Table S1.

ICP27-targeted genes identified by RNA-seq

No.	ICP27-mediated polyadenylation in intron 1 (132)						ICP27-mediated polyadenylation in intron 2 or alternative exon 2 (16)					ICP27-mediated use of alternative 5′ ss (12)			ICP27-mediated intron retention (78)
	Gene	PAS sequence	PAS to TSS	PAS to 5′ ss	5′ ss to TSS	Predicted size of novel ORF, aa	Gene	PAS sequence	PAS TO TSS	PAS TO 5′SS	Predicted size of novel ORF, aa	Gene	Affected 5′ ss to TSS	Predicted size of novel ORF, aa	Gene	Intron retained
1	ABHD6	AATAAA	1,269	858	411	None	CAD	AATAAA	1,369	753	<100	DESI2	308	<100	AKT1S1	Multiple introns
2	ACAD9	AATAAA	1,417	1,310	107	<100	CCT4	AATAAA	731	413	<100	HERPUD1	628	119	ALAS1	Intron 1 and 2
3	ACTR3B	AATAAA	1,696	1,518	178	<100	COQ4	AATAAA	1,046	410	<100	LEPR*	89	113	ALKBH6	Multiple introns
4	ADCY1	AATAAA	2,375	1,717	658	249	ELK1	AATAAA	1,847	1,163	None	NSUN4	743	<100	ANKRD9	Intron 1 and 2
5	AEBP2	ATTAAA	1,404	525	879	227	EIF4G3	AATAAA	1,605	459	144	PIGG	290	<100	ARFIP2	Last intron
6	AFTPH	AATAAA	2,176	1,868	308	None	EPC1	AATAAA	1,944	1,636	None	PPP1R8*	151	None)	ARMC5	Last two introns
7	AGPAT5	AATAAA	2,197	1,666	531	134	HOMEZ	AATAAA	2,144	1,956	None	RANGAP1	178	None	ATPIF1	Last intron
8	ALV9	AATAAA	1,241	864	377	<100	MDH2	AATAAA	1,147	939	<100	TACO1	492	122	ATPIP	Multiple introns
9	AMMCR1	AATAAA	1,330	986	344	None	MIB2	AATAAA	2,320	680	237	TMEM5	346	None	ATXN2L	Multiple introns
10	APPL1	AATAAA	860	659	201	<100	NFKBIL1	ATTAAA	2,002	413	121	TRMU	446	139	BRD4	Multiple introns
11	ARNTL	ATTAAA	1,686	1,489	197	None	SNX5	AATAAA	1,269	652	126	UBE2J2	189	None	CAND2	Last two introns
12	ASB13	AATAAA	1,727	1,640	87	<100	STON1	AATAAA	886	225	None	ZER1	349	None	CC2D2A	Last intron
13	ATP6V0A2	AATAAA	719	354	365	<100	TMEM127	AATAAA	2,471	1,595	112				CHMP2A	Intron 1
14	ATR	AATAAA	1053	872	181	<100	WWTR1	ATTAAA	1,855	627	None				CHTF8	Last intron
15	ATXN10	AATAAA	1134	752	382	<100	ZNF274	AATAAA	2,441	1,431	None				CREBBP	Last intron
16	AVL9	ATTAAA	1,241	864	377	<100	ZNF778	AATAAA	554	347	None				CRELD1	Multiple introns
17	BRSK2	AATAAA	1,903	1,426	477	224									CUL7	Multiple introns
18	BTBD2	AATAAA	3,542	3,135	407	205									DAXX	Last intron
19	CACHD1	AATAAA	1,952	1,802	150	<100									DMPK	Multiple introns
20	CACNA2D1	AATAAA	813	371	442	<100									DLG3	Intron 1
21	CAMSAP3	AATAAA	2,646	2,397	249	141									DLX4	Intron 1
22	CCDC85C	ATTAAA	4,804	3,922	882	379									DPP8	Intron 1
23	CCDC113	AATAAA	2,073	1,893	180	<100									DYRK1B	Last intron
24	CD99L2	AATAAA	1,071	776	295	<100									EMC6	Intron 1
25	CEP85L	AATAAA	2,586	1,925	661	240									ERF	Multiple introns
26	CLSTN1	AATAAA	2,122	1,238	884	<100									FBXO31	Last intron
27	CMTM4	AATAAA	1,715	1,347	368	<100									GTPBP3	Intron 1
28	C6ORF89	AATAAA	2,775	2,611	164	None)									IFT88	Intron 1
29	CPSF6	AATAAA	1,100	930	170	127									ILK	Intron 1
30	CTNNBIP1	AATAAA	1,274	1,100	174	None									JRK	Intron 1
31	CYP2U1	AATAAA	1,160	521	639	205									KLC2	Last two introns
32	DCAF10	AATAAA	979	339	640	180									LINC00476	Last intron
33	DGCR2	AATAAA	1,188	861	327	185									LPHN1	Multiple introns
34	DHRS4	AATAAA	1,113	931	182	<100									LPPR3	Multiple introns
35	DHX35	AATAAA	638	568	70	111									LRFN4	Intron 1
36	DUSP22	AATAAA	1,887	1,383	504	<100									MAP3K12	Multiple introns
37	DNMT3A	AATAAA	5,653	5,492	161	None									MFSD5	Intron 1
38	DYNC1I1	AATAAA	1,547	1,279	268	None)									MID1IP1	Intron 1
39	EFCAB5	AATAAA	1,902	1,789	113	None									MIDN	Multiple introns
40	ENDOD1	AATAAA	1,085	667	418	157									MIEF2	Last intron
41	EPN2	ATTAAA	2,214	2,059	155	None									NADK	Multiple introns
42	ERCC6	AATAAA	1,057	895	162	None)									NFS1	Intron1
43	ERLEC1	AATAAA	1,186	754	432	118									PHF12	Intron 1 and Last intron
44	EXTL3	AATAAA	1,036	849	187	None									P4HTM	Intron 1
45	FAM175A	AATAAA	641	463	178	128									PI4KB	Last intron
46	FAM178A	AATAAA	1,297	615	682	<100									PLEKH3	Multiple introns
47	FBXL5	AATAAA	1,952	1,743	209	<100									PMEL	Middle intron
48	FBXW11	AATAAA	1,430	1,014	416	117									PML	Multiple introns
49	FNIP1	AATAAA	1,248	1,014	234	<100									POLR2A	Last intron
50	FYCO1	AATAAA	1,520	1,417	103	None									PPPDE1	Intron 1
51	GIT1	AATAAA	3,257	2,991	266	205									PPP1R7	Last intron
52	GLCCI1	AATAAA	2,978	1,921	1,057	249									PRMT2	Intron 1
53	GREB1l	AATAAA	1,505	1,178	327	None									RELA	Last intron
54	GSKIP	AATAAA	1,551	1,434	117	None									RFT1	Last intron
55	GSR	AATAAA	1,500	1,060	440	190									SETD1A	Middle intron
56	HDAC7	AATAAA	2,709	2,262	447	160									SHISA5	Last intron
57	HILPDA	AATAAA	581	387	194	None									SLC10A3	Last intron
58	HNRNPLL	AATAAA	1,728	1548	180	None									SLC35A2	Last intron
59	HSDL1	AATAAA	1,040	924	116	None									SPATA2	Last intron
60	IFNAR2	AATAAA	2,418	2,096	322	None									STIM1	Last intron
61	INSR	AATAAA	1,899	1,690	209	173									STC2	Last intron
62	KLC1	AATAAA	1,060	753	307	None									TAPBP	Intron 1 and 2
63	LEPR	AATAAA	1,117	987	130	113									TCF3	Multiple introns
64	LRRC47	AATAAA	1,751	1,108	643	234									TMEM129	Multiple introns
65	MAML1	AATAAA	1,984	1,406	578	127									TMEM173	Intron 2
66	MAP3K3	AATAAA	1,581	1,026	555	183									TJAP1	Last intron
67	MAP3K7	AATAAA	1,291	753	538	<100									TSC22D4	Multiple introns
68	MBP	AATAAA	2,715	2,477	238	None									VARS	First intron
69	MCCC1	AATAAA	1,659	1,423	236	<100									WBP1L	Last intron
70	MEGF8	AATAAA	1,564	742	822	<100									WDR5	Intron 1
71	MKL1	AATAAA	2,983	2,741	242	None									YPEL3	Multiple introns
72	MLLT1	AATAAA	5,612	5,436	176	<100									ZC3H10	Intron 1
73	MOB1B	AATAAA	1,586	1,378	208	<100									ZNF107	Last intron
74	NAA16	AATAAA	887	509	378	118									ZNF200	Intron 1
75	NFKB1	AATAAA	1,164	704	460	None									ZNF416	Last intron
76	NUTM2B-AS1	AATAAA	1,804	1,407	397	None									ZNF580	Intron 1
77	PAFAH1B1	AATAAA	2,027	1,649	378	None									ZNF598	Multiple introns
78	PFKFB3	AATAAA	4,212	4,078	134	203									ZNF668	Last intron
79	PIP4K2B	ATTAAA	3,766	3,066	700	<100
80	PLAG1	AATAAA	1,047	915	132	None
81	PPM1E	AATAAA	2,143	1,550	593	154
82	PPP6C	AATAAA	953	575	378	118
83	PPP1R8	AATAAA	780	629	151	None
84	PPTC7	AATAAA	1,351	900	451	291
85	PRDM10	AATAAA	2,249	1917	332	None
86	PRDM15	AATAAA	1,050	837	213	226
87	PRKACB	AATAAA	1,255	858	397	None
88	QSOX2	AATAAA	2,650	2,284	366	186
89	RABL6	AATAAA	2,076	1,671	405	148
90	RBL1	AATAAA	891	663	228	133
91	R3HDM1	AATAAA	1,096	917	179	None
92	RFX2	AATAAA	2,944	2683	261	None
93	RIC1	AATAAA	2,009	1585	424	220
94	RMND5A	AATAAA	1,285	766	519	None
95	RRP1B	AATAAA	3,066	2,822	244	None
96	SCRN1	AATAAA	1,460	1,352	108	<100
97	SGSM2	AATAAA	1,155	921	234	180
98	SLC4A4	AATAAA	2,154	2,036	118	None
99	SLC22A5	AATAAA	1,115	453	662	139
100	SLC46A3	AATAAA	1,235	717	518	None
101	SNX25	AATAAA	754	528	226	None
102	SP3	ATTAAA	912	454	458	<100
103	SPTAN1	AATAAA	759	620	139	None
104	SSH2	AATAAA	1,069	767	302	<100
105	STXBP3	AATAAA	1,864	1,750	114	<100
106	SUPT16H	AATAAA	1,640	862	778	<100
107	TBC1D2B	ATTAAA	884	473	411	231
108	TIAM1	AATAAA	2,475	2,425	50	None
109	TIPRL	AATAAA	815	478	337	<100
110	TMEM116	AATAAA	2,772	2,554	218	None
111	TMEM170B	AATAAA	2,283	2,186	97	None
112	TMEM245	AATAAA	1,588	973	615	245
113	TRAF6	AATAAA	1,047	781	266	None
114	TSHZ3	AATAAA	1,054	949	105	None
115	TTC13	AATAAA	1,039	726	313	166
116	UBE2J1	AATAAA	1,117	755	362	<100
117	UNK	AATAAA	1,535	1,389	146	139
118	URI1	AATAAA	1,053	627	426	None
119	USP31	ATTAAA	1,098	465	633	280
120	WDYHV1	AATAAA	1,118	910	208	None
121	YWHAG	AATAAA	1,078	770	308	203
122	ZAK	AATAAA	1,459	1,293	166	None
123	ZC3H6	AATAAA	909	441	468	None
124	ZFP90	AATAAA	1,044	853	191	None
125	ZKSCAN1	AATAAA	981	826	155	None
126	ZMIZ2	AATAAA	4,051	3,667	384	None
127	ZNF75A	AATAAA	935	697	238	None
128	ZNF250	AATAAA	2,426	1,869	557	None
129	ZNF254	AATAAA	498	320	178	None
130	ZNF273	AATAAA	537	359	178	None
131	ZNF627	AATAAA	1,025	814	211	None
132	ZSCAN32	AATAAA	452	360	92	None

^*Use of both alternative 5′ splice sites (ss) and intronic PAS were observed for these genes.