Position dependent AATAA

From Table IIb: Position-dependent, orientation-dependent pentamers
AATAA
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: 9 genes

YBR202W	CDC47	MCM3 protein homolog (S. cerevisiae)

```
YDR033W		
```

YEL032W	MCM3	component of DNA replication initiator complex

YKL150W	MCR1	NADH-cytochrome b5 reductase

YML110C	COQ5	Putative mitochondrial C-methyltransferase

YMR256C	COX7	subunit VII of cytochrome c oxidase

```
YNR067C		
```
```
YOR065W	CYT1	Cytochrome c1
```
```
YPL158C		
```

early_g1: -499 to -401 nt upstream of the ATG start codon: 11 genes

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

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

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

YLR395C	COX8	Cytochrome-c oxidase chain VIII

```
YML109W	ZDS2	Zds1 homolog
```

YML110C	COQ5	Putative mitochondrial C-methyltransferase

```
YMR254C		
```
```
YNR067C		
```
```
YOR066W		
```
```
YPR002W		
```

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

```
YBR067C	TIP1	cell wall mannoprotein
```

YBR202W	CDC47	MCM3 protein homolog (S. cerevisiae)

```
YDL117W		
```

YGL055W	OLE1	delta-9-fatty acid desaturase

```
YGR035C		
```

YJL194W	CDC6	pre-initiation complex component

YKL185W	ASH1	probable purine nucleotide-binding protein

YLL040C	VPS13	component of peripheral vacuolar membrane protein complex

```
YLR050C		
```

YLR274W	CDC46	MCM initiator complex protein

YLR395C	COX8	Cytochrome-c oxidase chain VIII

```
YOR065W	CYT1	Cytochrome c1
```
```
YPL158C		
```

YPR019W	CDC54	Involved in initiation of DNA replication

early_g1: -301 to -203 nt upstream of the ATG start codon: 18 genes

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

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

```
YBR157C		
```
```
YCL040W	GLK1	Glucokinase
```
```
YDL181W	INH1	ATPase inhibitor
```

YDR368W	YPR1	similar to aldo-keto reductase

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

YGL055W	OLE1	delta-9-fatty acid desaturase

```
YJL157C	FAR1	Cdc28p kinase inhibitor
```

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

YKL185W	ASH1	probable purine nucleotide-binding protein

YLR079W	SIC1	Cdc28p-Clb5 protein kinase inhibitor

```
YLR254C		
```

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

```
YNR016C	ACC1	acetyl-CoA carboxylase
```
```
YOR066W		
```
```
YOR264W		
```

early_g1: -202 to -104 nt upstream of the ATG start codon: 16 genes

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

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

```
YBR157C		
```
```
YBR158W		
```

YBR202W	CDC47	MCM3 protein homolog (S. cerevisiae)

```
YDL117W		
```
```
YDR033W		
```
```
YJL157C	FAR1	Cdc28p kinase inhibitor
```

YKL150W	MCR1	NADH-cytochrome b5 reductase

```
YLR050C		
```
```
YLR254C		
```

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

YLR395C	COX8	Cytochrome-c oxidase chain VIII

```
YML109W	ZDS2	Zds1 homolog
```
```
YNR067C		
```

YPL058C	PDR12	multidrug resistance transporter

early_g1: -103 to -5 nt upstream of the ATG start codon: 29 genes

YBL023C	MCM2	Minichromosome maintenance protein, transcription factor

```
YBR067C	TIP1	cell wall mannoprotein
```

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

```
YBR157C		
```
```
YBR158W		
```

YBR202W	CDC47	MCM3 protein homolog (S. cerevisiae)

```
YBR231C		
```
```
YDL179W	PCL9	Cyclin
```
```
YDR033W		
```

YDR368W	YPR1	similar to aldo-keto reductase

```
YER111C	SWI4	transcription factor
```

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

```
YHL026C		
```

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

YKL150W	MCR1	NADH-cytochrome b5 reductase

YKL163W	PIR3	Protein containing tandem internal repeats

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

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

YMR256C	COX7	subunit VII of cytochrome c oxidase

YNR001C	CIT1	citrate synthase. Nuclear encoded mitochondrial protein.

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

YPL058C	PDR12	multidrug resistance transporter

```
YPL158C		
```

YPR019W	CDC54	Involved in initiation of DNA replication

late_g1: -598 to -500 nt upstream of the ATG start codon: 30 genes

```
YBR071W		
```
```
YCL022C		
```
```
YCL024W		Ser/Thr protein kinase
```

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
YDL105W	QRI2	
```
```
YDL156W		
```
```
YDR493W		
```

YFL008W	SMC1	omosome segregation protein

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

YIL026C	IRR1	involved in cell morphology

YIL159W	BNR1	involved in actin filament organization

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

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

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

YLR233C	EST1	involved in telomere length regulation

```
YLR286C	CTS1	Endochitinase
```

YML027W	YOX1	Homeobox-domain containing protein

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

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

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

```
YPL187W	MF(ALPHA)1	mating factor alpha
```
```
YLR236C		
```
```
YCL061C		
```

late_g1: -499 to -401 nt upstream of the ATG start codon: 29 genes

```
YBR071W		
```
```
YBR089W		
```
```
YCL022C		
```
```
YCL024W		Ser/Thr protein kinase
```

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDL127W	PCL2	G1 cyclin
```

YDL227C	HO	Homothallic switching endonuclease

```
YDR383C		
```
```
YGL028C	SCW11	soluble cell wall protein
```
```
YGL089C	MF(ALPHA)2	alpha mating factor
```

YHR110W	ERP5	p24 protein involved in membrane trafficking

```
YHR154W	ESC4	involved in silencing
```

YIL159W	BNR1	involved in actin filament organization

YKL045W	PRI2	p58 polypeptide of DNA primase

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

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

YLL022C	HIF1	interacts with histone acetyltransferase

YLR121C	YPS4	GPI-anchored aspartic protease

```
YLR326W		
```

YML060W	OGG1	43-kDa 8-oxo-guanine DNA glycosylase

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

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

```
YOL017W		
```

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

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

late_g1: -400 to -302 nt upstream of the ATG start codon: 23 genes

```
YAR003W		beta transducin domain
```
```
YBR070C		involved in osmotolerance
```

YBR073W	RDH54	Putative helicase similar to RAD54

```
YCL022C		
```

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

YDR297W	SUR2	Syringomycin response protein 2

```
YDR493W		
```

YFL008W	SMC1	omosome segregation protein

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

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

```
YHR039C		Aldehyde dehydrogenases
```

YIL159W	BNR1	involved in actin filament organization

YJL074C	SMC3	involved in sister chromatid cohesion

YLR103C	CDC45	omosomal DNA replication initiation protein

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
```
```
YML061C	PIF1	5' to 3' DNA helicase
```

YNL102W	POL1	DNA polymerase I alpha subunit, p180

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

late_g1: -301 to -203 nt upstream of the ATG start codon: 33 genes

YBR252W	DUT1	dUTP pyrophosphatase (dUTPase)

YDL227C	HO	Homothallic switching endonuclease

```
YDR383C		
```
```
YDR493W		
```

YFL008W	SMC1	omosome segregation protein

```
YHR153C	SPO16	sporulation protein
```

YIL159W	BNR1	involved in actin filament organization

```
YJL018W		
```

YJL074C	SMC3	involved in sister chromatid cohesion

```
YJL181W		
```

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

YJR148W	BAT2	Branched-Chain Amino Acid Transaminase

YKL042W	SPC42	component of the spindle pole body

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

```
YKR077W		
```
```
YKR083C		
```

YLL022C	HIF1	interacts with histone acetyltransferase

YLR032W	RAD5	putative ATPase/DNA helicase

YLR103C	CDC45	omosomal DNA replication initiation protein

```
YLR183C		
```
```
YLR234W	TOP3	DNA Topoisomerase III
```

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

YML060W	OGG1	43-kDa 8-oxo-guanine DNA glycosylase

YMR078C	CTF18	(putative) involved in chromosome transmission during mitosis

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

YNL272C	SEC2	GDP/GTP exchange factor for Sec4p

YNL273W	TOF1	Interacts with topoisomerase I

```
YNL300W		
```

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

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

YPL124W	NIP29	spindle pole body associated protein

```
YPL127C	HHO1	histone H1
```

late_g1: -202 to -104 nt upstream of the ATG start codon: 40 genes

```
YAR003W		beta transducin domain
```

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

YBL035C	POL12	B subunit of DNA polymerase alpha-primase complex

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

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
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

```
YDR493W		
```
```
YER070W	RNR1	ribonucleotide reductase
```

YFL008W	SMC1	omosome segregation protein

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

YGR152C	RSR1	GTP-binding protein, ras superfamily

```
YHR154W	ESC4	involved in silencing
```

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

```
YKR083C		
```

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

YLR103C	CDC45	omosomal DNA replication initiation protein

YLR121C	YPS4	GPI-anchored aspartic protease

```
YLR286C	CTS1	Endochitinase
```

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

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

YML060W	OGG1	43-kDa 8-oxo-guanine DNA glycosylase

YNL173C	MDG1	Involved in G-protein mediated signal transduction

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

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

```
YOR144C		
```

YOR316C	COT1	involved in cobalt accumulation

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

YPL153C	RAD53	protein kinase, Mec1p and Tel1p regulate rad53p phosphorylation

YPL241C	CIN2	involved in microtubule function

```
YPL267W		
```

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

```
YPR174C		
```
```
YCL061C		
```

late_g1: -103 to -5 nt upstream of the ATG start codon: 67 genes

```
YAR003W		beta transducin domain
```
```
YBR070C		involved in osmotolerance
```

YBR073W	RDH54	Putative helicase similar to RAD54

```
YBR089W		
```

YBR252W	DUT1	dUTP pyrophosphatase (dUTPase)

YBR278W	DPB3	C and C' subunits of DNA polymerase II

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

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
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

```
YDR493W		
```

YDR507C	GIN4	putative serine/threonine kinase

```
YGL027C	CWH41	glucosidase I
```
```
YGL028C	SCW11	soluble cell wall protein
```

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

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

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

```
YHR113W		Vacuolar aminopeptidase
```
```
YHR153C	SPO16	sporulation protein
```
```
YHR154W	ESC4	involved in silencing
```

YIL026C	IRR1	involved in cell morphology

YJL173C	RFA3	subunit 3 of replication factor-A

```
YJL181W		
```
```
YJL187C	SWE1	protein kinase homolog
```

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

YJR148W	BAT2	Branched-Chain Amino Acid Transaminase

YKL045W	PRI2	p58 polypeptide of DNA primase

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

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

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

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

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

```
YLR326W		
```
```
YLR376C		
```

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

YLR383W	RHC18	involved in recombination repair

```
YLR457C	NBP1	Nap1p binding protein
```

YMR078C	CTF18	(putative) involved in chromosome transmission during mitosis

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

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

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

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

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

```
YNL303W		
```

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.

```
YOR074C	CDC21	Thymidylate synthase
```

YOR317W	FAA1	long chain fatty acyl:CoA synthetase

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

YPL124W	NIP29	spindle pole body associated protein

```
YPL208W		
```
```
YPL267W		
```
```
YPR120C	CLB5	B-type cyclin
```

YPR175W	DPB2	DNA polymerase epsilon, subunit B

```
YLR236C		
```

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: 12 genes

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

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

```
YDL094C		
```

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

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

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

YJR137C	ECM17	Putative sulfite reductase

YJR155W	AAD10	Hypothetical aryl-alcohol dehydrogenase (AAD)

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

```
YNL176C		
```

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

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

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

```
YDL094C		
```

YDR252W	BTT1	negative regulator of RNA polymerase II

YDR488C	PAC11	similar to rat dynein intermediate chain

YER016W	BIM1	microtubule-binding protein

```
YER118C	SSU81	Transmembrane osmosensor
```
```
YFR026C		
```
```
YFR038W		
```

YGR140W	CBF2	110 kDa subunit of the centromere binding factor CBF3

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

YIL140W	SRO4	localizes to the plasma membrane

```
YJL115W	ASF1	involved in silencing
```

YKL067W	YNK1	Nucleoside diphosphate kinase

```
YLR151C		
```

s: -400 to -302 nt upstream of the ATG start codon: 21 genes

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

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

YBL052C	SAS3	involved in silencing at HMR

```
YBR156C		
```

YBR276C	PPS1	dual specificity protein phosphatase

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

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

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

YER016W	BIM1	microtubule-binding protein

```
YER118C	SSU81	Transmembrane osmosensor
```

YIL140W	SRO4	localizes to the plasma membrane

YIR017C	MET28	transcriptional activator in the Cbf1p-Met4p-Met28p complex

YJR006W	HYS2	DNA polymerase delta 55 KD subunit

YJR137C	ECM17	Putative sulfite reductase

YJR155W	AAD10	Hypothetical aryl-alcohol dehydrogenase (AAD)

YKR010C	TOF2	topoisomerase I interacting factor 2

```
YLR455W		
```

YNL073W	MSK1	mitochondrial lysine-tRNA synthetase

```
YOL019W		
```

YOR026W	BUB3	cell cycle checkpoint protein

YPL016W	SWI1	Zinc-finger transcription factor

s: -301 to -203 nt upstream of the ATG start codon: 20 genes

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

YAR008W	SEN34	34kDa subunit of the tetrameric tRNA splicing endonuclease

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

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

```
YDL096C		
```
```
YDR179C		
```

YDR252W	BTT1	negative regulator of RNA polymerase II

YER003C	PMI40	mannose-6-phosphate isomerase

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

YIL140W	SRO4	localizes to the plasma membrane

YKL067W	YNK1	Nucleoside diphosphate kinase

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

YMR198W	CIK1	spindle pole body associated protein

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

YPR141C	KAR3	kinesin-like nuclear fusion protein

s: -202 to -104 nt upstream of the ATG start codon: 23 genes

YAR008W	SEN34	34kDa subunit of the tetrameric tRNA splicing endonuclease

YBL052C	SAS3	involved in silencing at HMR

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

YBR276C	PPS1	dual specificity protein phosphatase

```
YDL096C		
```
```
YDR113C	PDS1	42-kDa nuclear protein
```
```
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

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

YER001W	MNN1	Alpha-1,3-mannosyltransferase

YER017C	AFG3	ATP-dependent metalloprotease

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

YGR140W	CBF2	110 kDa subunit of the centromere binding factor CBF3

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

YIL126W	STH1	helicase related protein, snf2 homolog

```
YJL118W		
```

YJR137C	ECM17	Putative sulfite reductase

YMR198W	CIK1	spindle pole body associated protein

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

YOR026W	BUB3	cell cycle checkpoint protein

YPL016W	SWI1	Zinc-finger transcription factor

s: -103 to -5 nt upstream of the ATG start codon: 28 genes

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

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

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

YDL197C	ASF2	Anti-silencing protein, involved in transcription

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

YDR252W	BTT1	negative regulator of RNA polymerase II

```
YEL018W		
```

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

YER017C	AFG3	ATP-dependent metalloprotease

```
YER118C	SSU81	Transmembrane osmosensor
```

YFR027W	ECO1	involved in establishment of cohesion between sister chromatids

YFR037C	RSC8	chromatin remodeling complex subunit

YIL126W	STH1	helicase related protein, snf2 homolog

```
YJL115W	ASF1	involved in silencing
```

YJR006W	HYS2	DNA polymerase delta 55 KD subunit

YJR137C	ECM17	Putative sulfite reductase

YJR155W	AAD10	Hypothetical aryl-alcohol dehydrogenase (AAD)

```
YKL066W		
```

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

YKR010C	TOF2	topoisomerase I interacting factor 2

YLL061W	MMP1	High affinity S-methylmethionine permease

```
YLR151C		
```

YLR228C	ECM22	involved in cell wall biogenesis (putative)

```
YMR048W		
```

YPL016W	SWI1	Zinc-finger transcription factor

YPR141C	KAR3	kinesin-like nuclear fusion protein

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

```
YJL092W	HPR5	DNA helicase
```

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

```
YLL047W		
```
```
YOR073W		
```
```
YOR273C		
```

YOR274W	MOD5	transfer RNA isopentenyl transferase

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

YCL014W	BUD3	involved in bud site selection

```
YCL063W		
```

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

```
YCR086W		
```
```
YDR451C		
```

YDR464W	SPP41	negative regulator of prp genes

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

```
YIL050W	PCL7	PHO85 cyclin
```
```
YIL131C	FKH1	
```
```
YIL158W		
```
```
YJL092W	HPR5	DNA helicase
```

YJL137C	GLG2	glycogen synthesis initiator

```
YKL053W		
```

YKL068W	NUP100	Nuclear pore complex protein homologous to Nup116p

```
YKL069W		
```

YPL116W	HOS3	sequence similar to the histone deacetylase Hda1p

g2: -400 to -302 nt upstream of the ATG start codon: 20 genes

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

YBR104W	YMC2	mitochondrial carrier protein

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

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

YDR464W	SPP41	negative regulator of prp genes

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

```
YIL050W	PCL7	PHO85 cyclin
```

YIL106W	MOB1	(putative) transcriptional regulator involved in mitosis

YJL099W	CHS6	involved in chitin biosynthesis

```
YJR110W		
```
```
YKL069W		
```
```
YLL046C	RNP1	ribonucleoprotein 1
```
```
YMR003W		
```

YOR188W	MSB1	involved in polarized growth

YPL116W	HOS3	sequence similar to the histone deacetylase Hda1p

YPR111W	DBF20	kinase required for late nuclear division

```
YMR299C		
```

g2: -301 to -203 nt upstream of the ATG start codon: 10 genes

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

```
YDR324C		
```
```
YDR325W		
```
```
YGL101W		
```

YJL137C	GLG2	glycogen synthesis initiator

```
YMR003W		
```
```
YMR215W		
```
```
YNR009W		
```

YPR111W	DBF20	kinase required for late nuclear division

```
YMR299C		
```

g2: -202 to -104 nt upstream of the ATG start codon: 16 genes

YBR104W	YMC2	mitochondrial carrier protein

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

YCL014W	BUD3	involved in bud site selection

```
YDR324C		
```

YDR464W	SPP41	negative regulator of prp genes

YIL106W	MOB1	(putative) transcriptional regulator involved in mitosis

YIL169C		serine-, threonine-rich protein

YJL099W	CHS6	involved in chitin biosynthesis

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

```
YJR110W		
```
```
YKL048C	ELM1	protein kinase
```
```
YLR015W		
```
```
YMR215W		
```

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

g2: -103 to -5 nt upstream of the ATG start codon: 22 genes

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

```
YBR038W	CHS2	chitin synthase 2
```

YBR104W	YMC2	mitochondrial carrier protein

```
YCR086W		
```
```
YDR451C		
```

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

```
YGL101W		
```

YGL255W	ZRT1	high-affinity zinc transport protein

YIL106W	MOB1	(putative) transcriptional regulator involved in mitosis

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

YJR112W	NNF1	involved in nuclear function

```
YKL048C	ELM1	protein kinase
```
```
YKL053W		
```

YKL068W	NUP100	Nuclear pore complex protein homologous to Nup116p

```
YLL047W		
```
```
YLR015W		
```

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

```
YOR273C		
```
```
YPL264C		
```

YPR111W	DBF20	kinase required for late nuclear division

```
YMR299C		
```

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

```
YBR138C	HDR1	Unknown
```
```
YCL038C		Membrane transporter
```

YCR042C	TSM1	TATA binding protein-associated factor (TAF)

```
YGL116W	CDC20	beta-transducin homolog
```
```
YJL051W		
```
```
YKR021W		
```

YLR131C	ACE2	zinc finger transcription factor

```
YLR190W		
```

YLR353W	BUD8	involved in bud site selection

```
YML034W		
```
```
YOL014W		
```
```
YOL137W		
```
```
YPL186C		
```

YPR167C	MET16	3'phosphoadenylylsulfate reductase

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

```
YAR018C	KIN3	protein kinase
```

YCR042C	TSM1	TATA binding protein-associated factor (TAF)

YGL201C	MCM6	component of MCM initiator complex involved in DNA replication

YGR230W	BNS1	similar to Spo12, involved in sporulation

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.

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

YLR353W	BUD8	involved in bud site selection

```
YML119W		
```

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

YMR032W	HOF1	SH3 domain containing-protein

```
YOL069W	NUF2	53-kDa coiled-coil protein
```
```
YOL070C		
```

YOR058C	ASE1	encodes component of the spindle midzone

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

```
YPR157W		
```

m: -400 to -302 nt upstream of the ATG start codon: 12 genes

```
YBR138C	HDR1	Unknown
```
```
YCL038C		Membrane transporter
```

YJR092W	BUD4	involved in bud site selection

```
YKL129C	MYO3	myosin I
```
```
YLR190W		
```

YLR353W	BUD8	involved in bud site selection

```
YML034W		
```

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

```
YNL057W		
```
```
YOL014W		
```

YOR058C	ASE1	encodes component of the spindle midzone

```
YPR157W		
```

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

```
YAR018C	KIN3	protein kinase
```

YCR042C	TSM1	TATA binding protein-associated factor (TAF)

```
YDR146C	SWI5	transcriptional activator
```
```
YGL116W	CDC20	beta-transducin homolog
```
```
YIL161W		
```
```
YJL051W		
```

YJR092W	BUD4	involved in bud site selection

```
YKL129C	MYO3	myosin I
```
```
YLR190W		
```
```
YML034W		
```
```
YNL057W		
```
```
YOL014W		
```

YOR025W	HST3	involved in telomeric silencing

YOR058C	ASE1	encodes component of the spindle midzone

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

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

```
YAR018C	KIN3	protein kinase
```
```
YDL138W	RGT2	glucose permease
```

YGL021W	ALK1	DNA damage-responsive protein

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

YGR230W	BNS1	similar to Spo12, involved in sporulation

YJR092W	BUD4	involved in bud site selection

```
YKL129C	MYO3	myosin I
```

YLR353W	BUD8	involved in bud site selection

```
YML119W		
```

YMR032W	HOF1	SH3 domain containing-protein

YNL053W	MSG5	Dual-specificity protein tyrosine phosphatase

YOR025W	HST3	involved in telomeric silencing

YOR058C	ASE1	encodes component of the spindle midzone

```
YOR229W	WTM2	Transcriptional modulator
```
```
YPL186C		
```

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

```
YDR146C	SWI5	transcriptional activator
```

YGL021W	ALK1	DNA damage-responsive protein

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

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.

YIL162W	SUC2	invertase (sucrose hydrolyzing enzyme)

```
YKR021W		
```

YLR131C	ACE2	zinc finger transcription factor

```
YLR190W		
```

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

```
YMR031C		
```
```
YNL057W		
```
```
YNL058C		
```
```
YOL069W	NUF2	53-kDa coiled-coil protein
```
```
YOL137W		
```

YPL242C	IQG1	Similar to mammalian IQGAP proteins

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