From Table Ib: Position-independent, orientation-dependent hexamers

AACGCG
is found in the upstream regions of these cell cycle-regulated yeast genes:

early_g1: 9 genes

• YGR183C	QCR9	7.3 kDa subunit 9 of the ubiquinol cytochrome c oxidoreductase complex

• YGR281W	YOR1	ABC transporter

• YKL116C		probable serine/threonine-specific protein kinase (EC 2.7.1.-)

• YLR049C		

• YLR274W	CDC46	MCM initiator complex protein

• YML110C	COQ5	Putative mitochondrial C-methyltransferase

• YNR001C	CIT1	citrate synthase. Nuclear encoded mitochondrial protein.

• YOR066W		

• YPL066W		

late_g1: 48 genes

• YBR073W	RDH54	Putative helicase similar to RAD54

• YBR088C	POL30	profilerating cell nuclear antigen (PCNA); accessory factor for DNA polymerase delta, mRNA increases in G1, peaks in S in mitosis, and increases prior to DNA synthesis in meiosis

• YCL024W		Ser/Thr protein kinase

• YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

• YDL010W		

• YDL018C	ERP3	p24 protein involved in membrane trafficking

• YDL105W	QRI2	

• YDL164C	CDC9	DNA ligase

• YDR013W		

• YDR097C	MSH6	Homolog of the human GTBP protein, forms a complex with Msh2p to repair both single-base and insertion-deletion mispairs, redundant with Msh3p in repair of insertion-deletion mispairs

• YDR297W	SUR2	Syringomycin response protein 2

• YDR507C	GIN4	putative serine/threonine kinase

• YER070W	RNR1	ribonucleotide reductase

• YFL008W	SMC1	omosome segregation protein

• YGR109C	CLB6	B-type cyclin

• YGR152C	RSR1	GTP-binding protein, ras superfamily

• YHR153C	SPO16	sporulation protein

• YIL026C	IRR1	involved in cell morphology

• YJL078C	PRY3	Similar to plant PR-1 class of pathogen related proteins

• YJR043C	POL32	third (55 kDa) subunit of DNA polymerase delta

• YKL113C	RAD27	42 kDa 5' to 3' exonuclease required for Okazaki fragment processing

• YKL165C	MCD4	(putative) involved in cell polarity

• YKR077W		

• YKR083C		

• YLL022C	HIF1	interacts with histone acetyltransferase

• YLR103C	CDC45	omosomal DNA replication initiation protein

• YLR183C		

• YLR212C	TUB4	gamma tubulin-like protein, interacts with Spc98p and Spc97p, the Tub4p-Spc98p-Spc97p complex may be part of the microtubule attachment site at the spindle pole body

• YLR234W	TOP3	DNA Topoisomerase III

• YLR313C	SPH1	homologous to Spa2p, localizes to sites of polarized growth

• YLR383W	RHC18	involved in recombination repair

• YML021C	UNG1	uracil DNA glycosylase

• YML027W	YOX1	Homeobox-domain containing protein

• YMR179W	SPT21	non-specific DNA binding protein

• YNL082W	PMS1	MutL homolog, similar to Mlh1p, associates with Mlh1p, possibly forming a heterodimer, Pms1p and Msh1p act in concert to bind to a Msh2p-heteroduplex complex containing a G-T mismatch

• YNL102W	POL1	DNA polymerase I alpha subunit, p180

• YNL262W	POL2	DNA polymerase II

• YNL312W	RFA2	subunit 2 of replication factor RF-A; 29% identical to the human p34 subunit of RF-A

• YOL017W		

• YOL090W	MSH2	MutS homolog encoding major mismatch repair activity in mitosis and meiosis.

• YOR144C		

• YPL124W	NIP29	spindle pole body associated protein

• YPL208W		

• YPL241C	CIN2	involved in microtubule function

• YPL256C	CLN2	G(sub)1 cyclin

• YPR120C	CLB5	B-type cyclin

• YPR174C		

• YPR175W	DPB2	DNA polymerase epsilon, subunit B

s: 11 genes

• YBL003C	HTA2	Histone H2A (HTA1 and HTA2 code for nearly identical proteins)

• YBR007C		

• YCR065W	HCM1	Transcription factor (fork head domain)

• YDR113C	PDS1	42-kDa nuclear protein

• YER016W	BIM1	microtubule-binding protein

• YER118C	SSU81	Transmembrane osmosensor

• YFR027W	ECO1	involved in establishment of cohesion between sister chromatids

• YIL140W	SRO4	localizes to the plasma membrane

• YJL115W	ASF1	involved in silencing

• YLR126C		

• YOR026W	BUB3	cell cycle checkpoint protein

g2: 2 genes

• YCR073C	SSK22	protein kinase

• YIL169C		serine-, threonine-rich protein

m: 1 genes

• YCL037C	SRO9	involved in actin filament organization