Position dependent ATATA

From Table IIa: Position-dependent, orientation-independent pentamers
ATATA and/or TATAT
are 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: 9 genes

```
YCL040W	GLK1	Glucokinase
```

YDR368W	YPR1	similar to aldo-keto reductase

YEL032W	MCM3	component of DNA replication initiator complex

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

YKL150W	MCR1	NADH-cytochrome b5 reductase

YLR079W	SIC1	Cdc28p-Clb5 protein kinase inhibitor

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

YLR395C	COX8	Cytochrome-c oxidase chain VIII

```
YOR066W		
```

early_g1: -499 to -401 nt upstream of the ATG start codon: 18 genes

YBL023C	MCM2	Minichromosome maintenance protein, transcription factor

```
YBR053C		
```

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

```
YBR200W	BEM1	contains two SH3 domains
```
```
YCL040W	GLK1	Glucokinase
```
```
YDL181W	INH1	ATPase inhibitor
```
```
YER111C	SWI4	transcription factor
```
```
YHR022C		RAS-related protein
```
```
YIL009W	FAA3	Acyl CoA synthase
```

YJL194W	CDC6	pre-initiation complex component

YKL185W	ASH1	probable purine nucleotide-binding protein

```
YLR049C		
```

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

```
YOR065W	CYT1	Cytochrome c1
```
```
YOR264W		
```
```
YPL158C		
```
```
YPR002W		
```

YPR019W	CDC54	Involved in initiation of DNA replication

early_g1: -400 to -302 nt upstream of the ATG start codon: 16 genes

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

```
YBR053C		
```

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

```
YBR158W		
```

YBR202W	CDC47	MCM3 protein homolog (S. cerevisiae)

```
YDR033W		
```

YGR044C	RME1	zinc finger protein; negative regulator of meiosis; directly repressed by a1-a2 regulator

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

YLL040C	VPS13	component of peripheral vacuolar membrane protein complex

```
YLR049C		
```

YLR258W	GSY2	Glycogen synthase (UDP-glucose--starch glucosyltransferase)

```
YNL078W		
```
```
YNR016C	ACC1	acetyl-CoA carboxylase
```
```
YPL066W		
```
```
YPL158C		
```
```
YPR002W		
```

early_g1: -301 to -203 nt upstream of the ATG start codon: 22 genes

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

```
YBR157C		
```
```
YBR158W		
```
```
YBR200W	BEM1	contains two SH3 domains
```
```
YDR511W		
```

YGL055W	OLE1	delta-9-fatty acid desaturase

```
YGR281W	YOR1	ABC transporter
```
```
YHL026C		
```

YKL150W	MCR1	NADH-cytochrome b5 reductase

YKL185W	ASH1	probable purine nucleotide-binding protein

```
YLR049C		
```
```
YLR050C		
```
```
YLR254C		
```

YLR395C	COX8	Cytochrome-c oxidase chain VIII

YMR256C	COX7	subunit VII of cytochrome c oxidase

```
YNL046W		
```
```
YNR067C		
```
```
YOR065W	CYT1	Cytochrome c1
```

YPL058C	PDR12	multidrug resistance transporter

```
YPL066W		
```
```
YPR002W		
```

YPR019W	CDC54	Involved in initiation of DNA replication

early_g1: -202 to -104 nt upstream of the ATG start codon: 30 genes

```
YBR067C	TIP1	cell wall mannoprotein
```

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

```
YCL040W	GLK1	Glucokinase
```

YDR368W	YPR1	similar to aldo-keto reductase

```
YDR511W		
```
```
YER111C	SWI4	transcription factor
```

YGL055W	OLE1	delta-9-fatty acid desaturase

```
YGR035C		
```

YGR044C	RME1	zinc finger protein; negative regulator of meiosis; directly repressed by a1-a2 regulator

```
YGR281W	YOR1	ABC transporter
```
```
YHL026C		
```

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

```
YHR022C		RAS-related protein
```
```
YIL009W	FAA3	Acyl CoA synthase
```
```
YJL157C	FAR1	Cdc28p kinase inhibitor
```

YJL194W	CDC6	pre-initiation complex component

YKL150W	MCR1	NADH-cytochrome b5 reductase

YKL163W	PIR3	Protein containing tandem internal repeats

YLL040C	VPS13	component of peripheral vacuolar membrane protein complex

```
YLR049C		
```

YLR258W	GSY2	Glycogen synthase (UDP-glucose--starch glucosyltransferase)

```
YMR007W		
```

YMR256C	COX7	subunit VII of cytochrome c oxidase

```
YNL046W		
```

YNR001C	CIT1	citrate synthase. Nuclear encoded mitochondrial protein.

```
YNR067C		
```
```
YOR264W		
```
```
YPL004C		
```

YPL058C	PDR12	multidrug resistance transporter

```
YPL158C		
```

early_g1: -103 to -5 nt upstream of the ATG start codon: 33 genes

YBL023C	MCM2	Minichromosome maintenance protein, transcription factor

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

```
YBR053C		
```
```
YBR200W	BEM1	contains two SH3 domains
```

YBR202W	CDC47	MCM3 protein homolog (S. cerevisiae)

```
YDL117W		
```
```
YDL179W	PCL9	Cyclin
```

YDR368W	YPR1	similar to aldo-keto reductase

YGL055W	OLE1	delta-9-fatty acid desaturase

```
YGR035C		
```
```
YGR281W	YOR1	ABC transporter
```

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

```
YJL157C	FAR1	Cdc28p kinase inhibitor
```

YJL194W	CDC6	pre-initiation complex component

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

YKL150W	MCR1	NADH-cytochrome b5 reductase

```
YLR049C		
```
```
YLR050C		
```
```
YLR254C		
```

YLR274W	CDC46	MCM initiator complex protein

YML110C	COQ5	Putative mitochondrial C-methyltransferase

```
YMR254C		
```

YMR256C	COX7	subunit VII of cytochrome c oxidase

```
YNL046W		
```

YNR001C	CIT1	citrate synthase. Nuclear encoded mitochondrial protein.

```
YNR016C	ACC1	acetyl-CoA carboxylase
```
```
YOR065W	CYT1	Cytochrome c1
```
```
YOR066W		
```
```
YOR264W		
```

YPL058C	PDR12	multidrug resistance transporter

```
YPL066W		
```
```
YPL158C		
```
```
YPR002W		
```

late_g1: -598 to -500 nt upstream of the ATG start codon: 26 genes

YBR252W	DUT1	dUTP pyrophosphatase (dUTPase)

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
YDL101C	DUN1	protein kinase
```

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

YFL008W	SMC1	omosome segregation protein

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

```
YHR113W		Vacuolar aminopeptidase
```

YIL026C	IRR1	involved in cell morphology

YJL074C	SMC3	involved in sister chromatid cohesion

```
YJL196C	ELO1	Elongation enzyme 1
```

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

YKL042W	SPC42	component of the spindle pole body

YKL165C	MCD4	(putative) involved in cell polarity

```
YLR183C		
```
```
YLR457C	NBP1	Nap1p binding protein
```

YML102W	CAC2	p60 subunit of the yeast omatin Assembly Factor-I (CAF-I)

YMR179W	SPT21	non-specific DNA binding protein

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

YNL273W	TOF1	Interacts with topoisomerase I

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

```
YOR144C		
```

YOR316C	COT1	involved in cobalt accumulation

```
YPL127C	HHO1	histone H1
```
```
YPR120C	CLB5	B-type cyclin
```
```
YLR349W		
```

late_g1: -499 to -401 nt upstream of the ATG start codon: 30 genes

YBL035C	POL12	B subunit of DNA polymerase alpha-primase complex

```
YBR070C		involved in osmotolerance
```

YBR252W	DUT1	dUTP pyrophosphatase (dUTPase)

```
YCL022C		
```
```
YCL024W		Ser/Thr protein kinase
```

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDL127W	PCL2	G1 cyclin
```

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

```
YER070W	RNR1	ribonucleotide reductase
```

YGR041W	BUD9	involved in bud-site selection

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

YGR152C	RSR1	GTP-binding protein, ras superfamily

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

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

YJR148W	BAT2	Branched-Chain Amino Acid Transaminase

YKL045W	PRI2	p58 polypeptide of DNA primase

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

YLR121C	YPS4	GPI-anchored aspartic protease

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

YLR383W	RHC18	involved in recombination repair

```
YML021C	UNG1	uracil DNA glycosylase
```

YML102W	CAC2	p60 subunit of the yeast omatin Assembly Factor-I (CAF-I)

```
YNL303W		
```
```
YNL310C		
```

YPL241C	CIN2	involved in microtubule function

YPR018W	RLF2	p90 subunit of yeast omatin Assembly Factor-I (CAF-I)

```
YPR174C		
```

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: 33 genes

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

```
YBR070C		involved in osmotolerance
```

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

```
YCL022C		
```
```
YCL024W		Ser/Thr protein kinase
```

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
YDL101C	DUN1	protein kinase
```
```
YDR383C		
```
```
YDR493W		
```
```
YGL089C	MF(ALPHA)2	alpha mating factor
```

YGR152C	RSR1	GTP-binding protein, ras superfamily

```
YHR039C		Aldehyde dehydrogenases
```
```
YHR113W		Vacuolar aminopeptidase
```

YIL159W	BNR1	involved in actin filament organization

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

YJL173C	RFA3	subunit 3 of replication factor-A

YKL042W	SPC42	component of the spindle pole body

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

YKL165C	MCD4	(putative) involved in cell polarity

```
YLR234W	TOP3	DNA Topoisomerase III
```
```
YLR286C	CTS1	Endochitinase
```
```
YML021C	UNG1	uracil DNA glycosylase
```

YML102W	CAC2	p60 subunit of the yeast omatin Assembly Factor-I (CAF-I)

YMR078C	CTF18	(putative) involved in chromosome transmission during mitosis

YMR179W	SPT21	non-specific DNA binding protein

YNL102W	POL1	DNA polymerase I alpha subunit, p180

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

YNL272C	SEC2	GDP/GTP exchange factor for Sec4p

```
YNL300W		
```

YOR317W	FAA1	long chain fatty acyl:CoA synthetase

```
YPL209C	IPL1	Protein kinase
```
```
YCL061C		
```

late_g1: -301 to -203 nt upstream of the ATG start codon: 46 genes

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

YBR073W	RDH54	Putative helicase similar to RAD54

```
YBR089W		
```
```
YCL022C		
```

YDL018C	ERP3	p24 protein involved in membrane trafficking

```
YDL101C	DUN1	protein kinase
```

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDL119C		
```
```
YDL156W		
```

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

```
YDR383C		
```
```
YER070W	RNR1	ribonucleotide reductase
```

YFL008W	SMC1	omosome segregation protein

```
YGL027C	CWH41	glucosidase I
```
```
YHR113W		Vacuolar aminopeptidase
```
```
YHR153C	SPO16	sporulation protein
```

YIL159W	BNR1	involved in actin filament organization

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

YJL173C	RFA3	subunit 3 of replication factor-A

```
YJL181W		
```

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

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

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

YLL022C	HIF1	interacts with histone acetyltransferase

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
```
```
YLR286C	CTS1	Endochitinase
```

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

```
YLR457C	NBP1	Nap1p binding protein
```
```
YML021C	UNG1	uracil DNA glycosylase
```

YMR078C	CTF18	(putative) involved in chromosome transmission during mitosis

YMR179W	SPT21	non-specific DNA binding protein

```
YMR199W	CLN1	G(sub)1 cyclin
```

YNL102W	POL1	DNA polymerase I alpha subunit, p180

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

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

YNL273W	TOF1	Interacts with topoisomerase I

```
YOL017W		
```
```
YOR144C		
```

YOR316C	COT1	involved in cobalt accumulation

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

YPL124W	NIP29	spindle pole body associated protein

```
YPL256C	CLN2	G(sub)1 cyclin
```
```
YPL267W		
```

YPR018W	RLF2	p90 subunit of yeast omatin Assembly Factor-I (CAF-I)

```
YLR236C		
```

late_g1: -202 to -104 nt upstream of the ATG start codon: 56 genes

```
YAR003W		beta transducin domain
```

YBL035C	POL12	B subunit of DNA polymerase alpha-primase complex

```
YBR071W		
```

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

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
YDL105W	QRI2	
```
```
YDL119C		
```
```
YDL124W		
```
```
YDL156W		
```

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

```
YDR493W		
```
```
YER070W	RNR1	ribonucleotide reductase
```
```
YGL028C	SCW11	soluble cell wall protein
```
```
YGL089C	MF(ALPHA)2	alpha mating factor
```
```
YGR109C	CLB6	B-type cyclin
```

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

```
YHR039C		Aldehyde dehydrogenases
```

YHR110W	ERP5	p24 protein involved in membrane trafficking

```
YHR153C	SPO16	sporulation protein
```
```
YHR154W	ESC4	involved in silencing
```
```
YJL018W		
```

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

YJL173C	RFA3	subunit 3 of replication factor-A

YJR148W	BAT2	Branched-Chain Amino Acid Transaminase

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

YKL165C	MCD4	(putative) involved in cell polarity

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

```
YKR077W		
```

YLL022C	HIF1	interacts with histone acetyltransferase

YLR121C	YPS4	GPI-anchored aspartic protease

```
YLR286C	CTS1	Endochitinase
```

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

```
YLR326W		
```
```
YLR376C		
```
```
YLR381W		
```

YLR383W	RHC18	involved in recombination repair

```
YML021C	UNG1	uracil DNA glycosylase
```

YML027W	YOX1	Homeobox-domain containing 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

YNL173C	MDG1	Involved in G-protein mediated signal transduction

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

```
YNL300W		
```

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

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

```
YOL017W		
```

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

YOR316C	COT1	involved in cobalt accumulation

```
YPL014W		
```

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

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

YPL241C	CIN2	involved in microtubule function

```
YPL256C	CLN2	G(sub)1 cyclin
```
```
YLR236C		
```
```
YLR349W		
```

late_g1: -103 to -5 nt upstream of the ATG start codon: 51 genes

```
YAR003W		beta transducin domain
```

YBL035C	POL12	B subunit of DNA polymerase alpha-primase complex

```
YBR071W		
```

YBR073W	RDH54	Putative helicase similar to RAD54

```
YDL010W		
```

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDL124W		
```

YDR297W	SUR2	Syringomycin response protein 2

```
YDR383C		
```
```
YDR493W		
```
```
YER070W	RNR1	ribonucleotide reductase
```
```
YGL027C	CWH41	glucosidase I
```
```
YGL028C	SCW11	soluble cell wall protein
```
```
YGL089C	MF(ALPHA)2	alpha mating factor
```

YGR152C	RSR1	GTP-binding protein, ras superfamily

```
YHR039C		Aldehyde dehydrogenases
```
```
YHR154W	ESC4	involved in silencing
```

YIL026C	IRR1	involved in cell morphology

YJL173C	RFA3	subunit 3 of replication factor-A

```
YJL196C	ELO1	Elongation enzyme 1
```

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

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

YKL165C	MCD4	(putative) involved in cell polarity

```
YKR083C		
```

YLR103C	CDC45	omosomal DNA replication initiation protein

YLR121C	YPS4	GPI-anchored aspartic protease

```
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

YLR233C	EST1	involved in telomere length regulation

```
YLR286C	CTS1	Endochitinase
```

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

```
YLR376C		
```

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

YLR383W	RHC18	involved in recombination repair

```
YML021C	UNG1	uracil DNA glycosylase
```

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

YNL273W	TOF1	Interacts with topoisomerase I

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

```
YOR074C	CDC21	Thymidylate synthase
```

YOR317W	FAA1	long chain fatty acyl:CoA synthetase

```
YPL014W		
```

YPL124W	NIP29	spindle pole body associated protein

YPL153C	RAD53	protein kinase, Mec1p and Tel1p regulate rad53p phosphorylation

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

YPL241C	CIN2	involved in microtubule function

```
YPL267W		
```

YPR018W	RLF2	p90 subunit of yeast omatin Assembly Factor-I (CAF-I)

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

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

s: -598 to -500 nt upstream of the ATG start codon: 17 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)

```
YBR156C		
```
```
YBR184W		
```

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

YCR065W	HCM1	Transcription factor (fork head domain)

```
YDR219C		
```
```
YEL018W		
```

YER001W	MNN1	Alpha-1,3-mannosyltransferase

```
YFR026C		
```
```
YFR038W		
```

YGR140W	CBF2	110 kDa subunit of the centromere binding factor CBF3

YKL067W	YNK1	Nucleoside diphosphate kinase

YLR228C	ECM22	involved in cell wall biogenesis (putative)

YMR190C	SGS1	has DNA helicase signature motifs

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

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

s: -499 to -401 nt upstream of the ATG start codon: 12 genes

YBL052C	SAS3	involved in silencing at HMR

```
YBL063W	KIP1	kinesin related protein
```

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

```
YDR179C		
```

YER003C	PMI40	mannose-6-phosphate isomerase

YIL140W	SRO4	localizes to the plasma membrane

YJR137C	ECM17	Putative sulfite reductase

YKL067W	YNK1	Nucleoside diphosphate kinase

YLR045C	STU2	spindle pole body component

```
YLR151C		
```

YLR228C	ECM22	involved in cell wall biogenesis (putative)

YMR198W	CIK1	spindle pole body associated protein

s: -400 to -302 nt upstream of the ATG start codon: 30 genes

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

YBL052C	SAS3	involved in silencing at HMR

```
YBL063W	KIP1	kinesin related protein
```

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

YBR276C	PPS1	dual specificity protein phosphatase

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

YCR065W	HCM1	Transcription factor (fork head domain)

```
YDR113C	PDS1	42-kDa nuclear protein
```
```
YDR179C		
```

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

YFR027W	ECO1	involved in establishment of cohesion between sister chromatids

YGR140W	CBF2	110 kDa subunit of the centromere binding factor CBF3

YHR061C	GIC1	interacts with GTPase, involved in bud emergence

YIL140W	SRO4	localizes to the plasma membrane

```
YJL118W		
```

YJR006W	HYS2	DNA polymerase delta 55 KD subunit

YJR137C	ECM17	Putative sulfite reductase

YJR155W	AAD10	Hypothetical aryl-alcohol dehydrogenase (AAD)

YKL067W	YNK1	Nucleoside diphosphate kinase

YKR010C	TOF2	topoisomerase I interacting factor 2

```
YLR126C		
```
```
YLR151C		
```

YMR190C	SGS1	has DNA helicase signature motifs

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		
```
```
YOR284W		
```

YPR141C	KAR3	kinesin-like nuclear fusion protein

s: -301 to -203 nt upstream of the ATG start codon: 24 genes

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

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

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

YBR276C	PPS1	dual specificity protein phosphatase

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

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

YDL197C	ASF2	Anti-silencing protein, involved in transcription

```
YDR179C		
```

YDR252W	BTT1	negative regulator of RNA polymerase II

```
YEL018W		
```

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

YER003C	PMI40	mannose-6-phosphate isomerase

YGR140W	CBF2	110 kDa subunit of the centromere binding factor CBF3

YIL126W	STH1	helicase related protein, snf2 homolog

YKR010C	TOF2	topoisomerase I interacting factor 2

```
YLL062C		
```

YLR045C	STU2	spindle pole body component

```
YLR151C		
```
```
YLR455W		
```

YMR190C	SGS1	has DNA helicase signature motifs

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

```
YOR284W		
```

s: -202 to -104 nt upstream of the ATG start codon: 31 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)

YBL052C	SAS3	involved in silencing at HMR

```
YBL063W	KIP1	kinesin related protein
```
```
YBR184W		
```
```
YBR296C	PHO89	Probable Na+/Pi symporter
```

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

YCR065W	HCM1	Transcription factor (fork head domain)

```
YDL094C		
```

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

```
YDR179C		
```

YDR488C	PAC11	similar to rat dynein intermediate chain

```
YEL017W		
```
```
YEL018W		
```

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

YER001W	MNN1	Alpha-1,3-mannosyltransferase

YER003C	PMI40	mannose-6-phosphate isomerase

```
YER018C	SPC25	component of spindle pole
```
```
YFR026C		
```

YJR006W	HYS2	DNA polymerase delta 55 KD subunit

YJR137C	ECM17	Putative sulfite reductase

YKL067W	YNK1	Nucleoside diphosphate kinase

```
YLR151C		
```
```
YLR455W		
```

YMR190C	SGS1	has DNA helicase signature motifs

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

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		
```

YOR026W	BUB3	cell cycle checkpoint protein

```
YOR284W		
```

YPR141C	KAR3	kinesin-like nuclear fusion protein

s: -103 to -5 nt upstream of the ATG start codon: 31 genes

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

YAR008W	SEN34	34kDa subunit of the tetrameric tRNA splicing endonuclease

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

```
YBR007C		
```

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

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

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

```
YDR179C		
```
```
YEL017W		
```

YER003C	PMI40	mannose-6-phosphate isomerase

YER017C	AFG3	ATP-dependent metalloprotease

YFR027W	ECO1	involved in establishment of cohesion between sister chromatids

YIL140W	SRO4	localizes to the plasma membrane

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

YJR006W	HYS2	DNA polymerase delta 55 KD subunit

YJR137C	ECM17	Putative sulfite reductase

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

YLL061W	MMP1	High affinity S-methylmethionine permease

```
YLR126C		
```
```
YLR151C		
```

YLR228C	ECM22	involved in cell wall biogenesis (putative)

```
YMR048W		
```

YMR190C	SGS1	has DNA helicase signature motifs

YMR198W	CIK1	spindle pole body associated protein

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

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		
```
```
YOR284W		
```

YPR141C	KAR3	kinesin-like nuclear fusion protein

g2: -598 to -500 nt upstream of the ATG start codon: 17 genes

```
YCL012W		
```
```
YCL012W		
```

YCL014W	BUD3	involved in bud site selection

YDL198C	YHM1	(putative) mitochondrial carrier protein

```
YDR366C		
```
```
YDR451C		
```

YER069W	ARG5,6	N-acetyl-gamma-glutamyl-phosphate reductase and acetylglutamate kinase

```
YIL050W	PCL7	PHO85 cyclin
```

YIL106W	MOB1	(putative) transcriptional regulator involved in mitosis

YIL169C		serine-, threonine-rich protein

```
YJR110W		
```

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

```
YKL069W		
```
```
YLR015W		
```

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

```
YOR273C		
```

YOR274W	MOD5	transfer RNA isopentenyl transferase

g2: -499 to -401 nt upstream of the ATG start codon: 16 genes

```
YBL032W		
```

YBR104W	YMC2	mitochondrial carrier protein

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

```
YCR086W		
```
```
YDR324C		
```
```
YDR325W		
```

YDR464W	SPP41	negative regulator of prp genes

YER069W	ARG5,6	N-acetyl-gamma-glutamyl-phosphate reductase and acetylglutamate kinase

```
YIL131C	FKH1	
```
```
YJL092W	HPR5	DNA helicase
```

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

```
YKL053W		
```
```
YNR009W		
```

YOR188W	MSB1	involved in polarized growth

YPL116W	HOS3	sequence similar to the histone deacetylase Hda1p

YPR111W	DBF20	kinase required for late nuclear division

g2: -400 to -302 nt upstream of the ATG start codon: 17 genes

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

YBR104W	YMC2	mitochondrial carrier protein

```
YCL063W		
```

YDL198C	YHM1	(putative) mitochondrial carrier protein

YDR464W	SPP41	negative regulator of prp genes

YER069W	ARG5,6	N-acetyl-gamma-glutamyl-phosphate reductase and acetylglutamate kinase

YGL255W	ZRT1	high-affinity zinc transport protein

```
YJL092W	HPR5	DNA helicase
```

YJL137C	GLG2	glycogen synthesis initiator

YJR112W	NNF1	involved in nuclear function

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

```
YKL053W		
```
```
YLL046C	RNP1	ribonucleoprotein 1
```
```
YLR015W		
```
```
YOR073W		
```

YOR188W	MSB1	involved in polarized growth

```
YMR299C		
```

g2: -301 to -203 nt upstream of the ATG start codon: 19 genes

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

```
YBR038W	CHS2	chitin synthase 2
```
```
YCR086W		
```
```
YGL101W		
```

YIL106W	MOB1	(putative) transcriptional regulator involved in mitosis

```
YIL131C	FKH1	
```
```
YIL158W		
```

YJL099W	CHS6	involved in chitin biosynthesis

YJL137C	GLG2	glycogen synthesis initiator

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

YJR112W	NNF1	involved in nuclear function

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

```
YLL046C	RNP1	ribonucleoprotein 1
```
```
YLL047W		
```
```
YMR003W		
```
```
YMR215W		
```

YOR188W	MSB1	involved in polarized growth

YPR111W	DBF20	kinase required for late nuclear division

```
YMR299C		
```

g2: -202 to -104 nt upstream of the ATG start codon: 17 genes

```
YBL032W		
```

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

YDL198C	YHM1	(putative) mitochondrial carrier protein

YDR389W	SAC7	GTPase activating protein (GAP) for RHO1

```
YDR451C		
```

YER069W	ARG5,6	N-acetyl-gamma-glutamyl-phosphate reductase and acetylglutamate kinase

```
YIL050W	PCL7	PHO85 cyclin
```

YIL169C		serine-, threonine-rich protein

YJL137C	GLG2	glycogen synthesis initiator

YJR112W	NNF1	involved in nuclear function

```
YKL048C	ELM1	protein kinase
```
```
YKL053W		
```
```
YLL046C	RNP1	ribonucleoprotein 1
```
```
YLL047W		
```
```
YMR215W		
```
```
YOR273C		
```
```
YMR299C		
```

g2: -103 to -5 nt upstream of the ATG start codon: 18 genes

```
YBL032W		
```

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

```
YBR038W	CHS2	chitin synthase 2
```

YCL014W	BUD3	involved in bud site selection

YDL198C	YHM1	(putative) mitochondrial carrier protein

```
YDR451C		
```

YDR464W	SPP41	negative regulator of prp genes

YER069W	ARG5,6	N-acetyl-gamma-glutamyl-phosphate reductase and acetylglutamate kinase

```
YGL101W		
```

YIL106W	MOB1	(putative) transcriptional regulator involved in mitosis

```
YKL053W		
```
```
YKL069W		
```
```
YMR003W		
```
```
YMR215W		
```
```
YNR009W		
```
```
YOR073W		
```
```
YOR273C		
```

YPL116W	HOS3	sequence similar to the histone deacetylase Hda1p

m: -598 to -500 nt upstream of the ATG start codon: 19 genes

YAL022C	FUN26	predicted membrane protein

```
YCL038C		Membrane transporter
```

YCR042C	TSM1	TATA binding protein-associated factor (TAF)

```
YGL116W	CDC20	beta-transducin homolog
```

YGR108W	CLB1	G(sub)2-specific B-type cyclin

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

YGR230W	BNS1	similar to Spo12, involved in sporulation

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

```
YHR151C		
```
```
YIL167W		
```

YJR092W	BUD4	involved in bud site selection

```
YLR190W		
```

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

YMR032W	HOF1	SH3 domain containing-protein

```
YNL058C		
```
```
YOL137W		
```
```
YPL186C		
```

YPR119W	CLB2	G(sub)2-specific B-type cyclin

YPR167C	MET16	3'phosphoadenylylsulfate reductase

m: -499 to -401 nt upstream of the ATG start codon: 18 genes

YAL022C	FUN26	predicted membrane protein

```
YAL040C	CLN3	G(sub)1 cyclin
```
```
YAR018C	KIN3	protein kinase
```

YGL201C	MCM6	component of MCM initiator complex involved in DNA replication

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

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

```
YIL167W		
```
```
YJL051W		
```

YJR092W	BUD4	involved in bud site selection

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

```
YMR031C		
```

YMR032W	HOF1	SH3 domain containing-protein

```
YNL058C		
```

YOR025W	HST3	involved in telomeric silencing

YOR058C	ASE1	encodes component of the spindle midzone

```
YPL186C		
```

YPR119W	CLB2	G(sub)2-specific B-type cyclin

YPR167C	MET16	3'phosphoadenylylsulfate reductase

m: -400 to -302 nt upstream of the ATG start codon: 13 genes

```
YAR018C	KIN3	protein kinase
```

YGL021W	ALK1	DNA damage-responsive protein

YGL201C	MCM6	component of MCM initiator complex involved in DNA replication

YGR092W	DBF2	Serine/threonine protein kinase

YGR108W	CLB1	G(sub)2-specific B-type cyclin

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

YLR131C	ACE2	zinc finger transcription factor

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

```
YMR031C		
```
```
YOL014W		
```

YPR119W	CLB2	G(sub)2-specific B-type cyclin

```
YPR157W		
```

m: -301 to -203 nt upstream of the ATG start codon: 18 genes

```
YBR138C	HDR1	Unknown
```
```
YDL138W	RGT2	glucose permease
```

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

```
YIL161W		
```
```
YJL051W		
```

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

```
YKL129C	MYO3	myosin I
```
```
YKL130C	SHE2	involved in cell polarity
```
```
YKR021W		
```
```
YML033W		
```
```
YML034W		
```
```
YML119W		
```

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

YMR032W	HOF1	SH3 domain containing-protein

```
YNL057W		
```
```
YOL014W		
```
```
YOL070C		
```

YPL242C	IQG1	Similar to mammalian IQGAP proteins

m: -202 to -104 nt upstream of the ATG start codon: 20 genes

YCL037C	SRO9	involved in actin filament organization

YCR042C	TSM1	TATA binding protein-associated factor (TAF)

```
YDL048C	STP4	involved in tRNA splicing
```
```
YDL138W	RGT2	glucose permease
```
```
YDR146C	SWI5	transcriptional activator
```

YGL021W	ALK1	DNA damage-responsive protein

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

```
YKL129C	MYO3	myosin I
```
```
YML034W		
```

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

```
YMR031C		
```

YMR032W	HOF1	SH3 domain containing-protein

YNL053W	MSG5	Dual-specificity protein tyrosine phosphatase

```
YNL057W		
```
```
YNL058C		
```
```
YOL069W	NUF2	53-kDa coiled-coil protein
```
```
YOL137W		
```

YOR025W	HST3	involved in telomeric silencing

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

m: -103 to -5 nt upstream of the ATG start codon: 23 genes

```
YAR018C	KIN3	protein kinase
```
```
YCL038C		Membrane transporter
```
```
YDL138W	RGT2	glucose permease
```
```
YDR146C	SWI5	transcriptional activator
```
```
YGL116W	CDC20	beta-transducin homolog
```

YGR092W	DBF2	Serine/threonine protein kinase

YGR108W	CLB1	G(sub)2-specific B-type cyclin

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

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

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		
```

YJR092W	BUD4	involved in bud site selection

```
YMR031C		
```

YMR032W	HOF1	SH3 domain containing-protein

```
YNL057W		
```
```
YOL070C		
```
```
YOL137W		
```

YOR025W	HST3	involved in telomeric silencing

YOR058C	ASE1	encodes component of the spindle midzone

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

YPL242C	IQG1	Similar to mammalian IQGAP proteins

YPR167C	MET16	3'phosphoadenylylsulfate reductase

From Table IIa: Position-dependent, orientation-independent pentamers ATATA and/or TATAT are found in the upstream regions of these cell cycle-regulated yeast genes in the following intervals:

From Table IIa: Position-dependent, orientation-independent pentamers
ATATA and/or TATAT
are found in the upstream regions of these cell cycle-regulated yeast genes in the following intervals: