Table 2. List of novel splice sites in previously unknown spliced genes and transcripts identified in the ICP27 mutant virus and wide-type HSV-1 (KOS) infected cells.

Novel Spliced Viral Genes /transcripts	5’ Splice Junction	3’ Splice Junction	Reads (d27-1)	Reads (KOS)	Strand	Size of Intron (nt)	Classes	Verified by Sequencing
ICP34.5	125650	124046	804	3	-	1604	γ1, nonessential	Fig 5
	124467	124046	15	78	-	421		Fig 5
	124467	123186	0	46	-	1281		Fig 5
	125650	124073	35	0	-	1577		?
	125650	123186	96	33	-	2464		?
UL5	13881	13397	221	24	-	484	β, essential	Fig 7
UL52	109052	111003	93	6	+	1951	β, essential	Fig 7
	111281	114960	39	0	+	3679		Ref [38]
pri-miR-H6/UDG	6722	9770	65	2	+	3048	Unknown	Fig 6
	7618	9770	38	9	+	2152		Fig 6
gL (UL1)	9253	9770	123	4	+	517	γ1, essential	Fig 6
UL37	85696	80961	512	2	-	4735	γ1, essential	Fig 8
	83293	80961	465	4	-	2332		?
	81121	80961	89	1	-	160		?
	81571	80961	51	1	-	610		?
	83293	80864	35	0	-	2429		?
	85696	80864	58	0	-	4832		?
US3	135089	135293	1162	78	+	204	γ1, nonessential	Fig 8
	135089	135198	133	24	+	109		Fig 8
gH (UL22)	45630	44531	358	0	-	1099	γ, essential	Fig 8
	45626	44531	39	0	-	1095		?
UL12	25375	25140	749	0	-	235	β, nonessential	Fig 8
	27748	25140	39	0	-	2608		?
gE (US8)	142539	142641	706	0	+	102	γ1, nonessential	?
	142539	142666	38	0	+	122		?
	141171	142666	152	0	+	1495		Fig 8
	141171	142491	44	0	+	2420		?
UL24	47482	48016	44	9	+	534	γ1, nonessential	Fig 8
	46712	48016	7	246	+	1304		?
	47480	47943	35	0	+	491		?
UL34	69536	69868	35	1	+	332	γ1, essential	Fig 8
VHS (UL41)	91311	91237	185	1	-	74	γ, nonessential	Fig 8
	91311	91166	142	1	-	145		Fig 8
ICP8(UL29)	61447	60735	556	0	-	712	β, essential	Fig 8
	61447	60834	82	0	-	613		?
	61122	60735	172	1	-	387		?
	61122	60834	122	1	-	288		?
	62239	61395	77	0	-	844		?
	62148	61395	53	0	-	753		?
TK (UL23)	47416	46696	82	0	-	720	β, nonessential	Fig 8
US11 /ICP47/US10	145111	144553	96	0	-	558	γ, nonessential	Fig 8
	145130	144553	95	0	-	577		Fig 8
gD (US6)	138918	139058	249	3	+	140	γ, essential	Fig 8
	137670	138846	1	36	+	1176		?
	138252	138750	33	0	+	498		?
gB (UL27)	54946	54453	338	0	-	493	γ1, essential	Fig 8
	54454	54366	298	0	-	88		?
	54454	53733	123	0	-	721		?
	53923	53733	111	0	-	190		?
	55947	55220	149	0	-	727		?
	54454	54377	55	0	-	77		?
	55236	55079	46	103	-	157		?
UL46 (VP11/12)	99924	99253	38	0	-	671	γ1, essential	Fig 8
UL42b	93048 (93052)	94152	30	384	+	1104	β, essential	Fig 8
UL4-5C	12377	12921	14	381	+	544	Unknown	Fig 8
	12137	12921	5	96	+	784		?
UL22C	45684	46578	8	52	+	894	Unknown	Fig 8
UL26/UL26.5a	51974	52447	0	41	+	473	Unknown	Fig 8

^a intron is flanked by GC-AG.

^b A GC-AG intron was predicted by MapSplice 2 for UL42 (93052^94152); however, RT-PCR and sequencing results suggest that a GT(U)-AG intron is used for UL42 (93048^94152).