Table 1. Transcription and translation coordinates, timing of expression, and function of latent, early lytic and delayed early lytic ORFs.

Gene	Str	TSS-PolyA	Start-Stop	Ann	Variant	Timing	Function	Ref
ORFK1	+	38–2956	105–959	P		Latent	Glycoprotein	[89]
ORF4	+	1097–2956	1127–2779	P	Sp.Var	24 h	Complement binding protein	[90]
ORF6U	+	3137–7013	3194–6592	P		24–48 h	ssDNA Binding protein	[91]
ORF11U	+	15610–17054	15771–16994	P		8 h	Predicted dUTPase	[92]
vIL6U	−	17960–17163	17856–17242	P		Latent	viral Interleukine 6 homolog	[93]
ORFK3	−	21099–18575	19557–18589	P	Internal	24 h	Immune modulator	[94], [95]
ORF70	−	21099–18575	21051–20038	P	Alt. Start	8 h	thymidylate synthasee	[96]
ORFK4	−	21898–21274	21779–21495	P		8 h	vMIP-II	[97]
ORFK4.1	−	22864–21274	N/A	P		8 h	N/A
1.4 kb	+	24175–25394	multiple	P		8 h	N/A	[28]
ORFK5U	−	26692–25501	26433–25663	P		8 h	RING-CH E3 Ubiquitin ligase	[94], [95]
ORFK6	−	27472–26843	27374–27422	P	Alt. Start	8 h	vMIP-IA	[94], [95]
PAN	+	28616–29690	multiple	P		8 h	Late gene expression	[33], [38]
ORF16	+	29770–30566	29962–30489	P		8 h	Bcl2 homolog	[98], [99]
ORF17.5	−	31536–30563	31505–30639	P		24 h	Assembly protein	[100]
ORF18	+	N/A-33273	32242–33015	P		24 h	Late gene regulationMHV68	[101]
ORF34U	+	54379–58691	54491–55474	M		24 h–48 h	N/A	[102]
ORF35U	+	55381–58691	55455–55907	M		24 h–48 h	N/A	[103]
ORF36	+	N/A-58691	N/A-57126	M		24 h–48 h	Serine protein kinase	[104]
ORF37U	+	N/A-58691	57089–58549	M		24 h–48 h	Sox	[50]
ORF38U	+	58186–58691	58504–58689	P		24 h–48 h	Myristylated protein	[61]
ORF39	−	60050–58701	59991–58789	P		24 h–48 h	Glycoprotein M	[105]
ORF45U	−	68683–67140	68392–67169	P		8 h	RSK activator	[106]
ORF46	−	69782–67140	69220–68453	P		24 h	Uracil deglycosylase	[107]
ORF47U	−	69782–67140	69731–69228	M		24 h	glycoprotein L	[96], [108]
ORF50	+	71374–76554	71412–74445	P	AS-ORF	8 h	RTA	[109]
ORFK8	+	74660–76554	74675–75607	P	Sp. Var	8 h–24 h	bZIP	[110]
ORF57	+	81819–83453	81886–83361	P	Sp. Var	8 h	mRNA export/splicing	[61]
ORF58	−	96613–94287	95363–94290	P		24 h	N/A	[61]
ORF59	−	96613–94287	96558–95368	P		24 h	Processivity factor	[61], [62]
ORF60	−	100149–94287	97606–96689	P		24 h–48 h	Ribonucleoprotein reductase	[61]
ORF61U	−	100149–94287	100013–97635	P		24 h–48 h	Ribonucleoprotein reductase	[61]
ORFK12	−	119205–117250	119075–117738	P	Alt. Start	Latent	Kaposin	[111]
ORF71	−	124220–122513	123154–122588	M		Latent	vFLIP	[112]
ORF72U	−	124220–122513	124010–123236	M		Latent	vCyclin	[112]
ORF73	−	128213–122513	127623–124252	M		Latent	LANA	[112]

Transcription and translation coordinates for the primary viral ORFs were annotated from in silico predictions and/or by manually curating mRNA-seq and Ribo-seq data. Timing was determined according to the time of transcription. Functions were gathered from the literature. U: uORF in leader region; Str: Strand; TSS: transcription start site; N/A, not determined in silico or by manual annotation; Ann: Annotation; P: predicted; M: manual annotation; Sp. Var: ORF with splice variant, Alt. Start: ORF with alternative starts; Internal: ORF with internal ORFs; AS-ORF: Antisense ORFs; MHV68: Function annotated in MHV68.