Table 2.

The genome organization and predicted viral proteins encoded by TCoV

Gene	Frame	Start	Stop	Size (nt)	Size (aa)
5′ UTR		1	528	528
ORF1a	+1	529	12381	11853	3951
ORF1ab		529	20333	19806	6601
S	+2	20360	24037	3678	1226
G3a	+3	23988	24158	171	57
G3b	+2	24161	24352	192	64
G3c (E)	+3	24336	24632	297	99
M	+2	24637	25305	669	223
ORF-X	+1	25309	25590	282	94
G5a	+1	25669	25863	195	65
G5b	+3	25863	26108	246	82
N	+2	26054	27280	1227	409
3′ UTR		27281	27632	352

ORF1a/1ab non-structural proteins for positions and sizes
Proteins	Genomica positions (nt)	1a/1ab positions (aa)	C-end cleavage	Size (aa)	Identityb to IBV (%)	Possiblec motif
NSP1	529–?	M1-?	?	?
NSP2	?–2547	?-673G	AG/GK	∼673	91.4	P87
NSP3	2548–7323	G674–2265G	AG/GI	1592	89.1	PLP
NSP4	7324–8865	G2266–2779Q	LQ/AG	514	87.4
NSP5	8866–9786	A2780–3086Q	LQ/SS	307	92.8	3CLP
NSP6	9787–10665	S3087–3379Q	VQ/SK	293	92.5	HD
NSP7	10666–10914	S3380–3462Q	LQ/SV	83	96.4
NSP8	10915–11544	S3463–3672Q	LQ/NN	210	96.2
NSP9	11545–11877	N3673–3783Q	LQ/SK	111	99.1
NSP10	11878–12312	S3784–3928Q	VQ/SV	145	95.2	GFL
NSP11	12313–12381	S3929–3951Q		23	91.3
NSP12	12313–15131	S3929–4870Q	LQ/SC	941	97.2	RdRp
NSP13	15132–16931	S4871–5470Q	LQ/GT	600	97.3	HEL
NSP14	16932–18485	G5471–5988Q	LQ/SI	518	96.2	ExonN
NSP15	18486–19499	S5989–6326Q	LQ/SA	338	95.3	NendoU
NSP16	19500–20333	S6327–6604S		278	95.0	2-O-MT

^aNot including stop codons.

^bIBV Beaudette (GenBank accession NC_001451).

^cPLP, papain-like protease; HD: hydrophobic domain; 3CLP, 3C-like proteinase; GFL: growth factor-like domain; RdRp: RNA-dependant RNA polymerase; HEL, helicase domain; ExonN, exoribonuclease; NendoU, nidoviral uridylate-specific endoribonuclease; 2′O-MT, 2′-O-ribose methyltransferase.