Table 1. List of splice sites of previously known spliced genes and transcripts identified in the ICP27 mutant virus and wild-type HSV-1 (KOS) infected cell.

	Viral Genes	5’ Splice Junction	3’ Splice Junction	Reads (d27-1)	Reads (KOS)	Strand	Size of Intron (nt)	Classes	Verified by Sequencing
Known spliced genes	LAT	119352	121311	4	429	+	1959	Latent; γ²	Fig 4
		119628a	121311	0	56	+	1683		Fig 4
	UL15	29990	33581	3573	2098	+	3591	γ, essential	Fig 4
		28566	33581	206	3	+	5015		Fig 4
		33431	33581	169	283	+	150		Fig 4
		27364	33581	94	26	+	6217		Fig 4
		28566	29957	130	6	+	1391		Fig 4
		29033	29957	87	2	+	924		Fig 4
	ICP0 (intron 1)	123950	123186	16873	28617	-	764	α, nonessential at high multiplicities	Fig 4
		123402	123186	5	1045	-	216		Fig 4
	ICP0 (intron 2)	122520	122380	2903	4677	-	140		Fig 4
		122520	122377	1868	3475	-	143		Fig 4
	ICP22 (US1)*	132232	132400	30190	30732	+	168	α, nonessential	Fig 8
		132213	132400	171	102	+	187		?
	ICP47 (US12)*	145457	145625	75081	66113	-	168	α, nonessential	Fig 8
		145457	145644	354	202	-	187		?
	gC (UL44)	97641	97867	173	215	+	226	γ², nonessential	Ref [21]
		96231a	96364	0	57	+	133		?
Spliced transcripts recently identified using PAC-Bio sequencing	UL41-42C (Intron 1)	91042	91334	28	870	+	292	Unknown	Ref [69]
		90999	91334	4	369	+	335		?
		91042	91439	1	91	+	397		?
	UL41-42C (Intron 2)	91472	92456	6	3387	+	984		Ref [69]
		91472	97867	0	5	+	6395		Ref [69]
	AST-2 Intron 2	79818	80026	8	5	+	208	Unknown	Ref [69]

Splice junctions were identified by MapSplice 2 using RNA-Seq data from KOS and d27-1 infected cells at 7 hpi (S1 and S2 Tables). Previously identified splice junctions are labeled in bold italics. For previously reported splice junctions, only the splice junctions with read counts ≥ 1 from either KOS or d27-1 infected cells were included in the table. For previously unreported splice junctions, only the splice junctions with read counts ≥ 30 from either KOS or d27-1 infected cells are listed. ^a intron is flanked by GC-AG. * ICP47 and ICP22 share the same splice sites in their 5’ UTR.? denotes that the isoform has not been confirmed by RT-PCR and sequencing. Classification of related viral genes is noted accordingly [1]. KOS complete genome [JQ673480] was used as the reference genome. ORF: Open-reading frame. Aa: amino acid. UL49sp [22] that appears to use GC-AG splice sites was not detected in this study.