LOCUS       Exported               14715 bp ds-DNA     circular SYN 17-DEC-2018
DEFINITION  Cloning vector pCHIKV-LS3-MCS, complete sequence.
ACCESSION   JX911336
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 14715)
  AUTHORS   Scholte FE, Tas A, Martina BE, Cordioli P, Narayanan K, Makino S, 
            Snijder EJ, van Hemert MJ.
  TITLE     Characterization of Synthetic Chikungunya Viruses Based on the 
            Consensus Sequence of Recent E1-226V Isolates
  JOURNAL   PLoS ONE 8 (8), E71047 (2013)
  PUBMED    23936484
REFERENCE   2  (bases 1 to 14715)
  AUTHORS   Scholte FEM., Tas A, Snijder EJ, van Hemert MJ.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-OCT-2012) Medical Microbiology, Leiden University 
            Medical Center, Albinusdreef 2, Leiden, Zuid-Holland 2333 ZA, The 
            Netherlands
REFERENCE   3  (bases 1 to 14715)
  AUTHORS   .
  TITLE     Direct Submission
FEATURES             Location/Qualifiers
     source          1..14715
                     /organism="Cloning vector pCHIKV-LS3-MCS"
                     /mol_type="other DNA"
                     /note="infectious cDNA clone of Chikungunya virus strain 
                     LS3 with a duplicated subgenomic promoter"
                     /db_xref="taxon:1343679"
     primer_bind     379..395
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     regulatory      410..430
                     /regulatory_class="promoter"
     5UTR           430..505
     CDS             506..7930
                     /codon_start=1
                     /transl_except="(pos: 6074 .. 6076,  aa: OTHER)"
                     /product="nonstructural polyprotein"
                     /label=nonstructural polyprotein
                     /note="encodes nonstructural proteins 1 through 4"
                     /protein_id="AGN96203.1"
                     /translation="MDPVYVDIDADSAFLKALQRAYPMFEVEPRQVTPNDHANARAFSH
                     LAIKLIEQEIDPDSTILDIGSAPARRMMSDRKYHCVCPMRSAEDPERLANYARKLASAA
                     GKVLDRNISGKIGDLQAVMAVPDKETPTFCLHTDVSCRQRADVAIYQDVYAVHAPTSLY
                     HQAIKGVRVAYWVGFDTTPFMYNAMAGAYPSYSTNWADEQVLKAKNIGLCSTDLTEGRR
                     GKLSIMRGKKLKPCDRVLFSVGSTLYPESRKLLKSWHLPSVFHLKGKLSFTCRCDTVVS
                     CEGYVVKRITMSPGLYGKTTGYAVTHHADGFLMCKTTDTVDGERVSFSVCTYVPATICD
                     QMTGILATEVTPEDAQKLLVGLNQRIVVNGRTQRNMNTMKNYLLPVVAQAFSKWAKECR
                     KDMEDEKLLGVRERTLTCCCLWAFKKQKTHTVYKRPDTQSIQKVQAEFDSFVVPSLWSS
                     GLSIPLRTRIKWLLSKVPKTDLIPYSGDAREARDAEKEAEEEREAELTREALPPLQAAQ
                     EDVQVEIDVEQLEDRAGAGIIETPRGAIKVTAQPTDHVVGEYLVLSPQTVLRSQKLSLI
                     HALAEQVKTCTHNGRAGRYAVEAYDGRVLVPSGYAISPEDFQSLSESATMVYNEREFVN
                     RKLHHIAMHGPALNTDEESYELVRAERTEHEYVYDVDQRRCCKKEEAAGLVLVGDLTNP
                     PYHEFAYEGLKIRPACPYKIAVIGVFGVPGSGKSAIIKNLVTRQDLVTSGKKENCQEIT
                     TDVMRQRGLEISARTVDSLLLNGCNRPVDVLYVDEAFACHSGTLLALIALVRPRQKVVL
                     CGDPKQCGFFNMMQMKVNYNHNICTQVYHKSISRRCTLPVTAIVSSLHYEGKMRTTNEY
                     NKPIVVDTTGSTKPDPGDLVLTCFRGWVKQLQIDYRGYEVMTAAASQGLTRKGVYAVRQ
                     KVNENPLYASTSEHVNVLLTRTEGKLVWKTLSGDPWIKTLQNPPKGNFKATIKEWEVEH
                     ASIMAGICSHQMTFDTFQNKANVCWAKSLVPILETAGIKLNDRQWSQIIQAFKEDKAYS
                     PEVALNEICTRMYGVDLDSGLFSKPLVSVYYADNHWDNRPGGKMFGFNPEAASILERKY
                     PFTKGKWNINKQICVTTRRIEDFNPTTNIIPANRRLPHSLVAEHRPVKGERMEWLVNKI
                     NGHHVLLVSGYNLALPTKRVTWVAPLGVRGADYTYNLELGLPATLGRYDLVVINIHTPF
                     RIHHYQQCVDHAMKLQMLGGDSLRLLKPGGSLLIRAYGYADRTSERVICVLGRKFRSSR
                     ALKPPCVTSNTEMFFLFSNFDNGRRNFTTHVMNNQLNAAFVGQVTRAGCAPSYRVKRMD
                     IAKNDEECVVNAANPRGLPGDGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAV
                     GPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHL
                     FTAMDSTDADVVIYCRDKEWEKKISEAIQMRTQVELLDEHISIDCDIVRVHPDSSLAGR
                     KGYSTTEGALYSYLEGTRFHQTAVDMAEIHTMWPKQTEANEQVCLYALGESIESIRQKC
                     PVDDADASSPPKTVPCLCRYAMTPERVTRLRMNHVTSIIVCSSFPLPKYKIEGVQKVKC
                     SKVMLFDHNVPSRVSPREYRSSQESAQEASTITSLTHSQFDLSVDGEILPVPSDLDADA
                     PALEPALDDGATHTLPSTTGNLAAVSDWVMSTVPVAPPRRRRGRNLTVTCDEREGNITP
                     MASVRFFRAELCPVVQETAETRDTAMSLQAPPSTATEPNHPPISFGASSETFPITFGDF
                     NEGEIESLSSELLTFGDFLPGEVDDLTDSDWSTCSDTDDEL*LDRAGGYIFSSDTGPGH
                     LQQKSVRQSVLPVNTLEEVHEEKCYPPKLDEAKEQLLLKKLQESASMANRSRYQSRKVE
                     NMKAAIIQRLKRGCRLYLMSETPKVPTYRTTYPAPVYSPPINVRLSNPESAVAACNEFL
                     ARNYPTVSSYQITDEYDAYLDMVDGSESCLDRATFNPSKLRSYPKQHAYHAPSIRSAVP
                     SPFQNTLQNVLAAATKRNCNVTQMRELPTLDSAVFNVECFKKFACNQEYWEEFAASPIR
                     ITTENLATYVTKLKGPKAAALFAKTHNLLPLQEVPMDRFTVDMKRDVKVTPGTKHTEER
                     PKVQVIQAAEPLATAYLCGIHRELVRRLNAVLLPNVHTLFDMSAEDFDAIIAAHFKPGD
                     TVLETDIASFDKSQDDSLALTALMLLEDLGVDHSLLDLIEAAFGEISSCHLPTGTRFKF
                     GAMMKSGMFLTLFVNTLLNITIASRVLEDRLTKSACAAFIGDDNIIHGVVSDELMAARC
                     ATWMNMEVKIIDAVVSLKAPYFCGGFILHDTVTGTACRVADPLKRLFKLGKPLAAGDEQ
                     DEDRRRALADEVIRWQRTGLIDELEKAVYSRYEVQGISVVVMSMATFASSRSNFEKLRG
                     PVITLYGGPK"
     regulatory      7909..7928
                     /regulatory_class="promoter"
     regulatory      8092..8111
                     /regulatory_class="promoter"
     CDS             8179..11925
                     /codon_start=1
                     /product="structural polyprotein"
                     /label=structural polyprotein
                     /note="contains C, E3, E2, 6K and E1"
                     /protein_id="AGN96201.1"
                     /translation="MEFIPTQTFYNRRYQPRPWTPRSTIQVIRPRPRPQRQAGQLAQLI
                     SAVNKLTMRAVPQQKPRRNRKNKKQKQKQQAPQNNTNQKKQPPKKKPAQKKKKPGRRER
                     MCMKIENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLE
                     CAQIPVHMKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKG
                     RVVAIVLGGANEGARTALSVVTWNKDIVTKITPEGAEEWSLAIPVMCLLANTTFPCSQP
                     PCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSPHRQRRSTKDNFNVYKATRPY
                     LAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDNHM
                     PADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHSCTHPFHHDP
                     PVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSGNVKITV
                     NGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNAELGDR
                     KGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNYQEEW
                     VMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYYELYPTMTVV
                     VVSVATFILLSMVGMAAGMCMCARRRCITPYELTPGATVPFLLSLICCIRTAKAATYQE
                     AAIYLWNEQQPLFWLQALIPLAALIVLCNCLRLLPCCCKTLAFLAVMSVGAHTVSAYEH
                     VTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKC
                     CGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASA
                     YRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVY
                     KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAVGTVHVPYSQAPSG
                     FKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTD
                     MSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFS
                     TALASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISATAMSWVQKITGG
                     VGLVVAVAALILIVVLCVSFSRH"
     3UTR           11926..12463
     primer_bind     complement(12494..12510)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     protein_bind    12518..12534
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     promoter        complement(12542..12572)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    12587..12608
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     rep_origin      12881..13494
     rep_origin      complement(12896..13484)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     CDS             complement(13655..14515)
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=bla
                     /note="confers ampicillin resistance"
                     /protein_id="AGN96202.1"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     gene            complement(13655..14515)
                     /gene="bla"
                     /label=bla
     promoter        complement(14516..14620)
                     /gene="bla"
                     /label=AmpR promoter