacc atctagcaga 7381 tcctctagcc aaggcacagt ctcaaccgtg cctaaagaag ttttggactc ctggactggc 7441 gccttcaaca cgcgcaggca gcctctcttc gctcacattc gtaagcgagg ggagtcacgg 7501 gtataa //