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The Nobel Prize in Physiology or Medicine 2020 "for the discovery of Hepatitis C virus".


Entry details : AY859526


GENERAL INFORMATION
ID AY859526; SV 1; linear; genomic RNA; STD; VRL; 9355 BP.
Primary AC AY859526
Creation Date 20-JAN-2005 (Rel. 82, 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), no 3'UTR.
Genotype
Deposited 6a
Provisional 6a
Confirmed 6a
Isolate 6a33
Keywords partial genome;  partial 5'UTR;  complete CDS;  C;  E1;  E2;  P7;  NS2;  NS3;  NS4A;  NS4B;  NS5A;  NS5B; 
Organism
OS Hepatitis C virus
Common Name isolate 6a33
OC Viruses;  ssRNA positive-strand viruses, no DNA stage;  Flaviviridae;  Hepacivirus; 
REFERENCES
[1]
1 - 9355
RA Zhou D.X.;  Chan P.K.;  Zhang T.;  Tully D.C.;  Tam J.S.; 
RT Sequence diversity of hepatitis C virus 6a within the extended interferon sensitivity-determining region correlates with interferon-alpha/ribavirin treatment outcomes
RL Virus Res. 153(1):44-49(2010).
RX DOI: 10.1016/j.virusres.2010.07.004  
PUBMED: 20624431  
[2]
1 - 9355
RA Zhou X.M.;  Chan P.K.S.;  Tam J.S.L.; 
RT Full genome sequence of HCV 6a virus strains isolated in Hong Kong
RL Unpublished.
[3]
1 - 9355
RA Zhou X.M.;  Chan P.K.S.;  Tam J.S.L.; 
RL Submitted (17-DEC-2004) to the EMBL/GenBank/DDBJ databases. Department of Microbiology, Faculty of Medcine, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, P.R. of China
FEATURES
source
1..9355
(9355)
country country : Hong Kong
sub-region :
db_xref taxon : 356391
db_xref EMBL : AY859526
db_xref euHCVdb : AF009606
isolation_source patient resistant to IFN combo treatment
mol_type genomic RNA
note genotype: 6a
organism Hepatitis C virus (isolate 6a33)
strain 6a33
5'UTR
<1..295
(295)

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..308
(308)

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..72
(72)

5UTR-dII
function 5'UTR domain II is a component of the IRES
standard_name 5UTR-dII
stem_loop
79..277
(199)

5UTR-dIII
function 5'UTR domain III is a component of the IRES
standard_name 5UTR-dIII
stem_loop
285..308
(24)

5UTR-dIV
function 5'UTR domain IV is a component of the IRES
standard_name 5UTR-dIV
misc_feature
823..1246
(424)

5UTR-dIV
note C/E1 genotyping region
misc_feature
8254..8593
(340)

5UTR-dIV
note NS5B genotyping region
gene
296..9355
(9060)

5UTR-dIV
locus_tag HCVORF1
CDS
296..9355
(9060)

5UTR-dIV
codon_start offset : 1
db_xref UniProtKB/Swiss-Prot : Q5I2N3
locus_tag HCVORF1
product Complete HCV polyprotein (contains C, E1, E2, P7, NS2, NS3, NS4A, NS4B, NS5A, NS5B).
translation VIEW
mat_peptide
296..868
(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
869..1444
(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
1445..2548
(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..409  (26) Hypervariable region 1 (HVR1)
prod_ft
site 472..480  (9) 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
2549..2737
(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
2738..3388
(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
3389..5281
(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
5282..5443
(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
5444..6226
(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
6227..7579
(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 2332..2340  (9) Nuclear localisation signal (NLS)
prod_ft
site 2363..2390  (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
7580..9352
(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
SEQUENCES
Sequence VIEW
Translation(s)
locus_tag HCVORF1 VIEW

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