LOCUS       Exported               13826 bp ds-DNA     circular SYN 17-DEC-2018
DEFINITION  Cloning vector pCHIK-37997ic, complete sequence.
ACCESSION   EU224270
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 13826)
  AUTHORS   Tsetsarkin KA, Vanlandingham DL, Higgs S.
  TITLE     Full length infectious clone of Chikungunya virus strain 37997
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 13826)
  AUTHORS   Tsetsarkin KA, Vanlandingham DL, Higgs S.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-OCT-2007) Pathology, University of Texas Medical 
            Branch, University Blvd, Galveston, TX 77555-0609, USA
REFERENCE   3  (bases 1 to 13826)
  AUTHORS   .
  TITLE     Direct Submission
FEATURES             Location/Qualifiers
     source          1..13826
                     /organism="Cloning vector pCHIK-37997ic"
                     /mol_type="other DNA"
                     /note="derived from Chikungunya virus strain LR2006 OPY1 
                     and plasmid pSinRep5 which serves to propagate the viral 
                     cDNA in Escherichia coli"
                     /db_xref="taxon:481787"
     5UTR           1..77
     CDS             78..7502
                     /codon_start=1
                     /transl_except="(pos: 5646 .. 5648,  aa: OTHER)"
                     /product="nonstructural polyprotein"
                     /label=nonstructural polyprotein
                     /note="encodes nonstructural proteins 1 through 4"
                     /protein_id="ABX40010.1"
                     /translation="MDPVYVDIDADSAFLKALQRAYPMFEVEPRQVTPNDHANARAFSH
                     LAIKLIEQEIDPDSTILDIGSAPARRMMSDRKYHCVCPMRSAEDPERLANYARKLASAA
                     GKVLDRNISEKIGDLQAVMAVPDAETPTFCLHTDVSCRQRADVAIYQDVYAVHAPTSLY
                     HQAIKGVRVAYWIGFDTTPFMYNAMAGAYPSYSTNWADEQVLKAKNIGLCSTDLTEGRR
                     GKLSIMRGKKMKPCDRVLFSVGSTLYPESRKLLKSWHLPSVFHLKGKLSFTCRCDTVVS
                     CEGYVVKRITISPGLYGKTTGYAVTHHADGFLMCKTTDTVDGERVSFSVCTYVPATICD
                     QMTGILATEVTPEDAQKLLVGLNQRIVVNGRTQRNTNTMKNYLLPVVAQALSKWAKECR
                     KDMEDEKLLGIRERTLTCCCLWAFKKQKTHTVYKRPDTQSIQKVPAEFDSFVVPSLWSS
                     GLSIPLRTRIKWLLSKVPKTDLIPYSGDAKEARDAEKEAEEEREAELTREALPPLQAAQ
                     DDVQVEIDVEQLEDRAGAGIIETPRGAIKVTAQPTDHVVGEYLVLSPQTVLRSQKLSLI
                     HALAEQVKTCTHSGRAGRYAVEAYDGRILVPSGYAISPEDFQSLSESATMVYNEREFVN
                     RKLHHIALHGPALNTDEESYELVRAERTEHEYVYDVDQRRCCKKEEAAGLVLVGDLTNP
                     PYHEFAYEGLRIRPACPYKTAVIGVFGVPGSGKSAIIKNLVTRQDLVTSGKKENCQEIS
                     TDVMRQRNLEISARTVDSLLLNGCNRPVDVLYVDEAFACHSGTLLALIALVRPRQKVVL
                     CGDPKQCGFFNMMQMKVNYNHNICTQVYHKSISRRCTLPVTAIVSSLHYEGKMRTTNEY
                     NKPIVVDTTGSTKPDPGDLVLTCFRGWVKQLQIDYRGHEVMTAAASQGLTRKGVYAVRQ
                     KVNENPLYASTSEHVNVLLTRTEGKLVWKTLSGDPWIKTLQNPPKGNFKATIKEWEVEH
                     ASIMAGICNHQVTFDTFQNKANVCWAKSLVPILETAGIKLNDRQWSQIIQAFKEDRAYS
                     PEVALNEICTRMYGVDLDSGLFSKPLVSVHHADNHWDNRPGGKMFGFNPEAASILERKY
                     PFTKGKWNTNKQICVTTRRIEDFNPNTNIIPANRRLPHSLVAEHRPVKGERMEWLVNKI
                     NGHHVLLVSGYNLVLPTKRVTWVAPLGIRGADYTYNLELGLPATLGRYDLVIINIHTPF
                     RIHHYQQCVDHAMKLQMLGGDSLRLLKPGGSLLIRAYGYADRTSERVVCVLGRKFRSSR
                     ALKPPCVTSNTEMFFLFSNFDNGRRNFTTHVMNNQLNAAFVGQATRAGCAPSYRVKRMD
                     IAKNDEECVVNAANPRGLPGDGVCKAVYKKWPESFKNSATPVGTAKTVMCGTYPVIHAV
                     GPNFSNYSESEGDRELAAAYREVAKEVTRLGVNSVAIPLLSTGVYSGGKDRLTQSLNHL
                     FTALDSTDADVVIYCRDKEWEKKIAEAIQMRTQVELLDEHISVDCDIIRVHPDSSLAGR
                     KGYSTTEGSLYSYLEGTRFHQTAVDMAEVYTMWPKQTEANEQVCLYALGESIESIRQKC
                     PVDDADASSPPKTVPCLCRYAMTPERVTRLRMNHVTSIIVCSSFPLPKYKIEGVQKVKC
                     SKVMLFDHNVPSRVSPREYKSPQETAQEVSSTTSLTHSQFDLSVDGEELPAPSDLEADA
                     PIPEPTPDDRAVLTLPPTIDNFSAVSDWVMNTAPVAPPRRRRGKNLNVTCDEREGNVLP
                     MASVRFFRADLHSIVQETAEIRDTAASLQAPLSVATEPNQLPISFGAPNETFPITFGDF
                     DEGEIESLSSELLTFGDFSPGEVDDLTDSDWSTCSDTDDEL*LDRAGGYIFSSDTGPGH
                     LQQRSVRQTVLPVNTLEEVQEEKCYPPKLDEVKEQLLLKKLQESASMANRSRYQSRKVE
                     NMKATIVQRLKGGCKLYLMSETPKVPTYRTTYPAPVYSPPINIRLSNPESAVAACNEFL
                     ARNYPTVASYQITDEYDAYLDMVDGSESCLDRATFNPSKLRSYPKQHSYHAPTIRSAVP
                     SPFQNTLQNVLAAATKRNCNVTQMRELPTLDSAVFNVECFKKFACNQEYWKEFAASPIR
                     ITTENLTTYVTKLKGPKAAALFAKTHNLLPLQEVPMDRFTVDMKRDVKVTPGTKHTEER
                     PKVQVIQAAEPLATAYLCGIHRELVRRLNAVLLPNVHTLFDMSAEDFDAIIAAHFKPGD
                     AVLETDIASFDKSQDDSLALTALMLLEDLGVDHPLLDLIEAAFGEISSCHLPTGTRFKF
                     GAMMKSGMFLTLFVNTLLNITIASRVLEDRLTRSACAAFIGDDNIIHGVVSDELMAARC
                     ATWMNMEVKIIDAVVSQKAPYFCGGFILYDTVAGTACRVADPLKRLFKLGKPLAAGDEQ
                     DDDRRRALADEVVRWQRTGLTDELEKAVHSRYEVQGISVVVMSMATFASSRSNFEKLRG
                     PVVTLYGGPK"
     RBS             4355..4363
                     /label=Shine-Dalgarno sequence
                     /note="full consensus sequence for ribosome-binding sites 
                     upstream of start codons in E. coli; complementary to a 
                     region in the 3 end of the 16S rRNA (Chen et al., 1994)"
     regulatory      7480..7500
                     /regulatory_class="promoter"
                     /note="subgenomic promoter"
     CDS             7569..11315
                     /codon_start=1
                     /product="structural polyprotein"
                     /label=structural polyprotein
                     /protein_id="ABX40011.1"
                     /translation="MEFIPTQTFYNRRYQPRPWAPRPTIQVIRPRPRPQRQAGQLAQLI
                     SAVNKLTMRAVPQQKPRRNRKNKKQRQKKQAPQNDPKQKKQPPQKKPAQKKKKPGRRER
                     MCMKIENDCIFEVKHEGKVMGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLE
                     CAQIPVHMKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKG
                     RVVAIVLGGANEGARTALSVVTWNKDIVTKITPEGAEEWSLALPVLCLLANTTFPCSQP
                     PCTPCCYEKEPESTLRMLEDNVMRPGYYQLLKASLTCSPHRQRRSTKDNFNVYKATRPY
                     LAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDSHT
                     PADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHTCTHPFHHEP
                     PVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQSGNVKITV
                     NGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPRNAELGDR
                     KGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEPNYHEEW
                     VTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYPTMTVV
                     IVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCVRTTKAATYYE
                     AAAYLWNEQQPLFWLQALIPLAALIVLCNCLKLLPCCCKTLAFLAVMSIGAHTVSAYEH
                     VTVIPNTVGVPYKTLVNRPGYSPMVLEMELQSVTLEPTLSLDYITCEYKTVIPSPYVKC
                     CGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASA
                     YRAHTASASAKLRVLYQGNNITVAAYANGDHAVTVKDAKFVVGPMSSAWTPFDNKIVVY
                     KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSG
                     FKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNIPISIDIPDAAFTRVVDAPSVTD
                     MSCEVPACTHSSDFGGVAIIKYTASKKGKCAVHSMTNAVTIREADVEVEGNSQLQISFS
                     TALASAEFRVQVCSTQVHCAAACHPPKDHIVNYPASHTTLGVQDISTTAMSWVQKITGG
                     VGLIVAVAALILIVVLCVSFSRH"
     3UTR           11316..11881
     polyA_site      11882
     promoter        11997..12101
                     /gene="bla"
                     /label=AmpR promoter
     CDS             12102..12962
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     rep_origin      13133..13721
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     regulatory      13807..13826
                     /regulatory_class="promoter"
                     /note="Sp6 promoter"
     promoter        13809..1
                     /label=SP6 promoter
                     /note="promoter for bacteriophage SP6 RNA polymerase"