Position dependent AACGC

From Table IIa: Position-dependent, orientation-independent pentamers
AACGC and/or GCGTT
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: 8 genes

```
YER111C	SWI4	transcription factor
```
```
YGR035C		
```
```
YGR281W	YOR1	ABC transporter
```

YML110C	COQ5	Putative mitochondrial C-methyltransferase

```
YNL046W		
```

YNR001C	CIT1	citrate synthase. Nuclear encoded mitochondrial protein.

```
YNR067C		
```
```
YPR002W		
```

early_g1: -499 to -401 nt upstream of the ATG start codon: 9 genes

```
YBR231C		
```
```
YDR511W		
```
```
YGR281W	YOR1	ABC transporter
```

YLL040C	VPS13	component of peripheral vacuolar membrane protein complex

```
YLR049C		
```
```
YLR254C		
```
```
YMR007W		
```

YNR001C	CIT1	citrate synthase. Nuclear encoded mitochondrial protein.

```
YOR066W		
```

early_g1: -400 to -302 nt upstream of the ATG start codon: 10 genes

```
YBR053C		
```

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

```
YER111C	SWI4	transcription factor
```

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

```
YHR022C		RAS-related protein
```

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

```
YLR049C		
```

YLR079W	SIC1	Cdc28p-Clb5 protein kinase inhibitor

YLR274W	CDC46	MCM initiator complex protein

```
YNL046W		
```

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

YDR368W	YPR1	similar to aldo-keto reductase

```
YDR511W		
```

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

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

```
YNL078W		
```
```
YPL066W		
```

YPR019W	CDC54	Involved in initiation of DNA replication

early_g1: -202 to -104 nt upstream of the ATG start codon: 11 genes

```
YBR067C	TIP1	cell wall mannoprotein
```
```
YDL181W	INH1	ATPase inhibitor
```

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

```
YGR281W	YOR1	ABC transporter
```
```
YHR022C		RAS-related protein
```

YJL194W	CDC6	pre-initiation complex component

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

YLL040C	VPS13	component of peripheral vacuolar membrane protein complex

```
YML109W	ZDS2	Zds1 homolog
```
```
YMR007W		
```
```
YPL004C		
```

early_g1: -103 to -5 nt upstream of the ATG start codon: 3 genes

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

```
YHR022C		RAS-related protein
```
```
YML109W	ZDS2	Zds1 homolog
```

late_g1: -598 to -500 nt upstream of the ATG start codon: 19 genes

```
YBR070C		involved in osmotolerance
```
```
YDL010W		
```

YDR309C	GIC2	Cdc42 binding protein, involved in bud emergence

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

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

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

YJR148W	BAT2	Branched-Chain Amino Acid Transaminase

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

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

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

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

YNL173C	MDG1	Involved in G-protein mediated signal transduction

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

```
YNL303W		
```
```
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: -499 to -401 nt upstream of the ATG start codon: 18 genes

```
YDL010W		
```

YDL018C	ERP3	p24 protein involved in membrane trafficking

```
YDL156W		
```

YDR297W	SUR2	Syringomycin response protein 2

```
YER070W	RNR1	ribonucleotide reductase
```

YFL008W	SMC1	omosome segregation protein

```
YGL089C	MF(ALPHA)2	alpha mating factor
```
```
YJL196C	ELO1	Elongation enzyme 1
```

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

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

```
YLR234W	TOP3	DNA Topoisomerase III
```

YML027W	YOX1	Homeobox-domain containing protein

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

```
YNL262W	POL2	DNA polymerase II
```

YNL273W	TOF1	Interacts with topoisomerase I

```
YOR144C		
```
```
YPR120C	CLB5	B-type cyclin
```

YPR175W	DPB2	DNA polymerase epsilon, subunit B

late_g1: -400 to -302 nt upstream of the ATG start codon: 24 genes

```
YAR003W		beta transducin domain
```
```
YBR089W		
```

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
YDL119C		
```

YDR309C	GIC2	Cdc42 binding protein, involved in bud emergence

YDR507C	GIN4	putative serine/threonine kinase

```
YER070W	RNR1	ribonucleotide reductase
```
```
YGR109C	CLB6	B-type cyclin
```

YJL074C	SMC3	involved in sister chromatid cohesion

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

YKL045W	PRI2	p58 polypeptide of DNA primase

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

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

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

```
YKR077W		
```
```
YLR234W	TOP3	DNA Topoisomerase III
```

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

YNL273W	TOF1	Interacts with topoisomerase I

```
YNL303W		
```

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

```
YPL256C	CLN2	G(sub)1 cyclin
```
```
YCL061C		
```

late_g1: -301 to -203 nt upstream of the ATG start codon: 25 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

```
YDL119C		
```

YDL227C	HO	Homothallic switching endonuclease

YDR309C	GIC2	Cdc42 binding protein, involved in bud emergence

YDR507C	GIN4	putative serine/threonine kinase

```
YGL027C	CWH41	glucosidase I
```
```
YGR109C	CLB6	B-type cyclin
```

YGR152C	RSR1	GTP-binding protein, ras superfamily

```
YLR183C		
```
```
YLR326W		
```

YML027W	YOX1	Homeobox-domain containing protein

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

YMR179W	SPT21	non-specific DNA binding protein

YNL102W	POL1	DNA polymerase I alpha subunit, p180

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

YNL309W	STB1	Interacts with the putative transcription factor Sin3p

```
YOR144C		
```

YOR317W	FAA1	long chain fatty acyl:CoA synthetase

YPL153C	RAD53	protein kinase, Mec1p and Tel1p regulate rad53p phosphorylation

```
YPL208W		
```
```
YPL209C	IPL1	Protein kinase
```

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

```
YPR120C	CLB5	B-type cyclin
```

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

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

late_g1: -202 to -104 nt upstream of the ATG start codon: 53 genes

YBR073W	RDH54	Putative helicase similar to RAD54

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

```
YCL022C		
```
```
YCL024W		Ser/Thr protein kinase
```
```
YDL010W		
```

YDL018C	ERP3	p24 protein involved in membrane trafficking

```
YDL101C	DUN1	protein kinase
```
```
YDL105W	QRI2	
```
```
YDL119C		
```
```
YDL156W		
```
```
YDL164C	CDC9	DNA ligase
```

YDL227C	HO	Homothallic switching endonuclease

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

YFL008W	SMC1	omosome segregation protein

YGR152C	RSR1	GTP-binding protein, ras superfamily

```
YHR039C		Aldehyde dehydrogenases
```

YHR110W	ERP5	p24 protein involved in membrane trafficking

```
YHR154W	ESC4	involved in silencing
```

YIL026C	IRR1	involved in cell morphology

YJL074C	SMC3	involved in sister chromatid cohesion

```
YJL181W		
```

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

YKL042W	SPC42	component of the spindle pole body

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

YKL165C	MCD4	(putative) involved in cell polarity

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

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

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

YLR233C	EST1	involved in telomere length regulation

```
YLR234W	TOP3	DNA Topoisomerase III
```

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

YLR383W	RHC18	involved in recombination repair

```
YLR457C	NBP1	Nap1p binding protein
```

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

YMR179W	SPT21	non-specific DNA binding protein

YNL102W	POL1	DNA polymerase I alpha subunit, p180

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

```
YNL262W	POL2	DNA polymerase II
```

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.

```
YOR074C	CDC21	Thymidylate synthase
```
```
YOR144C		
```

YPL124W	NIP29	spindle pole body associated protein

```
YPL127C	HHO1	histone H1
```
```
YPL209C	IPL1	Protein kinase
```
```
YPL267W		
```
```
YPR174C		
```

YPR175W	DPB2	DNA polymerase epsilon, subunit B

late_g1: -103 to -5 nt upstream of the ATG start codon: 25 genes

YBR073W	RDH54	Putative helicase similar to RAD54

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDL164C	CDC9	DNA ligase
```
```
YDR013W		
```
```
YDR493W		
```
```
YER070W	RNR1	ribonucleotide reductase
```
```
YGR109C	CLB6	B-type cyclin
```
```
YHR113W		Vacuolar aminopeptidase
```
```
YHR153C	SPO16	sporulation protein
```

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

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

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

YLL022C	HIF1	interacts with histone acetyltransferase

YLR103C	CDC45	omosomal DNA replication initiation protein

```
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

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

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

```
YNL310C		
```
```
YPL208W		
```

YPL241C	CIN2	involved in microtubule function

```
YPR120C	CLB5	B-type cyclin
```
```
YLR349W		
```
```
YCL061C		
```

s: -598 to -500 nt upstream of the ATG start codon: 4 genes

YDR252W	BTT1	negative regulator of RNA polymerase II

```
YER018C	SPC25	component of spindle pole
```
```
YNL176C		
```

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

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

YAR008W	SEN34	34kDa subunit of the tetrameric tRNA splicing endonuclease

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

```
YBR007C		
```
```
YBR156C		
```

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

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

YIL140W	SRO4	localizes to the plasma membrane

YKL067W	YNK1	Nucleoside diphosphate kinase

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

```
YMR048W		
```

YMR190C	SGS1	has DNA helicase signature motifs

YPL016W	SWI1	Zinc-finger transcription factor

s: -400 to -302 nt upstream of the ATG start codon: 9 genes

```
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)

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

YER001W	MNN1	Alpha-1,3-mannosyltransferase

```
YER118C	SSU81	Transmembrane osmosensor
```

YIL140W	SRO4	localizes to the plasma membrane

YLR228C	ECM22	involved in cell wall biogenesis (putative)

YPL016W	SWI1	Zinc-finger transcription factor

s: -301 to -203 nt upstream of the ATG start codon: 17 genes

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

```
YBR156C		
```

YCR065W	HCM1	Transcription factor (fork head domain)

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

YDL197C	ASF2	Anti-silencing protein, involved in transcription

```
YDR219C		
```
```
YER018C	SPC25	component of spindle pole
```
```
YER118C	SSU81	Transmembrane osmosensor
```

YFR037C	RSC8	chromatin remodeling complex subunit

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

```
YJL115W	ASF1	involved in silencing
```

YLL061W	MMP1	High affinity S-methylmethionine permease

```
YLR151C		
```

YMR190C	SGS1	has DNA helicase signature motifs

```
YNL176C		
```

YOR026W	BUB3	cell cycle checkpoint protein

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

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

YCR065W	HCM1	Transcription factor (fork head domain)

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

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

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

YER016W	BIM1	microtubule-binding protein

YER017C	AFG3	ATP-dependent metalloprotease

YFR027W	ECO1	involved in establishment of cohesion between sister chromatids

YFR037C	RSC8	chromatin remodeling complex subunit

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

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

```
YJL115W	ASF1	involved in silencing
```
```
YLL062C		
```
```
YLR126C		
```

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		
```

YPL016W	SWI1	Zinc-finger transcription factor

s: -103 to -5 nt upstream of the ATG start codon: 8 genes

YDR252W	BTT1	negative regulator of RNA polymerase II

```
YEL018W		
```

YER001W	MNN1	Alpha-1,3-mannosyltransferase

YER017C	AFG3	ATP-dependent metalloprotease

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

YGR140W	CBF2	110 kDa subunit of the centromere binding factor CBF3

```
YJL118W		
```

g2: -598 to -500 nt upstream of the ATG start codon: 5 genes

```
YBR038W	CHS2	chitin synthase 2
```
```
YIL131C	FKH1	
```

YJL099W	CHS6	involved in chitin biosynthesis

```
YKL069W		
```

YOR274W	MOD5	transfer RNA isopentenyl transferase

g2: -499 to -401 nt upstream of the ATG start codon: 4 genes

```
YCL012W		
```
```
YCL012W		
```
```
YCR073C	SSK22	protein kinase
```
```
YCR085W		
```

g2: -400 to -302 nt upstream of the ATG start codon: 3 genes

```
YDR451C		
```

YIL169C		serine-, threonine-rich protein

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

g2: -301 to -203 nt upstream of the ATG start codon: 5 genes

```
YIL158W		
```

YIL169C		serine-, threonine-rich protein

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

YOR188W	MSB1	involved in polarized growth

g2: -202 to -104 nt upstream of the ATG start codon: 4 genes

```
YGL101W		
```

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

```
YKL069W		
```

YOR188W	MSB1	involved in polarized growth

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

```
YDR366C		
```

YDR464W	SPP41	negative regulator of prp genes

```
YIL131C	FKH1	
```
```
YKL048C	ELM1	protein kinase
```
```
YKL069W		
```

m: -598 to -500 nt upstream of the ATG start codon: 5 genes

YCL037C	SRO9	involved in actin filament organization

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

```
YIL161W		
```
```
YML034W		
```

YMR032W	HOF1	SH3 domain containing-protein

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

```
YAR018C	KIN3	protein kinase
```

YCL037C	SRO9	involved in actin filament organization

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

```
YKR021W		
```
```
YOL014W		
```
```
YOL069W	NUF2	53-kDa coiled-coil protein
```

YPL242C	IQG1	Similar to mammalian IQGAP proteins

m: -400 to -302 nt upstream of the ATG start codon: 5 genes

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

YGR092W	DBF2	Serine/threonine protein kinase

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

```
YMR031C		
```
```
YOR229W	WTM2	Transcriptional modulator
```

m: -301 to -203 nt upstream of the ATG start codon: 5 genes

```
YBR138C	HDR1	Unknown
```
```
YDL048C	STP4	involved in tRNA splicing
```
```
YJL051W		
```

YJR092W	BUD4	involved in bud site selection

YMR032W	HOF1	SH3 domain containing-protein

m: -202 to -104 nt upstream of the ATG start codon: 5 genes

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

```
YJL051W		
```

YNL053W	MSG5	Dual-specificity protein tyrosine phosphatase

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

m: -103 to -5 nt upstream of the ATG start codon: 7 genes

YAL022C	FUN26	predicted membrane protein

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

```
YIL161W		
```

YIL162W	SUC2	invertase (sucrose hydrolyzing enzyme)

```
YMR031C		
```
```
YOL070C		
```
```
YOR315W		
```

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