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Entry details : D90208

[General] [References] [Features] [Sequences] [Text Entry]    [LANL]
GENERAL INFORMATION
ID D90208; SV 1; linear; genomic RNA; STD; VRL; 9413 BP.
Primary AC D90208
Creation Date 16-JAN-1991 (Rel. 26, 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 1b
Provisional 1b
Confirmed 1b
Isolate HCV-J
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
OC Viruses;  ssRNA positive-strand viruses, no DNA stage;  Flaviviridae;  Hepacivirus; 
[General] [References] [Features] [Sequences] [Text Entry]    [LANL]
REFERENCES
[1]
RA Kato N.;  Hijikata M.;  Ootsuyama Y.;  Nakagawa M.;  Ohkoshi S.;  Shimotohno K.; 
RT A structural protein encoded by the 5' region of the hepatitis C virus genome efficiently detects viral infection
RL Jpn. J. Cancer Res. 81(11):1092-1094(1990).
RX PUBMED: 2176200  
[2]
1 - 9413
RA Kato N.;  Hijikata M.;  Ootsuyama Y.;  Nakagawa M.;  Ohkoshi S.;  Sugimura T.;  Shimotohno K.; 
RT Molecular cloning of the human hepatitis C virus genome from Japanese patients with non-A, non-B hepatitis
RL Proc. Natl. Acad. Sci. U.S.A. 87(24):9524-9528(1990).
RX DOI: 10.1073/pnas.87.24.9524  
PUBMED: 2175903  
[3]
RA Hotta H.;  Doi H.;  Hayashi T.;  Purwanta M.;  Soemarto W.;  Mizokami M.;  Ohba K.;  Homma M.; 
RT Analysis of the core and E1 envelope region sequences of a novel variant of hepatitis C virus obtained in Indonesia
RL Arch. Virol. 136(1-2):53-62(1994).
RX DOI: 10.1007/BF01538816  
PUBMED: 7545932  
[4]
RA Mink M.;  Benichou S.;  Madaule P.;  Tiollais P.;  Prince A.;  Inchauspe G.; 
RT Characterization and mapping of a B-cell immunogenic domain in hepatitis C virus E2 glycoprotein using a yeast peptide library
RL Virology 200(1):246-255(1994).
RX DOI: 10.1006/viro.1994.1182  
PUBMED: 7510436  
[General] [References] [Features] [Sequences] [Text Entry]    [LANL]
FEATURES
source
 1..9413
(9413)
db_xref taxon : 11103
db_xref EMBL : D90208
db_xref euHCVdb : AF009606
isolation_source human plasma
mol_type genomic RNA
organism Hepatitis C virus
strain J
5'UTR
 <1..329
(329)

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
 32..342
(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
 <1..8
(8)

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
 32..106
(75)

5UTR-dII
function 5'UTR domain II is a component of the IRES
standard_name 5UTR-dII
stem_loop
 113..311
(199)

5UTR-dIII
function 5'UTR domain III is a component of the IRES
standard_name 5UTR-dIII
stem_loop
 319..342
(24)

5UTR-dIV
function 5'UTR domain IV is a component of the IRES
standard_name 5UTR-dIV
misc_feature
 857..1280
(424)

5UTR-dIV
note C/E1 genotyping region
misc_feature
 8261..8600
(340)

5UTR-dIV
note NS5B genotyping region
gene
 330..9362
(9033)

5UTR-dIV
locus_tag HCVORF1
CDS
 330..9362
(9033)

5UTR-dIV
codon_start offset : 1
db_xref UniProtKB/Swiss-Prot : P26662
locus_tag HCVORF1
product Complete HCV polyprotein (contains C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B).
translation VIEW
mat_peptide
 330..902
(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
 903..1478
(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
 1479..2567
(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
 2568..2756
(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
 2757..3407
(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  
standard_name NS2
mat_peptide
 3408..5300
(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  
standard_name NS3
mat_peptide
 5301..5462
(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  
standard_name NS4A
mat_peptide
 5463..6245
(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
 6246..7586
(1341)

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..2419  (447) 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  
standard_name NS5A
mat_peptide
 7587..9359
(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 2420..3010  (591) RNA-dependent RNA polymerase (NS5B protein) (P68)
prod_ft
model3d 2422..2985  (564) NS5B RNA-dependent RNA polymerase homology molecular model using template PDB: 1c2pB  
standard_name NS5B
3'UTR
 9363..>9413
(51)

3UTR
function 3'UTR (contains a polypyrimidine stretch and the conserved X region)
standard_name 3UTR
[General] [References] [Features] [Sequences] [Text Entry]    [LANL]
SEQUENCES
Sequence VIEW
Translation(s)
locus_tag HCVORF1 VIEW
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