GenomeNet

Database: RefSeq
Entry: NC_002640
LinkDB: NC_002640
Original site: NC_002640 
LOCUS       NC_002640              10649 bp ss-RNA     linear   VRL 11-JUL-2019
DEFINITION  Dengue virus 4, complete genome.
ACCESSION   NC_002640
VERSION     NC_002640.1
DBLINK      BioProject: PRJNA485481
KEYWORDS    RefSeq.
SOURCE      dengue virus type 4
  ORGANISM  dengue virus type 4
            Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Flasuviricetes;
            Amarillovirales; Flaviviridae; Orthoflavivirus; Orthoflavivirus
            denguei.
REFERENCE   1  (bases 1 to 10649)
  AUTHORS   Durbin,A.P., Karron,R.A., Sun,W., Vaughn,D.W., Reynolds,M.J.,
            Perreault,J.R., Men,R.H., Lai,C.J., Elkins,W.R., Chanock,R.M.,
            Murphy,B.R. and Whitehead,S.S.
  TITLE     A live attenuated dengue virus type 4 vaccine candidate with a 30
            nucleotide deletion in the 3' untranslated region is highly
            attenuated and immunogenic in humans
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 10649)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (12-JAN-2001) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 10649)
  AUTHORS   Whitehead,S.S.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-DEC-2000) LID, NIAID, 7 Center Drive, Bethesda, MD
            20892, USA
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AF326825.
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..10649
                     /organism="dengue virus type 4"
                     /mol_type="genomic RNA"
                     /db_xref="taxon:11070"
                     /clone="rDEN4"
     5'UTR           1..101
     stem_loop       2..69
                     /note="stem-loop A (SLA)"
     regulatory      70..80
                     /regulatory_class="other"
                     /note="oligo U track spacer"
     regulatory      81..96
                     /regulatory_class="promoter"
                     /note="5' upstream AUG region (UAR)"
     stem_loop       81..95
                     /note="stem-loop B (SLB)"
     gene            102..10265
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /db_xref="GeneID:5075729"
     CDS             102..10265
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="NP_073286.1"
                     /db_xref="GeneID:5075729"
                     /translation="MNQRKKVVRPPFNMLKRERNRVSTPQGLVKRFSTGLFSGKGPLR
                     MVLAFITFLRVLSIPPTAGILKRWGQLKKNKAIKILIGFRKEIGRMLNILNGRKRSTI
                     TLLCLIPTVMAFSLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCED
                     TVTYKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSGMGLET
                     RAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQRTVFFVLMMLVAP
                     SYGMRCVGVGNRDFVEGVSGGAWVDLVLEHGGCVTTMAQGKPTLDFELTKTTAKEVAL
                     LRTYCIEASISNITTATRCPTQGEPYLKEEQDQQYICRRDVVDRGWGNGCGLFGKGGV
                     VTCAKFSCSGKITGNLVQIENLEYTVVVTVHNGDTHAVGNDTSNHGVTAMITPRSPSV
                     EVKLPDYGELTLDCEPRSGIDFNEMILMKMKKKTWLVHKQWFLDLPLPWTAGADTSEV
                     HWNYKERMVTFKVPHAKRQDVTVLGSQEGAMHSALAGATEVDSGDGNHMFAGHLKCKV
                     RMEKLRIKGMSYTMCSGKFSIDKEMAETQHGTTVVKVKYEGAGAPCKVPIEIRDVNKE
                     KVVGRIISSTPLAENTNSVTNIELEPPFGDSYIVIGVGNSALTLHWFRKGSSIGKMFE
                     STYRGAKRMAILGETAWDFGSVGGLFTSLGKAVHQVFGSVYTTMFGGVSWMIRILIGF
                     LVLWIGTNSRNTSMAMTCIAVGGITLFLGFTVQADMGCVASWSGKELKCGSGIFVVDN
                     VHTWTEQYKFQPESPARLASAILNAHKDGVCGIRSTTRLENVMWKQITNELNYVLWEG
                     GHDLTVVAGDVKGVLTKGKRALTPPVSDLKYSWKTWGKAKIFTPEARNSTFLIDGPDT
                     SECPNERRAWNSLEVEDYGFGMFTTNIWMKFREGSSEVCDHRLMSAAIKDQKAVHADM
                     GYWIESSKNQTWQIEKASLIEVKTCLWPKTHTLWSNGVLESQMLIPKSYAGPFSQHNY
                     RQGYATQTVGPWHLGKLEIDFGECPGTTVTIQEDCDHRGPSLRTTTASGKLVTQWCCR
                     SCTMPPLRFLGEDGCWYGMEIRPLSEKEENMVKSQVTAGQGTSETFSMGLLCLTLFVE
                     ECLRRRVTRKHMILVVVITLCAIILGGLTWMDLLRALIMLGDTMSGRIGGQIHLAIMA
                     VFKMSPGYVLGVFLRKLTSRETALMVIGMAMTTVLSIPHDLMELIDGISLGLILLKIV
                     TQFDNTQVGTLALSLTFIRSTMPLVMAWRTIMAVLFVVTLIPLCRTSCLQKQSHWVEI
                     TALILGAQALPVYLMTLMKGASRRSWPLNEGIMAVGLVSLLGSALLKNDVPLAGPMVA
                     GGLLLAAYVMSGSSADLSLEKAANVQWDEMADITGSSPIVEVKQDEDGSFSIRDVEET
                     NMITLLVKLALITVSGLYPLAIPVTMTLWYMWQVKTQRSGALWDVPSPAATKKAALSE
                     GVYRIMQRGLFGKTQVGVGIHMEGVFHTMWHVTRGSVICHETGRLEPSWADVRNDMIS
                     YGGGWRLGDKWDKEEDVQVLAIEPGKNPKHVQTKPGLFKTLTGEIGAVTLDFKPGTSG
                     SPIINRKGKVIGLYGNGVVTKSGDYVSAITQAERIGEPDYEVDEDIFRKKRLTIMDLH
                     PGAGKTKRILPSIVREALKRRLRTLILAPTRVVAAEMEEALRGLPIRYQTPAVKSEHT
                     GREIVDLMCHATFTTRLLSSTRVPNYNLIVMDEAHFTDPSSVAARGYISTRVEMGEAA
                     AIFMTATPPGATDPFPQSNSPIEDIEREIPERSWNTGFDWITDYQGKTVWFVPSIKAG
                     NDIANCLRKSGKKVIQLSRKTFDTEYPKTKLTDWDFVVTTDISEMGANFRAGRVIDPR
                     RCLKPVILPDGPERVILAGPIPVTPASAAQRRGRIGRNPAQEDDQYVFSGDPLKNDED
                     HAHWTEAKMLLDNIYTPEGIIPTLFGPEREKTQAIDGEFRLRGEQRKTFVELMRRGDL
                     PVWLSYKVASAGISYEDREWCFTGERNNQILEENMEVEIWTREGEKKKLRPRWLDARV
                     YADPMALKDFKEFASGRKSITLDILTEIASLPTYLSSRAKLALDNIVMLHTTERGGRA
                     YQHALNELPESLETLMLVALLGAMTAGIFLFFMQGKGIGKLSMGLITIAVASGLLWVA
                     EIQPQWIAASIILEFFLMVLLIPEPEKQRTPQDNQLIYVILTILTIIGLIAANEMGLI
                     EKTKTDFGFYQVKTETTILDVDLRPASAWTLYAVATTILTPMLRHTIENTSANLSLAA
                     IANQAAVLMGLGKGWPLHRMDLGVPLLAMGCYSQVNPTTLTASLVMLLVHYAIIGPGL
                     QAKATREAQKRTAAGIMKNPTVDGITVIDLEPISYDPKFEKQLGQVMLLVLCAGQLLL
                     MRTTWAFCEVLTLATGPILTLWEGNPGRFWNTTIAVSTANIFRGSYLAGAGLAFSLIK
                     NAQTPRRGTGTTGETLGEKWKRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKI
                     KHAVSRGSSKIRWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGPG
                     HEEPIPMATYGWNLVKLHSGVDVFYKPTEQVDTLLCDIGESSSNPTIEEGRTLRVLKM
                     VEPWLSSKPEFCIKVLNPYMPTVIEELEKLQRKHGGNLVRCPLSRNSTHEMYWVSGAS
                     GNIVSSVNTTSKMLLNRFTTRHRKPTYEKDVDLGAGTRSVSTETEKPDMTIIGRRLQR
                     LQEEHKETWHYDQENPYRTWAYHGSYEAPSTGSASSMVNGVVKLLTKPWDVIPMVTQL
                     AMTDTTPFGQQRVFKEKVDTRTPQPKPGTRMVMTTTANWLWALLGKKKNPRLCTREEF
                     ISKVRSNAAIGAVFQEEQGWTSASEAVNDSRFWELVDKERALHQEGKCESCVYNMMGK
                     REKKLGEFGRAKGSRAIWYMWLGARFLEFEALGFLNEDHWFGRENSWSGVEGEGLHRL
                     GYILEEIDKKDGDLMYADDTAGWDTRITEDDLQNEELITEQMAPHHKILAKAIFKLTY
                     QNKVVKVLRPTPRGAVMDIISRKDQRGSGQVGTYGLNTFTNMEVQLIRQMEAEGVITQ
                     DDMQNPKGLKERVEKWLKECGVDRLKRMAISGDDCVVKPLDERFGTSLLFLNDMGKVR
                     KDIPQWEPSKGWKNWQEVPFCSHHFHKIFMKDGRSLVVPCRNQDELIGRARISQGAGW
                     SLRETACLGKAYAQMWSLMYFHRRDLRLASMAICSAVPTEWFPTSRTTWSIHAHHQWM
                     TTEDMLKVWNRVWIEDNPNMTDKTPVHSWEDIPYLGKREDLWCGSLIGLSSRATWAKN
                     IHTAITQVRNLIGKEEYVDYMPVMKRYSAPSESEGVL"
     mat_peptide     102..440
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="anchored capsid protein ancC"
                     /protein_id="NP_740314.1"
     mat_peptide     102..398
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="capsid protein C"
                     /note="virion capsid protein"
                     /protein_id="NP_740313.1"
     misc_feature    111..440
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Flavivirus capsid protein C; Region: Flavi_capsid;
                     pfam01003"
                     /db_xref="CDD:366413"
     mat_peptide     441..938
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="membrane glycoprotein precursor prM"
                     /protein_id="NP_740315.1"
     mat_peptide     441..713
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="protein pr"
                     /note="peptide pr"
                     /protein_id="YP_009164957.1"
     misc_feature    456..692
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Flavivirus polyprotein propeptide; Region:
                     Flavi_propep; pfam01570"
                     /db_xref="CDD:366710"
     mat_peptide     714..938
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="membrane glycoprotein M"
                     /protein_id="NP_740316.1"
     misc_feature    714..938
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Flavivirus envelope glycoprotein M; Region:
                     Flavi_M; cd17038"
                     /db_xref="CDD:341208"
     misc_feature    order(714..716,720..749,753..761,765..770,795..797,
                     885..887,918..920)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="glycoprotein E binding interface [polypeptide
                     binding]; other site"
                     /db_xref="CDD:341208"
     mat_peptide     939..2423
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="envelope protein E"
                     /protein_id="NP_740317.1"
     misc_feature    942..1826
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Flavivirus glycoprotein, central and dimerization
                     domains; Region: Flavi_glycoprot; pfam00869"
                     /db_xref="CDD:395698"
     misc_feature    1851..2120
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Immunoglobulin-like domain III (C-terminal domain)
                     of Flavivirus envelope glycoprotein E; Region: Flavi_E_C;
                     cd12149"
                     /db_xref="CDD:213392"
     misc_feature    order(1866..1871,1875..1880,1899..1904,2034..2036)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="homodimer interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:213392"
     misc_feature    order(1887..1889,1938..1940,1992..2003,2007..2009)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="low pH domain interface [polypeptide binding];
                     other site"
                     /db_xref="CDD:213392"
     misc_feature    order(1890..1892,1938..1940,1986..1994,2046..2048)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="low pH trimer interface [polypeptide binding];
                     other site"
                     /db_xref="CDD:213392"
     misc_feature    2133..2423
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="flavivirus envelope glycoprotein E, stem/anchor
                     domain; Region: flavi_E_stem; TIGR04240"
                     /db_xref="CDD:213897"
     mat_peptide     2424..3479
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="nonstructural protein NS1"
                     /protein_id="NP_740318.1"
     misc_feature    2430..3488
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Flavivirus non-structural Protein NS1; Region:
                     Flavi_NS1; pfam00948"
                     /db_xref="CDD:279316"
     mat_peptide     3480..4133
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="nonstructural protein NS2A"
                     /protein_id="NP_740319.1"
     misc_feature    3981..4256
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="MerC mercury resistance protein; Region: MerC;
                     pfam03203"
                     /db_xref="CDD:427195"
     mat_peptide     4134..4523
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="nonstructural protein NS2B"
                     /protein_id="NP_740320.1"
     mat_peptide     4524..6377
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="nonstructural protein NS3"
                     /protein_id="NP_740321.1"
     misc_feature    4575..5024
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Peptidase S7, Flavivirus NS3 serine protease;
                     Region: Peptidase_S7; pfam00949"
                     /db_xref="CDD:395758"
     misc_feature    5076..5513
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Flavivirus DEAD domain; Region: Flavi_DEAD;
                     pfam07652"
                     /db_xref="CDD:400138"
     misc_feature    5517..5951
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="C-terminal helicase domain of viral helicase;
                     Region: SF2_C_viral; cd18806"
                     /db_xref="CDD:350193"
     misc_feature    order(5538..5540,5553..5555,5562..5567,5829..5837)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="homodimer interface [polypeptide binding]; other
                     site"
                     /db_xref="CDD:350193"
     misc_feature    order(5901..5903,5910..5912)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="putative ATP binding site [chemical binding]; other
                     site"
                     /db_xref="CDD:350193"
     mat_peptide     6378..6758
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="nonstructural protein NS4A"
                     /protein_id="NP_740322.1"
     misc_feature    6390..6821
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Flavivirus non-structural protein NS4A; Region:
                     Flavi_NS4A; pfam01350"
                     /db_xref="CDD:279666"
     mat_peptide     6759..6827
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="protein 2K"
                     /protein_id="NP_740323.1"
     mat_peptide     6828..7562
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="nonstructural protein NS4B"
                     /protein_id="NP_740324.1"
     misc_feature    6828..7541
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Flavivirus non-structural protein NS4B; Region:
                     Flavi_NS4B; pfam01349"
                     /db_xref="CDD:279665"
     mat_peptide     7563..10262
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /product="RNA-dependent RNA polymerase NS5"
                     /protein_id="NP_740325.1"
     misc_feature    7596..8288
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="Cap-0 specific (nucleoside-2'-O-)-methyltransferase
                     of flaviviridae; Region: capping_2-OMTase_Flaviviridae;
                     cd20761"
                     /db_xref="CDD:467736"
     misc_feature    order(7602..7604,7611..7616,7620..7622,8010..8015,
                     8202..8204)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="nucleic acid substrate binding site [nucleotide
                     binding]; other site"
                     /db_xref="CDD:467736"
     misc_feature    order(7803..7811,7818..7823,7872..7877,7950..7955,
                     7998..8003)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="SAM binding site [chemical binding]; other site"
                     /db_xref="CDD:467736"
     misc_feature    8520..10214
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="catalytic core domain of RNA-dependent RNA
                     polymerase (RdRp) in the genus Flavivirus, within the
                     family Flaviviridae of positive-sense single-stranded RNA
                     (+ssRNA) viruses; Region: Flavivirus_RdRp; cd23204"
                     /db_xref="CDD:438054"
     misc_feature    order(8766..8768,8778..8780,8799..8804,8994..8996,
                     9006..9008,9018..9020,9039..9041,9363..9383,9939..9941,
                     9948..9950,9954..9956)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="inhibitor binding site [chemical binding];
                     inhibition site"
                     /db_xref="CDD:438054"
     misc_feature    8922..8987
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="conserved polymerase motif F; other site"
                     /db_xref="CDD:438054"
     misc_feature    order(8931..8933,8982..8984,8988..8990,9006..9008,
                     9018..9020,9030..9032,9042..9044,9081..9083,9087..9095,
                     9363..9374,9378..9383,9546..9557,9690..9695,9750..9752,
                     9774..9776,9822..9827,9834..9839,9843..9848)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="RNA binding site [nucleotide binding]; other site"
                     /db_xref="CDD:438054"
     misc_feature    order(8934..8936,8943..8945,8967..8969,8976..8978,
                     9177..9179,9360..9365,9390..9392,9552..9557,9693..9695,
                     9750..9752,9774..9776,9945..9953)
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="NTP binding site [chemical binding]; other site"
                     /db_xref="CDD:438054"
     misc_feature    9147..9191
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="conserved polymerase motif A; other site"
                     /db_xref="CDD:438054"
     misc_feature    9357..9428
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="conserved polymerase motif B; other site"
                     /db_xref="CDD:438054"
     misc_feature    9525..9575
                     /gene="POLY"
                     /locus_tag="DV4_gp1"
                     /gene_synonym="polyprotein gene"
                     /note="conserved polymerase motif C; other site"
                     /db_xref="CDD:438054"
     stem_loop       118..134
                     /note="capsid region hairpin (cHP)"
     regulatory      136..146
                     /regulatory_class="other"
                     /note="5' conserved sequence (CS); also called cyclization
                     sequence"
     3'UTR           10266..10649
     ncRNA           10292..10649
                     /ncRNA_class="lncRNA"
                     /product="sfRNA2"
                     /note="subgenomic flavivirus RNA"
     stem_loop       10296..10364
                     /note="flaviviral nuclease-resistant RNA 2 (fNR2); also
                     called stem-loop 2 or xrRNA2"
     ncRNA           10372..10649
                     /ncRNA_class="lncRNA"
                     /product="sfRNA3"
                     /note="subgenomic flavivirus RNA"
     stem_loop       10376..10462
                     /note="dumbbell 1 (DBI); also called xrRNA3"
     ncRNA           10464..10649
                     /ncRNA_class="lncRNA"
                     /product="sfRNA4"
                     /note="subgenomic flavivirus RNA"
     stem_loop       10467..10547
                     /note="dumbbell 2 (DBII); also called xrRNA4"
     regulatory      10544..10554
                     /regulatory_class="other"
                     /note="3' conserved sequence (CS); also called cyclization
                     sequence"
     stem_loop       10557..10570
                     /note="short hairpin (sHP)"
     regulatory      10568..10584
                     /regulatory_class="promoter"
                     /note="3' upstream AUG region (UAR)"
     stem_loop       10571..10649
                     /note="3' stem-loop (3'SL)"
ORIGIN      
        1 agttgttagt ctgtgtggac cgacaaggac agttccaaat cggaagcttg cttaacacag
       61 ttctaacagt ttgtttgaat agagagcaga tctctggaaa aatgaaccaa cgaaaaaagg
      121 tggttagacc acctttcaat atgctgaaac gcgagagaaa ccgcgtatca acccctcaag
      181 ggttggtgaa gagattctca accggacttt tttctgggaa aggaccctta cggatggtgc
      241 tagcattcat cacgtttttg cgagtccttt ccatcccacc aacagcaggg attctgaaga
      301 gatggggaca gttgaagaaa aataaggcca tcaagatact gattggattc aggaaggaga
      361 taggccgcat gctgaacatc ttgaacggga gaaaaaggtc aacgataaca ttgctgtgct
      421 tgattcccac cgtaatggcg ttttccctca gcacaagaga tggcgaaccc ctcatgatag
      481 tggcaaaaca tgaaaggggg agacctctct tgtttaagac aacagagggg atcaacaaat
      541 gcactctcat tgccatggac ttgggtgaaa tgtgtgagga cactgtcacg tataaatgcc
      601 ccctactggt caataccgaa cctgaagaca ttgattgctg gtgcaacctc acgtctacct
      661 gggtcatgta tgggacatgc acccagagcg gagaacggag acgagagaag cgctcagtag
      721 ctttaacacc acattcagga atgggattgg aaacaagagc tgagacatgg atgtcatcgg
      781 aaggggcttg gaagcatgct cagagagtag agagctggat actcagaaac ccaggattcg
      841 cgctcttggc aggatttatg gcttatatga ttgggcaaac aggaatccag cgaactgtct
      901 tctttgtcct aatgatgctg gtcgccccat cctacggaat gcgatgcgta ggagtaggaa
      961 acagagactt tgtggaagga gtctcaggtg gagcatgggt cgacctggtg ctagaacatg
     1021 gaggatgcgt cacaaccatg gcccagggaa aaccaacctt ggattttgaa ctgactaaga
     1081 caacagccaa ggaagtggct ctgttaagaa cctattgcat tgaagcctca atatcaaaca
     1141 taactacggc aacaagatgt ccaacgcaag gagagcctta tctgaaagag gaacaggacc
     1201 aacagtacat ttgccggaga gatgtggtag acagagggtg gggcaatggc tgtggcttgt
     1261 ttggaaaagg aggagttgtg acatgtgcga agttttcatg ttcggggaag ataacaggca
     1321 atttggtcca aattgagaac cttgaataca cagtggttgt aacagtccac aatggagaca
     1381 cccatgcagt aggaaatgac acatccaatc atggagttac agccatgata actcccaggt
     1441 caccatcggt ggaagtcaaa ttgccggact atggagaact aacactcgat tgtgaaccca
     1501 ggtctggaat tgactttaat gagatgattc tgatgaaaat gaaaaagaaa acatggctcg
     1561 tgcataagca atggtttttg gatctgcctc ttccatggac agcaggagca gacacatcag
     1621 aggttcactg gaattacaaa gagagaatgg tgacatttaa ggttcctcat gccaagagac
     1681 aggatgtgac agtgctggga tctcaggaag gagccatgca ttctgccctc gctggagcca
     1741 cagaagtgga ctccggtgat ggaaatcaca tgtttgcagg acatcttaag tgcaaagtcc
     1801 gtatggagaa attgagaatc aagggaatgt catacacgat gtgttcagga aagttttcaa
     1861 ttgacaaaga gatggcagaa acacagcatg ggacaacagt ggtgaaagtc aagtatgaag
     1921 gtgctggagc tccgtgtaaa gtccccatag agataagaga tgtaaacaag gaaaaagtgg
     1981 ttgggcgtat catctcatcc acccctttgg ctgagaatac caacagtgta accaacatag
     2041 aattagaacc cccctttggg gacagctaca tagtgatagg tgttggaaac agcgcattaa
     2101 cactccattg gttcaggaaa gggagttcca ttggcaagat gtttgagtcc acatacagag
     2161 gtgcaaaacg aatggccatt ctaggtgaaa cagcttggga ttttggttcc gttggtggac
     2221 tgttcacatc attgggaaag gctgtgcacc aggtttttgg aagtgtgtat acaaccatgt
     2281 ttggaggagt ctcatggatg attagaatcc taattgggtt cttagtgttg tggattggca
     2341 cgaactcgag gaacacttca atggctatga cgtgcatagc tgttggagga atcactctgt
     2401 ttctgggctt cacagttcaa gcagacatgg gttgtgtggc gtcatggagt gggaaagaat
     2461 tgaagtgtgg aagcggaatt tttgtggttg acaacgtgca cacttggaca gaacagtaca
     2521 aatttcaacc agagtcccca gcgagactag cgtctgcaat attaaatgcc cacaaagatg
     2581 gggtctgtgg aattagatca accacgaggc tggaaaatgt catgtggaag caaataacca
     2641 acgagctaaa ctatgttctc tgggaaggag gacatgacct cactgtagtg gctggggatg
     2701 tgaagggggt gttgaccaaa ggcaagagag cactcacacc cccagtgagt gatctgaaat
     2761 attcatggaa gacatgggga aaagcaaaaa tcttcacccc agaagcaaga aatagcacat
     2821 ttttaataga cggaccagac acctctgaat gccccaatga acgaagagca tggaactctc
     2881 ttgaggtgga agactatgga tttggcatgt tcacgaccaa catatggatg aaattccgag
     2941 aaggaagttc agaagtgtgt gaccacaggt taatgtcagc tgcaattaaa gatcagaaag
     3001 ctgtgcatgc tgacatgggt tattggatag agagctcaaa aaaccagacc tggcagatag
     3061 agaaagcatc tcttattgaa gtgaaaacat gtctgtggcc caagacccac acactgtgga
     3121 gcaatggagt gctggaaagc cagatgctca ttccaaaatc atatgcgggc cctttttcac
     3181 agcacaatta ccgccagggc tatgccacgc aaaccgtggg cccatggcac ttaggcaaat
     3241 tagagataga ctttggagaa tgccccggaa caacagtcac aattcaggag gattgtgacc
     3301 atagaggccc atctttgagg accaccactg catctggaaa actagtcacg caatggtgct
     3361 gccgctcctg cacgatgcct cccttaaggt tcttgggaga agatgggtgc tggtatggga
     3421 tggagattag gcccttgagt gaaaaagaag agaacatggt caaatcacag gtgacggccg
     3481 gacagggcac atcagaaact ttttctatgg gtctgttgtg cctgaccttg tttgtggaag
     3541 aatgcttgag gagaagagtc actaggaaac acatgatatt agttgtggtg atcactcttt
     3601 gtgctatcat cctgggaggc ctcacatgga tggacttact acgagccctc atcatgttgg
     3661 gggacactat gtctggtaga ataggaggac agatccacct agccatcatg gcagtgttca
     3721 agatgtcacc aggatacgtg ctgggtgtgt ttttaaggaa actcacttca agagagacag
     3781 cactaatggt aataggaatg gccatgacaa cggtgctttc aattccacat gaccttatgg
     3841 aactcattga tggaatatca ctgggactaa ttttgctaaa aatagtaaca cagtttgaca
     3901 acacccaagt gggaacctta gctctttcct tgactttcat aagatcaaca atgccattgg
     3961 tcatggcttg gaggaccatt atggctgtgt tgtttgtggt cacactcatt cctttgtgca
     4021 ggacaagctg tcttcaaaaa cagtctcatt gggtagaaat aacagcactc atcctaggag
     4081 cccaagctct gccagtgtac ctaatgactc ttatgaaagg agcctcaaga agatcttggc
     4141 ctcttaacga gggcataatg gctgtgggtt tggttagtct cttaggaagc gctcttttaa
     4201 agaatgatgt ccctttagct ggcccaatgg tggcaggagg cttacttctg gcggcttacg
     4261 tgatgagtgg tagctcagca gatctgtcac tagagaaggc cgccaacgtg cagtgggatg
     4321 aaatggcaga cataacaggc tcaagcccaa tcgtagaagt gaagcaggat gaagatggct
     4381 ctttctccat acgggacgtc gaggaaacca atatgataac ccttttggtg aaactggcac
     4441 tgataacagt gtcaggtctc taccccttgg caattccagt cacaatgacc ttatggtaca
     4501 tgtggcaagt gaaaacacaa agatcaggag ccctgtggga cgtcccctca cccgctgcca
     4561 ctaaaaaagc cgcactgtct gaaggagtgt acaggatcat gcaaagaggg ttattcggga
     4621 aaactcaggt tggagtaggg atacacatgg aaggtgtatt tcacacaatg tggcatgtaa
     4681 caagaggatc agtgatctgc cacgagactg ggagattgga gccatcttgg gctgacgtca
     4741 ggaatgacat gatatcatac ggtgggggat ggaggcttgg agacaaatgg gacaaagaag
     4801 aagacgttca ggtcctcgcc atagaaccag gaaaaaatcc taaacatgtc caaacgaaac
     4861 ctggcctttt caagacccta actggagaaa ttggagcagt aacattagat ttcaaacccg
     4921 gaacgtctgg ttctcccatc atcaacagga aaggaaaagt catcggactc tatggaaatg
     4981 gagtagttac caaatcaggt gattacgtca gtgccataac gcaagccgaa agaattggag
     5041 agccagatta tgaagtggat gaggacattt ttcgaaagaa aagattaact ataatggact
     5101 tacaccccgg agctggaaag acaaaaagaa ttcttccatc aatagtgaga gaagccttaa
     5161 aaaggaggct acgaactttg attttagctc ccacgagagt ggtggcggcc gagatggaag
     5221 aggccctacg tggactgcca atccgttatc agaccccagc tgtgaaatca gaacacacag
     5281 gaagagagat tgtagacctc atgtgtcatg caaccttcac aacaagactt ttgtcatcaa
     5341 ccagggttcc aaattacaac cttatagtga tggatgaagc acatttcacc gatccttcta
     5401 gtgtcgcggc tagaggatac atctcgacca gggtggaaat gggagaggca gcagccatct
     5461 tcatgaccgc aacccctccc ggagcgacag atccctttcc ccagagcaac agcccaatag
     5521 aagacatcga gagggaaatt ccggaaaggt catggaacac agggttcgac tggataacag
     5581 actaccaagg gaaaactgtg tggtttgttc ccagcataaa agctggaaat gacattgcaa
     5641 attgtttgag aaagtcggga aagaaagtta tccagttgag taggaaaacc tttgatacag
     5701 agtatccaaa aacgaaactc acggactggg actttgtggt cactacagac atatctgaaa
     5761 tgggggccaa ttttagagcc gggagagtga tagaccctag aagatgcctc aagccagtta
     5821 tcctaccaga tgggccagag agagtcattt tagcaggtcc tattccagtg actccagcaa
     5881 gcgctgctca gagaagaggg cgaataggaa ggaacccagc acaagaagac gaccaatacg
     5941 ttttctccgg agacccacta aaaaatgatg aagatcatgc ccactggaca gaagcaaaga
     6001 tgctgcttga caatatctac accccagaag ggatcattcc aacattgttt ggtccggaaa
     6061 gggaaaaaac ccaagccatt gatggagagt ttcgcctcag aggggaacaa aggaagactt
     6121 ttgtggaatt aatgaggaga ggagaccttc cggtgtggct gagctataag gtagcttctg
     6181 ctggcatttc ttacgaagat cgggaatggt gcttcacagg ggaaagaaat aaccaaattt
     6241 tagaagaaaa catggaggtt gaaatttgga ctagagaggg agaaaagaaa aagctaaggc
     6301 caagatggtt agatgcacgt gtatacgctg accccatggc tttgaaggat ttcaaggagt
     6361 ttgccagtgg aaggaagagt ataactctcg acatcctaac agagattgcc agtttgccaa
     6421 cttacctttc ctctagggcc aagctcgccc ttgataacat agtcatgctc cacacaacag
     6481 aaagaggagg gagggcctat caacacgccc tgaacgaact tccggagtca ctggaaacac
     6541 tcatgcttgt agctttacta ggtgctatga cagcaggcat cttcctgttt ttcatgcaag
     6601 ggaaaggaat agggaaattg tcaatgggtt tgataaccat tgcggtggct agtggcttgc
     6661 tctgggtagc agaaattcaa ccccagtgga tagcggcctc aatcatacta gagttttttc
     6721 tcatggtact gttgataccg gaaccagaaa aacaaaggac cccacaagac aatcaattga
     6781 tctacgtcat attgaccatt ctcaccatca ttggtctaat agcagccaac gagatggggc
     6841 tgattgaaaa aacaaaaacg gattttgggt tttaccaggt aaaaacagaa accaccatcc
     6901 tcgatgtgga cttgagacca gcttcagcat ggacgctcta tgcagtagcc accacaattc
     6961 tgactcccat gctgagacac accatagaaa acacgtcggc caacctatct ctagcagcca
     7021 ttgccaacca ggcagccgtc ctaatggggc ttggaaaagg atggccgctc cacagaatgg
     7081 acctcggtgt gccgctgtta gcaatgggat gctattctca agtgaaccca acaaccttga
     7141 cagcatcctt agtcatgctt ttagtccatt atgcaataat aggcccagga ttgcaggcaa
     7201 aagccacaag agaggcccag aaaaggacag ctgctgggat catgaaaaat cccacagtgg
     7261 acgggataac agtaatagat ctagaaccaa tatcctatga cccaaaattt gaaaagcaat
     7321 tagggcaggt catgctacta gtcttgtgtg ctggacaact actcttgatg agaacaacat
     7381 gggctttctg tgaagtcttg actttggcca caggaccaat cttgaccttg tgggagggca
     7441 acccgggaag gttttggaac acgaccatag ccgtatccac cgccaacatt ttcaggggaa
     7501 gttacttggc gggagctgga ctggcttttt cactcataaa gaatgcacaa acccctagga
     7561 ggggaactgg gaccacagga gagacactgg gagagaagtg gaagagacag ctaaactcat
     7621 tagacagaaa agagtttgaa gagtataaaa gaagtggaat actagaagtg gacaggactg
     7681 aagccaagtc tgccctgaaa gatgggtcta aaatcaagca tgcagtatca agagggtcca
     7741 gtaagatcag atggattgtt gagagaggga tggtaaagcc aaaagggaaa gttgtagatc
     7801 ttggctgtgg gagaggagga tggtcttatt acatggcgac actcaagaac gtgactgaag
     7861 tgaaagggta tacaaaagga ggtccaggac atgaagaacc gattcccatg gctacttatg
     7921 gttggaattt ggtcaaactc cattcagggg ttgacgtgtt ctacaaaccc acagagcaag
     7981 tggacaccct gctctgtgat attggggagt catcttctaa tccaacaata gaggaaggaa
     8041 gaacattaag agttttgaag atggtggagc catggctctc ttcaaaacct gaattctgca
     8101 tcaaagtcct taacccctac atgccaacag tcatagaaga gctggagaaa ctgcagagaa
     8161 aacatggtgg gaaccttgtc agatgcccgc tgtccaggaa ctccacccat gagatgtatt
     8221 gggtgtcagg agcgtcggga aacattgtga gctctgtgaa cacaacatca aagatgttgt
     8281 tgaacaggtt cacaacaagg cataggaaac ccacttatga gaaggacgta gatcttgggg
     8341 caggaacgag aagtgtctcc actgaaacag aaaaaccaga catgacaatc attgggagaa
     8401 ggcttcagcg attgcaagaa gagcacaaag aaacctggca ttatgatcag gaaaacccat
     8461 acagaacctg ggcgtatcat ggaagctatg aagctccttc gacaggctct gcatcctcca
     8521 tggtgaacgg ggtggtaaaa ctgctaacaa aaccctggga tgtgattcca atggtgactc
     8581 agttagccat gacagataca accccttttg ggcaacaaag agtgttcaaa gagaaggtgg
     8641 ataccagaac accacaacca aaacccggta cacgaatggt tatgaccacg acagccaatt
     8701 ggctgtgggc cctccttgga aagaagaaaa atcccagact gtgcacaagg gaagagttca
     8761 tctcaaaagt tagatcaaac gcagccatag gcgcagtctt tcaggaagaa cagggatgga
     8821 catcagccag tgaagctgtg aatgacagcc ggttttggga actggttgac aaagaaaggg
     8881 ccctacacca ggaagggaaa tgtgaatcgt gtgtctataa catgatggga aaacgtgaga
     8941 aaaagttagg agagtttggc agagccaagg gaagccgagc aatctggtac atgtggctgg
     9001 gagcgcggtt tctggaattt gaagccctgg gttttttgaa tgaagatcac tggtttggca
     9061 gagaaaattc atggagtgga gtggaagggg aaggtctgca cagattggga tatatcctgg
     9121 aggagataga caagaaggat ggagacctaa tgtatgctga tgacacagca ggctgggaca
     9181 caagaatcac tgaggatgac cttcaaaatg aggaactgat cacggaacag atggctcccc
     9241 accacaagat cctagccaaa gccattttca aactaaccta tcaaaacaaa gtggtgaaag
     9301 tcctcagacc cacaccgcgg ggagcggtga tggatatcat atccaggaaa gaccaaagag
     9361 gtagtggaca agttggaaca tatggtttga acacattcac caacatggaa gttcaactca
     9421 tccgccaaat ggaagctgaa ggagtcatca cacaagatga catgcagaac ccaaaagggt
     9481 tgaaagaaag agttgagaaa tggctgaaag agtgtggtgt cgacaggtta aagaggatgg
     9541 caatcagtgg agacgattgc gtggtgaagc ccctagatga gaggtttggc acttccctcc
     9601 tcttcttgaa cgacatggga aaggtgagga aagacattcc gcagtgggaa ccatctaagg
     9661 gatggaaaaa ctggcaagag gttccttttt gctcccacca ctttcacaag atctttatga
     9721 aggatggccg ctcactagtt gttccatgta gaaaccagga tgaactgata gggagagcca
     9781 gaatctcgca gggagctgga tggagcttaa gagaaacagc ctgcctgggc aaagcttacg
     9841 cccagatgtg gtcgcttatg tacttccaca gaagggatct gcgtttagcc tccatggcca
     9901 tatgctcagc agttccaacg gaatggtttc caacaagcag aacaacatgg tcaatccacg
     9961 ctcatcacca gtggatgacc actgaagata tgctcaaagt gtggaacaga gtgtggatag
    10021 aagacaaccc taatatgact gacaagactc cagtccattc gtgggaagat ataccttacc
    10081 tagggaaaag agaggatttg tggtgtggat ccctgattgg actttcttcc agagccacct
    10141 gggcgaagaa cattcatacg gccataaccc aggtcaggaa cctgatcgga aaagaggaat
    10201 acgtggatta catgccagta atgaaaagat acagtgctcc ttcagagagt gaaggagttc
    10261 tgtaattacc aacaacaaac accaaaggct attgaagtca ggccacttgt gccacggttt
    10321 gagcaaaccg tgctgcctgt agctccgcca ataatgggag gcgtaataat ccccagggag
    10381 gccatgcgcc acggaagctg tacgcgtggc atattggact agcggttaga ggagacccct
    10441 cccatcactg ataaaacgca gcaaaagggg gcccgaagcc aggaggaagc tgtactcctg
    10501 gtggaaggac tagaggttag aggagacccc cccaacacaa aaacagcata ttgacgctgg
    10561 gaaagaccag agatcctgct gtctctgcaa catcaatcca ggcacagagc gccgcaagat
    10621 ggattggtgt tgttgatcca acaggttct
//
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