Positioning of ATAAA

From Table IVb: Position-dependent pentamers: Clustered pentamers
ATAAA
is found in the upstream regions of these late_g1 yeast genes in the following intervals:

-551 to -600 nt upstream of the ATG start codon
13 elements found in 12 genes

```
YDR493W		
```

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

```
YHR113W		Vacuolar aminopeptidase
```

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

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

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

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

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

```
YLR349W		
```

-501 to -550 nt upstream of the ATG start codon
14 elements found in 12 genes

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

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

```
YHR153C	SPO16	sporulation protein
```

YKL042W	SPC42	component of the spindle pole body

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.-)

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

```
YLR234W	TOP3	DNA Topoisomerase III
```
```
YPL187W	MF(ALPHA)1	mating factor alpha
```
```
YCL061C		
```

-451 to -500 nt upstream of the ATG start codon
22 elements found in 19 genes

```
YBR089W		
```
```
YDL127W	PCL2	G1 cyclin
```

YDL227C	HO	Homothallic switching endonuclease

```
YDR383C		
```

YDR507C	GIN4	putative serine/threonine kinase

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

YGR152C	RSR1	GTP-binding protein, ras superfamily

```
YJL196C	ELO1	Elongation enzyme 1
```

YKL042W	SPC42	component of the spindle pole body

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

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

YNL273W	TOF1	Interacts with topoisomerase I

```
YOL017W		
```

YPL153C	RAD53	protein kinase, Mec1p and Tel1p regulate rad53p phosphorylation

```
YPL187W	MF(ALPHA)1	mating factor alpha
```
```
YPL267W		
```
```
YLR236C		
```

-401 to -450 nt upstream of the ATG start codon
13 elements found in 13 genes

```
YBR071W		
```

YBR252W	DUT1	dUTP pyrophosphatase (dUTPase)

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
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

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

YKL045W	PRI2	p58 polypeptide of DNA primase

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

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

YNL272C	SEC2	GDP/GTP exchange factor for Sec4p

```
YOL017W		
```

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

-351 to -400 nt upstream of the ATG start codon
15 elements found in 15 genes

```
YBR070C		involved in osmotolerance
```

YDL018C	ERP3	p24 protein involved in membrane trafficking

```
YDR383C		
```
```
YGL027C	CWH41	glucosidase I
```
```
YGL028C	SCW11	soluble cell wall protein
```

YGR041W	BUD9	involved in bud-site selection

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

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

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

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

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

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

YNL102W	POL1	DNA polymerase I alpha subunit, p180

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

```
YPR174C		
```

-301 to -350 nt upstream of the ATG start codon
25 elements found in 22 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		
```

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		
```

YFL008W	SMC1	omosome segregation protein

```
YGL089C	MF(ALPHA)2	alpha mating factor
```
```
YHR039C		Aldehyde dehydrogenases
```
```
YHR113W		Vacuolar aminopeptidase
```

YJL173C	RFA3	subunit 3 of replication factor-A

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

YLR103C	CDC45	omosomal DNA replication initiation protein

```
YLR286C	CTS1	Endochitinase
```

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

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

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

YNL102W	POL1	DNA polymerase I alpha subunit, p180

YNL173C	MDG1	Involved in G-protein mediated signal transduction

```
YPL209C	IPL1	Protein kinase
```
```
YPR174C		
```
```
YCL061C		
```

-251 to -300 nt upstream of the ATG start codon
20 elements found in 20 genes

YBR073W	RDH54	Putative helicase similar to RAD54

YDL018C	ERP3	p24 protein involved in membrane trafficking

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YHR039C		Aldehyde dehydrogenases
```

YIL159W	BNR1	involved in actin filament organization

```
YJL181W		
```

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

YLR032W	RAD5	putative ATPase/DNA helicase

YLR103C	CDC45	omosomal DNA replication initiation protein

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

YMR078C	CTF18	(putative) involved in chromosome transmission during mitosis

YMR179W	SPT21	non-specific DNA binding protein

```
YNL262W	POL2	DNA polymerase II
```
```
YOL017W		
```

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

```
YOR074C	CDC21	Thymidylate synthase
```

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		
```

-201 to -250 nt upstream of the ATG start codon
16 elements found in 14 genes

```
YDL101C	DUN1	protein kinase
```

YDL227C	HO	Homothallic switching endonuclease

```
YDR383C		
```

YKL042W	SPC42	component of the spindle pole body

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

YLL022C	HIF1	interacts with histone acetyltransferase

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

```
YML021C	UNG1	uracil DNA glycosylase
```

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

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

```
YNL300W		
```
```
YOL017W		
```

YPL241C	CIN2	involved in microtubule function

```
YPR174C		
```

-151 to -200 nt upstream of the ATG start codon
25 elements found in 19 genes

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

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		
```

YFL008W	SMC1	omosome segregation protein

YHR110W	ERP5	p24 protein involved in membrane trafficking

YKL042W	SPC42	component of the spindle pole body

YLR032W	RAD5	putative ATPase/DNA helicase

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

```
YLR381W		
```
```
YML061C	PIF1	5' to 3' DNA helicase
```

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

```
YNL300W		
```
```
YOL017W		
```
```
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

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

-101 to -150 nt upstream of the ATG start codon
31 elements found in 27 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

```
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		
```

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDL105W	QRI2	
```

YDL227C	HO	Homothallic switching endonuclease

YDR297W	SUR2	Syringomycin response protein 2

```
YER070W	RNR1	ribonucleotide reductase
```
```
YGL089C	MF(ALPHA)2	alpha mating factor
```
```
YHR154W	ESC4	involved in silencing
```

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

```
YKR083C		
```

YLR032W	RAD5	putative ATPase/DNA helicase

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

YNL173C	MDG1	Involved in G-protein mediated signal transduction

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

```
YOR144C		
```
```
YPL014W		
```
```
YPL209C	IPL1	Protein kinase
```

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

```
YLR236C		
```

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

```
YCL061C		
```

-51 to -100 nt upstream of the ATG start codon
44 elements found in 40 genes

```
YAR003W		beta transducin domain
```

YBL035C	POL12	B subunit of DNA polymerase alpha-primase complex

```
YBR071W		
```

YBR073W	RDH54	Putative helicase similar to RAD54

```
YBR089W		
```

YBR252W	DUT1	dUTP pyrophosphatase (dUTPase)

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

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

```
YDL105W	QRI2	
```
```
YDL127W	PCL2	G1 cyclin
```
```
YDL156W		
```
```
YDL164C	CDC9	DNA ligase
```
```
YDR383C		
```

YFL008W	SMC1	omosome segregation protein

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

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

```
YHR154W	ESC4	involved in silencing
```

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

YJL173C	RFA3	subunit 3 of replication factor-A

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

YJR148W	BAT2	Branched-Chain Amino Acid Transaminase

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

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

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

```
YLR234W	TOP3	DNA Topoisomerase III
```

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

```
YLR326W		
```

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

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

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

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

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

YPL124W	NIP29	spindle pole body associated protein

```
YPL209C	IPL1	Protein kinase
```
```
YPL267W		
```

YPR175W	DPB2	DNA polymerase epsilon, subunit B

-1 to -50 nt upstream of the ATG start codon
32 elements found in 27 genes

YBR073W	RDH54	Putative helicase similar to RAD54

YBR278W	DPB3	C and C' subunits of DNA polymerase II

```
YCL022C		
```

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDR013W		
```
```
YDR493W		
```

YFL008W	SMC1	omosome segregation protein

```
YHR113W		Vacuolar aminopeptidase
```
```
YHR153C	SPO16	sporulation protein
```

YIL026C	IRR1	involved in cell morphology

YIL159W	BNR1	involved in actin filament organization

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

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

YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

YLR383W	RHC18	involved in recombination repair

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

YNL102W	POL1	DNA polymerase I alpha subunit, p180

YNL272C	SEC2	GDP/GTP exchange factor for Sec4p

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

```
YOR074C	CDC21	Thymidylate synthase
```

YOR317W	FAA1	long chain fatty acyl:CoA synthetase

```
YPL187W	MF(ALPHA)1	mating factor alpha
```
```
YPL267W		
```

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

From Table IVb: Position-dependent pentamers: Clustered pentamers ATAAA is found in the upstream regions of these late_g1 yeast genes in the following intervals:

From Table IVb: Position-dependent pentamers: Clustered pentamers
ATAAA
is found in the upstream regions of these late_g1 yeast genes in the following intervals: