Position dependent AAACA

From Table IIb: Position-dependent, orientation-dependent pentamers
AAACA
is found in the upstream regions of these cell cycle-regulated yeast genes in the following intervals:

early_g1: -598 to -500 nt upstream of the ATG start codon: 14 genes

```
YDR033W		
```

YDR368W	YPR1	similar to aldo-keto reductase

```
YER111C	SWI4	transcription factor
```
```
YGR035C		
```

YHR005C	GPA1	alpha subunit of G protein coupled to mating factor receptors

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

```
YLR049C		
```
```
YLR050C		
```

YLR273C	PIG1	Protein similar to Gac1p, a putative type 1 protein phosphatase targeting subunit

YLR274W	CDC46	MCM initiator complex protein

YML110C	COQ5	Putative mitochondrial C-methyltransferase

```
YOR264W		
```
```
YPL004C		
```

YPR019W	CDC54	Involved in initiation of DNA replication

early_g1: -499 to -401 nt upstream of the ATG start codon: 7 genes

```
YDR033W		
```
```
YLR254C		
```
```
YNR016C	ACC1	acetyl-CoA carboxylase
```
```
YOR065W	CYT1	Cytochrome c1
```

YPL058C	PDR12	multidrug resistance transporter

```
YPR002W		
```

YPR019W	CDC54	Involved in initiation of DNA replication

early_g1: -400 to -302 nt upstream of the ATG start codon: 14 genes

YBL023C	MCM2	Minichromosome maintenance protein, transcription factor

YBR083W	TEC1	transcription factor of the TEA/ATTS DNA-binding domain family, regulator of Ty1 expression

YDR368W	YPR1	similar to aldo-keto reductase

YEL032W	MCM3	component of DNA replication initiator complex

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

```
YHL026C		
```
```
YHR022C		RAS-related protein
```

YKL185W	ASH1	probable purine nucleotide-binding protein

```
YLR050C		
```

YLR273C	PIG1	Protein similar to Gac1p, a putative type 1 protein phosphatase targeting subunit

YLR274W	CDC46	MCM initiator complex protein

YMR256C	COX7	subunit VII of cytochrome c oxidase

```
YOR066W		
```
```
YPL066W		
```

early_g1: -301 to -203 nt upstream of the ATG start codon: 7 genes

YBL023C	MCM2	Minichromosome maintenance protein, transcription factor

```
YCL040W	GLK1	Glucokinase
```
```
YDL117W		
```
```
YDR033W		
```

YKL150W	MCR1	NADH-cytochrome b5 reductase

YLR079W	SIC1	Cdc28p-Clb5 protein kinase inhibitor

YPR019W	CDC54	Involved in initiation of DNA replication

early_g1: -202 to -104 nt upstream of the ATG start codon: 8 genes

YBR054W	YRO2	Homolog to HSP30 heat shock protein YRO1 (S. cerevisiae) 7

YBR083W	TEC1	transcription factor of the TEA/ATTS DNA-binding domain family, regulator of Ty1 expression

YEL032W	MCM3	component of DNA replication initiator complex

```
YLR050C		
```
```
YMR007W		
```
```
YPL004C		
```

YPL058C	PDR12	multidrug resistance transporter

```
YPL158C		
```

early_g1: -103 to -5 nt upstream of the ATG start codon: 18 genes

YBR052C		Homolog to YCR004, obr1 (S. pombe), trp repressor binding protein (E. coli)

YBR083W	TEC1	transcription factor of the TEA/ATTS DNA-binding domain family, regulator of Ty1 expression

```
YDL117W		
```

YGL055W	OLE1	delta-9-fatty acid desaturase

```
YGR035C		
```

YKL163W	PIR3	Protein containing tandem internal repeats

YKL185W	ASH1	probable purine nucleotide-binding protein

```
YLR049C		
```
```
YLR050C		
```

YLR395C	COX8	Cytochrome-c oxidase chain VIII

```
YMR007W		
```

YMR256C	COX7	subunit VII of cytochrome c oxidase

```
YNL078W		
```

YNR001C	CIT1	citrate synthase. Nuclear encoded mitochondrial protein.

```
YNR016C	ACC1	acetyl-CoA carboxylase
```
```
YNR067C		
```
```
YPL158C		
```
```
YPR002W		
```

late_g1: -598 to -500 nt upstream of the ATG start codon: 20 genes

YBL035C	POL12	B subunit of DNA polymerase alpha-primase complex

YBR252W	DUT1	dUTP pyrophosphatase (dUTPase)

```
YDL127W	PCL2	G1 cyclin
```

YDR297W	SUR2	Syringomycin response protein 2

YDR309C	GIC2	Cdc42 binding protein, involved in bud emergence

YGR152C	RSR1	GTP-binding protein, ras superfamily

YGR238C	KEL2	involved in cell fusion and morphology; contains six Kelch repeats

```
YHR113W		Vacuolar aminopeptidase
```

YKL108W	SLD2	Synthetically lethal with dpb11-1; required for DNA replication

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

YLR103C	CDC45	omosomal DNA replication initiation protein

YLR121C	YPS4	GPI-anchored aspartic protease

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

```
YLR376C		
```
```
YML021C	UNG1	uracil DNA glycosylase
```

YMR179W	SPT21	non-specific DNA binding protein

YNL173C	MDG1	Involved in G-protein mediated signal transduction

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

```
YPL014W		
```

YPL153C	RAD53	protein kinase, Mec1p and Tel1p regulate rad53p phosphorylation

late_g1: -499 to -401 nt upstream of the ATG start codon: 31 genes

YBL035C	POL12	B subunit of DNA polymerase alpha-primase complex

```
YBR089W		
```
```
YCL024W		Ser/Thr protein kinase
```

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDL156W		
```
```
YDR383C		
```

YDR507C	GIN4	putative serine/threonine kinase

```
YER070W	RNR1	ribonucleotide reductase
```

YFL008W	SMC1	omosome segregation protein

```
YGL028C	SCW11	soluble cell wall protein
```
```
YGL089C	MF(ALPHA)2	alpha mating factor
```

YGR152C	RSR1	GTP-binding protein, ras superfamily

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

```
YHR113W		Vacuolar aminopeptidase
```

YJR148W	BAT2	Branched-Chain Amino Acid Transaminase

YKL108W	SLD2	Synthetically lethal with dpb11-1; required for DNA replication

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

YKL161C		probable serine/threonine-specific protein kinase (EC 2.7.1.-)

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

YLR103C	CDC45	omosomal DNA replication initiation protein

```
YLR286C	CTS1	Endochitinase
```

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

```
YLR457C	NBP1	Nap1p binding protein
```

YNL102W	POL1	DNA polymerase I alpha subunit, p180

YNL272C	SEC2	GDP/GTP exchange factor for Sec4p

```
YOL017W		
```

YPL124W	NIP29	spindle pole body associated protein

```
YPL256C	CLN2	G(sub)1 cyclin
```

YMR076C	PDS5	(putative) involved in sister chromosome cohesion during mitosis

YMR076C	PDS5	(putative) involved in sister chromosome cohesion during mitosis

late_g1: -400 to -302 nt upstream of the ATG start codon: 26 genes

```
YBR071W		
```

YBR073W	RDH54	Putative helicase similar to RAD54

```
YCL024W		Ser/Thr protein kinase
```

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

YDL018C	ERP3	p24 protein involved in membrane trafficking

```
YDL101C	DUN1	protein kinase
```
```
YDL119C		
```

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

YDR309C	GIC2	Cdc42 binding protein, involved in bud emergence

```
YGR109C	CLB6	B-type cyclin
```

YGR152C	RSR1	GTP-binding protein, ras superfamily

```
YHR153C	SPO16	sporulation protein
```
```
YJL018W		
```
```
YJL196C	ELO1	Elongation enzyme 1
```

YKL108W	SLD2	Synthetically lethal with dpb11-1; required for DNA replication

YKL161C		probable serine/threonine-specific protein kinase (EC 2.7.1.-)

```
YKR083C		
```

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

YLR103C	CDC45	omosomal DNA replication initiation protein

YLR233C	EST1	involved in telomere length regulation

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

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

YMR179W	SPT21	non-specific DNA binding protein

YNL272C	SEC2	GDP/GTP exchange factor for Sec4p

YPL241C	CIN2	involved in microtubule function

```
YCL061C		
```

late_g1: -301 to -203 nt upstream of the ATG start codon: 27 genes

```
YBR089W		
```
```
YCL024W		Ser/Thr protein kinase
```

YDL227C	HO	Homothallic switching endonuclease

```
YGL028C	SCW11	soluble cell wall protein
```

YGL200C	EMP24	type I transmemebrane protein, component of COPII-coated, ER-derived transport vesicles

```
YJL181W		
```
```
YJL196C	ELO1	Elongation enzyme 1
```

YKL042W	SPC42	component of the spindle pole body

YKL045W	PRI2	p58 polypeptide of DNA primase

YKL101W	HSL1	Putative protein kinase homologous to S. pombe cdr1/nim1

YKL108W	SLD2	Synthetically lethal with dpb11-1; required for DNA replication

YKR013W	PRY2	Similar to plant PR-1 class of pathogen related proteins

YLR032W	RAD5	putative ATPase/DNA helicase

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

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

```
YLR457C	NBP1	Nap1p binding protein
```
```
YNL262W	POL2	DNA polymerase II
```
```
YNL303W		
```

YOL007C	CSI2	Appears to be a structural component of the chitin synthase 3 complex

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

```
YOR144C		
```

YPL153C	RAD53	protein kinase, Mec1p and Tel1p regulate rad53p phosphorylation

```
YPL187W	MF(ALPHA)1	mating factor alpha
```

YPL241C	CIN2	involved in microtubule function

```
YPR174C		
```
```
YLR349W		
```
```
YCL061C		
```

late_g1: -202 to -104 nt upstream of the ATG start codon: 31 genes

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

```
YCL022C		
```
```
YDL010W		
```

YDL018C	ERP3	p24 protein involved in membrane trafficking

```
YDL105W	QRI2	
```
```
YDL124W		
```
```
YDL127W	PCL2	G1 cyclin
```

YFL008W	SMC1	omosome segregation protein

YGL200C	EMP24	type I transmemebrane protein, component of COPII-coated, ER-derived transport vesicles

```
YHR153C	SPO16	sporulation protein
```

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

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

YKL161C		probable serine/threonine-specific protein kinase (EC 2.7.1.-)

YKR013W	PRY2	Similar to plant PR-1 class of pathogen related proteins

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

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

```
YLR381W		
```
```
YLR457C	NBP1	Nap1p binding protein
```
```
YML061C	PIF1	5' to 3' DNA helicase
```

YMR078C	CTF18	(putative) involved in chromosome transmission during mitosis

YNL233W	BNI4	Is required to link Chs3p and Chs4p to the septins

YNL272C	SEC2	GDP/GTP exchange factor for Sec4p

YNL289W	PCL1	G(sub)1 cyclin that associates with PHO85

```
YNL303W		
```
```
YPL014W		
```

YPL124W	NIP29	spindle pole body associated protein

```
YPL208W		
```

YPL241C	CIN2	involved in microtubule function

```
YLR349W		
```

YMR076C	PDS5	(putative) involved in sister chromosome cohesion during mitosis

YMR076C	PDS5	(putative) involved in sister chromosome cohesion during mitosis

late_g1: -103 to -5 nt upstream of the ATG start codon: 35 genes

YAR007C	RFA1	69 kDa subunit of the heterotrimeric RPA (RF-A) single-stranded DNA binding protein, binds URS1 and CAR1

YBR252W	DUT1	dUTP pyrophosphatase (dUTPase)

YBR278W	DPB3	C and C' subunits of DNA polymerase II

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
YDL010W		
```
```
YDL127W	PCL2	G1 cyclin
```

YDR309C	GIC2	Cdc42 binding protein, involved in bud emergence

YGL200C	EMP24	type I transmemebrane protein, component of COPII-coated, ER-derived transport vesicles

YGR152C	RSR1	GTP-binding protein, ras superfamily

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

YIL026C	IRR1	involved in cell morphology

YJL074C	SMC3	involved in sister chromatid cohesion

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

```
YJL187C	SWE1	protein kinase homolog
```

YJR148W	BAT2	Branched-Chain Amino Acid Transaminase

YKL042W	SPC42	component of the spindle pole body

YKL108W	SLD2	Synthetically lethal with dpb11-1; required for DNA replication

YKR013W	PRY2	Similar to plant PR-1 class of pathogen related proteins

YLR032W	RAD5	putative ATPase/DNA helicase

YLR103C	CDC45	omosomal DNA replication initiation protein

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

```
YLR381W		
```

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

YML027W	YOX1	Homeobox-domain containing protein

YMR078C	CTF18	(putative) involved in chromosome transmission during mitosis

YNL102W	POL1	DNA polymerase I alpha subunit, p180

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

YNL289W	PCL1	G(sub)1 cyclin that associates with PHO85

YOL007C	CSI2	Appears to be a structural component of the chitin synthase 3 complex

```
YOL017W		
```
```
YOR074C	CDC21	Thymidylate synthase
```

YOR317W	FAA1	long chain fatty acyl:CoA synthetase

YPL057C	SUR1	Multicopy suppressor of cls2-2; also suppresses rvs161 mutations

```
YPL187W	MF(ALPHA)1	mating factor alpha
```
```
YPL209C	IPL1	Protein kinase
```

s: -598 to -500 nt upstream of the ATG start codon: 9 genes

```
YBR156C		
```

YER001W	MNN1	Alpha-1,3-mannosyltransferase

YER016W	BIM1	microtubule-binding protein

YFR027W	ECO1	involved in establishment of cohesion between sister chromatids

YHR061C	GIC1	interacts with GTPase, involved in bud emergence

YHR172W	SPC97	spindle pole body component, associates in a complex with Spc98p and Tub4p perhaps as part of the microtubule attachment site of the SBP

YJR155W	AAD10	Hypothetical aryl-alcohol dehydrogenase (AAD)

YKR001C	VPS1	putative GTP-binding protein; similar to mammalian Mx proteins

YLR228C	ECM22	involved in cell wall biogenesis (putative)

s: -499 to -401 nt upstream of the ATG start codon: 13 genes

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

```
YBL063W	KIP1	kinesin related protein
```
```
YDR179C		
```
```
YEL017W		
```

YER001W	MNN1	Alpha-1,3-mannosyltransferase

YFR027W	ECO1	involved in establishment of cohesion between sister chromatids

YGR140W	CBF2	110 kDa subunit of the centromere binding factor CBF3

YIL140W	SRO4	localizes to the plasma membrane

```
YKL066W		
```
```
YLR455W		
```

YNL073W	MSK1	mitochondrial lysine-tRNA synthetase

YNL126W	SPC98	spindle pole body component, associates in a complex with Spc97p and Tub4p perhaps as part of the microtubule attachment site of the SBP

```
YOL019W		
```

s: -400 to -302 nt upstream of the ATG start codon: 19 genes

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

```
YBL063W	KIP1	kinesin related protein
```

YBR275C	RIF1	RAP1-interacting factor, involved in establishment of repressed chromatin

YCR065W	HCM1	Transcription factor (fork head domain)

YDL093W	PMT5	dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase

```
YDL094C		
```
```
YDL096C		
```
```
YDR219C		
```

YIL126W	STH1	helicase related protein, snf2 homolog

YJR155W	AAD10	Hypothetical aryl-alcohol dehydrogenase (AAD)

YKR010C	TOF2	topoisomerase I interacting factor 2

YLR045C	STU2	spindle pole body component

```
YLR126C		
```
```
YLR455W		
```

YNL072W	RNH35	RNase H(35), a 35 kDa ribonuclease H

YNL304W	YPT11	similar to Ypt1 and other Ras-like GTP-binding proteins

YOR026W	BUB3	cell cycle checkpoint protein

```
YOR284W		
```

YPL016W	SWI1	Zinc-finger transcription factor

s: -301 to -203 nt upstream of the ATG start codon: 15 genes

YBL002W	HTB2	Histone H2B (HTB1 and HTB2 code for nearly identical proteins)

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

```
YBR007C		
```

YCR035C	RRP43	Component of the exosome 3->5 exoribonuclease complex with Rrp4p, Rrp41p, Rrp42p and Dis3p (Rrp44p).

YCR065W	HCM1	Transcription factor (fork head domain)

YDR252W	BTT1	negative regulator of RNA polymerase II

YGR140W	CBF2	110 kDa subunit of the centromere binding factor CBF3

YHR061C	GIC1	interacts with GTPase, involved in bud emergence

YIL126W	STH1	helicase related protein, snf2 homolog

```
YLR455W		
```
```
YMR048W		
```

YNL072W	RNH35	RNase H(35), a 35 kDa ribonuclease H

```
YNL176C		
```
```
YOR284W		
```

YPR141C	KAR3	kinesin-like nuclear fusion protein

s: -202 to -104 nt upstream of the ATG start codon: 17 genes

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

YBL052C	SAS3	involved in silencing at HMR

YBR276C	PPS1	dual specificity protein phosphatase

```
YBR296C	PHO89	Probable Na+/Pi symporter
```
```
YDL094C		
```
```
YDR113C	PDS1	42-kDa nuclear protein
```
```
YDR219C		
```

YDR356W	NUF1	component of the spindle pole body that interacts with Spc42p, calmodulin, and a 35 kDa protein

YHR172W	SPC97	spindle pole body component, associates in a complex with Spc98p and Tub4p perhaps as part of the microtubule attachment site of the SBP

YJR155W	AAD10	Hypothetical aryl-alcohol dehydrogenase (AAD)

YKR001C	VPS1	putative GTP-binding protein; similar to mammalian Mx proteins

YKR010C	TOF2	topoisomerase I interacting factor 2

```
YLL062C		
```

YMR198W	CIK1	spindle pole body associated protein

YNL126W	SPC98	spindle pole body component, associates in a complex with Spc97p and Tub4p perhaps as part of the microtubule attachment site of the SBP

```
YNL176C		
```
```
YOL019W		
```

s: -103 to -5 nt upstream of the ATG start codon: 33 genes

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

```
YBL063W	KIP1	kinesin related protein
```
```
YBR007C		
```
```
YBR156C		
```
```
YBR184W		
```

YBR276C	PPS1	dual specificity protein phosphatase

```
YBR296C	PHO89	Probable Na+/Pi symporter
```
```
YDL094C		
```

YDL095W	PMT1	dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase

YDL197C	ASF2	Anti-silencing protein, involved in transcription

```
YDR179C		
```
```
YDR219C		
```

YDR252W	BTT1	negative regulator of RNA polymerase II

YDR356W	NUF1	component of the spindle pole body that interacts with Spc42p, calmodulin, and a 35 kDa protein

YDR488C	PAC11	similar to rat dynein intermediate chain

```
YEL017W		
```

YEL061C	CIN8	kinesin-related protein involved in establishment and maintenance of mitotic spindle

YER003C	PMI40	mannose-6-phosphate isomerase

YER016W	BIM1	microtubule-binding protein

```
YER018C	SPC25	component of spindle pole
```
```
YER118C	SSU81	Transmembrane osmosensor
```

YGR140W	CBF2	110 kDa subunit of the centromere binding factor CBF3

YIL126W	STH1	helicase related protein, snf2 homolog

```
YJL115W	ASF1	involved in silencing
```
```
YJL118W		
```

YJR137C	ECM17	Putative sulfite reductase

YKL067W	YNK1	Nucleoside diphosphate kinase

```
YLL062C		
```

YLR045C	STU2	spindle pole body component

```
YLR126C		
```

YNL072W	RNH35	RNase H(35), a 35 kDa ribonuclease H

```
YOL019W		
```

YOR026W	BUB3	cell cycle checkpoint protein

g2: -598 to -500 nt upstream of the ATG start codon: 7 genes

YCR084C	TUP1	glucose repression regulatory protein, exhibits similarity to beta subunits of G proteins

YDR389W	SAC7	GTPase activating protein (GAP) for RHO1

YGL255W	ZRT1	high-affinity zinc transport protein

```
YIL158W		
```
```
YKL069W		
```
```
YMR003W		
```

YOL012C	HTA3	An evolutionarily conserved member of the histone H2A F/Z family of histone variants

g2: -499 to -401 nt upstream of the ATG start codon: 15 genes

YBL097W	BRN1	involved in chromosome maintenance; similar to Drosophila barren, Xenopus XCAP-H, and human BRRN1

YBR104W	YMC2	mitochondrial carrier protein

YCR084C	TUP1	glucose repression regulatory protein, exhibits similarity to beta subunits of G proteins

```
YCR085W		
```
```
YCR086W		
```
```
YDR366C		
```
```
YIL158W		
```

YJR112W	NNF1	involved in nuclear function

YKL049C	CSE4	high similarity to histone H3 and to human centromere protein CENP-A

```
YKL053W		
```

YKL068W	NUP100	Nuclear pore complex protein homologous to Nup116p

```
YLR015W		
```
```
YNR009W		
```

YOR274W	MOD5	transfer RNA isopentenyl transferase

```
YPL264C		
```

g2: -400 to -302 nt upstream of the ATG start codon: 15 genes

```
YBR038W	CHS2	chitin synthase 2
```

YBR104W	YMC2	mitochondrial carrier protein

YCL014W	BUD3	involved in bud site selection

```
YCL063W		
```

YCR084C	TUP1	glucose repression regulatory protein, exhibits similarity to beta subunits of G proteins

```
YCR085W		
```

YDR389W	SAC7	GTPase activating protein (GAP) for RHO1

YGL255W	ZRT1	high-affinity zinc transport protein

```
YJL092W	HPR5	DNA helicase
```

YJL099W	CHS6	involved in chitin biosynthesis

YJR076C	CDC11	Component of 10 nm filaments of mother-bud neck

YKL049C	CSE4	high similarity to histone H3 and to human centromere protein CENP-A

YKL068W	NUP100	Nuclear pore complex protein homologous to Nup116p

YPL116W	HOS3	sequence similar to the histone deacetylase Hda1p

```
YPL264C		
```

g2: -301 to -203 nt upstream of the ATG start codon: 13 genes

```
YCL063W		
```

YCR084C	TUP1	glucose repression regulatory protein, exhibits similarity to beta subunits of G proteins

YDL198C	YHM1	(putative) mitochondrial carrier protein

```
YDR324C		
```
```
YDR451C		
```
```
YJL092W	HPR5	DNA helicase
```

YKL049C	CSE4	high similarity to histone H3 and to human centromere protein CENP-A

```
YLL047W		
```

YLR014C	PPR1	zinc-finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type

```
YNR009W		
```
```
YOR273C		
```

YPL116W	HOS3	sequence similar to the histone deacetylase Hda1p

```
YPL264C		
```

g2: -202 to -104 nt upstream of the ATG start codon: 22 genes

```
YBL032W		
```

YCL014W	BUD3	involved in bud site selection

YCR084C	TUP1	glucose repression regulatory protein, exhibits similarity to beta subunits of G proteins

YDL198C	YHM1	(putative) mitochondrial carrier protein

```
YDR325W		
```

YDR464W	SPP41	negative regulator of prp genes

```
YIL050W	PCL7	PHO85 cyclin
```

YIL106W	MOB1	(putative) transcriptional regulator involved in mitosis

```
YIL131C	FKH1	
```

YJL099W	CHS6	involved in chitin biosynthesis

YJL137C	GLG2	glycogen synthesis initiator

YJR076C	CDC11	Component of 10 nm filaments of mother-bud neck

```
YJR110W		
```
```
YKL048C	ELM1	protein kinase
```
```
YKL053W		
```
```
YMR215W		
```
```
YNR009W		
```

YOL012C	HTA3	An evolutionarily conserved member of the histone H2A F/Z family of histone variants

```
YOR073W		
```

YOR188W	MSB1	involved in polarized growth

YOR274W	MOD5	transfer RNA isopentenyl transferase

YPR111W	DBF20	kinase required for late nuclear division

g2: -103 to -5 nt upstream of the ATG start codon: 24 genes

```
YBR038W	CHS2	chitin synthase 2
```
```
YBR043C		
```
```
YCL063W		
```
```
YCR086W		
```

YDL198C	YHM1	(putative) mitochondrial carrier protein

```
YDR325W		
```
```
YDR366C		
```

YDR464W	SPP41	negative regulator of prp genes

```
YGL101W		
```

YGL255W	ZRT1	high-affinity zinc transport protein

YIL106W	MOB1	(putative) transcriptional regulator involved in mitosis

```
YIL158W		
```

YIL169C		serine-, threonine-rich protein

YJL099W	CHS6	involved in chitin biosynthesis

YJR112W	NNF1	involved in nuclear function

YKL049C	CSE4	high similarity to histone H3 and to human centromere protein CENP-A

```
YKL053W		
```
```
YKL069W		
```

YLR014C	PPR1	zinc-finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type

```
YNR009W		
```

YOL012C	HTA3	An evolutionarily conserved member of the histone H2A F/Z family of histone variants

YPL116W	HOS3	sequence similar to the histone deacetylase Hda1p

```
YPL264C		
```
```
YMR299C		
```

m: -598 to -500 nt upstream of the ATG start codon: 14 genes

```
YAR018C	KIN3	protein kinase
```
```
YBR138C	HDR1	Unknown
```

YCR042C	TSM1	TATA binding protein-associated factor (TAF)

YIL162W	SUC2	invertase (sucrose hydrolyzing enzyme)

YLR353W	BUD8	involved in bud site selection

```
YML033W		
```

YMR001C	CDC5	protein kinase which functions at the G(sub)2/M boundary

```
YMR031C		
```

YNL053W	MSG5	Dual-specificity protein tyrosine phosphatase

```
YOL014W		
```

YOR058C	ASE1	encodes component of the spindle midzone

```
YOR315W		
```
```
YPL186C		
```

YPL242C	IQG1	Similar to mammalian IQGAP proteins

m: -499 to -401 nt upstream of the ATG start codon: 14 genes

YAL022C	FUN26	predicted membrane protein

YCR042C	TSM1	TATA binding protein-associated factor (TAF)

YGR092W	DBF2	Serine/threonine protein kinase

```
YHR023W	MYO1	Class II Myosin
```

YHR152W	SPO12	20 kDa protein with negatively charged C-terminus required for function; thought to be a positive regulator of exit from M-phase in mitosis and meiosis. Spo12p interacts with Dbf2p and Dbf20p protein kinases.

```
YKR021W		
```

YMR001C	CDC5	protein kinase which functions at the G(sub)2/M boundary

YMR032W	HOF1	SH3 domain containing-protein

```
YNL058C		
```
```
YOL070C		
```

YOR058C	ASE1	encodes component of the spindle midzone

```
YOR229W	WTM2	Transcriptional modulator
```

YPL242C	IQG1	Similar to mammalian IQGAP proteins

YPR167C	MET16	3'phosphoadenylylsulfate reductase

m: -400 to -302 nt upstream of the ATG start codon: 8 genes

```
YAL040C	CLN3	G(sub)1 cyclin
```

YGR279C	SCW4	soluble cell wall protein; can be released from SDS-extracted cell walls under reducing conditions

```
YKL130C	SHE2	involved in cell polarity
```

YLR131C	ACE2	zinc finger transcription factor

```
YOL014W		
```

YOR058C	ASE1	encodes component of the spindle midzone

```
YOR315W		
```
```
YPR157W		
```

m: -301 to -203 nt upstream of the ATG start codon: 12 genes

```
YDR146C	SWI5	transcriptional activator
```

YGL201C	MCM6	component of MCM initiator complex involved in DNA replication

YGR092W	DBF2	Serine/threonine protein kinase

YGR143W	SKN1	encodes a predicted type II membrane protein highly homologous to Kre6p

YHR152W	SPO12	20 kDa protein with negatively charged C-terminus required for function; thought to be a positive regulator of exit from M-phase in mitosis and meiosis. Spo12p interacts with Dbf2p and Dbf20p protein kinases.

```
YJL051W		
```
```
YKL130C	SHE2	involved in cell polarity
```

YLR353W	BUD8	involved in bud site selection

YNL053W	MSG5	Dual-specificity protein tyrosine phosphatase

```
YOL014W		
```
```
YOL070C		
```

YOR058C	ASE1	encodes component of the spindle midzone

m: -202 to -104 nt upstream of the ATG start codon: 18 genes

YAL022C	FUN26	predicted membrane protein

```
YBR138C	HDR1	Unknown
```

YCL037C	SRO9	involved in actin filament organization

```
YDL048C	STP4	involved in tRNA splicing
```

YGL021W	ALK1	DNA damage-responsive protein

YHL028W	WSC4	Putative integral membrane protein containing novel cysteine motif. Similarity to SLG1 (WSC1), WSC2 and WSC3

```
YHR023W	MYO1	Class II Myosin
```

YHR152W	SPO12	20 kDa protein with negatively charged C-terminus required for function; thought to be a positive regulator of exit from M-phase in mitosis and meiosis. Spo12p interacts with Dbf2p and Dbf20p protein kinases.

YJL079C	PRY1	Similar to plant PR-1 class of pathogen related proteins

YJR092W	BUD4	involved in bud site selection

```
YKL130C	SHE2	involved in cell polarity
```

YLR131C	ACE2	zinc finger transcription factor

```
YML119W		
```

YMR001C	CDC5	protein kinase which functions at the G(sub)2/M boundary

YMR032W	HOF1	SH3 domain containing-protein

YNL053W	MSG5	Dual-specificity protein tyrosine phosphatase

```
YNL058C		
```

YPL242C	IQG1	Similar to mammalian IQGAP proteins

m: -103 to -5 nt upstream of the ATG start codon: 16 genes

YCL037C	SRO9	involved in actin filament organization

```
YCL038C		Membrane transporter
```

YGL021W	ALK1	DNA damage-responsive protein

YGR143W	SKN1	encodes a predicted type II membrane protein highly homologous to Kre6p

YHR152W	SPO12	20 kDa protein with negatively charged C-terminus required for function; thought to be a positive regulator of exit from M-phase in mitosis and meiosis. Spo12p interacts with Dbf2p and Dbf20p protein kinases.

YJR092W	BUD4	involved in bud site selection

```
YKL129C	MYO3	myosin I
```
```
YLR190W		
```
```
YML034W		
```
```
YML119W		
```

YMR032W	HOF1	SH3 domain containing-protein

YNL053W	MSG5	Dual-specificity protein tyrosine phosphatase

```
YNL058C		
```
```
YOL069W	NUF2	53-kDa coiled-coil protein
```
```
YOR315W		
```

YPL242C	IQG1	Similar to mammalian IQGAP proteins

From Table IIb: Position-dependent, orientation-dependent pentamers AAACA is found in the upstream regions of these cell cycle-regulated yeast genes in the following intervals:

From Table IIb: Position-dependent, orientation-dependent pentamers
AAACA
is found in the upstream regions of these cell cycle-regulated yeast genes in the following intervals: