Position dependent GCGAA

From Table IIa: Position-dependent, orientation-independent pentamers
GCGAA and/or TTCGC
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: 4 genes

```
YHL026C		
```
```
YIL009W	FAA3	Acyl CoA synthase
```

YLR079W	SIC1	Cdc28p-Clb5 protein kinase inhibitor

YNR001C	CIT1	citrate synthase. Nuclear encoded mitochondrial protein.

early_g1: -499 to -401 nt upstream of the ATG start codon: 5 genes

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

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

YNR001C	CIT1	citrate synthase. Nuclear encoded mitochondrial protein.

YPL058C	PDR12	multidrug resistance transporter

early_g1: -400 to -302 nt upstream of the ATG start codon: 5 genes

```
YBR157C		
```

YEL032W	MCM3	component of DNA replication initiator complex

YGL055W	OLE1	delta-9-fatty acid desaturase

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

```
YMR007W		
```

early_g1: -301 to -203 nt upstream of the ATG start codon: 14 genes

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

```
YDL181W	INH1	ATPase inhibitor
```
```
YDR033W		
```

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

```
YGR281W	YOR1	ABC transporter
```
```
YIL009W	FAA3	Acyl CoA synthase
```
```
YJL157C	FAR1	Cdc28p kinase inhibitor
```

YKL163W	PIR3	Protein containing tandem internal repeats

YLL040C	VPS13	component of peripheral vacuolar membrane protein complex

```
YLR049C		
```
```
YLR050C		
```
```
YOR264W		
```
```
YPL004C		
```
```
YPL158C		
```

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

```
YBR200W	BEM1	contains two SH3 domains
```
```
YBR231C		
```
```
YDR511W		
```
```
YLR049C		
```

YLR079W	SIC1	Cdc28p-Clb5 protein kinase inhibitor

YLR274W	CDC46	MCM initiator complex protein

```
YNL046W		
```

YPR019W	CDC54	Involved in initiation of DNA replication

early_g1: -103 to -5 nt upstream of the ATG start codon: 1 genes

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

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

```
YBR070C		involved in osmotolerance
```
```
YDL127W	PCL2	G1 cyclin
```

YDL227C	HO	Homothallic switching endonuclease

```
YDR383C		
```

YGR041W	BUD9	involved in bud-site selection

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

```
YJL187C	SWE1	protein kinase homolog
```

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

```
YLR326W		
```
```
YMR199W	CLN1	G(sub)1 cyclin
```
```
YNL262W	POL2	DNA polymerase II
```

YNL309W	STB1	Interacts with the putative transcription factor Sin3p

```
YPL014W		
```

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

YPL124W	NIP29	spindle pole body associated protein

YPL153C	RAD53	protein kinase, Mec1p and Tel1p regulate rad53p phosphorylation

```
YPL209C	IPL1	Protein kinase
```

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: 21 genes

YBR278W	DPB3	C and C' subunits of DNA polymerase II

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
YDL124W		
```
```
YDL164C	CDC9	DNA ligase
```
```
YGL027C	CWH41	glucosidase I
```
```
YGL028C	SCW11	soluble cell wall protein
```

YGR152C	RSR1	GTP-binding protein, ras superfamily

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

YJL173C	RFA3	subunit 3 of replication factor-A

```
YJL187C	SWE1	protein kinase homolog
```

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

YLR233C	EST1	involved in telomere length regulation

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

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

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

```
YNL303W		
```
```
YPL209C	IPL1	Protein kinase
```
```
YPL256C	CLN2	G(sub)1 cyclin
```

late_g1: -400 to -302 nt upstream of the ATG start codon: 22 genes

```
YBR070C		involved in osmotolerance
```
```
YBR071W		
```

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
YDL127W	PCL2	G1 cyclin
```

YDL227C	HO	Homothallic switching endonuclease

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

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

```
YHR154W	ESC4	involved in silencing
```
```
YJL187C	SWE1	protein kinase homolog
```

YKL042W	SPC42	component of the spindle pole body

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

YLR383W	RHC18	involved in recombination repair

YML027W	YOX1	Homeobox-domain containing protein

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

```
YNL300W		
```
```
YNL310C		
```

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

```
YOR074C	CDC21	Thymidylate synthase
```
```
YPL014W		
```
```
YPL208W		
```
```
YPL256C	CLN2	G(sub)1 cyclin
```

YPR175W	DPB2	DNA polymerase epsilon, subunit B

late_g1: -301 to -203 nt upstream of the ATG start codon: 22 genes

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

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

```
YDL010W		
```
```
YDR013W		
```

YDR507C	GIN4	putative serine/threonine kinase

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

YGR152C	RSR1	GTP-binding protein, ras superfamily

```
YJL187C	SWE1	protein kinase homolog
```

YKL042W	SPC42	component of the spindle pole body

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

YLR103C	CDC45	omosomal DNA replication initiation protein

YLR121C	YPS4	GPI-anchored aspartic protease

```
YLR183C		
```

YLR233C	EST1	involved in telomere length regulation

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

YML027W	YOX1	Homeobox-domain containing protein

YNL173C	MDG1	Involved in G-protein mediated signal transduction

YNL273W	TOF1	Interacts with topoisomerase I

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

YOR317W	FAA1	long chain fatty acyl:CoA synthetase

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

late_g1: -202 to -104 nt upstream of the ATG start codon: 46 genes

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

```
YBR089W		
```
```
YCL024W		Ser/Thr protein kinase
```
```
YDL010W		
```

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDL164C	CDC9	DNA ligase
```

YDR309C	GIC2	Cdc42 binding protein, involved in bud emergence

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

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

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

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

YIL159W	BNR1	involved in actin filament organization

```
YJL181W		
```

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

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

YKL165C	MCD4	(putative) involved in cell polarity

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

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

YLR121C	YPS4	GPI-anchored aspartic protease

YLR233C	EST1	involved in telomere length regulation

```
YLR234W	TOP3	DNA Topoisomerase III
```
```
YLR376C		
```
```
YLR381W		
```

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

```
YLR457C	NBP1	Nap1p binding protein
```

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

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

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

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

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

```
YOR144C		
```

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

```
YPL127C	HHO1	histone H1
```
```
YPL267W		
```

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

```
YPR174C		
```

YPR175W	DPB2	DNA polymerase epsilon, subunit B

late_g1: -103 to -5 nt upstream of the ATG start codon: 28 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

YBR278W	DPB3	C and C' subunits of DNA polymerase II

```
YDR013W		
```

YDR309C	GIC2	Cdc42 binding protein, involved in bud emergence

```
YDR383C		
```

YDR507C	GIN4	putative serine/threonine kinase

```
YGL027C	CWH41	glucosidase I
```

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
```
```
YLR376C		
```
```
YLR381W		
```

YLR383W	RHC18	involved in recombination repair

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

YNL309W	STB1	Interacts with the putative transcription factor Sin3p

```
YNL310C		
```
```
YOR144C		
```
```
YPL014W		
```

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

YPL241C	CIN2	involved in microtubule function

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

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: 8 genes

YAR008W	SEN34	34kDa subunit of the tetrameric tRNA splicing endonuclease

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

YDR488C	PAC11	similar to rat dynein intermediate chain

```
YFR038W		
```
```
YJL118W		
```

YJR155W	AAD10	Hypothetical aryl-alcohol dehydrogenase (AAD)

YLL061W	MMP1	High affinity S-methylmethionine permease

```
YOL019W		
```

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

```
YBR156C		
```
```
YDR219C		
```

YDR488C	PAC11	similar to rat dynein intermediate chain

YER001W	MNN1	Alpha-1,3-mannosyltransferase

YFR027W	ECO1	involved in establishment of cohesion between sister chromatids

```
YJL115W	ASF1	involved in silencing
```

YJR006W	HYS2	DNA polymerase delta 55 KD subunit

YJR155W	AAD10	Hypothetical aryl-alcohol dehydrogenase (AAD)

YLL061W	MMP1	High affinity S-methylmethionine permease

```
YLL062C		
```

YMR190C	SGS1	has DNA helicase signature motifs

```
YOL019W		
```

s: -400 to -302 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)

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

YBR276C	PPS1	dual specificity protein phosphatase

YCR065W	HCM1	Transcription factor (fork head domain)

YER003C	PMI40	mannose-6-phosphate isomerase

```
YFR038W		
```

YIL126W	STH1	helicase related protein, snf2 homolog

YIL140W	SRO4	localizes to the plasma membrane

YLR045C	STU2	spindle pole body component

YMR190C	SGS1	has DNA helicase signature motifs

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

s: -301 to -203 nt upstream of the ATG start codon: 8 genes

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

YFR027W	ECO1	involved in establishment of cohesion between sister chromatids

YHR061C	GIC1	interacts with GTPase, involved in bud emergence

YKL067W	YNK1	Nucleoside diphosphate kinase

```
YLL062C		
```
```
YLR151C		
```
```
YNL176C		
```
```
YOR284W		
```

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

YAR008W	SEN34	34kDa subunit of the tetrameric tRNA splicing endonuclease

```
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

```
YDR179C		
```

YDR488C	PAC11	similar to rat dynein intermediate chain

YER001W	MNN1	Alpha-1,3-mannosyltransferase

YER003C	PMI40	mannose-6-phosphate isomerase

YFR027W	ECO1	involved in establishment of cohesion between sister chromatids

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

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

YNL073W	MSK1	mitochondrial lysine-tRNA synthetase

YPL016W	SWI1	Zinc-finger transcription factor

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

YAL001C	TFC3	transcription factor tau (TFIIIC) subunit 138

```
YBL063W	KIP1	kinesin related protein
```
```
YDR113C	PDS1	42-kDa nuclear protein
```

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

```
YEL017W		
```

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

YER016W	BIM1	microtubule-binding protein

YGR140W	CBF2	110 kDa subunit of the centromere binding factor CBF3

```
YJL118W		
```

YJR006W	HYS2	DNA polymerase delta 55 KD subunit

YLR228C	ECM22	involved in cell wall biogenesis (putative)

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

YNL073W	MSK1	mitochondrial lysine-tRNA synthetase

```
YNL176C		
```

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

YOR026W	BUB3	cell cycle checkpoint protein

g2: -598 to -500 nt upstream of the ATG start codon: 8 genes

```
YCL063W		
```

YDR464W	SPP41	negative regulator of prp genes

```
YKL052C		
```
```
YLL046C	RNP1	ribonucleoprotein 1
```
```
YOR273C		
```

YOR274W	MOD5	transfer RNA isopentenyl transferase

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

g2: -499 to -401 nt upstream of the ATG start codon: 6 genes

```
YCR073C	SSK22	protein kinase
```
```
YIL050W	PCL7	PHO85 cyclin
```
```
YIL158W		
```

YIL169C		serine-, threonine-rich protein

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

```
YMR215W		
```

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

```
YCR085W		
```
```
YDR366C		
```

YDR389W	SAC7	GTPase activating protein (GAP) for RHO1

g2: -301 to -203 nt upstream of the ATG start codon: 11 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		
```

YDL198C	YHM1	(putative) mitochondrial carrier protein

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

```
YJL092W	HPR5	DNA helicase
```
```
YKL053W		
```
```
YLL047W		
```
```
YNR009W		
```

YOR274W	MOD5	transfer RNA isopentenyl transferase

g2: -202 to -104 nt upstream of the ATG start codon: 15 genes

```
YCL063W		
```
```
YCR073C	SSK22	protein kinase
```

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

```
YCR085W		
```

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

```
YIL158W		
```
```
YJL092W	HPR5	DNA helicase
```

YKL068W	NUP100	Nuclear pore complex protein homologous to Nup116p

```
YLR015W		
```
```
YMR215W		
```
```
YNR009W		
```

YOR188W	MSB1	involved in polarized growth

```
YOR273C		
```

YOR274W	MOD5	transfer RNA isopentenyl transferase

```
YPL264C		
```

g2: -103 to -5 nt upstream of the ATG start codon: 6 genes

```
YCL063W		
```

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

```
YCR086W		
```
```
YLL047W		
```

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

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

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

YCR042C	TSM1	TATA binding protein-associated factor (TAF)

```
YDR146C	SWI5	transcriptional activator
```

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.

YIL162W	SUC2	invertase (sucrose hydrolyzing enzyme)

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

```
YKL129C	MYO3	myosin I
```

YLR353W	BUD8	involved in bud site selection

```
YNL058C		
```

m: -499 to -401 nt upstream of the ATG start codon: 5 genes

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.

```
YML119W		
```
```
YOL069W	NUF2	53-kDa coiled-coil protein
```
```
YOR229W	WTM2	Transcriptional modulator
```

m: -400 to -302 nt upstream of the ATG start codon: 7 genes

YGL201C	MCM6	component of MCM initiator complex involved in DNA replication

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

```
YHR151C		
```
```
YML033W		
```
```
YOR315W		
```

YPL242C	IQG1	Similar to mammalian IQGAP proteins

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

m: -301 to -203 nt upstream of the ATG start codon: 6 genes

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

YGL201C	MCM6	component of MCM initiator complex involved in DNA replication

YGR092W	DBF2	Serine/threonine protein kinase

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.

YPL242C	IQG1	Similar to mammalian IQGAP proteins

```
YPR157W		
```

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

```
YDL138W	RGT2	glucose permease
```
```
YHR151C		
```
```
YKR021W		
```

YLR353W	BUD8	involved in bud site selection

```
YOR315W		
```

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

YGL201C	MCM6	component of MCM initiator complex involved in DNA replication

```
YHR023W	MYO1	Class II Myosin
```
```
YHR151C		
```

YIL162W	SUC2	invertase (sucrose hydrolyzing enzyme)

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

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