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ORF1ab ORF1a polyprotein;ORF1ab polyprotein [ Severe acute respiratory syndrome coronavirus 2 ]

Gene ID: 43740578, updated on 12-Jun-2021

Summary

Gene symbol
ORF1ab
Gene description
ORF1a polyprotein;ORF1ab polyprotein
Locus tag
GU280_gp01
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Severe acute respiratory syndrome coronavirus 2 (isolate: Wuhan-Hu-1, nat-host: Homo sapiens)
Lineage
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; Betacoronavirus; Sarbecovirus
Summary
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped, positive-sense, single-stranded RNA virus that causes coronavirus disease 2019 (COVID-19). Virus particles include the RNA genetic material and structural proteins needed for invasion of host cells. Once inside the cell the infecting RNA is used to encode structural proteins that make up virus particles, nonstructural proteins that direct virus assembly, transcription, replication and host control and accessory proteins whose function has not been determined.~ ORF1ab, the largest gene, contains overlapping open reading frames that encode polyproteins PP1ab and PP1a. The polyproteins are cleaved to yield 16 nonstructural proteins, NSP1-16. Production of the longer (PP1ab) or shorter protein (PP1a) depends on a -1 ribosomal frameshifting event. The proteins, based on similarity to other coronaviruses, include the papain-like proteinase protein (NSP3), 3C-like proteinase (NSP5), RNA-dependent RNA polymerase (NSP12, RdRp), helicase (NSP13, HEL), endoRNAse (NSP15), 2'-O-Ribose-Methyltransferase (NSP16) and other nonstructural proteins. SARS-CoV-2 nonstructural proteins are responsible for viral transcription, replication, proteolytic processing, suppression of host immune responses and suppression of host gene expression. The RNA-dependent RNA polymerase is a target of antiviral therapies.
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Genomic context

Sequence:
NC_045512.2 (266..21555)

NC_045512.2Genomic Context describing neighboring genes Neighboring gene surface glycoprotein Neighboring gene ORF3a protein

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

stem_loop

  • Loc: 13476-13503 function = Coronavirus frameshifting stimulation element stem-loop 1 , inference = COORDINATES: profile:Rfam-release-14.1:RF00507,Infernal:1.1.2
  • Loc: 13488-13542 function = Coronavirus frameshifting stimulation element stem-loop 2 , inference = COORDINATES: profile:Rfam-release-14.1:RF00507,Infernal:1.1.2

General protein information

Preferred Names
ORF1a polyprotein;ORF1ab polyprotein
Names
leader protein
nsp2
nsp3
nsp4
3C-like proteinase
nsp6
nsp7
nsp8
nsp9
nsp10
RNA-dependent RNA polymerase
helicase
3'-to-5' exonuclease
endoRNAse
2'-O-ribose methyltransferase
leader protein
nsp2
nsp3
nsp4
3C-like proteinase
nsp6
nsp7
nsp8
nsp9
nsp10
nsp11
YP_009724389.1
  • pp1ab; translated by -1 ribosomal frameshift
YP_009725295.1
  • pp1a

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_045512.2 Reference assembly

    Range
    266..21555
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. YP_009724389.1 ORF1ab polyprotein [Severe acute respiratory syndrome coronavirus 2]

    Status: PROVISIONAL

    Conserved Domains (29) summary
    pfam11633
    Location:13511493
    SUD-M; Single-stranded poly(A) binding domain
    cd21401
    Location:53255419
    ZBD_cv_Nsp13-like; Cys/His rich zinc-binding domain (CH/ZBD) of coronavirus SARS NSP13 helicase and related proteins
    cd21409
    Location:54745552
    1B_cv_Nsp13-like; 1B domain of coronavirus SARS NSP13 helicase and related proteins
    cd21473
    Location:27773157
    cv_Nsp4_TM; coronavirus non-structural protein 4 (Nsp4) transmembrane domain
    cd21525
    Location:14961561
    SUD_C_SARS-CoV_Nsp3; C-terminal SARS-Unique Domain (SUD) of non-structural protein 3 (Nsp3) from Severe Acute Respiratory Syndrome coronavirus and related betacoronaviruses in the B lineage
    cd21560
    Location:35703859
    betaCoV-Nsp6; betacoronavirus non-structural protein 6
    cd21516
    Location:182818
    cv_beta_Nsp2_SARS-like; betacoronavirus non-structural protein 2 (Nsp2) similar to SARS-CoV Nsp2, and related proteins from betacoronaviruses in the B lineage
    cd21557
    Location:10541177
    Macro_X_Nsp3-like; X-domain of viral non-structural protein 3 and related macrodomains
    cd21666
    Location:32673563
    betaCoV_Nsp5_Mpro; betacoronavirus non-structural protein 5, also called Main protease (Mpro)
    cd21591
    Location:43975324
    SARS-CoV-like_RdRp; Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the B lineage: responsible for replication and transcription of the viral RNA genome
    cd21171
    Location:64536513
    NTD_alpha_beta_cv_Nsp15-like; N-terminal domain of alpha- and beta-coronavirus Nonstructural protein 15 (Nsp15), and related proteins
    cd21167
    Location:65176648
    M_alpha_beta_cv_Nsp15-like; middle domain of alpha- and beta-coronavirus Nonstructural protein 15 (Nsp15), and related proteins
    cd21161
    Location:66466796
    NendoU_cv_Nsp15-like; Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural Protein 15 (Nsp15) and related proteins
    cd21659
    Location:59306450
    betaCoV_Nsp14; nonstructural protein 14 of betacoronavirus
    pfam06460
    Location:68007095
    NSP13; Coronavirus NSP13
    pfam08717
    Location:39434139
    nsp8; nsp8 replicase
    pfam12379
    Location:8801050
    DUF3655; Protein of unknown function (DUF3655)
    pfam16348
    Location:31693261
    Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus
    cd21827
    Location:38603942
    betaCoV_Nsp7; betacoronavirus non-structural protein 7
    cd21901
    Location:42544384
    alpha_betaCoV_Nsp10; alphacoronavirus and betacoronavirus non-structural protein 14
    cd21898
    Location:41414253
    betaCoV_Nsp9; betacoronavirus non-structural protein 9
    cd21796
    Location:13127
    SARS-CoV-like_Nsp1_N; N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage
    cd21822
    Location:19132019
    SARS-CoV-like_Nsp3_NAB; nucleic acid binding domain of non-structural protein 3 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage
    cd21814
    Location:20442159
    SARS-CoV-like_Nsp3_betaSM; betacoronavirus-specific marker of non-structural protein 3 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage
    cd21732
    Location:15661868
    betaCoV_PLPro; betacoronavirus papain-like protease
    cd21722
    Location:55755914
    betaCoV_Nsp13-helicase; helicase domain of betacoronavirus non-structural protein 13
    cd21717
    Location:22322762
    TM_Y_SARS-CoV-like_Nsp3_C; C-terminus of non-structural protein 3, including transmembrane and Y domains, from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage
    cd21689
    Location:54235470
    stalk_CoV_Nsp13-like; stalk domain of coronavirus Nsp13 helicase and related proteins
    cl00019
    Location:12331358
    Macro_SF; macrodomain superfamily
  2. YP_009725297.1 leader protein

    Conserved Domains (1) summary
    pfam11501
    Location:13127
    Nsp1; Non structural protein Nsp1
  3. YP_009725298.1 nsp2

  4. YP_009725299.1 nsp3

    Conserved Domains (8) summary
    pfam12124
    Location:680743
    Nsp3_PL2pro; Coronavirus polyprotein cleavage domain
    pfam12379
    Location:102169
    DUF3655; Protein of unknown function (DUF3655)
    pfam16251
    Location:10891201
    NAR; Nucleic acid-binding domain (NAR)
    pfam11633
    Location:533675
    SUD-M; Single-stranded poly(A) binding domain
    cd14964
    Location:14971519
    7tm_GPCRs; TM helix 5 [structural motif]
    pfam01661
    Location:240340
    Macro; Macro domain
    pfam08715
    Location:7461064
    Viral_protease; Papain like viral protease
    cl28897
    Location:14941563
    7tm_GPCRs; seven-transmembrane G protein-coupled receptor superfamily
  5. YP_009725300.1 nsp4

    Conserved Domains (1) summary
    pfam16348
    Location:406498
    Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus
  6. YP_009725301.1 3C-like proteinase

    Conserved Domains (1) summary
    cd21666
    Location:4300
    betaCoV_Nsp5_Mpro; betacoronavirus non-structural protein 5, also called Main protease (Mpro)
  7. YP_009725302.1 nsp6

  8. YP_009725303.1 nsp7

    Conserved Domains (1) summary
    pfam08716
    Location:183
    nsp7; nsp7 replicase
  9. YP_009725304.1 nsp8

    Conserved Domains (1) summary
    pfam08717
    Location:1198
    nsp8; nsp8 replicase
  10. YP_009725305.1 nsp9

    Conserved Domains (1) summary
    pfam08710
    Location:1113
    nsp9; nsp9 replicase
  11. YP_009725306.1 nsp10

    Conserved Domains (1) summary
    pfam09401
    Location:12131
    NSP10; RNA synthesis protein NSP10
  12. YP_009725307.1 RNA-dependent RNA polymerase

    Conserved Domains (1) summary
    pfam06478
    Location:14366
    Corona_RPol_N; Coronavirus RPol N-terminus
  13. YP_009725308.1 helicase

    Conserved Domains (2) summary
    COG1112
    Location:323592
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    cd17934
    Location:272443
    DEXXQc_Upf1-like; DEXXQ-box helicase domain of Upf1-like helicase
  14. YP_009725309.1 3'-to-5' exonuclease

    Conserved Domains (1) summary
    pfam06471
    Location:3527
    NSP11
  15. YP_009725310.1 endoRNAse

    Conserved Domains (1) summary
    pfam06471
    Location:168
    NSP11
  16. YP_009725311.1 2'-O-ribose methyltransferase

    Conserved Domains (1) summary
    pfam06460
    Location:2297
    NSP13; Coronavirus NSP13
  17. YP_009725295.1 ORF1a polyprotein [Severe acute respiratory syndrome coronavirus 2]

    Status: PROVISIONAL

    Conserved Domains (19) summary
    pfam11633
    Location:13511493
    SUD-M; Single-stranded poly(A) binding domain
    cd21473
    Location:27773157
    cv_Nsp4_TM; coronavirus non-structural protein 4 (Nsp4) transmembrane domain
    cd21525
    Location:14961561
    SUD_C_SARS-CoV_Nsp3; C-terminal SARS-Unique Domain (SUD) of non-structural protein 3 (Nsp3) from Severe Acute Respiratory Syndrome coronavirus and related betacoronaviruses in the B lineage
    cd21560
    Location:35703859
    betaCoV-Nsp6; betacoronavirus non-structural protein 6
    cd21516
    Location:182818
    cv_beta_Nsp2_SARS-like; betacoronavirus non-structural protein 2 (Nsp2) similar to SARS-CoV Nsp2, and related proteins from betacoronaviruses in the B lineage
    cd21557
    Location:10541177
    Macro_X_Nsp3-like; X-domain of viral non-structural protein 3 and related macrodomains
    cd21666
    Location:32673563
    betaCoV_Nsp5_Mpro; betacoronavirus non-structural protein 5, also called Main protease (Mpro)
    pfam08717
    Location:39434139
    nsp8; nsp8 replicase
    pfam12379
    Location:8801050
    DUF3655; Protein of unknown function (DUF3655)
    pfam16348
    Location:31693261
    Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus
    cd21827
    Location:38603942
    betaCoV_Nsp7; betacoronavirus non-structural protein 7
    cd21901
    Location:42544384
    alpha_betaCoV_Nsp10; alphacoronavirus and betacoronavirus non-structural protein 14
    cd21898
    Location:41414253
    betaCoV_Nsp9; betacoronavirus non-structural protein 9
    cd21796
    Location:13127
    SARS-CoV-like_Nsp1_N; N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage
    cd21822
    Location:19132019
    SARS-CoV-like_Nsp3_NAB; nucleic acid binding domain of non-structural protein 3 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage
    cd21732
    Location:15661868
    betaCoV_PLPro; betacoronavirus papain-like protease
    cd21717
    Location:22322762
    TM_Y_SARS-CoV-like_Nsp3_C; C-terminus of non-structural protein 3, including transmembrane and Y domains, from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage
    cl00019
    Location:12331358
    Macro_SF; macrodomain superfamily
    cl41743
    Location:20442159
    betaCoV_Nsp3_betaSM; betacoronavirus-specific marker of betacoronavirus non-structural protein 3
  18. YP_009742608.1 leader protein

    Conserved Domains (1) summary
    pfam11501
    Location:13127
    Nsp1; Non structural protein Nsp1
  19. YP_009742609.1 nsp2

  20. YP_009742610.1 nsp3

    Conserved Domains (8) summary
    pfam12124
    Location:680743
    Nsp3_PL2pro; Coronavirus polyprotein cleavage domain
    pfam12379
    Location:102169
    DUF3655; Protein of unknown function (DUF3655)
    pfam16251
    Location:10891201
    NAR; Nucleic acid-binding domain (NAR)
    pfam11633
    Location:533675
    SUD-M; Single-stranded poly(A) binding domain
    cd14964
    Location:14971519
    7tm_GPCRs; TM helix 5 [structural motif]
    pfam01661
    Location:240340
    Macro; Macro domain
    pfam08715
    Location:7461064
    Viral_protease; Papain like viral protease
    cl28897
    Location:14941563
    7tm_GPCRs; seven-transmembrane G protein-coupled receptor superfamily
  21. YP_009742611.1 nsp4

    Conserved Domains (1) summary
    pfam16348
    Location:406498
    Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus
  22. YP_009742612.1 3C-like proteinase

    Conserved Domains (1) summary
    cd21666
    Location:4300
    betaCoV_Nsp5_Mpro; betacoronavirus non-structural protein 5, also called Main protease (Mpro)
  23. YP_009742613.1 nsp6

  24. YP_009742614.1 nsp7

    Conserved Domains (1) summary
    pfam08716
    Location:183
    nsp7; nsp7 replicase
  25. YP_009742615.1 nsp8

    Conserved Domains (1) summary
    pfam08717
    Location:1198
    nsp8; nsp8 replicase
  26. YP_009742616.1 nsp9

    Conserved Domains (1) summary
    pfam08710
    Location:1113
    nsp9; nsp9 replicase
  27. YP_009742617.1 nsp10

    Conserved Domains (1) summary
    pfam09401
    Location:12131
    NSP10; RNA synthesis protein NSP10
  28. YP_009725312.1 nsp11

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