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Table 1 The SARS-CoV-2 proteome (NCBI reference genome NC_045512.2)

From: Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models

Gene Protein length Position in the genome Description
nsp1 180 266–805 Interferes with host mRNA translation and processing [9].
nsp2 638 806–2719 Specific function is not known, it may play an auxiliary role to other viral proteins [10, 11].
nsp3 1945 2720–8554 Papain-like protease with phosphatase activity. Performs proteolytic cleavage of the polyproteins, membrane arrangements and [12, 13, 14].
nsp4 500 8555–10054 Involved in membrane rearrangements during viral infection [14].
nsp5 306 10055–10972 3C-like proteinase that cleave the viral polyprotein to produce the active forms of the nonstructural proteins [15, 16, 17, 18].
nsp6 290 10973–11842 Involved in membrane rearrangements during viral infection and autophagy [15].
nsp7 83 11843–12091 Forms an hexadecameric complex with nsp8 that helps in viral RNA replication [19].
nsp8 198 12092–12685 Forms an hexadecameric complex with nsp7 that helps in viral RNA replication [19].
nsp9 113 12686–13024 Binds and protects the viral genome from host degradation during replication [20, 21].
nsp10 139 13025–13441 Interacts with nsp14 and nsp16 to perform 3′–5′ exoribonuclease and 2′-O-methyltransferase activities, respectively [22, 23].
nsp11 13 13442–13480 Short peptide with potential role in RNA synthesis [24].
nsp12 932 13442–16236 RNA-dependent RNA polymerase [25, 26].
nsp13 601 16237–18039 Viral RNA helicase [27].
nsp14 527 18040–19620 3′-to-5′ exonuclease with proofreading activity [28, 29].
nsp15 346 19621–20658 Nidoviral RNA uridylate-specific endoribonuclease (NendoU) [30].
nsp16 298 20659–21552 2′-O-ribose methyltransferase. Involved in capping of viral mRNA to protect it from host degradation [31].
S 1273 21563–25384 Spike glycoprotein. Interacts with human ACE2 to enter target cells [32].
M 222 26523–27191 Membrane glycoprotein. Required for viral particle assembly [33].
N 419 28274–29533 Nucleocapsid protein. Binds viral RNA during viral particle formation [34].
E 75 26245–26472 Envelope protein. Forms ion channels in host ER membranes. Involved in exaggerated immune response [35, 36, 37].
ORF3a 275 25393–26220 Form ion channels in the host membrane. Linked to inflammatory, IFN signaling, innate immunity, apoptosis, and cell cycle regulation [38, 39, 40, 41, 42].
ORF6 61 27202–27387 Viral replication enhancer [43, 44].
ORF7a 121 27394–27759 Prevents virus tethering at the plasma membrane by inactivation BTS-2 protein [45].
ORF7b 43 27756–27887 Integral transmembrane protein. Its function has not been discovered yet [46, 47].
ORF8 121 27894–28259 Virus replication enhancer [48].
ORF9b* 97 28284–28580 Expressed from an alternative reading frame in the N gene. Suppresses host antiviral responses by promoting MAVS degradation [49, 50].
ORF10 38 29558–29674 Potential role in hijacking components of the host ubiquitin-proteasome system (UPS) [50].
ORF14** 73 28734–28946 Expressed from an alternative reading frame in the N gene. Unknown function.
  1. *Annotated by Gordon et al. [50]
  2. **Annotated by Wu et al. [51]