Positioning of AATAA

From Table IVb: Position-dependent pentamers: Clustered pentamers
AATAA
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
21 elements found in 18 genes

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

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

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

YFL008W	SMC1	omosome segregation protein

```
YHR154W	ESC4	involved in silencing
```

YIL159W	BNR1	involved in actin filament organization

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

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
```
```
YCL061C		
```

-501 to -550 nt upstream of the ATG start codon
15 elements found in 15 genes

```
YBR071W		
```
```
YHR153C	SPO16	sporulation protein
```

YIL026C	IRR1	involved in cell morphology

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

YLR032W	RAD5	putative ATPase/DNA helicase

YLR233C	EST1	involved in telomere length regulation

```
YLR286C	CTS1	Endochitinase
```

YML027W	YOX1	Homeobox-domain containing protein

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

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

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

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

YDL227C	HO	Homothallic switching endonuclease

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

YHR110W	ERP5	p24 protein involved in membrane trafficking

YIL159W	BNR1	involved in actin filament organization

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

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

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
```

-401 to -450 nt upstream of the ATG start codon
14 elements found in 12 genes

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

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDL127W	PCL2	G1 cyclin
```
```
YDR383C		
```
```
YGL089C	MF(ALPHA)2	alpha mating factor
```
```
YHR154W	ESC4	involved in silencing
```

YKL045W	PRI2	p58 polypeptide of DNA primase

YLL022C	HIF1	interacts with histone acetyltransferase

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

YNL272C	SEC2	GDP/GTP exchange factor for Sec4p

-351 to -400 nt upstream of the ATG start codon
11 elements found in 11 genes

```
YAR003W		beta transducin domain
```
```
YBR070C		involved in osmotolerance
```
```
YDL101C	DUN1	protein kinase
```

YDR297W	SUR2	Syringomycin response protein 2

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

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

YJL074C	SMC3	involved in sister chromatid cohesion

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

```
YLR457C	NBP1	Nap1p binding protein
```

YNL102W	POL1	DNA polymerase I alpha subunit, p180

```
YPL209C	IPL1	Protein kinase
```

-301 to -350 nt upstream of the ATG start codon
16 elements found in 14 genes

YBR073W	RDH54	Putative helicase similar to RAD54

```
YCL022C		
```

YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

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

```
YHR039C		Aldehyde dehydrogenases
```

YIL159W	BNR1	involved in actin filament organization

YLR103C	CDC45	omosomal DNA replication initiation protein

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

```
YCL061C		
```

-251 to -300 nt upstream of the ATG start codon
20 elements found in 17 genes

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

YFL008W	SMC1	omosome segregation protein

YIL159W	BNR1	involved in actin filament organization

YLR103C	CDC45	omosomal DNA replication initiation protein

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

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

-201 to -250 nt upstream of the ATG start codon
22 elements found in 21 genes

YBR252W	DUT1	dUTP pyrophosphatase (dUTPase)

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

```
YHR153C	SPO16	sporulation protein
```
```
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

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

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

```
YNL300W		
```
```
YPL127C	HHO1	histone H1
```

-151 to -200 nt upstream of the ATG start codon
21 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

YBL035C	POL12	B subunit of DNA polymerase alpha-primase complex

```
YCL022C		
```
```
YER070W	RNR1	ribonucleotide reductase
```

YKL042W	SPC42	component of the spindle pole body

YKL165C	MCD4	(putative) involved in cell polarity

YLL002W	KIM2	diepoxybutane and mitomycin C resistance

YLR103C	CDC45	omosomal DNA replication initiation protein

```
YLR286C	CTS1	Endochitinase
```

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

```
YLR457C	NBP1	Nap1p binding protein
```

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

YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

```
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		
```

-101 to -150 nt upstream of the ATG start codon
26 elements found in 25 genes

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

YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

```
YDL156W		
```
```
YDR493W		
```
```
YER070W	RNR1	ribonucleotide reductase
```

YFL008W	SMC1	omosome segregation protein

```
YGL028C	SCW11	soluble cell wall protein
```
```
YGR109C	CLB6	B-type cyclin
```

YGR152C	RSR1	GTP-binding protein, ras superfamily

```
YHR154W	ESC4	involved in silencing
```

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

```
YKR083C		
```

YLR103C	CDC45	omosomal DNA replication initiation protein

YLR121C	YPS4	GPI-anchored aspartic protease

```
YLR286C	CTS1	Endochitinase
```

YNL173C	MDG1	Involved in G-protein mediated signal transduction

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

YNL272C	SEC2	GDP/GTP exchange factor for Sec4p

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

YPL241C	CIN2	involved in microtubule function

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

```
YPR174C		
```
```
YLR236C		
```
```
YCL061C		
```

-51 to -100 nt upstream of the ATG start codon
50 elements found in 41 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

```
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

YDR507C	GIN4	putative serine/threonine kinase

```
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
```
```
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

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

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
```
```
YLR286C	CTS1	Endochitinase
```
```
YLR326W		
```

YLR383W	RHC18	involved in recombination repair

YMR078C	CTF18	(putative) involved in chromosome transmission during mitosis

```
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

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

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

YPL124W	NIP29	spindle pole body associated protein

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

YPR175W	DPB2	DNA polymerase epsilon, subunit B

-1 to -50 nt upstream of the ATG start codon
43 elements found in 34 genes

YBR073W	RDH54	Putative helicase similar to RAD54

YBR252W	DUT1	dUTP pyrophosphatase (dUTPase)

```
YCL022C		
```
```
YDR493W		
```

YDR507C	GIN4	putative serine/threonine kinase

```
YGL027C	CWH41	glucosidase I
```

YHR038W	FIL1	Putative mitochondrial ribosome recycling factor

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

YIL026C	IRR1	involved in cell morphology

YKL045W	PRI2	p58 polypeptide of DNA primase

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

YOR317W	FAA1	long chain fatty acyl:CoA synthetase

```
YPL267W		
```

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

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

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