ID HQ731075; SV 1; linear; genomic RNA; STD; VRL; 7310 BP. XX AC HQ731075; XX DT 08-MAY-2011 (Rel. 108, Created) DT 27-MAY-2011 (Rel. 109, Last updated, Version 2) XX DE Cutthroat trout virus isolate Heenan88, complete genome. XX KW . XX OS Cutthroat trout virus OC Viruses; Riboviria; Hepeviridae; Piscihepevirus. XX RN [1] RP 1-7310 RX DOI; 10.1016/j.virusres.2011.03.019. RX PUBMED; 21458509. RA Batts W., Yun S., Hedrick R., Winton J.; RT "A novel member of the family Hepeviridae from cutthroat trout RT (Oncorhynchus clarkii)"; RL Virus Res. 158(1-2):116-123(2011). XX RN [2] RP 1-7310 RA Batts W.N.; RT ; RL Submitted (20-DEC-2010) to the INSDC. RL Virology, Western Fisheries Research Center, 6505 NE 65th Street, Seattle, RL WA 98115, USA XX DR MD5; 75cd556670af92a983f0b477193e54c2. DR EuropePMC; PMC3624379; 23388713. DR EuropePMC; PMC4442536; 25741007. XX FH Key Location/Qualifiers FH FT source 1..7310 FT /organism="Cutthroat trout virus" FT /host="cutthroat trout" FT /isolate="Heenan88" FT /mol_type="genomic RNA" FT /country="USA:Heenan Lake, California" FT /collection_date="1988" FT /PCR_primers="fwd_seq: actgttacacctcatgtagc, rev_seq: FT gactttactagcagtgtggat" FT /db_xref="taxon:1016879" FT 5'UTR 1..100 FT CDS 101..5224 FT /codon_start=1 FT /product="polyprotein" FT /note="non-structural; ORF1" FT /db_xref="GOA:F5BB17" FT /db_xref="InterPro:IPR001788" FT /db_xref="InterPro:IPR002588" FT /db_xref="InterPro:IPR002589" FT /db_xref="InterPro:IPR007094" FT /db_xref="InterPro:IPR027351" FT /db_xref="InterPro:IPR027417" FT /db_xref="UniProtKB/TrEMBL:F5BB17" FT /protein_id="AED98521.1" FT /translation="MDLDCFAHRDHDKVKLAISDCIEKSAGAYVNTSHVITVVLTPEQL FT EQAKKAFSPQPVTYQPRVCLPHALAKHYTTVLEGQLKNAIRGRPYIEAGPAPHQINSRP FT KDTHFCLVRGDARNHVRFATAPNNGLSRKVKRIYQGIQKEDATACLNGYQGCHQPRATS FT IAIHSTYDIPLKEFCRGMNNHKSDLAHVIMHMPSEITFPPGVFVNDMTGYRLDTTGETA FT KFTYLEDTSNGYDHSKADWLEWTTVTALIVDGFTFHVEVQRRLGSVVYLIIYRSTLPVK FT ITRPLDPLCSTSFVFDPYGPTSGHTAPTSYVRSLHSYACGLPDETFSYTRLVIYAKGLA FT FRAKIGAVALNEGWNPDTTAFSAVVAGVFMDVAVKRYLRSKGISNCMKELKKEQNAGFW FT SLLWQRICIWFGDSNEHRHMDHNTLKGWVSSGMILDPACMVLQGQANLNVLSLTTTQSG FT EFEIIGWLASSFEKILDYPNHHHDYLKDLMPGFTPDRAEHYENLLHTVLHTKERQGETD FT GELTDRLTEYINVPYEEVHALVTNRLDLRTRHHIQPKSCLTTPAPTPIPTPQSSRSSSP FT SRTRSSSVSSSSSVSTSVISFQMERESQFEARNQPQINLLDTPLDANLDLTQATFLQPS FT APPDTNQNQTALQDQARAITPTQNPPDTATLPSTRVLPAATPVDINTTLQPSPSTGAIR FT KTSPRVPPTVVPPPQNAQVTPIQLPQTGQNPRSNIRYHNTSIFDTHCCIAVNPAHPTLK FT PGGGLSALFHRQFPDLAAKTAPHTTSFERLPPYAVSTKVNAVGNISEVVHAIGPDRGRG FT QTSYNQLLCTYQLAMQVASGPAAFPLLGANIFGWSPEDSLRAFMEADTQDMHHLYIYDP FT SDPGRFRRLIGKDPTDGDQRPPTRDSMVREINGVIEPPRPTLAESIGSTLGLAPSWYKP FT TTHRYDDMACKAINSNMGMEKGKGGDSKVFAELVASAPLIEPFIFKYHLTEGVPGSGKS FT HAAKKLNKSTCVVVPTGELKSDWKQSGFKNTVTPHVAIKYGIKSKFLVVDEVFSIPPHL FT LATILYKHRDNNILLGDSKQIAACDFDNFRNFDIIAPKLTPSVYLNLTYRLPQDITRYL FT QRDYPGIHTASKVPVSISFYPPPSGTPCQVIGYRQLIKEQPPWKKTANTSHELQGATRK FT AVHLHLLTGDVEMIRSSRSHTIVALSRHTDQIFITGDAESIQTLQLTDKMENIIINYAP FT TTLVNDGATLEITSTPDDDTHVTAPAADSTAVGEILQACTNHLYAPISAVVLDCEKINQ FT GSLTVKCAVPDERIIPKTNFTEIEHCRRANASSTWTTVRTLIGRYTKLTINPAHVHDTI FT QAVNKTFWKCLTVDTMNCLPTTAELAELVRSMKDKGADPTLIHDLDFNDISVTKMTFFQ FT KECDKFTMDEPVQHNKPGQGISAWPKTLCFIYGLFFRKLEKELRQALKPSIIFSNPYTE FT EQLARAVSKCTTGTTVFYENDFSAFDSTQNLVSLGNEFLILVQCGMPPALAEVYFNLRL FT KWTLDARVASLRGTSKKHSGEPGTMLFNTIWNMTAVFHTTSFTRMTLALFKGDDSLVCC FT DSSILTPTAKEFISQNGLVMKQKTSHLGSFTCSLVTRTSYVPDVIRFACRLNNKDFTDT FT KRIEDLQRATDDFIKRATVTTNYGSTCSINGRYYGVPSDTIECVVGFLQDFALTGKIDL FT QTSYKPILKY" FT mat_peptide 284..835 FT /product="methyltransferase" FT mat_peptide 1388..1897 FT /product="protease" FT misc_feature 1808..1888 FT /note="serine-rich region of protease" FT misc_difference 2851 FT /note="heterogeneity site showing 70% T and 30% A" FT mat_peptide 2999..3763 FT /product="helicase" FT misc_feature 3044..3067 FT /note="conserved helicase sequence motif GVPGSGKS" FT misc_feature 3215..3226 FT /note="semi-conserved DEVF; DEAP region" FT mat_peptide 3770..5221 FT /product="RNA-dependent RNA polymerase" FT misc_feature 4814..4822 FT /note="conserved GDD tripeptide motif" FT misc_difference 5162 FT /note="heterogeneity site with 70% G and 30% C; codon FT encodes for Asp or His" FT CDS 5289..7193 FT /codon_start=1 FT /product="capsid protein" FT /note="ORF2" FT /db_xref="GOA:F5BB18" FT /db_xref="InterPro:IPR004261" FT /db_xref="InterPro:IPR029053" FT /db_xref="UniProtKB/TrEMBL:F5BB18" FT /protein_id="AED98522.1" FT /translation="MADSNAVVPSAQSKPRRTRRPKMDPSQIPDTVKTFRLTTDPIMAP FT PPGEIDSLLYTSGLSPAVVLSFSSFTSPAVVFAANYEKYKILSFKATVLSLAPEAISSY FT NLSVVWFPDASEGPTSLQATNLSMVRRYHSILPGQSGSLSLTASELLHGIAEKYVDPTH FT SDALSAFCGLFMVVCHGAPFNHYRDTQYLGPLFKIQFEFKLSVFGYSPGNIPVKVQGAS FT ATEIVSFGTVDGKATFDTPSAIALHASYQSGPPNSPGPSIGQVLLTVADTVSAALPFPF FT SILAKVGLFFIRKITGANGTSFMVYKSYGDAIRNRPLPSRSSHQLGNALVRQTTFGTND FT DSVLPPQPISQFTFHFKTGDVLVIQGSFKAPTSRPNNWNVQEFSISRILNITNGTSTTN FT ILVFEKWTLDGNLPQIKNTYGLIGVHYFPASISPVGTSTFDNIIGDCKVFAGTATDSML FT TPGPGSITVTFLSQTRGFLSQTELTQGLIAASSTMDTTDSSLTRQASQPMEVDGFLSGL FT IPSTPLCNMVNNTFSCGNSDSQATSRSAVHSLGPNCDKCGLDLNLRVTPCIATRLQHTP FT KACPHCSFLLGLTAYTVDCMRPSDTTDSTVDALLNPLNSLDLESESEPSDDDLIQFDD" FT CDS 5986..6663 FT /codon_start=1 FT /product="phosphoprotein" FT /note="ORF3" FT /db_xref="UniProtKB/TrEMBL:F5BB19" FT /protein_id="AED98523.1" FT /translation="MGKLPLTPLPQLLSMLHTKVAHQIHPGLLSAKYSSQWLTPCQLRS FT LSLSVYLQKLVSSLSARLLEPMELPSWSTNPMEMQFATAHYPHAQAINWAMHLSARPHS FT ALTMTQFSHPSPSASSPSTSRLAMSLSSRVPSRPQPVDPIIGMFRNSPFRESLTSLMGP FT PLQTFLCLKSGLWMVTSHRSRTPTVSSGSTTSRLPLVLLAPAPSTTSLVIAKSLQAPQL FT TAC" FT misc_feature 7137..7190 FT /note="50% acidic region" FT 3'UTR 7191..7310 XX SQ Sequence 7310 BP; 2018 A; 2221 C; 1390 G; 1681 T; 0 other; tgagcgttag taatttttcg ttcagaggtt tcaccgcctc tattctgtac cctagacttc 60 gtgtctctta agtaccgggc cgtaaaagga ttcgcccacc atggatcttg attgtttcgc 120 acaccgcgac cacgacaagg tcaagctcgc catctctgac tgcatagaga aatcggctgg 180 agcttacgtg aatacatctc acgtcatcac agttgttctt acacctgaac aactagagca 240 agccaagaag gctttttcac cccaacccgt cacctaccaa cctcgggttt gcctacccca 300 tgcactagca aagcactaca ccacagtcct cgaagggcaa ctcaaaaatg ccataagagg 360 gcggccttac attgaagccg gaccagctcc acatcaaatc aattctagac ctaaggacac 420 ccacttttgc ctagttcgag gagatgctcg caatcatgta aggtttgcca ccgccccaaa 480 caacgggctc agccgtaaag tcaagagaat atatcaaggc atccaaaaag aggacgccac 540 cgcctgcttg aacggctatc aaggttgtca tcagcctagg gcaacctcca ttgccataca 600 ctctacctat gacattcctc ttaaagagtt ctgtcgaggt atgaacaacc acaaatcaga 660 cctagcccat gtcataatgc acatgccatc tgaaatcaca tttccccctg gagtgtttgt 720 caatgacatg actggctaca gactcgatac cacaggtgag acagcaaagt tcacctactt 780 agaggacaca tccaatggtt atgatcactc taaagccgac tggctagagt ggactacggt 840 gacagcattg atagtggacg gcttcacatt ccacgtcgaa gtacagcgcc ggctcggctc 900 tgtcgtctat ctcatcattt accgctcgac tcttccagtc aagatcacaa gaccattaga 960 cccactctgc tccaccagct ttgtcttcga cccgtatggg cccacctcag gtcacacagc 1020 acccaccagc tatgttagat cactgcactc ctatgcttgt ggtttgcctg acgaaacctt 1080 ctcttatacc agacttgtca tttatgccaa aggtctggca ttcagagcaa agataggtgc 1140 agtcgctctc aatgaaggct ggaacccaga cacaacagcc ttcagtgcag tggttgccgg 1200 ggtctttatg gatgttgctg taaagcgata cctaagatct aagggtatta gcaactgcat 1260 gaaagagctc aagaaagagc aaaatgctgg gttctggtca ctcttgtggc agcgtatttg 1320 catctggttc ggagatagca atgaacaccg acacatggat cacaacacac tcaaaggatg 1380 ggtcagttca ggcatgatcc ttgatcctgc ttgcatggtc ctccagggcc aagccaactt 1440 aaatgtcctc tcactcacaa ctacccagtc aggcgagttc gaaatcatag gctggcttgc 1500 cagctctttt gagaagatac tggactaccc aaaccaccac cacgactacc tgaaggatct 1560 aatgccaggc ttcacaccag accgcgctga gcactacgag aacctgctac acaccgtttt 1620 gcacactaag gagcgccaag gcgaaactga tggtgagctc accgaccgac tcacagagta 1680 cattaatgta ccctatgaag aagtccatgc gcttgtgact aaccgactcg acctccgaac 1740 tcgtcatcac atccagccaa agagctgttt gacaaccccg gctcccaccc caatcccaac 1800 accacaaagt tccagatcca gtagtccatc tagaacccgc agttcatcag tgtctagctc 1860 tagctcagta agtacatcag tcatttcatt ccaaatggag agggagagtc agttcgaggc 1920 tcgtaaccaa ccccaaatca acctcctcga cacacctcta gacgctaatc ttgatctaac 1980 ccaagcaact tttctacaac cgtcagcgcc tcctgatacc aatcaaaacc aaacagctct 2040 ccaagaccaa gctagggcca tcacacccac tcagaaccca cctgacactg ccacactacc 2100 gagtactaga gtgttaccag cagctacacc cgtcgacata aacaccacac tgcaacccag 2160 cccctccaca ggagctatcc gtaagacaag ccctagagtc ccacctaccg ttgttcctcc 2220 accacagaac gcgcaagtca ctccaatcca actaccccag accgggcaga accccagatc 2280 caacatccgt taccacaaca cctcgatctt tgacactcac tgctgcattg cagtaaaccc 2340 ggcccacccc accctaaaac caggaggcgg tctgagtgcg ctattccaca ggcaatttcc 2400 agatctagca gcaaagacag caccacacac aactagtttc gagcgtctcc caccctatgc 2460 agtgtccacc aaagtgaatg cagtaggcaa catctcagaa gtcgttcatg caattggacc 2520 tgacagagga agaggtcaga cctcatacaa ccagctgctc tgcacatatc aacttgccat 2580 gcaggtagct tcaggtcctg cggctttccc cctgctagga gccaacattt ttggttggtc 2640 tccagaagac tctctcaggg catttatgga agctgatact caagacatgc accatctcta 2700 catttatgac ccctccgacc ctggcagatt tagaaggcta atcggtaaag acccaacaga 2760 cggtgatcag agaccgccca caagggattc tatggtcagg gaaatcaacg gtgtgatcga 2820 gccccccaga cccacactgg ccgaaagtat tggcagcaca ctcggactgg cacccagctg 2880 gtacaaacca accactcatc gctacgacga tatggcttgt aaagccatca acagcaacat 2940 gggcatggaa aaaggtaaag gtggtgattc taaggtattt gctgagctag ttgcttctgc 3000 tcctctcatc gaacccttta tattcaagta tcatctcaca gaaggcgttc ccggttcagg 3060 aaagtcccac gctgctaaga agctcaacaa aagtacttgt gtggtggttc caaccggcga 3120 actcaagagc gactggaagc aaagtgggtt caaaaacact gttacacccc atgtagccat 3180 caaatacggc atcaaatcta aatttctcgt cgtcgacgaa gtcttcagca tcccacccca 3240 cctgttggca accatcctct acaaacacag agacaacaac atcctacttg gggattctaa 3300 gcaaatagct gcctgtgatt ttgacaactt ccgcaacttt gatataattg ctccaaaact 3360 caccccgtcc gtctacctca atctcaccta caggctccca caagacatca ccaggtacct 3420 gcagcgcgac tacccgggca tccacactgc tagtaaagtc cccgtctcaa tctctttcta 3480 tccgcccccc tcaggcaccc cttgtcaagt tatcggctac cgtcaattga tcaaagaaca 3540 accaccgtgg aagaaaactg ccaacacatc tcatgagctc cagggtgcta cccgtaaagc 3600 cgtgcactta cacctgctta caggcgatgt ggagatgata cggtcatcca gatctcatac 3660 tattgtggca ctctcacgtc acactgacca aattttcatc acaggagacg cagagtccat 3720 tcaaacactc cagctcactg ataaaatgga aaacatcatc atcaactacg ctcctaccac 3780 tttagttaat gatggtgcga ccttggagat caccagcaca cctgacgatg acactcatgt 3840 cacagctcct gccgcagatt cgacagccgt aggtgagata ctccaggctt gcacaaatca 3900 tctatatgcc cccatttcag ctgtcgtact agactgcgag aaaataaatc aaggttcact 3960 caccgtcaag tgcgctgtac cagatgaacg catcatacca aaaaccaact tcacagagat 4020 agaacactgt cgtcgtgcaa atgccagcag cacctggacg acagtgcgca ccctcatagg 4080 ccgctacacc aaacttacca tcaacccagc tcatgtacac gataccatcc aagcagttaa 4140 caaaacattc tggaaatgcc tcacagtcga caccatgaat tgcttaccta caacagcaga 4200 gctcgccgag cttgtccgca gcatgaagga caagggagca gaccccactc tcatacacga 4260 tctggacttc aacgacatct ctgttacgaa gatgacgttc ttccaaaagg agtgtgataa 4320 gttcaccatg gatgaaccag tccaacacaa caagcctgga caagggattt cagcatggcc 4380 aaagacccta tgttttatct acgggctttt cttcagaaaa ctagaaaagg aactaagaca 4440 ggctctgaaa ccaagcatca tcttctcaaa cccttacaca gaggaacaac ttgcaagagc 4500 tgtctccaag tgcaccacag gaaccacagt cttctatgag aacgatttct cagcatttga 4560 cagcacacag aatctagttt ctcttggcaa tgagtttctc atcttggtac aatgtggaat 4620 gccacctgca ctcgctgaag tctacttcaa cctccgcctg aagtggactc ttgacgctag 4680 agttgccagt ctccgtggta catccaagaa gcactctggg gagccaggca ccatgctttt 4740 taacaccatt tggaacatga ccgctgtctt ccacaccact agtttcacca gaatgaccct 4800 cgccctcttc aaaggagatg actcgcttgt gtgctgtgac tccagcatac tcaccccaac 4860 tgccaaggag ttcatttctc agaacgggct cgtcatgaaa cagaagacgt cccacctcgg 4920 ctcctttacg tgcagtctcg tcacccgcac aagctatgtt ccggatgtca tcaggttcgc 4980 ttgcaggttg aacaacaagg acttcacaga caccaagcgc atcgaggatc tccagagggc 5040 cacagacgat ttcatcaaga gagcgactgt caccactaac tacggttcca cttgctcgat 5100 caacggcaga tactatggtg tcccttctga caccattgag tgtgttgttg gcttcctcca 5160 agattttgct ctcaccggaa aaatagacct ccaaacatca tacaaaccaa tcttaaaata 5220 ttaaaataag agaagaaatt aaataagttg gacattagtt gtgtgcgttt gagatagata 5280 cattcacaat ggcagattct aatgcagtcg tcccttccgc acaatctaaa ccacgtcgca 5340 ctaggcgccc aaagatggac ccctctcaga tcccagatac agtcaaaacc ttccgtctca 5400 caaccgaccc tatcatggca cccccacctg gtgaaattga ttcacttctc tatacatcag 5460 gcctctcacc tgcagttgtc ctttccttct cctcattcac ctcacctgca gttgtcttcg 5520 ctgccaacta tgagaaatac aagatcttgt ctttcaaagc tactgtcctc tccctagcac 5580 cagaagctat ttccagttac aacctctctg tcgtctggtt cccagatgca tcagaaggac 5640 ccacctccct ccaagctaca aacttgtcca tggtccgccg ctaccactca atcttaccag 5700 gacaatctgg ttctctctcc cttaccgcat ctgagctcct ccacggtata gctgagaagt 5760 acgtcgaccc cactcactct gatgcattat ccgctttctg cgggctcttc atggtagtgt 5820 gccacggagc ccctttcaac cactaccgtg acactcagta ccttggccct ctgttcaaga 5880 tccaattcga gttcaagctg tcagtcttcg gttactctcc cggcaacatt ccagttaaag 5940 ttcagggcgc ctcagctact gagattgtct catttggaac agttgatggg aaagctacct 6000 ttgacacccc ttccgcaatt gctctccatg cttcatacca aagtggccca ccaaattcac 6060 ccgggccttc tatcggccaa gtactcctca cagtggctga caccgtgtca gctgcgctcc 6120 ctttcccttt cagtatactt gcaaaagttg gtctcttctt tatccgcaag attactggag 6180 ccaatggaac ttccttcatg gtctacaaat cctatggaga tgcaattcgc aaccgcccac 6240 taccctcacg ctcaagccat caactgggca atgcacttgt ccgccagacc acattcggca 6300 ctaacgatga ctcagttctc ccaccccagc ccatcagcca gttcaccttc cacttcaaga 6360 ctggcgatgt ccttgtcatc cagggttcct tcaaggcccc aaccagtcga cccaataatt 6420 ggaatgttca ggaattctcc atttcgagaa tccttaacat cactaatggg acctccacta 6480 caaacattct tgtgtttgaa aagtggactc tggatggtaa cctcccacag atcaagaaca 6540 cctacggtct catcggggtc cactacttcc cggcttccat tagtcctgtt ggcaccagca 6600 ccttcgacaa catcattggt gattgcaaag tctttgcagg caccgcaact gacagcatgt 6660 taacgcctgg tccaggttct atcacagtaa cattcctatc ccaaacccgc ggcttcctca 6720 gtcagactga gctcacacaa ggtctcatag ccgcttcaag caccatggac accacagact 6780 catctctcac ccgacaagca tcccaaccaa tggaggtgga tggcttcctt tccggtctaa 6840 tcccctccac acccctctgc aacatggtga acaacacctt ctcctgcggc aacagcgaca 6900 gtcaagccac ttcccggtca gctgttcact ctcttggccc caattgtgat aaatgcggac 6960 tagatctcaa cctaagagtg acaccctgca ttgccactcg cctccaacac acaccaaaag 7020 catgccctca ctgctccttc ctcctcggtc tcactgccta cacagtggac tgtatgcgtc 7080 cttccgacac cactgattct accgtggacg ctctccttaa cccactcaac tctctcgatc 7140 ttgagtctga gtcagaacct tctgatgacg acctgatcca attcgatgac taaacatcat 7200 ttggcctact atctcttcta ttaatcctct aacttttctt atatattcac cctattcagt 7260 tatacaccca aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa 7310 //