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Entry details : D63821

[General] [References] [Features] [Sequences] [Text Entry]    [LANL]
GENERAL INFORMATION
ID D63821; SV 1; linear; genomic RNA; STD; VRL; 9450 BP.
Primary AC D63821
Creation Date 09-FEB-1996 (Rel. 46, 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 10a
Provisional 3k
Confirmed 3k
Isolate JK049
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
Common Name isolate JK049
OC Viruses;  ssRNA positive-strand viruses, no DNA stage;  Flaviviridae;  Hepacivirus; 
[General] [References] [Features] [Sequences] [Text Entry]    [LANL]
REFERENCES
[1]
1 - 9450
RA Okamoto H.; 
RL Submitted (10-AUG-1995) to the EMBL/GenBank/DDBJ databases. Hiroaki Okamoto, Jichi Medical School, Immunology Division; Minamikawachi-machi, Kawachi-gun, Tochigi 329-04, Japan (E-mail: hokamoto@jichi.ac.jp, Tel:0285-44-2111(ex.3334), Fax:0285-44-1557)
[2]
RA Tokita H.;  Okamoto H.;  Iizuka H.;  Kishimoto J.;  Tsuda F.;  Lesmana L.A.;  Miyakawa Y.;  Mayumi M.; 
RT Hepatitis C virus variants from Jakarta, Indonesia classifiable into novel genotypes in the second (2e and 2f), tenth (10a) and eleventh (11a) genetic groups
RL J. Gen. Virol. 77:293-301(1996).
RX PUBMED: 8627233  
[General] [References] [Features] [Sequences] [Text Entry]    [LANL]
FEATURES
source
 1..9450
(9450)
db_xref taxon : 356417
db_xref EMBL : D63821
db_xref euHCVdb : AF009606
mol_type genomic RNA
organism Hepatitis C virus (isolate JK049)
5'UTR
 1..339
(339)

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
 42..352
(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..18
(14)

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
 42..116
(75)

5UTR-dII
function 5'UTR domain II is a component of the IRES
standard_name 5UTR-dII
stem_loop
 123..321
(199)

5UTR-dIII
function 5'UTR domain III is a component of the IRES
standard_name 5UTR-dIII
stem_loop
 329..352
(24)

5UTR-dIV
function 5'UTR domain IV is a component of the IRES
standard_name 5UTR-dIV
misc_feature
 867..1290
(424)

5UTR-dIV
note C/E1 genotyping region
misc_feature
 8298..8637
(340)

5UTR-dIV
note NS5B genotyping region
gene
 340..9399
(9060)

5UTR-dIV
locus_tag HCVORF1
CDS
 340..9399
(9060)

5UTR-dIV
codon_start offset : 1
db_xref UniProtKB/Swiss-Prot : Q68801
locus_tag HCVORF1
product Complete HCV polyprotein (contains C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B).
translation VIEW
mat_peptide
 340..912
(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
 913..1488
(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
 1489..2592
(1104)

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..751  (368) 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 664..675  (12) PKR/eIF2aplha phosporylation homology domain (PePHD)
prod_ft
transmem 723..746  (24) Potential transmembrane region of E2
standard_name E2
mat_peptide
 2593..2781
(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 752..814  (63) P7 protein
standard_name P7
mat_peptide
 2782..3432
(651)

NS2
function NS2 protein coding sequence (ns2 sequence)
locus_tag HCVORF1
product NS2 protein. Produced by autoproteolytic processing
prod_ft
chain 815..1031  (217) Cysteine protease (NS2 protein) (P23)
prod_ft
model3d 908..1031  (124) NS2-3 autoprotease catalytic domain domain (domain I) homology molecular model using template PDB:2hd0  
standard_name NS2
mat_peptide
 3433..5325
(1893)

NS3
function NS3 protein coding sequence (ns3 sequence)
locus_tag HCVORF1
product NS3 protein. Produced by autoproteolytic processing
prod_ft
chain 1032..1662  (631) NS3 protein (P70) [Includes: N-ter serine protease; C-ter NTPase and RNA helicase]
prod_ft
domain 1032..1211  (180) NS3 protease domain
prod_ft
domain 1218..1662  (445) NS3 helicase domain
prod_ft
model3d 1034..1662  (629) NS3 protein homology molecular model using template PDB:1cu1A  
standard_name NS3
mat_peptide
 5326..5487
(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 1663..1716  (54) NS4A protein (P8)
prod_ft
domain 1683..1694  (12) NS3 protease cofactor
prod_ft
model3d 1683..1694  (12) NS4A homology molecular model using template PDB:1cu1Z  
standard_name NS4A
mat_peptide
 5488..6270
(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 1717..1977  (261) NS4B protein (P27)
standard_name NS4B
mat_peptide
 6271..7623
(1353)

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 1978..2428  (451) Serine phosphoprotein (NS5A protein) (P58)
prod_ft
site 2214..2253  (40) Interferon sensitivity determining region (ISDR)
prod_ft
domain 2214..2279  (66) PKR binding domain
prod_ft
site 2331..2339  (9) Nuclear localisation signal (NLS)
prod_ft
site 2362..2389  (28) Variable region V3
prod_ft
model3d 2013..2175  (163) NS5A zinc-binding domain (domain I) homology molecular model using template PDB:1zh1  
standard_name NS5A
mat_peptide
 7624..9396
(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 2429..3019  (591) RNA-dependent RNA polymerase (NS5B protein) (P68)
prod_ft
model3d 2431..2994  (564) NS5B RNA-dependent RNA polymerase homology molecular model using template PDB: 1c2pB  
standard_name NS5B
3'UTR
 9400..>9450
(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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