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Entry details : AF009606


GENERAL INFORMATION
ID AF009606; SV 1; linear; genomic RNA; STD; VRL; 9646 BP.
Primary AC AF009606
Creation Date 23-AUG-1997 (Rel. 52, Created)
Update Date 23-JAN-2011 (Rel. 122, Last updated , Version 0)
Description Hepatitis C virus complete genome, complete 5'UTR, complete CDS (Contains: C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B), complete 3'UTR.
Genotype
Deposited 1a
Provisional 1a
Confirmed 1a
Isolate H77
Keywords complete genome;  complete 5'UTR;  complete CDS;  C;  E1;  E2;  P7;  NS2;  NS3;  NS4A;  NS4B;  NS5A;  NS5B;  complete 3'UTR; 
Organism
OS Hepatitis C virus subtype 1a
OC Viruses;  ssRNA positive-strand viruses, no DNA stage;  Flaviviridae;  Hepacivirus; 
REFERENCES
[1]
1 - 9646
RA Kolykhalov A.A.;  Agapov E.V.;  Blight K.J.;  Mihalik K.;  Feinstone S.M.;  Rice C.M.; 
RT Transmission of hepatitis C by intrahepatic inoculation with transcribed RNA
RL Science 277(5325):570-574(1997).
RX DOI: 10.1126/science.277.5325.570  
PUBMED: 9228008  
[2]
1 - 9646
RA Kolykhalov A.A.;  Rice C.M.; 
RL Submitted (19-JUN-1997) to the EMBL/GenBank/DDBJ databases. Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Ave., St. Louis, MO 63110-1093, USA
DATABASES CROSS-REFERENCES
GOA P0C045
InterPro IPR002522  (HCV_core_N)
UniProtKB/Swiss-Prot P0C045  (F_HCVH)
FEATURES
source
1..9646
(9646)
db_xref taxon : 31646
db_xref EMBL : AF009606
db_xref euHCVdb : AF009606
mol_type genomic RNA
note assembled from cDNA library representing a population of Hepatitis C virus genomes; viable virus can be reconstituted from this sequence
organism Hepatitis C virus subtype 1a
5'UTR
1..341
(341)

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
44..354
(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..20
(16)

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
44..118
(75)

5UTR-dII
function 5'UTR domain II is a component of the IRES
standard_name 5UTR-dII
stem_loop
125..323
(199)

5UTR-dIII
function 5'UTR domain III is a component of the IRES
standard_name 5UTR-dIII
stem_loop
331..354
(24)

5UTR-dIV
function 5'UTR domain IV is a component of the IRES
standard_name 5UTR-dIV
misc_feature
869..1292
(424)

5UTR-dIV
note C/E1 genotyping region
misc_feature
8276..8615
(340)

5UTR-dIV
note NS5B genotyping region
gene
342..9377
(9036)

5UTR-dIV
locus_tag HCVORF1
CDS
342..9377
(9036)

5UTR-dIV
codon_start offset : 1
db_xref UniProtKB/Swiss-Prot : P27958
locus_tag HCVORF1
product Complete HCV polyprotein (contains C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B).
translation VIEW
mat_peptide
342..914
(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
915..1490
(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
1491..2579
(1089)

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..746  (363) 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 659..670  (12) PKR/eIF2aplha phosporylation homology domain (PePHD)
prod_ft
transmem 718..741  (24) Potential transmembrane region of E2
standard_name E2
mat_peptide
2580..2768
(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 747..809  (63) P7 protein
standard_name P7
mat_peptide
2769..3419
(651)

NS2
function NS2 protein coding sequence (ns2 sequence)
locus_tag HCVORF1
product NS2 protein. Produced by autoproteolytic processing
prod_ft
chain 810..1026  (217) Cysteine protease (NS2 protein) (P23)
prod_ft
model3d 903..1026  (124) NS2-3 autoprotease catalytic domain domain (domain I) homology molecular model using template PDB:2hd0   [VIEW]   [euHCVdb3D]
standard_name NS2
mat_peptide
3420..5312
(1893)

NS3
function NS3 protein coding sequence (ns3 sequence)
locus_tag HCVORF1
product NS3 protein. Produced by autoproteolytic processing
prod_ft
chain 1027..1657  (631) NS3 protein (P70) [Includes: N-ter serine protease; C-ter NTPase and RNA helicase]
prod_ft
domain 1027..1206  (180) NS3 protease domain
prod_ft
domain 1213..1657  (445) NS3 helicase domain
prod_ft
model3d 1029..1657  (629) NS3 protein homology molecular model using template PDB:1cu1A   [VIEW]   [euHCVdb3D]
standard_name NS3
mat_peptide
5313..5474
(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 1658..1711  (54) NS4A protein (P8)
prod_ft
domain 1678..1689  (12) NS3 protease cofactor
prod_ft
model3d 1678..1689  (12) NS4A homology molecular model using template PDB:1cu1Z   [VIEW]   [euHCVdb3D]
standard_name NS4A
mat_peptide
5475..6257
(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 1712..1972  (261) NS4B protein (P27)
standard_name NS4B
mat_peptide
6258..7601
(1344)

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 1973..2420  (448) Serine phosphoprotein (NS5A protein) (P58)
prod_ft
site 2209..2248  (40) Interferon sensitivity determining region (ISDR)
prod_ft
domain 2209..2274  (66) PKR binding domain
prod_ft
site 2326..2334  (9) Nuclear localisation signal (NLS)
prod_ft
site 2356..2379  (24) Variable region V3
prod_ft
model3d 2008..2170  (163) NS5A zinc-binding domain (domain I) homology molecular model using template PDB:1zh1   [VIEW]   [euHCVdb3D]
standard_name NS5A
mat_peptide
7602..9374
(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 2421..3011  (591) RNA-dependent RNA polymerase (NS5B protein) (P68)
prod_ft
model3d 2423..2986  (564) NS5B RNA-dependent RNA polymerase homology molecular model using template PDB: 1c2pB   [VIEW]   [euHCVdb3D]
standard_name NS5B
3'UTR
9378..9646
(269)

3UTR
function 3'UTR (contains a polypyrimidine stretch and the conserved X region)
standard_name 3UTR
stem_loop
9549..9646
(98)

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