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Entry details : Y13184


GENERAL INFORMATION
ID Y13184; SV 1; linear; genomic RNA; STD; VRL; 9343 BP.
Primary AC Y13184
Creation Date 12-SEP-1997 (Rel. 52, Created)
Update Date 23-JAN-2011 (Rel. 122, Last updated , Version 0)
Description Hepatitis C virus partial genome, partial 5'UTR, complete CDS (Contains: C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B), partial 3'UTR.
Genotype
Deposited 5a
Provisional 5a
Confirmed 5a
Isolate EUH1480
Keywords partial genome;  partial 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 EUH1480
OC Viruses;  ssRNA positive-strand viruses, no DNA stage;  Flaviviridae;  Hepacivirus; 
REFERENCES
[1]
RA Chamberlain R.W.;  Adams N.J.;  Taylor L.A.;  Simmonds P.;  Elliot R.M.; 
RT The complete coding sequence of hepatitis C virus genotype 5a, the predominant genotype in South Africa
RL Biochem. Biophys. Res. Commun. 236(1):44-49(1997).
RX DOI: 10.1006/bbrc.1997.6902  
PUBMED: 9223423  
[2]
RA Chamberlain R.W.; 
RL Submitted (15-MAY-1997) to the EMBL/GenBank/DDBJ databases. R.W. Chamberlain, Institute of Virology, University of Glasgow, Church Street, Glasgow, G11 5JR, UK
[3]
1 - 9343
RA Chamberlain R.W.; 
RL Submitted (30-SEP-1997) to the EMBL/GenBank/DDBJ databases. R.W. Chamberlain, Institute of Virology, University of Glasgow, Church Street, Glasgow, G11 5JR, UK
FEATURES
source
1..9343
(9343)
db_xref taxon : 356419
db_xref EMBL : Y13184
db_xref euHCVdb : AF009606
mol_type genomic RNA
note Hepatitis C virus subtype 5a
organism Hepatitis C virus (isolate EUH1480)
strain EUH1480
5'UTR
<1..279
(279)

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
<1..292
(292)

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
<1..56
(56)

5UTR-dII
function 5'UTR domain II is a component of the IRES
standard_name 5UTR-dII
stem_loop
63..261
(199)

5UTR-dIII
function 5'UTR domain III is a component of the IRES
standard_name 5UTR-dIII
stem_loop
269..292
(24)

5UTR-dIV
function 5'UTR domain IV is a component of the IRES
standard_name 5UTR-dIV
misc_feature
807..1230
(424)

5UTR-dIV
note C/E1 genotyping region
misc_feature
8223..8562
(340)

5UTR-dIV
note NS5B genotyping region
gene
280..9324
(9045)

5UTR-dIV
locus_tag HCVORF1
CDS
280..9324
(9045)

5UTR-dIV
codon_start offset : 1
db_xref UniProtKB/Swiss-Prot : O39928
locus_tag HCVORF1
product Complete HCV polyprotein (contains C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B).
translation VIEW
mat_peptide
280..852
(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
853..1428
(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
1429..2520
(1092)

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..747  (364) E2 protein
prod_ft
site 384..410  (27) Hypervariable region 1 (HVR1)
prod_ft
site 473..480  (8) Hypervariable region 2 (HVR2)
prod_ft
domain 660..671  (12) PKR/eIF2aplha phosporylation homology domain (PePHD)
prod_ft
transmem 719..742  (24) Potential transmembrane region of E2
standard_name E2
mat_peptide
2521..2709
(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 748..810  (63) P7 protein
standard_name P7
mat_peptide
2710..3360
(651)

NS2
function NS2 protein coding sequence (ns2 sequence)
locus_tag HCVORF1
product NS2 protein. Produced by autoproteolytic processing
prod_ft
chain 811..1027  (217) Cysteine protease (NS2 protein) (P23)
prod_ft
model3d 904..1027  (124) NS2-3 autoprotease catalytic domain domain (domain I) homology molecular model using template PDB:2hd0   [VIEW]   [euHCVdb3D]
standard_name NS2
mat_peptide
3361..5253
(1893)

NS3
function NS3 protein coding sequence (ns3 sequence)
locus_tag HCVORF1
product NS3 protein. Produced by autoproteolytic processing
prod_ft
chain 1028..1658  (631) NS3 protein (P70) [Includes: N-ter serine protease; C-ter NTPase and RNA helicase]
prod_ft
domain 1028..1207  (180) NS3 protease domain
prod_ft
domain 1214..1658  (445) NS3 helicase domain
prod_ft
model3d 1030..1658  (629) NS3 protein homology molecular model using template PDB:1cu1A   [VIEW]   [euHCVdb3D]
standard_name NS3
mat_peptide
5254..5415
(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 1659..1712  (54) NS4A protein (P8)
prod_ft
domain 1679..1690  (12) NS3 protease cofactor
prod_ft
model3d 1679..1690  (12) NS4A homology molecular model using template PDB:1cu1Z   [VIEW]   [euHCVdb3D]
standard_name NS4A
mat_peptide
5416..6198
(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 1713..1973  (261) NS4B protein (P27)
standard_name NS4B
mat_peptide
6199..7548
(1350)

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 1974..2423  (450) Serine phosphoprotein (NS5A protein) (P58)
prod_ft
site 2210..2249  (40) Interferon sensitivity determining region (ISDR)
prod_ft
domain 2210..2275  (66) PKR binding domain
prod_ft
site 2328..2336  (9) Nuclear localisation signal (NLS)
prod_ft
site 2358..2385  (28) Variable region V3
prod_ft
model3d 2009..2171  (163) NS5A zinc-binding domain (domain I) homology molecular model using template PDB:1zh1   [VIEW]   [euHCVdb3D]
standard_name NS5A
mat_peptide
7549..9321
(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 2424..3014  (591) RNA-dependent RNA polymerase (NS5B protein) (P68)
prod_ft
model3d 2426..2989  (564) NS5B RNA-dependent RNA polymerase homology molecular model using template PDB: 1c2pB   [VIEW]   [euHCVdb3D]
standard_name NS5B
3'UTR
9325..>9343
(19)

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