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Entry details : AB047639


GENERAL INFORMATION
ID AB047639; SV 1; linear; genomic RNA; STD; VRL; 9678 BP.
Primary AC AB047639
Creation Date 25-FEB-2001 (Rel. 66, 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 2a
Provisional 2a
Confirmed 2a
Isolate JFH-1
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 JFH-1
OC Viruses;  ssRNA positive-strand viruses, no DNA stage;  Flaviviridae;  Hepacivirus; 
REFERENCES
[1]
1 - 9678
RA Kato T.;  Wakita T.;  Furusaka A.; 
RL Submitted (23-AUG-2000) to the EMBL/GenBank/DDBJ databases. Takanobu Kato, The Tokyo Metropolitan Institute for Neuroscience, Department of Microbiology; Musashidai 2-6, Fuchu, Tokyo 183-8526, Japan (E-mail:takato@tmin.ac.jp, Tel:81-423-25-3881(ex.4605), Fax:81-423-21-8678)
[2]
RA Kato T.;  Furusaka A.;  Miyamoto M.;  Date T.;  Yasui K.;  Hiramoto J.;  Nagayama K.;  Tanaka T.;  Wakita T.; 
RT Sequence analysis of hepatitis C virus isolated from a fulminant hepatitis patient
RL J. Med. Virol. 64(3):334-339(2001).
RX DOI: 10.1002/jmv.1055  
PUBMED: 11424123  
FEATURES
source
1..9678
(9678)
clone JFH-1
db_xref taxon : 356411
db_xref EMBL : AB047639
db_xref euHCVdb : AF009606
mol_type genomic RNA
note isolated from fulminant hepatitis patient/genotype 2a
organism Hepatitis C virus JFH-1
5'UTR
1..340
(340)

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
43..353
(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..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
43..117
(75)

5UTR-dII
function 5'UTR domain II is a component of the IRES
standard_name 5UTR-dII
stem_loop
124..322
(199)

5UTR-dIII
function 5'UTR domain III is a component of the IRES
standard_name 5UTR-dIII
stem_loop
330..353
(24)

5UTR-dIV
function 5'UTR domain IV is a component of the IRES
standard_name 5UTR-dIV
misc_feature
868..1291
(424)

5UTR-dIV
note C/E1 genotyping region
misc_feature
8341..8680
(340)

5UTR-dIV
note NS5B genotyping region
gene
341..9442
(9102)

5UTR-dIV
locus_tag HCVORF1
CDS
341..9442
(9102)

5UTR-dIV
codon_start offset : 1
db_xref UniProtKB/Swiss-Prot : Q99IB8
locus_tag HCVORF1
product Complete HCV polyprotein (contains C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B).
translation VIEW
mat_peptide
341..913
(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
914..1489
(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
1490..2590
(1101)

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..750  (367) E2 protein
prod_ft
site 384..410  (27) Hypervariable region 1 (HVR1)
prod_ft
site 474..481  (8) Hypervariable region 2 (HVR2)
prod_ft
domain 663..674  (12) PKR/eIF2aplha phosporylation homology domain (PePHD)
prod_ft
transmem 722..745  (24) Potential transmembrane region of E2
standard_name E2
mat_peptide
2591..2779
(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 751..813  (63) P7 protein
standard_name P7
mat_peptide
2780..3430
(651)

NS2
function NS2 protein coding sequence (ns2 sequence)
locus_tag HCVORF1
product NS2 protein. Produced by autoproteolytic processing
prod_ft
chain 814..1030  (217) Cysteine protease (NS2 protein) (P23)
prod_ft
model3d 907..1030  (124) NS2-3 autoprotease catalytic domain domain (domain I) homology molecular model using template PDB:2hd0  
standard_name NS2
mat_peptide
3431..5323
(1893)

NS3
function NS3 protein coding sequence (ns3 sequence)
locus_tag HCVORF1
product NS3 protein. Produced by autoproteolytic processing
prod_ft
chain 1031..1661  (631) NS3 protein (P70) [Includes: N-ter serine protease; C-ter NTPase and RNA helicase]
prod_ft
domain 1031..1210  (180) NS3 protease domain
prod_ft
domain 1217..1661  (445) NS3 helicase domain
prod_ft
model3d 1033..1661  (629) NS3 protein homology molecular model using template PDB:1cu1A  
standard_name NS3
mat_peptide
5324..5485
(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 1662..1715  (54) NS4A protein (P8)
prod_ft
domain 1682..1693  (12) NS3 protease cofactor
prod_ft
model3d 1682..1693  (12) NS4A homology molecular model using template PDB:1cu1Z  
standard_name NS4A
mat_peptide
5486..6268
(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 1716..1976  (261) NS4B protein (P27)
standard_name NS4B
mat_peptide
6269..7666
(1398)

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 1977..2442  (466) Serine phosphoprotein (NS5A protein) (P58)
prod_ft
site 2213..2248  (36) Interferon sensitivity determining region (ISDR)
prod_ft
domain 2213..2274  (62) PKR binding domain
prod_ft
site 2326..2334  (9) Nuclear localisation signal (NLS)
prod_ft
site 2357..2383  (27) Variable region V3
prod_ft
model3d 2012..2174  (163) NS5A zinc-binding domain (domain I) homology molecular model using template PDB:1zh1  
standard_name NS5A
mat_peptide
7667..9439
(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 2443..3033  (591) RNA-dependent RNA polymerase (NS5B protein) (P68)
prod_ft
model3d 2445..3008  (564) NS5B RNA-dependent RNA polymerase homology molecular model using template PDB: 1c2pB  
standard_name NS5B
3'UTR
9443..9678
(236)

3UTR
function 3'UTR (contains a polypyrimidine stretch and the conserved X region)
standard_name 3UTR
stem_loop
9581..9678
(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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