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Entry details : DQ835762


GENERAL INFORMATION
ID DQ835762; SV 1; linear; genomic RNA; STD; VRL; 9458 BP.
Primary AC DQ835762
Creation Date 24-APR-2007 (Rel. 91, Created)
Update Date 23-JAN-2011 (Rel. 122, Last updated , Version 0)
Description Hepatitis C virus partial genome, complete 5'UTR, complete CDS (Contains: C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B), partial 3'UTR.
Genotype
Deposited 6i
Provisional 6i
Confirmed 6i
Isolate C-0159
Keywords partial genome;  complete 5'UTR;  complete CDS;  C;  E1;  E2;  P7;  NS2;  NS3;  NS4A;  NS4B;  NS5A;  NS5B;  partial 3'UTR; 
Organism
OS Hepatitis C virus subtype 6i
OC Viruses;  ssRNA positive-strand viruses, no DNA stage;  Flaviviridae;  Hepacivirus; 
REFERENCES
[1]
1 - 9458
RA Lu L.;  Li C.;  Fu Y.;  Thaikruea L.;  Thongswat S.;  Maneekarn N.;  Apichartpiyakul C.;  Hotta H.;  Okamoto H.;  Netski D.;  Pybus O.G.;  Murphy D.;  Hagedorn C.H.;  Nelson K.E.; 
RT Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses
RL J. Gen. Virol. 88(Pt 5):1505-1518(2007).
RX DOI: 10.1099/vir.0.82604-0  
PUBMED: 17412980  
[2]
1 - 9458
RA Lu L.;  Fu Y.;  Li C.;  Thaikruea L.;  Thongswat S.;  Apichartpiyakul C.;  Hotta H.;  Okamoto H.;  Murphy D.;  Hagedorn C.H.;  Nelson K.E.; 
RL Submitted (23-JUN-2006) to the EMBL/GenBank/DDBJ databases. Division of Gastroenterology, Department of Medicine, University of Kansas Medical Center, Hixon 1000, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
FEATURES
source
1..9458
(9458)
country country : Thailand
sub-region :
db_xref taxon : 467337
db_xref EMBL : DQ835762
db_xref euHCVdb : AF009606
isolation_source serum of a Thai blood donor, C-0159
mol_type genomic RNA
note genotype: 6i
organism Hepatitis C virus subtype 6i
5'UTR
1..338
(338)

5UTR
function 5'UTR highly conserved genomic region (contains four structural domains (I to IV), domains II to IV make up the internal ribosome entry site (IRES))
standard_name 5UTR
RBS
41..351
(311)

IRES
function The internal ribosome entry site (IRES) is made up by domains II to IV of the 5'UTR
standard_name IRES
stem_loop
5..18
(14)

5UTR-dI
function 5'UTR domain I has a regulatory effect for the replication and translation of the genome
standard_name 5UTR-dI
stem_loop
41..115
(75)

5UTR-dII
function 5'UTR domain II is a component of the IRES
standard_name 5UTR-dII
stem_loop
122..320
(199)

5UTR-dIII
function 5'UTR domain III is a component of the IRES
standard_name 5UTR-dIII
stem_loop
328..351
(24)

5UTR-dIV
function 5'UTR domain IV is a component of the IRES
standard_name 5UTR-dIV
misc_feature
866..1289
(424)

5UTR-dIV
note C/E1 genotyping region
misc_feature
8288..8627
(340)

5UTR-dIV
note NS5B genotyping region
gene
339..9389
(9051)

5UTR-dIV
locus_tag HCVORF1
CDS
339..9389
(9051)

5UTR-dIV
codon_start offset : 1
db_xref UniProtKB/TrEMBL : A4ZHH7
locus_tag HCVORF1
product Complete HCV polyprotein (contains C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B).
translation VIEW
mat_peptide
339..911
(573)

C
function C protein coding sequence (c sequence)
locus_tag HCVORF1
product RNA binding nucleocapsid protein (p21) (capsid) (core protein) (nucleocapsid) (C protein). Produced by proteolytic processing by the host signal peptidases
prod_ft
chain 1..191  (191) C protein
prod_ft
init_met 1..1  (1) Removed from C protein by the cellular aminopeptidase
standard_name C
mat_peptide
912..1487
(576)

E1
function E1 protein coding sequence (e1 sequence)
locus_tag HCVORF1
product Envelope glycoprotein 1 (gp31) (E1 protein). Produced by proteolytic processing by the host signal peptidases. E1 forms heterodimers with the viral E2 envelope glycoprotein
prod_ft
chain 192..383  (192) E1 protein
prod_ft
transmem 353..381  (29) Potential transmembrane region of E1
standard_name E1
mat_peptide
1488..2582
(1095)

E2
function E2 protein coding sequence (e2 sequence)
locus_tag HCVORF1
product Envelope glycoprotein 2 (GP70) (E2 protein). Produced by proteolytic processing by the host signal peptidases. E2 forms heterodimers with the viral E1 envelope glycoprotein
prod_ft
chain 384..748  (365) E2 protein
prod_ft
site 384..410  (27) Hypervariable region 1 (HVR1)
prod_ft
site 473..481  (9) Hypervariable region 2 (HVR2)
prod_ft
domain 661..672  (12) PKR/eIF2aplha phosporylation homology domain (PePHD)
prod_ft
transmem 720..743  (24) Potential transmembrane region of E2
standard_name E2
mat_peptide
2583..2771
(189)

P7
function P7 protein coding sequence (p7 sequence)
locus_tag HCVORF1
product P7 protein. Produced by proteolytic processing by the host signal peptidases
prod_ft
chain 749..811  (63) P7 protein
standard_name P7
mat_peptide
2772..3422
(651)

NS2
function NS2 protein coding sequence (ns2 sequence)
locus_tag HCVORF1
product NS2 protein. Produced by autoproteolytic processing
prod_ft
chain 812..1028  (217) Cysteine protease (NS2 protein) (P23)
prod_ft
model3d 905..1028  (124) NS2-3 autoprotease catalytic domain domain (domain I) homology molecular model using template PDB:2hd0  
standard_name NS2
mat_peptide
3423..5315
(1893)

NS3
function NS3 protein coding sequence (ns3 sequence)
locus_tag HCVORF1
product NS3 protein. Produced by autoproteolytic processing
prod_ft
chain 1029..1659  (631) NS3 protein (P70) [Includes: N-ter serine protease; C-ter NTPase and RNA helicase]
prod_ft
domain 1029..1208  (180) NS3 protease domain
prod_ft
domain 1215..1659  (445) NS3 helicase domain
prod_ft
model3d 1031..1659  (629) NS3 protein homology molecular model using template PDB:1cu1A  
standard_name NS3
mat_peptide
5316..5477
(162)

NS4A
function NS4A protein coding sequence (ns4a sequence)
locus_tag HCVORF1
product NS4A protein. Produced by proteolytic processing by the HCV NS3 protease
prod_ft
chain 1660..1713  (54) NS4A protein (P8)
prod_ft
domain 1680..1691  (12) NS3 protease cofactor
prod_ft
model3d 1680..1691  (12) NS4A homology molecular model using template PDB:1cu1Z  
standard_name NS4A
mat_peptide
5478..6260
(783)

NS4B
function NS4B protein coding sequence (ns4b sequence)
locus_tag HCVORF1
product NS4B protein. Produced by proteolytic processing by the HCV NS3 protease
prod_ft
chain 1714..1974  (261) NS4B protein (P27)
standard_name NS4B
mat_peptide
6261..7613
(1353)

NS5A
function NS5A protein coding sequence (ns5a sequence)
locus_tag HCVORF1
product NS5A protein. Produced by proteolytic processing by the HCV NS3 protease. NS5A seems to have a transcriptional activatory role
prod_ft
chain 1975..2425  (451) Serine phosphoprotein (NS5A protein) (P58)
prod_ft
site 2211..2250  (40) Interferon sensitivity determining region (ISDR)
prod_ft
domain 2211..2276  (66) PKR binding domain
prod_ft
site 2329..2337  (9) Nuclear localisation signal (NLS)
prod_ft
site 2360..2385  (26) Variable region V3
prod_ft
model3d 2010..2172  (163) NS5A zinc-binding domain (domain I) homology molecular model using template PDB:1zh1  
standard_name NS5A
mat_peptide
7614..9386
(1773)

NS5B
function NS5B protein coding sequence (ns5b sequence)
locus_tag HCVORF1
product NS5B protein. Produced by proteolytic processing by the HCV NS3 protease. NS5B is a RNA-dependent RNA polymerase that plays an essential role in virus replication
prod_ft
chain 2426..3016  (591) RNA-dependent RNA polymerase (NS5B protein) (P68)
prod_ft
model3d 2428..2991  (564) NS5B RNA-dependent RNA polymerase homology molecular model using template PDB: 1c2pB  
standard_name NS5B
3'UTR
9390..>9458
(69)

3UTR
function 3'UTR (contains a polypyrimidine stretch and the conserved X region)
standard_name 3UTR
SEQUENCES
Sequence VIEW
Translation(s)
locus_tag HCVORF1 VIEW

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