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Entry details : D84262


GENERAL INFORMATION
ID D84262; SV 2; linear; genomic RNA; STD; VRL; 9628 BP.
Primary AC D84262
Creation Date 08-SEP-1998 (Rel. 56, 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 6b
Provisional 6b
Confirmed 6b
Isolate Th580
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
Common Name isolate Th580
OC Viruses;  ssRNA positive-strand viruses, no DNA stage;  Flaviviridae;  Hepacivirus; 
REFERENCES
[1]
1 - 9628
RA Okamoto H.;  Tokita H.;  Iizuka H.;  Kishimoto J.;  Tsuda F.;  Miyakawa Y.;  Mayumi M.; 
RL Submitted (29-MAR-1996) to the EMBL/GenBank/DDBJ databases. Hiroaki Okamoto, Jichi Medical School, Immunology Division; Yakushiji 3311-1, Minamikawachi-machi, Kawachi-gun, Tochigi 329-0498, Japan (E-mail: hokamoto@jichi.ac.jp, Tel:81-285-58-7404, Fax:81-285-44-1557)
[2]
RA Tokita H.;  Okamoto H.;  Iizuka H.;  Kishimoto J.;  Tsuda F.;  Miyakawa Y.;  Mayumi M.; 
RT The entire nucleotide sequences of three hepatitis C virus isolates in genetic groups 7-9 and comparison with those in the other eight genetic groups
RL J. Gen. Virol. 79:1847-1857(1998).
FEATURES
source
1..9628
(9628)
db_xref taxon : 356421
db_xref EMBL : D84262
db_xref euHCVdb : AF009606
mol_type genomic RNA
organism Hepatitis C virus (isolate Th580)
5'UTR
1..342
(342)

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
42..355
(314)

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..19
(15)

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
42..116
(75)

5UTR-dII
function 5'UTR domain II is a component of the IRES
standard_name 5UTR-dII
stem_loop
123..324
(202)

5UTR-dIII
function 5'UTR domain III is a component of the IRES
standard_name 5UTR-dIII
stem_loop
332..355
(24)

5UTR-dIV
function 5'UTR domain IV is a component of the IRES
standard_name 5UTR-dIV
misc_feature
870..1293
(424)

5UTR-dIV
note C/E1 genotyping region
misc_feature
8301..8640
(340)

5UTR-dIV
note NS5B genotyping region
gene
343..9402
(9060)

5UTR-dIV
locus_tag HCVORF1
CDS
343..9402
(9060)

5UTR-dIV
codon_start offset : 1
db_xref UniProtKB/Swiss-Prot : O92529
locus_tag HCVORF1
product Complete HCV polyprotein (contains C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B).
translation VIEW
mat_peptide
343..915
(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
916..1491
(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
1492..2595
(1104)

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..751  (368) E2 protein
prod_ft
site 384..409  (26) Hypervariable region 1 (HVR1)
prod_ft
site 472..481  (10) Hypervariable region 2 (HVR2)
prod_ft
domain 664..675  (12) PKR/eIF2aplha phosporylation homology domain (PePHD)
prod_ft
transmem 723..746  (24) Potential transmembrane region of E2
standard_name E2
mat_peptide
2596..2784
(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 752..814  (63) P7 protein
standard_name P7
mat_peptide
2785..3435
(651)

NS2
function NS2 protein coding sequence (ns2 sequence)
locus_tag HCVORF1
product NS2 protein. Produced by autoproteolytic processing
prod_ft
chain 815..1031  (217) Cysteine protease (NS2 protein) (P23)
prod_ft
model3d 908..1031  (124) NS2-3 autoprotease catalytic domain domain (domain I) homology molecular model using template PDB:2hd0  
standard_name NS2
mat_peptide
3436..5328
(1893)

NS3
function NS3 protein coding sequence (ns3 sequence)
locus_tag HCVORF1
product NS3 protein. Produced by autoproteolytic processing
prod_ft
chain 1032..1662  (631) NS3 protein (P70) [Includes: N-ter serine protease; C-ter NTPase and RNA helicase]
prod_ft
domain 1032..1211  (180) NS3 protease domain
prod_ft
domain 1218..1662  (445) NS3 helicase domain
prod_ft
model3d 1034..1662  (629) NS3 protein homology molecular model using template PDB:1cu1A  
standard_name NS3
mat_peptide
5329..5490
(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 1663..1716  (54) NS4A protein (P8)
prod_ft
domain 1683..1694  (12) NS3 protease cofactor
prod_ft
model3d 1683..1694  (12) NS4A homology molecular model using template PDB:1cu1Z  
standard_name NS4A
mat_peptide
5491..6273
(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 1717..1977  (261) NS4B protein (P27)
standard_name NS4B
mat_peptide
6274..7626
(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 1978..2428  (451) Serine phosphoprotein (NS5A protein) (P58)
prod_ft
site 2214..2253  (40) Interferon sensitivity determining region (ISDR)
prod_ft
domain 2214..2279  (66) PKR binding domain
prod_ft
site 2332..2340  (9) Nuclear localisation signal (NLS)
prod_ft
site 2365..2390  (26) Variable region V3
prod_ft
model3d 2013..2175  (163) NS5A zinc-binding domain (domain I) homology molecular model using template PDB:1zh1  
standard_name NS5A
mat_peptide
7627..9399
(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 2429..3019  (591) RNA-dependent RNA polymerase (NS5B protein) (P68)
prod_ft
model3d 2431..2994  (564) NS5B RNA-dependent RNA polymerase homology molecular model using template PDB: 1c2pB  
standard_name NS5B
3'UTR
9403..9628
(226)

3UTR
function 3'UTR (contains a polypyrimidine stretch and the conserved X region)
standard_name 3UTR
stem_loop
9531..9628
(98)

3UTR-rX
function 3'UTR conserved X region
standard_name 3UTR-rX
SEQUENCES
Sequence VIEW
Translation(s)
locus_tag HCVORF1 VIEW

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