Overall information

FSDB ID	EM1V0016	Type	-1 frameshifting
Data	EXPERIMENTAL	Kingdom	viruses
Definition	Porcine reproductive and respiratory syndrome virus isolate 16244B, 2/18/97(Nebraska)pass.3, complete genome. 15428 bp RNA linear VRL 17-MAR-1999
Resource	[1] Allende R, Lewis TL, Lu Z, Rock DL, Kutish GF, Ali A, Doster AR, Osorio FA. J Gen Virol. 1999 Feb;80 ( Pt 2):307-15.
Nucleic acid sequence		AF046869
Amino acid sequence
CDS	Click for details 190..7701 /note="cysteine protease/serine protease; ORF1a" /codon_start=1 /product="ORF1a polyprotein" /protein_id="AAC64691.1" /db_xref="GI:3776251" /translation="MSGILDRCTCTPNARVFVAEGQVYCTRCLSARSLLPLNLQVSEL GVLGLFYRPEEPLRWTLPRAFPTVECSPAGACWLSAIFPIARMTSGNLNFQQRMVRVA AEIYRAGQLTPAVLKALQVYERGCRWYPIVGPVPGVAVFANSLHVSDKPFPGATHVLT NLPLPQRPKPEDFCPFECAMATVYDIGHDAVMYVAEGKISWAPRGGDEVKFEAVPGEL KLIANRLRTSFPPHHAVDMSKFAFTAPGCGVSMRVERQHGCLPADTVPEGNCWWSLFD LLPLEVQDKEIRHANQFGYQTKHGVSGKYLQRRLQVNGLRAVTDSNGPIVVQYFSVKE SWIRHLKLAGEPSYSGFEDLLRIRVEPNTSPLANTEGKIFRFGSHKWYGAGKRARKAR SCATATVAGRALSVRETRQAKEHEVAGADKAEHLKHYSPPAEGNCGWHCISAIANRMV NSIFETTLPERVRPPDDWATDDDLANAIQILRLPAALDRNGACTSAKYVLKLEGEHWT VTVTPGMSPSLLPLECVQGCCEHKGGLGSPDAIEVSGFDPACLDWLAEVMHLPSSAIP AALAEMSGDSDRSASPVTTVWTVSQFFARHSGGNHPDQVRLGKIISLCQVIEDCCCSQ NKTNRVTPEEVAAKIDLYLRGATNLEECLARLEKARPPRVIDTSFDWDVVLPGVEAAT QTNKLPQVNQCRALVPVVTQKSLDNNSVPLTAFSLANYYYRAQGDEVRHRERLTAVLS KLEEVVREEYGLMPTEPGPRPTLPRGLDELKDQMEEDLLRLANAQATSDMMAWAVEQV DLKTWVKNYPRWTPPPPPPKVQPRKTKPVKSLPERKPVPAPRRKVGPDCGSPVSLGGD VPNSWEDLAVSSPLDLPTPPEPATLSSELVIVSSPQCIFRPATPLSEPAPIPAPRGTV SRPVTPLSEPIPVPAPRRKFQQVKRLSSAAAVPLHQNEPLDLSASSQTEYEASPSAPP QSGGVLGVEGHEAEETLSEISDMSGNIKPASVSSSSSLSSVEITRPKYSAQAIIDSGG PCSGHLQGVKETCLSVMREACDATKLDDPATQEWLSRMWDRVDMLTWRNTSVCQAIRT LDGRLKFLPKMILETPPPYPCEFVMMPHTPAPSVGAESDLTIGSVATEDVPRILEKIE NVGEMANQEPSAFSEDKPVDDQLVNDPRISSRRPDESTAAPSAGTGGAGSFTDLPSSD GADADGGGPFRTAKRKAERLFDQLSRQVFDLVSHLPVFFSRLFHPGGGYSTGDWGFAA FTLLCLFLCYSYPAFGIAPLLGVFSGTSRRVRMGVFGCWLAFAVGLFKPVSDPVGAAC EFDSPECRNILLSFELLKPWDPVRSLVVGPVGLGLAILGRLLGGARCIWHFLLRLGIV ADCILAGAYVLSQGRCKKCWGSCIRTAPNEVAFNVFPFTRATRSSLIDLCDRFCAPKG MDPIFLATGWRGCWAGRSPIEQPSEKPIAFAQLDEKKITARTVVAQPYDPNQAVKCLR VLQAGGAMVAEAVPKVVKVSAVPFRAPFFPTGVKVDPDCRVVVDPDTFTAALRSGYST TNLVLGVGDFAQLNGLKIRQISKPSGGGPHLMAALHVACSMALHMLTGIYVTAVGSCG TGTNDPWCANPFAVPGYGPGSLCTSRLCISQHGLTLPLTALVAGFGIQEIALVVLIFV SIGGMAHRLSCKADMLCILLAIASYVWVPLTWLLCVFPCWLRCFSLHPLTILWLVFFL ISVNMPSGILAMVLLVSLWLLGRYTNVAGLVTPYDIHHYTSGPRGVAALATAPDGTYL AAVRRAALTGRTMLFTPSQLGSLLEGAFRTRKPSLNTVNVIGSSMGSGGVFTIDGKVK CVTAAHVLTGNSARVSGVGFNQMLDFDVKGDFAIADCPNWQGAAPKAQFCADGWTGRA YWLTSSGVEPGVIGKGFAFCFTACGDSGSPVITEAGELVGVHTGSNKQGGGIVTRPSG QFCNVAPIKLSELSEFFAGPKVPLGDVKVGSHIIKDISEVPSDLCALLAAKPELEGGL STVQLLCVFFLLWRMMGHAWTPLVAVSFFILNEVLPAVLVRSVFSFGMFVLSWLTPWS AQILMIRLLTAALNRNRWSLAFFSLGAVTGFVADLAATQGHPLQAVMNLSTYAFLPRM MVVTSPVPVITCGVVHLLAIILYLFKYRGLHQILVGDGVFSAAFFLRYFAEGKLREGV SQSCGMNHESLTGALAMRLNDEDLDFLMKWTDFKCFVSASNMRNAAGQFIEAAYAKAL RVELAQLVQVDKVRGVLAKLEAFADTVAPQLSPGDIVVALGHTPVGSIFDLKVGSTKH TLQAIETRVLAGSKMTVARVVDPTPTPPPAPVPIPLPPKVLENGPNAWGDEDRLNKKK RRRMEALGIYVMGGKKYQKFWDKNSGDVFYEEVHNNTDEWECLRVGDPADFDPEKGTL CGHVTIENKAYHVYISPSGKKFLVPVNPENGRVQWEAAKLSMEQALGMMNVDGELTAK ELEKLKRIIDKLQGLTKEQCLNC"
CDS	Click for details 7680..12071 /note="RNA dependent RNA polymerase/zinc-finger/helicase; ORF1b" /codon_start=1 /product="ORF1b polyprotein" /protein_id="AAC64692.1" /db_xref="GI:3776252" /translation="GAVFKLLAASGLTRCGRGGLVVTETAVKIVKFHNRTFTLGPVNL KVASEVELKDAVEHNQHPVARPIDGGVVLLRSAVPSLIDVLISGADASPKLLAHHGPG NTGIDGTLWDFESEATKEEVALSAQIIQACDIRRGDAPKIGLPYKLYPVRGNPERVKG VLQNTRFGDIPYKTPSDTGSPVHAAACLTPNATPVTDGRSVLATTMPPGFELYVPTIP ASVLDYLDSRPDCPKQLTEHGCEDAALKDLSKYDLSTQGFVLPGVLRLVRKYLFAHVG KCPPVHRPSTYPAKNSMAGINGNRFPTKDIQSVPEIDVLCAQAVRENWQTVTPCTLKK QYCGKKKTRTILGTNNFIALAHRAALSGVTQGFMKKAFNSPIALGKNKFKELQTSVLG RCLEADLASCDRSTPAIVRWFAANLLYELACAEEHLPSYVLNCCHDLLVTQSGAVTKR GGLSSGDPITSVSNTIYSLVIYAQHMVLSYFKSGHPHGLLFLQDQLKFEDMLKVQPLI VYSDDLVLYAESPTMPNYHWWVEHLNLMLGFQTDPKKTAITDSPSFLGCRIINGRQLV PNRDRILAALAYHMKASNVSEYYASAAAILMDSCACLEYDPEWFEELVVGIAQCARKD GYSFPGTPFFMSMWEKLRSNYEGKKSRVCGYCGAPAPYATACGLDVCIYHTHFHQHCP VTIWCGHPAGSGSCSECKSPVGKGTSPLDEVLEQVPYKPPRTVIMHVEQGLTPLDPGR YQTRRGLVSVRRGIRGNEVELPDGDYASTALLPTCKEINMVAVASNVLRSRFIIGPPG AGKTYWLLQQVQDGDVIYTPTHQTMLDMIRALGTCRFNVPAGTTLQFPVPSRTGPWVR ILAGGWCPGKNSFLDEAAYCNHLDVLRLLSKTTLTCLGDFKQLHPVGFDSHCYVFDIM PQTQLKTIWRFGQNICDAIQPDYRDKLMSMVNTTRVTYVEKPVRYGQVLTPYHRDRED DAITIDSSQGATFDVVTLHLPTKDSLNRQRALVAITRARHAIFVYDPHRQLQGLFDLP AKGTPVNLAVHRDGQLIVLDRNNKECTVAQALGNGDKFRATDKRVVDSLRAICADLEG SSSPLPKVAHNLGFYFSPDLTQFAKLPVELAPHWPVVTTQNNEKWPDRLVASLRPIHK YSRACIGAGYMVGPSVFLGTPGVVSYYLTKFVKGEAQLLPETVFSTGRIEVDCREYLD DREREVAASLPHAFIGDVKGTTVGGCHHVTSRYLPRVLPKESVAVVGVSSPGKAAKAL CTLTDVYLPDLEAYLHPETQSKCWKMMLDFKEVRLMVWRDKTAYFQLEGRYFTWYQLA SYASYIRVPVNSTVYLDPCMGPALCNRRVVGSTHWGADLAVTPYDYGAKIILSSAYHG EMPPGYKILACAEFSLDDPVRYKHTWGFESDTAYLYEFTGNGEDWEDYNDAFRARQEG KIYKATATSLKFHFPPGPVIEPTLGLN"

Graphical view

7677 TAAGGAGCAGTG TTTAAAC TGCTA GCCGCCAGCGGCTTGACCCGCTGTGGTCGCGGCGGCTTGGTTGTTACTGAGACAGCGG
Stop codons	TAA (7677),
Slippery sequence	TTTAAAC (7689 - 7695)
Spacer	TGCTA (5 nt)
Stimulatory structure	GCCGCCAGCGGCTTGACCCGCTGTGGTCGCGGCGGCTTGGTTGTTACTGAGACAGCGG (7701 - 7758)
	Stimulatory structure from PseudoBase Visualized by PseudoViewer

Model

-1 frameshift signal

FSFinder parameters

Run FSFinder
(You can obtain the above result by running FSFinder with the sequence and parameter values. You may have to alternate frames to get the same result.)

Target gene

genes in viruses

Sequence type

Patial genome

Direction

+ strand

Pattern

Pattern
Match
Exceptions AAA UUU

spacer

nt

RNA structure

Stem Pseudoknot
- Stem1	<
- Stem2	<
- Loop1	<
- Loop2	<
- Loop3	<