Table 1  Canonical and alternative open reading frames (ORF) in SARS-CoV-2. iORF: internal OPF, extORF: extended ORF, upORF: upstream ORF.
Gene  Start  End  Protein  Protease Products  Frame
ORF1a.iORF1.ext  59  136  upORF1a1  -  Alternative
ORF1a.iORF2.ext  163  264  upORF1a2  -  Alternative
ORF1ab  266  13483  pp1a  leader protein  Canonical
nsp2
nsp3
nsp4
3C-like proteinase
nsp6
nsp7
nsp8
nsp9
nsp10
nsp11
ORF1ab  13468  21555  pp1ab  RNA-dependent RNA polymerase  Canonical
helicase
3′-to-5′ exonuclease
endoRNAse
2′-O-ribose methyltransferase
S  21563  25384  surface glycoprotein  S1  Canonical
S2
ORFS.iORF1  21744  21863  inORFS  -  Alternative
ORF3a  25393  26220  ORF3a protein  -  Canonical
ORF3a.iORF1  25457  25582  inORF3a1  -  Alternative
ORF3a.iORF2  25596  25697  inORF3a2  -  Alternative
E  26245  26472  envelope protein  -  Canonical
ORFM.ext  26484  27191  exORFM  -  Alternative
M  26523  27191  membrane glycoprotein  -  Canonical
ORFM.iORF  27151  27195  inORFM  -  Alternative
ORF6  27202  27387  ORF6 protein  -  Canonical
ORF7a  27394  27759  ORF7a protein  -  Canonical
ORF7b  27756  27887  ORF7b protein  -  Canonical
ORF7b.iORF2  27862  27897  inORF7b  -  Alternative
ORF8  27894  28259  ORF8 protein  -  Canonical
ORF8.iORF  27965  27994  inORF8  -  Alternative
N  28274  29533  nucleocapsid phosphoprotein  -  Canonical
ORFN.iORF1  28284  28577  ORF9b  -  Alternative
ORF10.upORF  29538  29570  upORF10  -  Alternative
ORF10  29558  29674  ORF10 protein  -  Canonical
ORF position is referred to the NC_045512.2 reference sequence.