Dengue virus 2, complete genome.
type: Entry
definition: Dengue virus 2, complete genome.
sequence version: NC_001474.2
sequence date: 2019-07-11
sequence: sequence
division: VRL
label: NC_001474.2
type: RefSeq
SIO_000068: refseq
dblink: PRJNA485481
keyword: RefSeq
source: Dengue virus 2
organism: Dengue virus 2
taxonomy: Viruses; Riboviria; Flaviviridae; Flavivirus.
reference: 1
references: 9143286
reference: 2
reference: 3
comment: REVIEWED REFSEQ: This record has been curated by NCBI staff. The\nreference sequence was derived from U87411.\nOn Nov 1, 2007 this sequence version replaced NC_001474.1.\nThe mature peptides were added by the NCBI staff following other\nannotations for Dengue virus with the kind help of Dr. Vladimir\nYamshchikov (Southern Research Institute, Birmingham, AL USA).\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000353
sequence length: 10723
topology: linear
so has quality: SO_0000987
location: 1..10723
location: region:1-10723:1
RO_0002162: 11060

NC_001474
type: RefSeq
SIO_000068: refseq

PRJNA485481
type: BioProject
SIO_000068: bioproject

1
title: Construction of infectious cDNA clones for dengue 2 virus: strain 16681 and its attenuated vaccine derivative, strain PDK-53
author: Kinney, R.M.
author: Butrapet, S.
author: Chang, G.J.
author: Tsuchiya, K.R.
author: Roehrig, J.T.
author: Bhamarapravati, N.
author: Gubler, D.J.
journal: Virology
volume: 230
issue: 2
pages: 300-308
year: 1997
pubmed: 9143286

9143286
type: PubMed
SIO_000068: pubmed

2
title: Direct Submission
journal: Submitted (01-NOV-2007) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA

3
title: Direct Submission
author: Kinney, R.M.
author: Butrapet, S.
author: Chang, G.J.
author: Tsuchiya, K.R.
author: Roehrig, J.T.
author: Bhamarapravati, N.
author: Gubler, D.J.
journal: Submitted (28-JAN-1997) Division of Vector-Borne Infectious Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Public Health Service, U.S. Department of Health and Human Services, P.O. Box 2087, Fort Collins, CO 80522, USA

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10723:1
position: 10723
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-10723:1:source
so part of: sequence
organism: Dengue virus 2
mol type: genomic RNA
strain: 16681
country: Thailand
collection date: 1964

11060
type: Taxonomy
SIO_000068: taxonomy

5'UTR
type: Five Prime UTR
subclass of: SO_0000204
RO_0002162: 11060
so part of: sequence
location: 1..96
location: region:1-96:1
so has part: feature:1-96:1:region

position:96:1
position: 96
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-96:1:region

stem_loop
type: Stem Loop
subclass of: SO_0000313
RO_0002162: 11060
note: stem-loop A (SLA)
so part of: sequence
location: 2..70
location: region:2-70:1
so has part: feature:2-70:1:region

position:2:1
position: 2
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:70:1
position: 70
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2-70:1:region

regulatory
type: Feature
subclass of: SO_0000001
RO_0002162: 11060
regulatory class: other
note: oligo U track spacer
so part of: sequence
location: 71..80
location: region:71-80:1
so has part: feature:71-80:1:region

position:71:1
position: 71
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:80:1
position: 80
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:71-80:1:region

regulatory
type: Feature
subclass of: SO_0000001
RO_0002162: 11060
regulatory class: promoter
note: 5' upstream AUG region (UAR)
so part of: sequence
location: 81..96
location: region:81-96:1
so has part: feature:81-96:1:region

position:81:1
position: 81
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:81-96:1:region

stem_loop
type: Stem Loop
subclass of: SO_0000313
RO_0002162: 11060
note: stem-loop B (SLB)
so part of: sequence
location: 81..95
location: region:81-95:1
so has part: feature:81-95:1:region

position:95:1
position: 95
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:81-95:1:region

DENV_gp1
type: Gene
subclass of: SO_0000704
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
so part of: sequence
location: 97..10272
location: region:97-10272:1
so has part: feature:97-10272:1:exon
subclass of: SO_0000010

1494449
type: Gene
SIO_000068: ncbigene

position:97:1
position: 97
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10272:1
position: 10272
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:97-10272:1:exon

DENV_gp1
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
note: contains structural proteins, C-prM/M-E and non-structural proteins, NS1-NS2A/B-NS3-NS4A/B-NS5
codon start: 1
product: polyprotein
translation: MNNQRKKAKNTPFNMLKRERNRVSTVQQLTKRFSLGMLQGRGPLKLFMALVAFLRFLTIPPTAGILKRWGTIKKSKAINVLRGFRKEIGRMLNILNRRRRSAGMIIMLIPTVMAFHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTITYKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTMGEHRREKRSVALVPHVGMGLETRTETWMSSEGAWKHVQRIETWILRHPGFTMMAAILAYTIGTTHFQRALIFILLTAVTPSMTMRCIGMSNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFRCKKNMEGKVVQPENLEYTIVITPHSGEEHAVGNDTGKHGKEIKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMENKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIGQMFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILIGVIITWIGMNSRSTSLSVTLVLVGIVTLYLGVMVQADSGCVVSWKNKELKCGSGIFITDNVHTWTEQYKFQPESPSKLASAIQKAHEEGICGIRSVTRLENLMWKQITPELNHILSENEVKLTIMTGDIKGIMQAGKRSLRPQPTELKYSWKTWGKAKMLSTESHNQTFLIDGPETAECPNTNRAWNSLEVEDYGFGVFTTNIWLKLKEKQDVFCDSKLMSAAIKDNRAVHADMGYWIESALNDTWKIEKASFIEVKNCHWPKSHTLWSNGVLESEMIIPKNLAGPVSQHNYRPGYHTQITGPWHLGKLEMDFDFCDGTTVVVTEDCGNRGPSLRTTTASGKLITEWCCRSCTLPPLRYRGEDGCWYGMEIRPLKEKEENLVNSLVTAGHGQVDNFSLGVLGMALFLEEMLRTRVGTKHAILLVAVSFVTLITGNMSFRDLGRVMVMVGATMTDDIGMGVTYLALLAAFKVRPTFAAGLLLRKLTSKELMMTTIGIVLLSQSTIPETILELTDALALGMMVLKMVRNMEKYQLAVTIMAILCVPNAVILQNAWKVSCTILAVVSVSPLLLTSSQQKTDWIPLALTIKGLNPTAIFLTTLSRTSKKRSWPLNEAIMAVGMVSILASSLLKNDIPMTGPLVAGGLLTVCYVLTGRSADLELERAADVKWEDQAEISGSSPILSITISEDGSMSIKNEEEEQTLTILIRTGLLVISGLFPVSIPITAAAWYLWEVKKQRAGVLWDVPSPPPMGKAELEDGAYRIKQKGILGYSQIGAGVYKEGTFHTMWHVTRGAVLMHKGKRIEPSWADVKKDLISYGGGWKLEGEWKEGEEVQVLALEPGKNPRAVQTKPGLFKTNAGTIGAVSLDFSPGTSGSPIIDKKGKVVGLYGNGVVTRSGAYVSAIAQTEKSIEDNPEIEDDIFRKRRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVVAAEMEEALRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSPVRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPIIDEEREIPERSWNSGHEWVTDFKGKTVWFVPSIKAGNDIAACLRKNGKKVIQLSRKTFDSEYVKTRTNDWDFVVTTDISEMGANFKAERVIDPRRCMKPVILTDGEERVILAGPMPVTHSSAAQRRGRIGRNPKNENDQYIYMGEPLENDEDCAHWKEAKMLLDNINTPEGIIPSMFEPEREKVDAIDGEYRL…
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 97..10272
location: region:97-10272:1
so has part: feature:97-10272:1:exon

NP_056776.2
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:97-10272:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: anchored capsid protein ancC
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 97..438
location: region:97-438:1
so has part: feature:97-438:1:exon

NP_739581.2
type: Protein
SIO_000068: ncbiprotein

position:438:1
position: 438
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:97-438:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: capsid protein C
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 97..396
location: region:97-396:1
so has part: feature:97-396:1:exon

NP_739591.2
type: Protein
SIO_000068: ncbiprotein

position:396:1
position: 396
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:97-396:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: membrane glycoprotein precursor prM
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 439..936
location: region:439-936:1
so has part: feature:439-936:1:exon

NP_739582.2
type: Protein
SIO_000068: ncbiprotein

position:439:1
position: 439
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:936:1
position: 936
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:439-936:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: protein pr
note: peptide pr
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 439..711
location: region:439-711:1
so has part: feature:439-711:1:exon

YP_009164954.1
type: Protein
SIO_000068: ncbiprotein

position:711:1
position: 711
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:439-711:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: membrane glycoprotein M
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 712..936
location: region:712-936:1
so has part: feature:712-936:1:exon

NP_739592.2
type: Protein
SIO_000068: ncbiprotein

position:712:1
position: 712
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:712-936:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: envelope protein E
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 937..2421
location: region:937-2421:1
so has part: feature:937-2421:1:exon

NP_739583.2
type: Protein
SIO_000068: ncbiprotein

position:937:1
position: 937
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2421:1
position: 2421
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:937-2421:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: nonstructural protein NS1
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 2422..3477
location: region:2422-3477:1
so has part: feature:2422-3477:1:exon

NP_739584.2
type: Protein
SIO_000068: ncbiprotein

position:2422:1
position: 2422
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3477:1
position: 3477
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2422-3477:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: nonstructural protein NS2A
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 3478..4131
location: region:3478-4131:1
so has part: feature:3478-4131:1:exon

NP_739585.2
type: Protein
SIO_000068: ncbiprotein

position:3478:1
position: 3478
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4131:1
position: 4131
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3478-4131:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: nonstructural protein NS2B
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 4132..4521
location: region:4132-4521:1
so has part: feature:4132-4521:1:exon

NP_739586.2
type: Protein
SIO_000068: ncbiprotein

position:4132:1
position: 4132
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4521:1
position: 4521
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4132-4521:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: nonstructural protein NS3
note: RNA-helicase; protease; ATPase; component of capping enzyme (RNA thriphosphatase)
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 4522..6375
location: region:4522-6375:1
so has part: feature:4522-6375:1:exon

NP_739587.2
type: Protein
SIO_000068: ncbiprotein

position:4522:1
position: 4522
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6375:1
position: 6375
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4522-6375:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: nonstructural protein NS4A
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 6376..6756
location: region:6376-6756:1
so has part: feature:6376-6756:1:exon

NP_739588.2
type: Protein
SIO_000068: ncbiprotein

position:6376:1
position: 6376
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6756:1
position: 6756
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6376-6756:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: protein 2K
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 6757..6825
location: region:6757-6825:1
so has part: feature:6757-6825:1:exon

NP_739593.2
type: Protein
SIO_000068: ncbiprotein

position:6757:1
position: 6757
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6825:1
position: 6825
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6757-6825:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: nonstructural protein NS4B
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 6826..7569
location: region:6826-7569:1
so has part: feature:6826-7569:1:exon

NP_739589.2
type: Protein
SIO_000068: ncbiprotein

position:6826:1
position: 6826
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7569:1
position: 7569
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6826-7569:1:exon

DENV_gp1
type: Mature Peptide
subclass of: SO_0000419
RO_0002162: 11060
alternative label: polyprotein gene
gene: POLY
locus tag: DENV_gp1
gene synonym: polyprotein gene
product: RNA-dependent RNA polymerase NS5
note: methyltransferase component of capping enzyme; nonstructural protein NS5
SIO_010081: DENV_gp1
subclass of: SO_0000673
so part of: DENV_gp1
location: 7570..10269
location: region:7570-10269:1
so has part: feature:7570-10269:1:exon

NP_739590.2
type: Protein
SIO_000068: ncbiprotein

position:7570:1
position: 7570
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10269:1
position: 10269
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7570-10269:1:exon

stem_loop
type: Stem Loop
subclass of: SO_0000313
RO_0002162: 11060
note: capsid region hairpin (cHP)
so part of: sequence
location: 116..132
location: region:116-132:1
so has part: feature:116-132:1:region

position:116:1
position: 116
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:132:1
position: 132
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:116-132:1:region

regulatory
type: Feature
subclass of: SO_0000001
RO_0002162: 11060
regulatory class: other
note: 5' conserved sequence (CS); also called cyclization sequence
so part of: sequence
location: 134..144
location: region:134-144:1
so has part: feature:134-144:1:region

position:134:1
position: 134
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:144:1
position: 144
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:134-144:1:region

3'UTR
type: Three Prime UTR
subclass of: SO_0000205
RO_0002162: 11060
so part of: sequence
location: 10273..10723
location: region:10273-10723:1
so has part: feature:10273-10723:1:region

position:10273:1
position: 10273
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10273-10723:1:region

ncRNA
type: Non Coding RNA
subclass of: SO_0000655
RO_0002162: 11060
nc RNA class: lncRNA
product: sfRNA1
note: subgenomic flavivirus RNA
so part of: sequence
location: 10299..10723
location: region:10299-10723:1
so has part: feature:10299-10723:1:region

position:10299:1
position: 10299
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10299-10723:1:region

stem_loop
type: Stem Loop
subclass of: SO_0000313
RO_0002162: 11060
note: flaviviral nuclease-resistant RNA 1 (fNR1); also called stem-loop 1 or xrRNA1
so part of: sequence
location: 10303..10368
location: region:10303-10368:1
so has part: feature:10303-10368:1:region

position:10303:1
position: 10303
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10368:1
position: 10368
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10303-10368:1:region

ncRNA
type: Non Coding RNA
subclass of: SO_0000655
RO_0002162: 11060
nc RNA class: lncRNA
product: sfRNA2
note: subgenomic flavivirus RNA
so part of: sequence
location: 10372..10723
location: region:10372-10723:1
so has part: feature:10372-10723:1:region

position:10372:1
position: 10372
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10372-10723:1:region

stem_loop
type: Stem Loop
subclass of: SO_0000313
RO_0002162: 11060
note: flaviviral nuclease-resistant RNA 2 (fNR2); also called stem-loop 2 or xrRNA2
so part of: sequence
location: 10376..10441
location: region:10376-10441:1
so has part: feature:10376-10441:1:region

position:10376:1
position: 10376
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10441:1
position: 10441
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10376-10441:1:region

ncRNA
type: Non Coding RNA
subclass of: SO_0000655
RO_0002162: 11060
nc RNA class: lncRNA
product: sfRNA3
note: subgenomic flavivirus RNA
so part of: sequence
location: 10449..10723
location: region:10449-10723:1
so has part: feature:10449-10723:1:region

position:10449:1
position: 10449
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10449-10723:1:region

stem_loop
type: Stem Loop
subclass of: SO_0000313
RO_0002162: 11060
note: dumbbell 1 (DBI); also called xrRNA3
so part of: sequence
location: 10453..10534
location: region:10453-10534:1
so has part: feature:10453-10534:1:region

position:10453:1
position: 10453
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10534:1
position: 10534
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10453-10534:1:region

ncRNA
type: Non Coding RNA
subclass of: SO_0000655
RO_0002162: 11060
nc RNA class: lncRNA
product: sfRNA4
note: subgenomic flavivirus RNA
so part of: sequence
location: 10536..10723
location: region:10536-10723:1
so has part: feature:10536-10723:1:region

position:10536:1
position: 10536
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10536-10723:1:region

stem_loop
type: Stem Loop
subclass of: SO_0000313
RO_0002162: 11060
note: dumbbell 2 (DBII); also called xrRNA4
so part of: sequence
location: 10540..10621
location: region:10540-10621:1
so has part: feature:10540-10621:1:region

position:10540:1
position: 10540
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10621:1
position: 10621
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10540-10621:1:region

regulatory
type: Feature
subclass of: SO_0000001
RO_0002162: 11060
regulatory class: other
note: 3' conserved sequence (CS); also called cyclization sequence
so part of: sequence
location: 10618..10628
location: region:10618-10628:1
so has part: feature:10618-10628:1:region

position:10618:1
position: 10618
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10628:1
position: 10628
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10618-10628:1:region

stem_loop
type: Stem Loop
subclass of: SO_0000313
RO_0002162: 11060
note: short hairpin (sHP)
so part of: sequence
location: 10631..10644
location: region:10631-10644:1
so has part: feature:10631-10644:1:region

position:10631:1
position: 10631
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10644:1
position: 10644
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10631-10644:1:region

regulatory
type: Feature
subclass of: SO_0000001
RO_0002162: 11060
regulatory class: promoter
note: 3' upstream AUG region (UAR)
so part of: sequence
location: 10642..10658
location: region:10642-10658:1
so has part: feature:10642-10658:1:region

position:10642:1
position: 10642
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:10658:1
position: 10658
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10642-10658:1:region

stem_loop
type: Stem Loop
subclass of: SO_0000313
RO_0002162: 11060
note: 3' stem-loop (3'SL)
so part of: sequence
location: 10645..10723
location: region:10645-10723:1
so has part: feature:10645-10723:1:region

position:10645:1
position: 10645
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10645-10723:1:region