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Entry details : EF108306


GENERAL INFORMATION
ID EF108306; SV 1; linear; genomic RNA; STD; VRL; 9357 BP.
Primary AC EF108306
Creation Date 07-NOV-2007 (Rel. 93, 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 n.a.
Provisional 7a
Confirmed n.a.
Isolate QC69
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
OC Viruses;  ssRNA positive-strand viruses, no DNA stage;  Flaviviridae;  Hepacivirus; 
REFERENCES
[1]
1 - 9357
RA Murphy D.; 
RT Complete coding region sequence of isolate QC69
RL Unpublished.
[2]
1 - 9357
RA Murphy D.; 
RL Submitted (08-NOV-2006) to the EMBL/GenBank/DDBJ databases. Biologie Moleculaire, Laboratoire de Sante Publique du Quebec, Institut National de Sante Publique du Quebec, 20045 Chemin Sainte-Marie, Sainte-Anne-de-Bellevue, Quebec H9X 3R5, Canada
FEATURES
source
1..9357
(9357)
country country : Canada
sub-region :
db_xref taxon : 11103
db_xref EMBL : EF108306
db_xref euHCVdb : AF009606
isolation_source plasma
mol_type genomic RNA
note emigrant from the Democratic Republic of Congo
organism Hepatitis C virus
5'UTR
<1..308
(308)

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
11..321
(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
11..85
(75)

5UTR-dII
function 5'UTR domain II is a component of the IRES
standard_name 5UTR-dII
stem_loop
92..290
(199)

5UTR-dIII
function 5'UTR domain III is a component of the IRES
standard_name 5UTR-dIII
stem_loop
298..321
(24)

5UTR-dIV
function 5'UTR domain IV is a component of the IRES
standard_name 5UTR-dIV
misc_feature
836..1259
(424)

5UTR-dIV
note C/E1 genotyping region
misc_feature
8249..8588
(340)

5UTR-dIV
note NS5B genotyping region
gene
309..9350
(9042)

5UTR-dIV
locus_tag HCVORF1
CDS
309..9350
(9042)

5UTR-dIV
codon_start offset : 1
db_xref UniProtKB/TrEMBL : A8QPD9
locus_tag HCVORF1
product Complete HCV polyprotein (contains C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B).
translation VIEW
mat_peptide
309..881
(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
882..1457
(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
1458..2558
(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 473..480  (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
2559..2747
(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
2748..3398
(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
3399..5291
(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
5292..5453
(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
5454..6236
(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
6237..7574
(1338)

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..2422  (446) Serine phosphoprotein (NS5A protein) (P58)
prod_ft
site 2213..2251  (39) Interferon sensitivity determining region (ISDR)
prod_ft
domain 2213..2277  (65) PKR binding domain
prod_ft
site 2329..2337  (9) Nuclear localisation signal (NLS)
prod_ft
site 2361..2385  (25) 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
7575..9347
(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 2423..3013  (591) RNA-dependent RNA polymerase (NS5B protein) (P68)
prod_ft
model3d 2425..2988  (564) NS5B RNA-dependent RNA polymerase homology molecular model using template PDB: 1c2pB  
standard_name NS5B
3'UTR
9351..>9357
(7)

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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