-551 to -600 nt upstream of the ATG start codon
4 elements found in 4 genes

• YGL028C	SCW11	soluble cell wall protein

• YHR113W		Vacuolar aminopeptidase

• YLR381W		

• YMR199W	CLN1	G(sub)1 cyclin

-501 to -550 nt upstream of the ATG start codon
6 elements found in 4 genes

• YHR154W	ESC4	involved in silencing

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

• YLL022C	HIF1	interacts with histone acetyltransferase

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

-451 to -500 nt upstream of the ATG start codon
5 elements found in 4 genes

• YDL010W		

• YER070W	RNR1	ribonucleotide reductase

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

• YML027W	YOX1	Homeobox-domain containing protein

-401 to -450 nt upstream of the ATG start codon
7 elements found in 6 genes

• YDR297W	SUR2	Syringomycin response protein 2

• YER070W	RNR1	ribonucleotide reductase

• YGR109C	CLB6	B-type cyclin

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

• YNL300W		

• YPR175W	DPB2	DNA polymerase epsilon, subunit B

-351 to -400 nt upstream of the ATG start codon
10 elements found in 9 genes

• YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

• YDL127W	PCL2	G1 cyclin

• YDR309C	GIC2	Cdc42 binding protein, involved in bud emergence

• YER070W	RNR1	ribonucleotide reductase

• YGR109C	CLB6	B-type cyclin

• YJL196C	ELO1	Elongation enzyme 1

• YLR382C	NAM2	mitochondrial leucyl tRNA synthetase

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

• YPR120C	CLB5	B-type cyclin

-301 to -350 nt upstream of the ATG start codon
9 elements found in 9 genes

• YBR071W		

• YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

• YDR297W	SUR2	Syringomycin response protein 2

• YDR507C	GIN4	putative serine/threonine kinase

• YER070W	RNR1	ribonucleotide reductase

• YJL196C	ELO1	Elongation enzyme 1

• YKR077W		

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

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

-251 to -300 nt upstream of the ATG start codon
11 elements found in 9 genes

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

• YBR071W		

• YDL003W	MCD1	involved in mitosis, similar to pombe Rad21

• YGR152C	RSR1	GTP-binding protein, ras superfamily

• YMR179W	SPT21	non-specific DNA binding protein

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

• YOR317W	FAA1	long chain fatty acyl:CoA synthetase

• YPL014W		

• YPL153C	RAD53	protein kinase, Mec1p and Tel1p regulate rad53p phosphorylation

-201 to -250 nt upstream of the ATG start codon
10 elements found in 8 genes

• YBL035C	POL12	B subunit of DNA polymerase alpha-primase complex

• YDL018C	ERP3	p24 protein involved in membrane trafficking

• YKL042W	SPC42	component of the spindle pole body

• YML061C	PIF1	5' to 3' DNA helicase

• YMR179W	SPT21	non-specific DNA binding protein

• YNL102W	POL1	DNA polymerase I alpha subunit, p180

• YNL310C		

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

-151 to -200 nt upstream of the ATG start codon
34 elements found in 26 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

• 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

• YCL024W		Ser/Thr protein kinase

• YDL010W		

• YDL018C	ERP3	p24 protein involved in membrane trafficking

• YDL101C	DUN1	protein kinase

• 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

• YHR154W	ESC4	involved in silencing

• YJL181W		

• YJL196C	ELO1	Elongation enzyme 1

• YKL045W	PRI2	p58 polypeptide of DNA primase

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

• YKR077W		

• YLR032W	RAD5	putative ATPase/DNA helicase

• YLR103C	CDC45	omosomal DNA replication initiation protein

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

• YLR383W	RHC18	involved in recombination repair

• YNL102W	POL1	DNA polymerase I alpha subunit, p180

• YNL273W	TOF1	Interacts with topoisomerase I

• YOL017W		

• YOR074C	CDC21	Thymidylate synthase

• YPL127C	HHO1	histone H1

• YPL209C	IPL1	Protein kinase

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

-101 to -150 nt upstream of the ATG start codon
40 elements found in 34 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

• YDL018C	ERP3	p24 protein involved in membrane trafficking

• YDL103C	QRI1	UDP-N-acetylglucosamine pyrophosphorylase

• YDL105W	QRI2	

• YDL164C	CDC9	DNA ligase

• YFL008W	SMC1	omosome segregation protein

• YGL027C	CWH41	glucosidase I

• YHR110W	ERP5	p24 protein involved in membrane trafficking

• YHR153C	SPO16	sporulation protein

• YHR154W	ESC4	involved in silencing

• YIL026C	IRR1	involved in cell morphology

• YIL159W	BNR1	involved in actin filament organization

• YJL074C	SMC3	involved in sister chromatid cohesion

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

• YKL045W	PRI2	p58 polypeptide of DNA primase

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

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

• YLL002W	KIM2	diepoxybutane and mitomycin C resistance

• YLR032W	RAD5	putative ATPase/DNA helicase

• 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

• YLR457C	NBP1	Nap1p binding protein

• YMR078C	CTF18	(putative) involved in chromosome transmission during mitosis

• YNL225C	CNM67	Spindle pole body protein involved in nuclear migration

• YNL262W	POL2	DNA polymerase II

• 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

• YOR074C	CDC21	Thymidylate synthase

• YOR144C		

• YPL267W		

• YPR174C		

• YPR175W	DPB2	DNA polymerase epsilon, subunit B

-51 to -100 nt upstream of the ATG start codon
5 elements found in 5 genes

• YDR383C		

• YLL022C	HIF1	interacts with histone acetyltransferase

• YML021C	UNG1	uracil DNA glycosylase

• YPL208W		

• YPL241C	CIN2	involved in microtubule function

-1 to -50 nt upstream of the ATG start codon
2 elements found in 2 genes

• 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

• YNL310C