TABLE A1.

List of all ORFs selected more than once by HA-Prp42p genome localization analysis

ORF	Gene	% Prp42 expts hita	% Pol II expts hitb	No. of introns in ORFc	Introns across or nearbyd
YAL003W	EFB1	100	100	1
YBL027W	RPL19B	100	100	1
YBL072C	RPS8A	100	100	1
YBR048W	RPS11B	100	100	1
YBR084C-A	RPL19A	100	100	1
YBR181C	RPS6B	100	67	1
YBR189W	RPS9B	100	100	1
YBR191W	RPL21A	100	100	1
YCR031C	RPS14A	100	100	1
YDL082W	RPL13A	100	100	1
YDL130W	RPP1B	100	100	1
YDL136W	RPL35B	100	100	1
YDL191W	RPL35A	100	100	1
YDR025W	RPS11A	100	67	1
YDR064W	RPS13	100	100	1
YDR447C	RPS17B	100	100	1
YDR450W	RPS18A	100	67	1
YDR471W	RPL27B	100	100	1
YDR500C	RPL37B	100	33	1
YER102W	RPS8B	100	100	1
YER117W	RPL23B	100	100	1
YFL034C-A	RPL22B	100	100	1
YFR031C-A	RPL2A	100	100	1
YGL030W	RPL30	100	100	1
YGL076C	RPL7A	100	100	2
YGL189C	RPS26A	100	100	1
YGR118W	RPS23A	100	100	1
YGR148C	RPL24B	100	33	1
YGR214W	RPS0A	100	100	1
YHL001W	RPL14B	100	100	1
YHR010W	RPL27A	100	100	1
YHR141C	RPL42B	100	67	1
YHR203C	RPS4B	100	100	1
YIL052C	RPL34B	100	100	1
YIL069C	RPS24B	100	67	1
YIL133C	RPL16A	100	100	1
YIL148W	RPL40A	100	100	1
YJL191W	RPS14B	100	100	1
YJR094W-A	RPL43B	100	100	1
YJR145C	RPS4A	100	100	1
YKL006W	RPL14A	100	100	1
YKR094C	RPL40B	100	100	1
YLR185W	RPL37A	100	100	1
YLR333C	RPS25B	100	100	1
YLR367W	RPS22B	100	100	2
YLR448W	RPL6B	100	100	1
YML024W	RPS17A	100	100	1
YMR142C	RPL13B	100	100	1
YMR194W	RPL36A	100	100	1
YNL096C	RPS7B	100	67	1
YNL162W	RPL42A	100	67	1
YNL301C	RPL18B	100	100	1
YNL302C	RPS19B	100	67	1
YOL120C	RPL18A	100	100	1
YOL121C	RPS19A	100	67	1
YOL127W	RPL25	100	100	1
YOR096W	RPS7A	100	100	1
YOR234C	RPL33B	100	0	1
YOR293W	RPS10A	100	100	1
YOR312C	RPL20B	100	67	1
YPL079W	RPL21B	100	67	1
YPL081W	RPS9A	100	100	1
YPL090C	RPS6A	100	67	1
YPL143W	RPL33A	100	67	1
YPL198W	RPL7B	100	67	2
YPR132W	RPS23B	100	100	1
YGL102C		100	100	0	RPL28
YHL033C	RPL8A	100	100	0	No
YJL188C	BUD19	100	100	0	RPL39
YLL044W		100	100	0	No
YLL045C	RPL8B	100	100	0	No
YLR062C	BUD28	100	100	0	RPL22A
YLR441C	RPS1A	100	100	0	No
YMR242C	RPL20A	100	67	0	No
YOL086C	ADH1	100	100	0	No
YPL142C		100	67	0	RPL33A
YPR044C		100	67	0	RPL43A
YBL087C	RPL23A	80	100	1
YBL092W	RPL32	80	100	1
YBR082C	UBC4	80	0	1
YER056C-A	RPL34A	80	67	1
YER074W	RPS24A	80	67	1
YER131W	RPS26B	80	0	1
YGL031C	RPL24A	80	33	1
YGL103W	RPL28	80	100	1
YGR027C	RPS25A	80	67	1
YGR034W	RPL26B	80	67	1
YHR021C	RPS27B	80	33	1
YIL018W	RPL2B	80	100	1
YJL136C	RPS21B	80	0	1
YLR048W	RPS0B	80	0	1
YLR061W	RPL22A	80	67	1
YLR344W	RPL26A	80	67	1
YML073C	RPL6A	80	100	1
YMR230W	RPS10B	80	67	1
YNL112W	DBP2	80	100	1
YOR122C	PFY1	80	0	1
YPL249C-A	RPL36B	80	100	1
YLR167W	RPS31	80	33	0	No
YLR355C	ILV5	80	100	0	No
YML063W	RPS1B	80	100	0	No
YNL190W		80	33	0	No
YPL197C		80	100	0	RPL7B
YBL040C	ERD2	60	0	1
YDL061C	RPS29B	60	0	1
YDL083C	RPS16B	60	0	1
YJL189W	RPL39	60	100	1
YKL180W	RPL17A	60	100	1
YLR406C	RPL31B	60	100	1
YMR116C	ASC1	60	100	1
YNR053C		60	67	1
YPR043W	RPL43A	60	33	1
YBR118W	TEF2	60	100	0	MUD1
YHR143W		60	100	0	No
YJL190C	RPS22A	60	100	0	RPS14B and RPL39
YKL060C	FBA1	60	100	0	No
YKL153W		60	100	0	No
YKR042W	UTH1	60	100	0	No
YLR009W	RLP24	60	33	0	No
YLR044C	PDC1	60	100	0	No
YMR217W	GUA1	60	67	0	No
YMR303C	ADH2	60	67	0	No
YMR307W	GAS1	60	100	0	No
YNL066W	SUN4	60	67	0	No
YPR080W	TEF1	60	100	0	No
YBL018C	POP8	40	0	1
YDR381W	YRA1	40	100	1
YFL039C	ACT1	40	0	1
YHR039C-B	VMA10	40	0	1
YJL001W	PRE3	40	0	1
YKL006C-A	SFT1	40	33	1
YKL081W	TEF4	40	100	1
YLR388W	RPS29A	40	0	1
YML026C	RPS18B	40	67	1
YMR079W	SEC14	40	0	1
YOR182C	RPS30B	40	0	1
YBR009C	HHF1	40	100	0	No
YBR016W		40	0	0	No
YBR062C		40	33	0	No
YBR196C	PGI1	40	0	0	No
YDR033W	MRH1	40	67	0	No
YDR224C	HTB1	40	100	0	No
YEL034W	HYP2	40	100	0	No
YGL106W	MLC1	40	0	0	No
YGR082W	TOM20	40	0	0	No
YGR192C	TDH3	40	100	0	No
YGR234W	YHB1	40	100	0	No
YHL015W	RPS20	40	100	0	No
YIL053W	RHR2	40	100	0	RPL34B
YJR009C	TDH2	40	100	0	No
YLR340W	RPP0	40	100	0	No
YML106W	URA5	40	33	0	No
YMR193C-A		40	0	0	RPL36A
YNL030W	HHF2	40	100	0	No
YNL043C		40	0	0	YIP3
YNL255C	GIS2	40	33	0	No
YNL282W	POP3	40	0	0	No
YOL039W	RPP2A	40	67	0	No
YOR153W	PDR5	40	100	0	No
YLR076C		40	100	0	No
YLR110C	CCW12	40	100	0	No

^aIndicates the percentage of microarray experiments (out of five) in which the ORF was selected by HA-Prp42 ChIP by using the >2 SD criterion.

^bIndicates the percentage of microarray experiments (out of three) in which the ORF was selected in parallel Myc-Pol II ChIPs using the >2 SD criterion.

^cIndicates the number of introns contained in the ORF selected.

^dIndicates the name of the intron-containing ORF(s) occurring on the strand opposite or within ≤500 bp of the selected intronless ORF. Because the ChIP template probes are double stranded and up to 400 bp long, ORFs may be detected due to Prp42p accumulation on ORFs nearby or on the opposite DNA strand.