YLR307C-A	14.9764	CUP2	YLR307C-A||S000028525|Putative protein of unknown function
YHR053C	14.5341	CUP2	YHR053C|CUP1-1|S000001095|Metallothionein, binds copper and mediates resistance to high concentrations of copper and cadmium; locus is variably amplified in different strains, with two copies, CUP1-1 and CUP1-2, in the genomic sequence reference strain S288C
YHR055C	14.1982	CUP2	YHR055C|CUP1-2|S000001097|Metallothionein, binds copper and mediates resistance to high concentrations of copper and cadmium; locus is variably amplified in different strains, with two copies, CUP1-1 and CUP1-2, in the genomic sequence reference strain S288C
YAR053W	13.4239	CUP2	YAR053W||S000000085|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YMR107W	12.8341	CUP2	YMR107W|SPG4|S000004713|Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources
YIL057C	11.121	CUP2	YIL057C||S000001319|Putative protein of unknown function; expression induced under carbon limitation and repressed under high glucose
YHR054W-A	10.7197	CUP2	YHR054W-A||S000028648|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps CUP1-2
YJL089W	10.5306	CUP2	YJL089W|SIP4|S000003625|C6 zinc cluster transcriptional activator that binds to the carbon source-responsive element (CSRE) of gluconeogenic genes; involved in the positive regulation of gluconeogenesis; regulated by Snf1p protein kinase; localized to the nucleus
YAR060C	9.85996	CUP2	YAR060C||S000000086|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YMR244W	9.23545	CUP2	YMR244W||S000004858|Putative protein of unknown function
YCR005C	8.64052	CUP2	YCR005C|CIT2|S000000598|Citrate synthase, catalyzes the condensation of acetyl coenzyme A and oxaloacetate to form citrate, peroxisomal isozyme involved in glyoxylate cycle; expression is controlled by Rtg1p and Rtg2p transcription factors
YIL162W	8.32245	CUP2	YIL162W|SUC2|S000001424|Invertase, sucrose hydrolyzing enzyme; a secreted, glycosylated form is regulated by glucose repression, and an intracellular, nonglycosylated enzyme is produced constitutively
YFR053C	8.17581	CUP2	YFR053C|HXK1|S000001949|Hexokinase isoenzyme 1, a cytosolic protein that catalyzes phosphorylation of glucose during glucose metabolism; expression is highest during growth on non-glucose carbon sources; glucose-induced repression involves the hexokinase Hxk2p
YKL217W	8.17197	CUP2	YKL217W|JEN1|S000001700|Lactate transporter, required for uptake of lactate and pyruvate; phosphorylated; expression is derepressed by transcriptional activator Cat8p during respiratory growth, and repressed in the presence of glucose, fructose, and mannose
YHR212C	7.76524	CUP2	YHR212C||S000001255|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDL210W	7.71717	CUP2	YDL210W|UGA4|S000002369|Permease that serves as a gamma-aminobutyrate (GABA) transport protein involved in the utilization of GABA as a nitrogen source; catalyzes the transport of putrescine and delta-aminolevulinic acid (ALA); localized to the vacuolar membrane
YHR096C	7.50078	CUP2	YHR096C|HXT5|S000001138|Hexose transporter with moderate affinity for glucose, induced in the presence of non-fermentable carbon sources, induced by a decrease in growth rate, contains an extended N-terminal domain relative to other HXTs
YFL030W	6.98814	CUP2	YFL030W|AGX1|S000001864|Alanine:glyoxylate aminotransferase (AGT), catalyzes the synthesis of glycine from glyoxylate, which is one of three pathways for glycine biosynthesis in yeast; has similarity to mammalian and plant alanine:glyoxylate aminotransferases
YPR007C	6.67651	CUP2	YPR007C|REC8|S000006211|Meiosis-specific component of sister chromatid cohesion complex; maintains cohesion between sister chromatids during meiosis I; maintains cohesion between centromeres of sister chromatids until meiosis II; homolog of S. pombe Rec8p
YHR054C	6.5699	CUP2	YHR054C||S000001096|Putative protein of unknown function
YJR095W	6.4178	CUP2	YJR095W|SFC1|S000003856|Mitochondrial succinate-fumarate transporter, transports succinate into and fumarate out of the mitochondrion; required for ethanol and acetate utilization
YCR007C	6.37664	CUP2	YCR007C||S000000600|Putative integral membrane protein, member of DUP240 gene family; YCR007C is not an essential gene
YBR117C	6.24212	CUP2	YBR117C|TKL2|S000000321|Transketolase, similar to Tkl1p; catalyzes conversion of xylulose-5-phosphate and ribose-5-phosphate to sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate in the pentose phosphate pathway; needed for synthesis of aromatic amino acids
YKL031W	6.10634	CUP2	YKL031W||S000001514|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species
YHR212W-A	5.98313	CUP2	YHR212W-A||S000028650|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YKL103C	5.8944	CUP2	YKL103C|LAP4|S000001586|Vacuolar aminopeptidase, often used as a marker protein in studies of autophagy and cytosol to vacuole targeting (CVT) pathway
YKL102C	5.2803	CUP2	YKL102C||S000001585|Dubious open reading frame unlikely to encode a functional protein; deletion confers sensitivity to citric acid; predicted protein would include a thiol-disulfide oxidoreductase active site
YFL011W	5.11912	CUP2	YFL011W|HXT10|S000001883|Putative hexose transporter, expressed at low levels and expression is repressed by glucose
YJR150C	5.11889	CUP2	YJR150C|DAN1|S000003911|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YNL117W	5.09066	CUP2	YNL117W|MLS1|S000005061|Malate synthase, enzyme of the glyoxylate cycle, involved in utilization of non-fermentable carbon sources; expression is subject to carbon catabolite repression; localizes in peroxisomes during growth in oleic acid medium
YNL144C	5.05629	CUP2	YNL144C||S000005088|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YNL144C is not an essential gene
YDR536W	5.02051	CUP2	YDR536W|STL1|S000002944|Glycerol proton symporter of the plasma membrane, subject to glucose-induced inactivation, strongly but transiently induced when cells are subjected to osmotic shock
YCL054W	4.98585	CUP2	YCL054W|SPB1|S000000559|AdoMet-dependent methyltransferase involved in rRNA processing and 60S ribosomal subunit maturation; methylates G2922 in the tRNA docking site of the large subunit rRNA and in the absence of snR52, U2921; suppressor of PAB1 mutants
YJL130C	4.80601	CUP2	YJL130C|URA2|S000003666|Bifunctional carbamoylphosphate synthetase (CPSase)-aspartate transcarbamylase (ATCase), catalyzes the first two enzymatic steps in the de novo biosynthesis of pyrimidines; both activities are subject to feedback inhibition by UTP
YPL240C	4.73792	CUP2	YPL240C|HSP82|S000006161|Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p
YFL051C	4.50095	CUP2	YFL051C||S000001843|Putative protein of unknown function; YFL051C is not an essential gene
YLR122C	4.42308	CUP2	YLR122C||S000004112|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YLR123C
YPL092W	4.41624	CUP2	YPL092W|SSU1|S000006013|Plasma membrane sulfite pump involved in sulfite metabolism and required for efficient sulfite efflux; major facilitator superfamily protein
YGL255W	4.41092	CUP2	YGL255W|ZRT1|S000003224|High-affinity zinc transporter of the plasma membrane, responsible for the majority of zinc uptake; transcription is induced under low-zinc conditions by the Zap1p transcription factor
YMR206W	4.34577	CUP2	YMR206W||S000004819|Putative protein of unknown function; YMR206W is not an essential gene
YCR021C	4.3087	CUP2	YCR021C|HSP30|S000000615|Hydrophobic plasma membrane localized, stress-responsive protein that negatively regulates the H(+)-ATPase Pma1p; induced by heat shock, ethanol treatment, weak organic acid, glucose limitation, and entry into stationary phase
YJR078W	4.27834	CUP2	YJR078W|BNA2|S000003839|Putative tryptophan 2,3-dioxygenase or indoleamine 2,3-dioxygenase, required for the de novo biosynthesis of NAD from tryptophan via kynurenine; expression regulated by Hst1p and Aft2p
YOR192C	4.10915	CUP2	YOR192C|THI72|S000005718|Transporter of thiamine or related compound; shares sequence similarity with Thi7p
YEL024W	4.10112	CUP2	YEL024W|RIP1|S000000750|Ubiquinol-cytochrome-c reductase, a Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex; transfers electrons from ubiquinol to cytochrome c1 during respiration
YBL043W	4.06916	CUP2	YBL043W|ECM13|S000000139|Non-essential protein of unknown function; induced by treatment with 8-methoxypsoralen and UVA irradiation
YJL037W	4.0052	CUP2	YJL037W|IRC18|S000003574|Putative protein of unknown function; expression induced in respiratory-deficient cells and in carbon-limited chemostat cultures; similar to adjacent ORF, YJL038C; null mutant displays increased levels of spontaneous Rad52p foci
YPR013C	3.9748	CUP2	YPR013C||S000006217|Putative zinc finger protein; YPR013C is not an essential gene
YAL062W	3.96692	CUP2	YAL062W|GDH3|S000000058|NADP(+)-dependent glutamate dehydrogenase, synthesizes glutamate from ammonia and alpha-ketoglutarate; rate of alpha-ketoglutarate utilization differs from Gdh1p; expression regulated by nitrogen and carbon sources
YAL039C	3.95262	CUP2	YAL039C|CYC3|S000000037|Cytochrome c heme lyase (holocytochrome c synthase), attaches heme to apo-cytochrome c (Cyc1p or Cyc7p) in the mitochondrial intermembrane space; human ortholog may have a role in microphthalmia with linear skin defects (MLS)
YOR192C-C	3.89995	CUP2	YOR192C-C||S000028857|Putative protein of unknown function; identified by expression profiling and mass spectrometry
YEL028W	3.84968	CUP2	YEL028W||S000000754|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR277C	3.79972	CUP2	YDR277C|MTH1|S000002685|Negative regulator of the glucose-sensing signal transduction pathway, required for repression of transcription by Rgt1p; interacts with Rgt1p and the Snf3p and Rgt2p glucose sensors; phosphorylated by Yck1p, triggering Mth1p degradation
YDR342C	3.78783	CUP2	YDR342C|HXT7|S000002750|High-affinity glucose transporter of the major facilitator superfamily, nearly identical to Hxt6p, expressed at high basal levels relative to other HXTs, expression repressed by high glucose levels
YIR039C	3.77479	CUP2	YIR039C|YPS6|S000001478|Putative GPI-anchored aspartic protease
YBR201C-A	3.71895	CUP2	YBR201C-A||S000087085|Putative protein of unknown function
YLR123C	3.69015	CUP2	YLR123C||S000004113|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YLR122C; contains characteristic aminoacyl-tRNA motif
YHR139C	3.67709	CUP2	YHR139C|SPS100|S000001181|Protein required for spore wall maturation; expressed during sporulation; may be a component of the spore wall
YOL052C-A	3.64986	CUP2	YOL052C-A|DDR2|S000005413|Multistress response protein, expression is activated by a variety of xenobiotic agents and environmental or physiological stresses
YMR103C	3.64461	CUP2	YMR103C||S000004709|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YIR027C	3.5877	CUP2	YIR027C|DAL1|S000001466|Allantoinase, converts allantoin to allantoate in the first step of allantoin degradation; expression sensitive to nitrogen catabolite repression
YPR010C-A	3.40004	CUP2	YPR010C-A||S000122558|Putative protein of unknown function; conserved among Saccharomyces sensu stricto species
YAR050W	3.39839	CUP2	YAR050W|FLO1|S000000084|Lectin-like protein involved in flocculation, cell wall protein that binds to mannose chains on the surface of other cells, confers floc-forming ability that is chymotrypsin sensitive and heat resistant; similar to Flo5p
YOR382W	3.39303	CUP2	YOR382W|FIT2|S000005909|Mannoprotein that is incorporated into the cell wall via a glycosylphosphatidylinositol (GPI) anchor, involved in the retention of siderophore-iron in the cell wall
YNL142W	3.39022	CUP2	YNL142W|MEP2|S000005086|Ammonium permease involved in regulation of pseudohyphal growth; belongs to a ubiquitous family of cytoplasmic membrane proteins that transport only ammonium (NH4+); expression is under the nitrogen catabolite repression regulation
YOR152C	3.34518	CUP2	YOR152C||S000005678|Putative protein of unknown function; has no similarity to any known protein; YOR152C is not an essential gene
YFL052W	3.34034	CUP2	YFL052W||S000001842|Putative zinc cluster protein that contains a DNA binding domain; null mutant sensitive to calcofluor white, low osmolarity and heat, suggesting a role for YFL052Wp in cell wall integrity
YDR034C	3.33741	CUP2	YDR034C|LYS14|S000002441|Transcriptional activator involved in regulation of genes of the lysine biosynthesis pathway; requires 2-aminoadipate semialdehyde as co-inducer
YKR097W	3.27853	CUP2	YKR097W|PCK1|S000001805|Phosphoenolpyruvate carboxykinase, key enzyme in gluconeogenesis, catalyzes early reaction in carbohydrate biosynthesis, glucose represses transcription and accelerates mRNA degradation, regulated by Mcm1p and Cat8p, located in the cytosol
YMR017W	3.27702	CUP2	YMR017W|SPO20|S000004619|Meiosis-specific subunit of the t-SNARE complex, required for prospore membrane formation during sporulation; similar to but not functionally redundant with Sec9p; SNAP-25 homolog
YAR035W	3.21438	CUP2	YAR035W|YAT1|S000000080|Outer mitochondrial carnitine acetyltransferase, minor ethanol-inducible enzyme involved in transport of activated acyl groups from the cytoplasm into the mitochondrial matrix; phosphorylated
YPL057C	3.16711	CUP2	YPL057C|SUR1|S000005978|Probable catalytic subunit of a mannosylinositol phosphorylceramide (MIPC) synthase, forms a complex with probable regulatory subunit Csg2p; function in sphingolipid biosynthesis is overlapping with that of Csh1p
YCL001W-B	3.16631	CUP2	YCL001W-B||S000007596|Putative protein of unknown function; identified by homology
YDR102C	3.11721	CUP2	YDR102C||S000002509|Dubious open reading frame; homozygous diploid deletion strain exhibits high budding index
YMR256C	3.09478	CUP2	YMR256C|COX7|S000004869|Subunit VII of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain
YIL077C	3.07963	CUP2	YIL077C||S000001339|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; deletion confers sensitivity to 4-(N-(S-glutathionylacetyl)amino) phenylarsenoxide (GSAO)
YBR296C	3.05764	CUP2	YBR296C|PHO89|S000000500|Na+/Pi cotransporter, active in early growth phase; similar to phosphate transporters of Neurospora crassa; transcription regulated by inorganic phosphate concentrations and Pho4p
YGR043C	3.05009	CUP2	YGR043C|NQM1|S000003275|Protein of unknown function; transcription is repressed by Mot1p and induced by alpha-factor and during diauxic shift; null mutant non-quiescent cells exhibit reduced reproductive capacity
YML089C	3.03156	CUP2	YML089C||S000004554|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data; expression induced by calcium shortage
YJR154W	3.02747	CUP2	YJR154W||S000003915|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YOR387C	3.02094	CUP2	YOR387C||S000005914|Putative protein of unknown function; regulated by the metal-responsive Aft1p transcription factor; highly inducible in zinc-depleted conditions; localizes to the soluble fraction
YHR048W	2.99564	CUP2	YHR048W|YHK8|S000001090|Presumed antiporter of the DHA1 family of multidrug resistance transporters; contains 12 predicted transmembrane spans; expression of gene is up-regulated in cells exhibiting reduced susceptibility to azoles
YOL154W	2.98251	CUP2	YOL154W|ZPS1|S000005514|Putative GPI-anchored protein; transcription is induced under low-zinc conditions, as mediated by the Zap1p transcription factor, and at alkaline pH
YLR307W	2.93906	CUP2	YLR307W|CDA1|S000004298|Chitin deacetylase, together with Cda2p involved in the biosynthesis ascospore wall component, chitosan; required for proper rigidity of the ascospore wall
YLR346C	2.93463	CUP2	YLR346C||S000004338|Putative protein of unknown function found in mitochondria; expression is regulated by transcription factors involved in pleiotropic drug resistance, Pdr1p and Yrr1p; YLR346C is not an essential gene
YEL059W	2.90097	CUP2	YEL059W||S000000785|Dubious open reading frame unlikely to encode a functional protein
YAR047C	2.86474	CUP2	YAR047C||S000000083|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YNL014W	2.85829	CUP2	YNL014W|HEF3|S000004959|Translational elongation factor EF-3; paralog of YEF3 and member of the ABC superfamily; stimulates EF-1 alpha-dependent binding of aminoacyl-tRNA by the ribosome; normally expressed in zinc deficient cells
YBR105C	2.85072	CUP2	YBR105C|VID24|S000000309|Peripheral membrane protein located at Vid (vacuole import and degradation) vesicles; regulates fructose-1,6-bisphosphatase (FBPase) targeting to the vacuole; involved in proteasome-dependent catabolite degradation of FBPase
YOR139C	2.81005	CUP2	YOR139C||S000005665|Hypothetical protein
YER065C	2.75673	CUP2	YER065C|ICL1|S000000867|Isocitrate lyase, catalyzes the formation of succinate and glyoxylate from isocitrate, a key reaction of the glyoxylate cycle; expression of ICL1 is induced by growth on ethanol and repressed by growth on glucose
YDR250C	2.73686	CUP2	YDR250C||S000002658|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data
YOR120W	2.71251	CUP2	YOR120W|GCY1|S000005646|Putative NADP(+) coupled glycerol dehydrogenase, proposed to be involved in an alternative pathway for glycerol catabolism; member of the aldo-keto reductase (AKR) family
YDR542W	2.6957	CUP2	YDR542W|PAU10|S000002950|Hypothetical protein
YKR102W	2.69342	CUP2	YKR102W|FLO10|S000001810|Lectin-like protein with similarity to Flo1p, thought to be involved in flocculation
YEL012W	2.67782	CUP2	YEL012W|UBC8|S000000738|Ubiquitin-conjugating enzyme that negatively regulates gluconeogenesis by mediating the glucose-induced ubiquitination of fructose-1,6-bisphosphatase (FBPase); cytoplasmic enzyme that catalyzes the ubiquitination of histones in vitro
YJL116C	2.65463	CUP2	YJL116C|NCA3|S000003652|Protein that functions with Nca2p to regulate mitochondrial expression of subunits 6 (Atp6p) and 8 (Atp8p ) of the Fo-F1 ATP synthase; member of the SUN family
YPR196W	2.64933	CUP2	YPR196W||S000006400|Putative maltose activator
YNR002C	2.63762	CUP2	YNR002C|ATO2|S000005285|Putative transmembrane protein involved in export of ammonia, a starvation signal that promotes cell death in aging colonies; phosphorylated in mitochondria; member of the TC 9.B.33 YaaH family; homolog of Ady2p and Y. lipolytica Gpr1p
YPL216W	2.62614	CUP2	YPL216W||S000006137|Putative protein of unknown function; YPL216W is not an essential gene
YDR216W	2.62137	CUP2	YDR216W|ADR1|S000002624|Carbon source-responsive zinc-finger transcription factor, required for transcription of the glucose-repressed gene ADH2, of peroxisomal protein genes, and of genes required for ethanol, glycerol, and fatty acid utilization
YPL054W	2.61796	CUP2	YPL054W|LEE1|S000005975|Zinc-finger protein of unknown function
YOR140W	2.61468	CUP2	YOR140W|SFL1|S000005666|Transcriptional repressor and activator; involved in repression of flocculation-related genes, and activation of stress responsive genes; negatively regulated by cAMP-dependent protein kinase A subunit Tpk2p
YLL053C	2.6036	CUP2	YLL053C||S000003976|Putative protein; in the Sigma 1278B strain background YLL053C is contiguous with AQY2 which encodes an aquaporin
YLR149C	2.57986	CUP2	YLR149C||S000004139|Putative protein of unknown function; YLR149C is not an essential gene
YMR034C	2.57817	CUP2	YMR034C||S000004637|Putative transporter, member of the SLC10 carrier family; identified in a transposon mutagenesis screen as a gene involved in azole resistance; YMR034C is not an essential gene
YMR280C	2.56544	CUP2	YMR280C|CAT8|S000004893|Zinc cluster transcriptional activator necessary for derepression of a variety of genes under non-fermentative growth conditions, active after diauxic shift, binds carbon source responsive elements
YDR251W	2.55944	CUP2	YDR251W|PAM1|S000002659|Essential protein of unknown function; exhibits variable expression during colony morphogenesis; overexpression permits survival without protein phosphatase 2A, inhibits growth, and induces a filamentous phenotype
YLR124W	2.52059	CUP2	YLR124W||S000004114|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR379C-A	2.50421	CUP2	YDR379C-A||S000007605|Hypothetical protein identified by homology. See FEBS Letters [2000] 487:31-36.
YLR311C	2.49294	CUP2	YLR311C||S000004302|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YHR033W	2.47811	CUP2	YHR033W||S000001075|Putative protein of unknown function; epitope-tagged protein localizes to the cytoplasm
YPL262W	2.4645	CUP2	YPL262W|FUM1|S000006183|Fumarase, converts fumaric acid to L-malic acid in the TCA cycle; cytosolic and mitochondrial localization determined by the N-terminal mitochondrial targeting sequence and protein conformation; phosphorylated in mitochondria
YIL113W	2.42976	CUP2	YIL113W|SDP1|S000001375|Stress-inducible dual-specificity MAP kinase phosphatase, negatively regulates Slt2p MAP kinase by direct dephosphorylation, diffuse localization under normal conditions shifts to punctate localization after heat shock
YMR096W	2.41019	CUP2	YMR096W|SNZ1|S000004702|Protein involved in vitamin B6 biosynthesis; member of a stationary phase-induced gene family; coregulated with SNO1; interacts with Sno1p and with Yhr198p, perhaps as a multiprotein complex containing other Snz and Sno proteins
YNL143C	2.40865	CUP2	YNL143C||S000005087|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YOR347C	2.40072	CUP2	YOR347C|PYK2|S000005874|Pyruvate kinase that appears to be modulated by phosphorylation; PYK2 transcription is repressed by glucose, and Pyk2p may be active under low glycolytic flux
YDR249C	2.37205	CUP2	YDR249C||S000002657|Putative protein of unknown function
YJL038C	2.36223	CUP2	YJL038C|LOH1|S000003575|Putative protein of unknown function; expression induced during sporulation and repressed during vegetative growth by Sum1p and Hst1p; similar to adjacent open reading frame, YJL037W
YCL038C	2.34555	CUP2	YCL038C|ATG22|S000000543|Vacuolar integral membrane protein required for efflux of amino acids during autophagic body breakdown in the vacuole; null mutation causes a gradual loss of viability during starvation
YEL070W	2.33492	CUP2	YEL070W|DSF1|S000000796|Deletion suppressor of mpt5 mutation
YEL008W	2.33166	CUP2	YEL008W||S000000734|Hypothetical protein predicted to be involved in metabolism
YLR125W	2.33038	CUP2	YLR125W||S000004115|Putative protein of unknown function; mutant has decreased Ty3 transposition; YLR125W is not an essential gene
YLL052C	2.32234	CUP2	YLL052C|AQY2|S000003975|Water channel that mediates the transport of water across cell membranes, only expressed in proliferating cells, controlled by osmotic signals, may be involved in freeze tolerance; disrupted by a stop codon in many S. cerevisiae strains
YLR136C	2.30856	CUP2	YLR136C|TIS11|S000004126|mRNA-binding protein expressed during iron starvation; binds to a sequence element in the 3'-untranslated regions of specific mRNAs to mediate their degradation; involved in iron homeostasis
YER150W	2.30553	CUP2	YER150W|SPI1|S000000952|GPI-anchored cell wall protein involved in weak acid resistance; basal expression requires Msn2p/Msn4p; expression is induced under conditions of stress and during the diauxic shift; similar to Sed1p
YGR256W	2.28773	CUP2	YGR256W|GND2|S000003488|6-phosphogluconate dehydrogenase (decarboxylating), catalyzes an NADPH regenerating reaction in the pentose phosphate pathway; required for growth on D-glucono-delta-lactone
YEL009C	2.28656	CUP2	YEL009C|GCN4|S000000735|Transcriptional activator of amino acid biosynthetic genes in response to amino acid starvation; expression is tightly regulated at both the transcriptional and translational levels
YBR116C	2.27602	CUP2	YBR116C||S000000320|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene TKL2
YBR241C	2.2541	CUP2	YBR241C||S000000445|Putative transporter, member of the sugar porter family; green fluorescent protein (GFP)-fusion protein localizes to the vacuolar membrane; YBR241C is not an essential gene
YKL044W	2.24602	CUP2	YKL044W||S000001527|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YJL217W	2.24149	CUP2	YJL217W||S000003753|Cytoplasmic protein of unknown function; expression induced by calcium shortage and via the copper sensing transciption factor Mac1p during conditons of copper deficiency; mRNA is cell cycle regulated, peaking in G1 phase
YDR103W	2.22716	CUP2	YDR103W|STE5|S000002510|Pheromone-response scaffold protein; binds kinases Ste11p, Ste7p, and Fus3p to form a MAPK cascade complex that interacts with the plasma membrane, via a PH (pleckstrin homology) and PM/NLS domain, and with Ste4p-Ste18p, during signaling
YLR296W	2.22382	CUP2	YLR296W||S000004287|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YJR077C	2.21769	CUP2	YJR077C|MIR1|S000003838|Mitochondrial phosphate carrier, imports inorganic phosphate into mitochondria; functionally redundant with Pic2p but more abundant than Pic2p under normal conditions; phosphorylated
YAL060W	2.20821	CUP2	YAL060W|BDH1|S000000056|NAD-dependent (R,R)-butanediol dehydrogenase, catalyzes oxidation of (R,R)-2,3-butanediol to (3R)-acetoin, oxidation of meso-butanediol to (3S)-acetoin, and reduction of acetoin; enhances use of 2,3-butanediol as an aerobic carbon source
YER033C	2.19507	CUP2	YER033C|ZRG8|S000000835|Protein of unknown function; authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; GFP-fusion protein is localized to the cytoplasm; transcription induced under conditions of zinc deficiency
YGL072C	2.16374	CUP2	YGL072C||S000003040|Dubious open reading frame unlikely to encode a protein; partially overlaps the verified gene HSF1; null mutant displays increased resistance to antifungal agents gliotoxin, cycloheximide and H2O2
YGL184C	2.16053	CUP2	YGL184C|STR3|S000003152|Cystathionine beta-lyase, converts cystathionine into homocysteine
YKL221W	2.15701	CUP2	YKL221W|MCH2|S000001704|Protein with similarity to mammalian monocarboxylate permeases, which are involved in transport of monocarboxylic acids across the plasma membrane; mutant is not deficient in monocarboxylate transport
YBR045C	2.15073	CUP2	YBR045C|GIP1|S000000249|Meiosis-specific regulatory subunit of the Glc7p protein phosphatase, regulates spore wall formation and septin organization, required for expression of some late meiotic genes and for normal localization of Glc7p
YLR111W	2.14729	CUP2	YLR111W||S000004101|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YIL155C	2.10526	CUP2	YIL155C|GUT2|S000001417|Mitochondrial glycerol-3-phosphate dehydrogenase; expression is repressed by both glucose and cAMP and derepressed by non-fermentable carbon sources in a Snf1p, Rsf1p, Hap2/3/4/5 complex dependent manner
YPL223C	2.10071	CUP2	YPL223C|GRE1|S000006144|Hydrophilin of unknown function; stress induced (osmotic, ionic, oxidative, heat shock and heavy metals); regulated by the HOG pathway
YMR194C-B	2.06991	CUP2	YMR194C-B||S000028514|Putative protein of unknown function
YOL081W	2.05733	CUP2	YOL081W|IRA2|S000005441|GTPase-activating protein that negatively regulates RAS by converting it from the GTP- to the GDP-bound inactive form, required for reducing cAMP levels under nutrient limiting conditions, has similarity to Ira1p and human neurofibromin
YGL104C	2.03652	CUP2	YGL104C|VPS73|S000003072|Mitochondrial protein; mutation affects vacuolar protein sorting; putative transporter; member of the sugar porter family
YNL092W	2.03395	CUP2	YNL092W||S000005036|Putative S-adenosylmethionine-dependent methyltransferase of the seven beta-strand family; YNL092W is not an essential gene
YGR065C	2.033	CUP2	YGR065C|VHT1|S000003297|High-affinity plasma membrane H+-biotin (vitamin H) symporter; mutation results in fatty acid auxotrophy; 12 transmembrane domain containing major facilitator subfamily member; mRNA levels negatively regulated by iron deprivation and biotin
YER014C-A	2.02742	CUP2	YER014C-A|BUD25|S000007590|Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern
YPR078C	2.02232	CUP2	YPR078C||S000006282|Putative protein of unknown function; possible role in DNA metabolism and/or in genome stability; expression is heat-inducible
YOR214C	2.02014	CUP2	YOR214C||S000005740|Putative protein of unknown function; YOR214C is not an essential gene
YML042W	1.9979	CUP2	YML042W|CAT2|S000004506|Carnitine acetyl-CoA transferase present in both mitochondria and peroxisomes, transfers activated acetyl groups to carnitine to form acetylcarnitine which can be shuttled across membranes
YDR259C	1.98086	CUP2	YDR259C|YAP6|S000002667|Putative basic leucine zipper (bZIP) transcription factor; overexpression increases sodium and lithium tolerance
YBR035C	1.97102	CUP2	YBR035C|PDX3|S000000239|Pyridoxine (pyridoxamine) phosphate oxidase, has homologs in E. coli and Myxococcus xanthus; transcription is under the general control of nitrogen metabolism
YHR217C	1.97049	CUP2	YHR217C||S000001260|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; located in the telomeric region TEL08R.
YER121W	1.96956	CUP2	YER121W||S000000923|Putative protein of unknown function; may be involved in phosphatase regulation and/or generation of precursor metabolites and energy
YOR343C	1.95445	CUP2	YOR343C||S000005870|Dubious open reading frame, unlikely to encode a functional protein; based on available experimental and comparative sequence data
YDL180W	1.95157	CUP2	YDL180W||S000002339|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole
YOR090C	1.94299	CUP2	YOR090C|PTC5|S000005616|Mitochondrial type 2C protein phosphatase involved in regulation of pyruvate dehydrogenase activity by dephosphorylating the ser-133 residue of the Pda1p subunit; acts in concert with kinases Pkp1p and Pkp2p and phosphatase Ptc6p
YLR295C	1.93484	CUP2	YLR295C|ATP14|S000004286|Subunit h of the F0 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis
YGL045W	1.92338	CUP2	YGL045W|RIM8|S000003013|Protein of unknown function, involved in the proteolytic activation of Rim101p in response to alkaline pH; has similarity to A. nidulans PalF
YDR124W	1.91803	CUP2	YDR124W||S000002531|Putative protein of unknown function; non-essential gene; expression is strongly induced by alpha factor
YFL003C	1.90456	CUP2	YFL003C|MSH4|S000001891|Protein involved in meiotic recombination, required for normal levels of crossing over, colocalizes with Zip2p to discrete foci on meiotic chromosomes, has homology to bacterial MutS protein
YOR348C	1.89626	CUP2	YOR348C|PUT4|S000005875|Proline permease, required for high-affinity transport of proline; also transports the toxic proline analog azetidine-2-carboxylate (AzC); PUT4 transcription is repressed in ammonia-grown cells
YDR042C	1.87372	CUP2	YDR042C||S000002449|Putative protein of unknown function; expression is increased in ssu72-ts69 mutant
YDR541C	1.87033	CUP2	YDR541C||S000002949|Putative dihydrokaempferol 4-reductase
YOL047C	1.85607	CUP2	YOL047C||S000005407|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YPL171C	1.83818	CUP2	YPL171C|OYE3|S000006092|Widely conserved NADPH oxidoreductase containing flavin mononucleotide (FMN), homologous to Oye2p with slight differences in ligand binding and catalytic properties; may be involved in sterol metabolism
YPR001W	1.83807	CUP2	YPR001W|CIT3|S000006205|Dual specificity mitochondrial citrate and methylcitrate synthase; catalyzes the condensation of acetyl-CoA and oxaloacetate to form citrate and that of propionyl-CoA and oxaloacetate to form 2-methylcitrate
YPR026W	1.836	CUP2	YPR026W|ATH1|S000006230|Acid trehalase required for utilization of extracellular trehalose
YHR130C	1.8348	CUP2	YHR130C||S000001172|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOR235W	1.82514	CUP2	YOR235W|IRC13|S000005761|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; null mutant displays increased levels of spontaneous Rad52 foci
YDR476C	1.82135	CUP2	YDR476C||S000002884|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YDR476C is not an essential gene
YPR027C	1.81647	CUP2	YPR027C||S000006231|Putative protein of unknown function
YML090W	1.81269	CUP2	YML090W||S000004555|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YML089C; exhibits growth defect on a non-fermentable (respiratory) carbon source
YPR023C	1.81129	CUP2	YPR023C|EAF3|S000006227|Esa1p-associated factor, nonessential component of the NuA4 acetyltransferase complex, homologous to Drosophila dosage compensation protein MSL3; plays a role in regulating Ty1 transposition
YGR045C	1.8016	CUP2	YGR045C||S000003277|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YHR202W	1.78903	CUP2	YHR202W||S000001245|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole, while HA-tagged protein is found in the soluble fraction, suggesting cytoplasmic localization
YHR211W	1.78083	CUP2	YHR211W|FLO5|S000001254|Lectin-like cell wall protein (flocculin) involved in flocculation, binds to mannose chains on the surface of other cells, confers floc-forming ability that is chymotrypsin resistant but heat labile; similar to Flo1p
YBR006W	1.77697	CUP2	YBR006W|UGA2|S000000210|Succinate semialdehyde dehydrogenase involved in the utilization of gamma-aminobutyrate (GABA) as a nitrogen source; part of the 4-aminobutyrate and glutamate degradation pathways; localized to the cytoplasm
YJL144W	1.7607	CUP2	YJL144W||S000003680|Cytoplasmic hydrophilin of unknown function, possibly involved in the dessication response; expression induced by osmotic stress, starvation and during stationary phase; GFP-fusion protein is induced by the DNA-damaging agent MMS
YBR223C	1.74336	CUP2	YBR223C|TDP1|S000000427|Tyrosyl-DNA Phosphodiesterase I, hydrolyzes 3'-phosphotyrosyl bonds to generate 3'-phosphate DNA and tyrosine, involved in the repair of DNA lesions created by topoisomerase I
YHR015W	1.74294	CUP2	YHR015W|MIP6|S000001057|Putative RNA-binding protein, interacts with Mex67p, which is a component of the nuclear pore involved in nuclear mRNA export
YOL082W	1.73855	CUP2	YOL082W|ATG19|S000005442|Receptor protein for the cytoplasm-to-vacuole targeting (Cvt) pathway; recognizes cargo proteins aminopeptidase I (Lap4p) and alpha-mannosidase (Ams1p) and delivers them to the preautophagosomal structure for packaging into Cvt vesicles
YOR138C	1.73611	CUP2	YOR138C|RUP1|S000005664|Protein involved in regulation of Rsp5p, which is an essential HECT ubiquitin ligase; required for binding of Rsp5p to Ubp2p; contains an UBA domain
YFR023W	1.72132	CUP2	YFR023W|PES4|S000001919|Poly(A) binding protein, suppressor of DNA polymerase epsilon mutation, similar to Mip6p
YBR224W	1.70249	CUP2	YBR224W||S000000428|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene TDP1
YKR009C	1.70132	CUP2	YKR009C|FOX2|S000001717|Multifunctional enzyme of the peroxisomal fatty acid beta-oxidation pathway; has 3-hydroxyacyl-CoA dehydrogenase and enoyl-CoA hydratase activities
YMR081C	1.69839	CUP2	YMR081C|ISF1|S000004686|Serine-rich, hydrophilic protein with similarity to Mbr1p; overexpression suppresses growth defects of hap2, hap3, and hap4 mutants; expression is under glucose control; cotranscribed with NAM7 in a cyp1 mutant
YDL114W	1.6945	CUP2	YDL114W||S000002272|Putative protein of unknown function with similarity to acyl-carrier-protein reductases; YDL114W is not an essential gene
YOR121C	1.69104	CUP2	YOR121C||S000005647|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; open reading frame overlaps the verified gene GCY1/YOR120W
YMR250W	1.68861	CUP2	YMR250W|GAD1|S000004862|Glutamate decarboxylase, converts glutamate into gamma-aminobutyric acid (GABA) during glutamate catabolism; involved in response to oxidative stress
YER116C	1.68854	CUP2	YER116C|SLX8|S000000918|Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate
YCR068W	1.68263	CUP2	YCR068W|ATG15|S000000664|Lipase, required for intravacuolar lysis of autophagosomes; located in the endoplasmic reticulum membrane and targeted to intravacuolar vesicles during autophagy via the multivesicular body (MVB) pathway
YDR443C	1.68219	CUP2	YDR443C|SSN2|S000002851|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; required for stable association of Srb10p-Srb11p kinase; essential for transcriptional regulation
YKL032C	1.68206	CUP2	YKL032C|IXR1|S000001515|Protein that binds DNA containing intrastrand cross-links formed by cisplatin, contains two HMG (high mobility group box) domains, which confer the ability to bend cisplatin-modified DNA; mediates aerobic transcriptional repression of COX5b
YMR135C	1.67164	CUP2	YMR135C|GID8|S000004742|Protein of unknown function, involved in proteasome-dependent catabolite inactivation of fructose-1,6-bisphosphatase; contains LisH and CTLH domains, like Vid30p; dosage-dependent regulator of START
YKL028W	1.6695	CUP2	YKL028W|TFA1|S000001511|TFIIE large subunit, involved in recruitment of RNA polymerase II to the promoter, activation of TFIIH, and promoter opening
YLR438W	1.66804	CUP2	YLR438W|CAR2|S000004430|L-ornithine transaminase (OTAse), catalyzes the second step of arginine degradation, expression is dually-regulated by allophanate induction and a specific arginine induction process; not nitrogen catabolite repression sensitive
YOR394W	1.66421	CUP2	YOR394W|PAU21|S000005921|Hypothetical protein
YER162C	1.66341	CUP2	YER162C|RAD4|S000000964|Protein that recognizes and binds damaged DNA (with Rad23p) during nucleotide excision repair; subunit of Nuclear Excision Repair Factor 2 (NEF2); homolog of human XPC protein
YLR023C	1.65722	CUP2	YLR023C|IZH3|S000004013|Membrane protein involved in zinc metabolism, member of the four-protein IZH family, expression induced by zinc deficiency; deletion reduces sensitivity to elevated zinc and shortens lag phase, overexpression reduces Zap1p activity
YNR050C	1.65524	CUP2	YNR050C|LYS9|S000005333|Saccharopine dehydrogenase (NADP+, L-glutamate-forming); catalyzes the formation of saccharopine from alpha-aminoadipate 6-semialdehyde, which is the seventh step in lysine biosynthesis pathway
YDR223W	1.65173	CUP2	YDR223W|CRF1|S000002631|Transcriptional corepressor involved in the regulation of ribosomal protein gene transcription via the TOR signaling pathway and protein kinase A, phosphorylated by activated Yak1p which promotes accumulation of Crf1p in the nucleus
YOR377W	1.65167	CUP2	YOR377W|ATF1|S000005904|Alcohol acetyltransferase with potential roles in lipid and sterol metabolism; responsible for the major part of volatile acetate ester production during fermentation
YDR119W-A	1.65151	CUP2	YDR119W-A||S000113555|Putative protein of unknown function
YDR381C-A	1.64076	CUP2	YDR381C-A||S000007650|Protein of unknown function, localized to the mitochondrial outer membrane
YIL160C	1.63901	CUP2	YIL160C|POT1|S000001422|3-ketoacyl-CoA thiolase with broad chain length specificity, cleaves 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA during beta-oxidation of fatty acids
YJL088W	1.63744	CUP2	YJL088W|ARG3|S000003624|Ornithine carbamoyltransferase (carbamoylphosphate:L-ornithine carbamoyltransferase), catalyzes the sixth step in the biosynthesis of the arginine precursor ornithine
YJR146W	1.61508	CUP2	YJR146W||S000003907|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene HMS2
YOR178C	1.61265	CUP2	YOR178C|GAC1|S000005704|Regulatory subunit for Glc7p type-1 protein phosphatase (PP1), tethers Glc7p to Gsy2p glycogen synthase, binds Hsf1p heat shock transcription factor, required for induction of some HSF-regulated genes under heat shock
YDR540C	1.60328	CUP2	YDR540C|IRC4|S000002948|Putative protein of unknown function; null mutant displays increased levels of spontaneous Rad52p foci; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus
YIL108W	1.5977	CUP2	YIL108W||S000001370|Putative metalloprotease
YJR160C	1.57366	CUP2	YJR160C|MPH3|S000003921|Alpha-glucoside permease, transports maltose, maltotriose, alpha-methylglucoside, and turanose; identical to Mph2p; encoded in a subtelomeric position in a region likely to have undergone duplication
YOL051W	1.57316	CUP2	YOL051W|GAL11|S000005411|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; affects transcription by acting as target of activators and repressors
YBR222C	1.56685	CUP2	YBR222C|PCS60|S000000426|Peroxisomal AMP-binding protein, localizes to both the peroxisomal peripheral membrane and matrix, expression is highly inducible by oleic acid, similar to E. coli long chain acyl-CoA synthetase
YGR110W	1.56486	CUP2	YGR110W||S000003342|Putative protein of unknown function; transcription is increased in response to genotoxic stress; plays a role in restricting Ty1 transposition
YCR010C	1.55235	CUP2	YCR010C|ADY2|S000000603|Acetate transporter required for normal sporulation; phosphorylated in mitochondria
YOR031W	1.54589	CUP2	YOR031W|CRS5|S000005557|Copper-binding metallothionein, required for wild-type copper resistance
YGR268C	1.54333	CUP2	YGR268C|HUA1|S000003500|Cytoplasmic protein containing a zinc finger domain with sequence similarity to that of Type I J-proteins; computational analysis of large-scale protein-protein interaction data suggests a possible role in actin patch assembly
YOR339C	1.54044	CUP2	YOR339C|UBC11|S000005866|Ubiquitin-conjugating enzyme most similar in sequence to Xenopus ubiquitin-conjugating enzyme E2-C, but not a true functional homolog of this E2; unlike E2-C, not required for the degradation of mitotic cyclin Clb2
YIL017C	1.53782	CUP2	YIL017C|VID28|S000001279|Protein involved in proteasome-dependent catabolite degradation of fructose-1,6-bisphosphatase (FBPase); localized to the nucleus and the cytoplasm
YGR225W	1.52817	CUP2	YGR225W|AMA1|S000003457|Activator of meiotic anaphase promoting complex (APC/C); Cdc20p family member; required for initiation of spore wall assembly; required for Clb1p degradation during meiosis
YOR221C	1.52505	CUP2	YOR221C|MCT1|S000005747|Predicted malonyl-CoA:ACP transferase, putative component of a type-II mitochondrial fatty acid synthase that produces intermediates for phospholipid remodeling
YPR015C	1.52131	CUP2	YPR015C||S000006219|Putative protein of unknown function
YER084W	1.51402	CUP2	YER084W||S000000886|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YPL183W-A	1.50245	CUP2	YPL183W-A|RTC6|S000007224|Homolog of the prokaryotic ribosomal protein L36, likely to be a mitochondrial ribosomal protein coded in the nuclear genome; null mutation suppresses cdc13-1 temperature sensitivity
YGL192W	1.49081	CUP2	YGL192W|IME4|S000003160|Probable mRNA N6-adenosine methyltransferase that is required for IME1 transcript accumulation and for sporulation; expression is induced in starved MATa/MAT alpha diploid cells
YNL013C	1.48933	CUP2	YNL013C||S000004958|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF HEF3/YNL014W
YMR095C	1.48572	CUP2	YMR095C|SNO1|S000004701|Protein of unconfirmed function, involved in pyridoxine metabolism; expression is induced during stationary phase; forms a putative glutamine amidotransferase complex with Snz1p, with Sno1p serving as the glutaminase
YOL128C	1.47538	CUP2	YOL128C|YGK3|S000005488|Protein kinase related to mammalian glycogen synthase kinases of the GSK-3 family; GSK-3 homologs (Mck1p, Rim11p, Mrk1p, Ygk3p) are involved in control of Msn2p-dependent transcription of stress responsive genes and in protein degradation
YPR192W	1.46955	CUP2	YPR192W|AQY1|S000006396|Spore-specific water channel that mediates the transport of water across cell membranes, developmentally controlled; may play a role in spore maturation, probably by allowing water outflow, may be involved in freeze tolerance
YLR308W	1.4659	CUP2	YLR308W|CDA2|S000004299|Chitin deacetylase, together with Cda1p involved in the biosynthesis ascospore wall component, chitosan; required for proper rigidity of the ascospore wall
YJR108W	1.46461	CUP2	YJR108W|ABM1|S000003869|Protein of unknown function, required for normal microtubule organization
YJL213W	1.44713	CUP2	YJL213W||S000003749|Protein of unknown function that may interact with ribosomes; periodically expressed during the yeast metabolic cycle; phosphorylated in vitro by the mitotic exit network (MEN) kinase complex, Dbf2p/Mob1p
YMR271C	1.43874	CUP2	YMR271C|URA10|S000004884|Minor orotate phosphoribosyltransferase (OPRTase) isozyme that catalyzes the fifth enzymatic step in the de novo biosynthesis of pyrimidines, converting orotate into orotidine-5'-phosphate; major OPRTase encoded by URA5
YMR316C-B	1.43082	CUP2	YMR316C-B||S000004934|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YHR051W	1.42992	CUP2	YHR051W|COX6|S000001093|Subunit VI of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; expression is regulated by oxygen levels
YKL109W	1.42681	CUP2	YKL109W|HAP4|S000001592|Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression; provides the principal activation function of the complex
YGL193C	1.42619	CUP2	YGL193C||S000003161|Haploid-specific gene repressed by a1-alpha2, turned off in sir3 null strains, absence enhances the sensitivity of rad52-327 cells to campothecin almost 100-fold
YDL244W	1.42511	CUP2	YDL244W|THI13|S000002403|Protein involved in synthesis of the thiamine precursor hydroxymethylpyrimidine (HMP); member of a subtelomeric gene family including THI5, THI11, THI12, and THI13
YOR027W	1.42316	CUP2	YOR027W|STI1|S000005553|Hsp90 cochaperone, interacts with the Ssa group of the cytosolic Hsp70 chaperones; activates the ATPase activity of Ssa1p; homolog of mammalian Hop protein
YBL048W	1.41885	CUP2	YBL048W||S000000144|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data
YGR191W	1.41669	CUP2	YGR191W|HIP1|S000003423|High-affinity histidine permease, also involved in the transport of manganese ions
YPL135W	1.41167	CUP2	YPL135W|ISU1|S000006056|Conserved protein of the mitochondrial matrix, performs a scaffolding function during assembly of iron-sulfur clusters, interacts physically and functionally with yeast frataxin (Yfh1p); isu1 isu2 double mutant is inviable
YDR093W	1.40802	CUP2	YDR093W|DNF2|S000002500|Aminophospholipid translocase (flippase) that localizes primarily to the plasma membrane; contributes to endocytosis, protein transport and cell polarity; type 4 P-type ATPase
YGL121C	1.40205	CUP2	YGL121C|GPG1|S000003089|Proposed gamma subunit of the heterotrimeric G protein that interacts with the receptor Grp1p; involved in regulation of pseudohyphal growth; requires Gpb1p or Gpb2p to interact with Gpa2p
YGL117W	1.39709	CUP2	YGL117W||S000003085|Putative protein of unknown function
YJL005W	1.38566	CUP2	YJL005W|CYR1|S000003542|Adenylate cyclase, required for cAMP production and cAMP-dependent protein kinase signaling; the cAMP pathway controls a variety of cellular processes, including metabolism, cell cycle, stress response, stationary phase, and sporulation
YGL258W-A	1.38369	CUP2	YGL258W-A||S000007607|Putative protein of unknown function
YLR437C-A	1.38295	CUP2	YLR437C-A||S000028684|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF CAR2/YLR438W
YBR212W	1.3809	CUP2	YBR212W|NGR1|S000000416|RNA binding protein that negatively regulates growth rate; interacts with the 3' UTR of the mitochondrial porin (POR1) mRNA and enhances its degradation; overexpression impairs mitochondrial function; expressed in stationary phase
YGL173C	1.38082	CUP2	YGL173C|KEM1|S000003141|Evolutionarily-conserved 5'-3' exonuclease component of cytoplasmic processing (P) bodies involved in mRNA decay; plays a role in microtubule-mediated processes, filamentous growth, ribosomal RNA maturation, and telomere maintenance
YPL196W	1.36818	CUP2	YPL196W|OXR1|S000006117|Protein of unknown function required for normal levels of resistance to oxidative damage, null mutants are sensitive to hydrogen peroxide; member of a conserved family of proteins found in eukaryotes but not in prokaryotes
YDR456W	1.36078	CUP2	YDR456W|NHX1|S000002864|Endosomal Na+/H+ exchanger, required for intracellular sequestration of Na+; required for osmotolerance to acute hypertonic shock
YEL009C-A	1.35949	CUP2	YEL009C-A||S000028741|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLL060C	1.35388	CUP2	YLL060C|GTT2|S000003983|Glutathione S-transferase capable of homodimerization; functional overlap with Gtt2p, Grx1p, and Grx2p
YDR455C	1.35342	CUP2	YDR455C||S000002863|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YDR456W
YBR054W	1.35282	CUP2	YBR054W|YRO2|S000000258|Putative protein of unknown function; the authentic, non-tagged protein is detected in a phosphorylated state in highly purified mitochondria in high-throughput studies; transcriptionally regulated by Haa1p
YGR281W	1.35172	CUP2	YGR281W|YOR1|S000003513|Plasma membrane ATP-binding cassette (ABC) transporter, multidrug transporter mediates export of many different organic anions including oligomycin
YMR317W	1.34783	CUP2	YMR317W||S000004936|Putative protein of unknown function with some similarity to sialidase from Trypanosoma; YMR317W is not an essential gene
YER163C	1.34677	CUP2	YER163C||S000000965|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus
YKL163W	1.34624	CUP2	YKL163W|PIR3|S000001646|O-glycosylated covalently-bound cell wall protein required for cell wall stability; expression is cell cycle regulated, peaking in M/G1 and also subject to regulation by the cell integrity pathway
YNL283C	1.3453	CUP2	YNL283C|WSC2|S000005227|Partially redundant sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway involved in maintenance of cell wall integrity and recovery from heat shock; secretory pathway Wsc2p is required for the arrest of secretion response
YLR356W	1.34493	CUP2	YLR356W||S000004348|Putative protein of unknown function with similarity to SCM4; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YLR356W is not an essential gene
YBR200W-A	1.33941	CUP2	YBR200W-A||S000028535|Putative protein of unknown function; identified by fungal homology and RT-PCR
YHR198C	1.33916	CUP2	YHR198C|AIM18|S000001241|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YMR306W	1.33417	CUP2	YMR306W|FKS3|S000004923|Protein involved in spore wall assembly, has similarity to 1,3-beta-D-glucan synthase catalytic subunits Fks1p and Gsc2p; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YKL141W	1.33347	CUP2	YKL141W|SDH3|S000001624|Cytochrome b subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p), which couples the oxidation of succinate to the transfer of electrons to ubiquinone
YPR083W	1.32763	CUP2	YPR083W|MDM36|S000006287|Protein required for normal mitochondrial morphology and inheritance
YMR040W	1.32686	CUP2	YMR040W|YET2|S000004643|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; homolog of human BAP31 protein
YGR144W	1.32439	CUP2	YGR144W|THI4|S000003376|Thiazole synthase, catalyzes formation of the thiazole moiety of thiamin pyrophosphate; required for thiamine biosynthesis and for mitochondrial genome stability
YNR073C	1.32287	CUP2	YNR073C||S000005356|Putative mannitol dehydrogenase
YAR023C	1.31251	CUP2	YAR023C||S000000074|Putative integral membrane protein, member of DUP240 gene family
YJR004C	1.31146	CUP2	YJR004C|SAG1|S000003764|Alpha-agglutinin of alpha-cells, binds to Aga1p during agglutination, N-terminal half is homologous to the immunoglobulin superfamily and contains binding site for a-agglutinin, C-terminal half is highly glycosylated and contains GPI anchor
YDL085W	1.3087	CUP2	YDL085W|NDE2|S000002243|Mitochondrial external NADH dehydrogenase, catalyzes the oxidation of cytosolic NADH; Nde1p and Nde2p are involved in providing the cytosolic NADH to the mitochondrial respiratory chain
YLR037C	1.30592	CUP2	YLR037C|DAN2|S000004027|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YDR538W	1.30529	CUP2	YDR538W|PAD1|S000002946|Phenylacrylic acid decarboxylase, confers resistance to cinnamic acid, decarboxylates aromatic carboxylic acids to the corresponding vinyl derivatives; homolog of E. coli UbiX
YML091C	1.30474	CUP2	YML091C|RPM2|S000004556|Protein subunit of mitochondrial RNase P, has roles in nuclear transcription, cytoplasmic and mitochondrial RNA processing, and mitochondrial translation; distributed to mitochondria, cytoplasmic processing bodies, and the nucleus
YBR225W	1.30434	CUP2	YBR225W||S000000429|Putative protein of unknown function; non-essential gene identified in a screen for mutants affected in mannosylphophorylation of cell wall components
YHR177W	1.29986	CUP2	YHR177W||S000001220|Putative protein of unknown function
YPL021W	1.29965	CUP2	YPL021W|ECM23|S000005942|Non-essential protein of unconfirmed function; affects pre-rRNA processing, may act as a negative regulator of the transcription of genes involved in pseudohyphal growth; homologous to Srd1p
YML133C	1.29839	CUP2	YML133C||S000004602|Putative protein of unknown function with similarity to helicases; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YML133C contains an intron
YOR065W	1.29451	CUP2	YOR065W|CYT1|S000005591|Cytochrome c1, component of the mitochondrial respiratory chain; expression is regulated by the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex
YML132W	1.28843	CUP2	YML132W|COS3|S000004601|Protein involved in salt resistance; interacts with sodium:hydrogen antiporter Nha1p; member of the DUP380 subfamily of conserved, often subtelomerically-encoded proteins
YLL013C	1.28718	CUP2	YLL013C|PUF3|S000003936|Protein of the mitochondrial outer surface, links the Arp2/3 complex with the mitochore during anterograde mitochondrial movement; also binds to and promotes degradation of mRNAs for select nuclear-encoded mitochondrial proteins
YHR126C	1.28332	CUP2	YHR126C||S000001168|Putative protein of unknown function; transcription dependent upon Azf1p
YPR042C	1.28314	CUP2	YPR042C|PUF2|S000006246|Member of the PUF protein family, which is defined by the presence of Pumilio homology domains that confer RNA binding activity; preferentially binds mRNAs encoding membrane-associated proteins
YLL029W	1.28233	CUP2	YLL029W|FRA1|S000003952|Protein involved in negative regulation of transcription of iron regulon; forms an iron independent complex with Fra2p, Grx3p, and Grx4p; cytosolic; mutant fails to repress transcription of iron regulon and is defective in spore formation
YNL086W	1.27908	CUP2	YNL086W||S000005030|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to endosomes
YDR032C	1.25833	CUP2	YDR032C|PST2|S000002439|Protein with similarity to members of a family of flavodoxin-like proteins; induced by oxidative stress in a Yap1p dependent manner; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YMR243C	1.25676	CUP2	YMR243C|ZRC1|S000004856|Vacuolar membrane zinc transporter, transports zinc from the cytosol into the vacuole for storage; also has a role in resistance to zinc shock resulting from a sudden influx of zinc into the cytoplasm
YML081C-A	1.25646	CUP2	YML081C-A|ATP18|S000007247|Subunit of the mitochondrial F1F0 ATP synthase, which is a large enzyme complex required for ATP synthesis; termed subunit I or subunit j; does not correspond to known ATP synthase subunits in other organisms
YLL020C	1.25176	CUP2	YLL020C||S000003943|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene KNS1
YDL138W	1.24963	CUP2	YDL138W|RGT2|S000002297|Plasma membrane glucose receptor, highly similar to Snf3p; both Rgt2p and Snf3p serve as transmembrane glucose sensors generating an intracellular signal that induces expression of glucose transporter (HXT) genes
YPR030W	1.24605	CUP2	YPR030W|CSR2|S000006234|Nuclear protein with a potential regulatory role in utilization of galactose and nonfermentable carbon sources; overproduction suppresses the lethality at high temperature of a chs5 spa2 double null mutation; potential Cdc28p substrate
YPR065W	1.24545	CUP2	YPR065W|ROX1|S000006269|Heme-dependent repressor of hypoxic genes; contains an HMG domain that is responsible for DNA bending activity
YDR298C	1.23783	CUP2	YDR298C|ATP5|S000002706|Subunit 5 of the stator stalk of mitochondrial F1F0 ATP synthase, which is an evolutionarily conserved enzyme complex required for ATP synthesis; homologous to bovine subunit OSCP (oligomycin sensitivity-conferring protein); phosphorylated
YKL043W	1.23571	CUP2	YKL043W|PHD1|S000001526|Transcriptional activator that enhances pseudohyphal growth; regulates expression of FLO11, an adhesin required for pseudohyphal filament formation; similar to StuA, an A. nidulans developmental regulator; potential Cdc28p substrate
YDR269C	1.23248	CUP2	YDR269C||S000002677|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLL056C	1.23109	CUP2	YLL056C||S000003979|Putative protein of unknown function, transcription is activated by paralogous transcription factors Yrm1p and Yrr1p along with genes involved in pleiotropic drug resistance (PDR) phenomenon; YLL056C is not an essential gene
YPL186C	1.22565	CUP2	YPL186C|UIP4|S000006107|Protein that interacts with Ulp1p, a Ubl (ubiquitin-like protein)-specific protease for Smt3p protein conjugates; detected in a phosphorylated state in the mitochondrial outer membrane; also detected in ER and nuclear envelope
YNL094W	1.22434	CUP2	YNL094W|APP1|S000005038|Protein of unknown function, interacts with Rvs161p and Rvs167p; computational analysis of protein-protein interactions in large-scale studies suggests a possible role in actin filament organization
YJR061W	1.22387	CUP2	YJR061W||S000003822|Putative protein of unknown function; non-essential gene with similarity to Mnn4, a putative membrane protein involved in glycosylation; transcription repressed by Rm101p
YHL040C	1.22372	CUP2	YHL040C|ARN1|S000001032|Transporter, member of the ARN family of transporters that specifically recognize siderophore-iron chelates; responsible for uptake of iron bound to ferrirubin, ferrirhodin, and related siderophores
YHR218W	1.21586	CUP2	YHR218W||S000001261|Helicase-like protein encoded within the telomeric Y' element
YPR150W	1.19609	CUP2	YPR150W||S000006354|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene SUE1/YPR151C
YKR091W	1.19609	CUP2	YKR091W|SRL3|S000001799|Cytoplasmic protein that, when overexpressed, suppresses the lethality of a rad53 null mutation; potential Cdc28p substrate
YLR216C	1.19453	CUP2	YLR216C|CPR6|S000004206|Peptidyl-prolyl cis-trans isomerase (cyclophilin), catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; binds to Hsp82p and contributes to chaperone activity
YMR195W	1.19399	CUP2	YMR195W|ICY1|S000004808|Protein of unknown function, required for viability in rich media of cells lacking mitochondrial DNA; mutants have an invasive growth defect with elongated morphology; induced by amino acid starvation
YDR059C	1.18883	CUP2	YDR059C|UBC5|S000002466|Ubiquitin-conjugating enzyme that mediates selective degradation of short-lived and abnormal proteins, central component of the cellular stress response; expression is heat inducible
YLR252W	1.18863	CUP2	YLR252W||S000004242|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data; partially overlaps the verified gene SYM1, a mitochondrial protein involved in ethanol metabolism
YBL093C	1.18852	CUP2	YBL093C|ROX3|S000000189|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme
YBR230C	1.18847	CUP2	YBR230C|OM14|S000000434|Integral mitochondrial outer membrane protein; abundance is decreased in cells grown in glucose relative to other carbon sources; appears to contain 3 alpha-helical transmembrane segments; ORF encodes a 97-basepair intron
YMR118C	1.18834	CUP2	YMR118C||S000004724|Protein of unknown function with similarity to succinate dehydrogenase cytochrome b subunit; YMR118C is not an essential gene
YIL012W	1.18672	CUP2	YIL012W||S000001274|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YBR147W	1.1808	CUP2	YBR147W|RTC2|S000000351|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays fluconazole resistance and suppresses cdc13-1 temperature sensitivity
YDR085C	1.18	CUP2	YDR085C|AFR1|S000002492|Alpha-factor pheromone receptor regulator, negatively regulates pheromone receptor signaling; required for normal mating projection (shmoo) formation; required for Spa2p to recruit Mpk1p to shmoo tip during mating; interacts with Cdc12p
YMR035W	1.17545	CUP2	YMR035W|IMP2|S000004638|Catalytic subunit of the mitochondrial inner membrane peptidase complex, required for maturation of mitochondrial proteins of the intermembrane space; complex contains Imp1p and Imp2p (both catalytic subunits), and Som1p
YLR217W	1.1717	CUP2	YLR217W||S000004207|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene CPR6
YGR190C	1.15552	CUP2	YGR190C||S000003422|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene HIP1/YGR191W
YJL199C	1.15204	CUP2	YJL199C|MBB1|S000003735|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; protein detected in large-scale protein-protein interaction studies
YDR405W	1.14993	CUP2	YDR405W|MRP20|S000002813|Mitochondrial ribosomal protein of the large subunit
YDR537C	1.14784	CUP2	YDR537C||S000002945|Dubious open reading frame unlikely to encode a protein, almost completely overlaps verified ORF PAD1/YDR538W
YER158C	1.14503	CUP2	YER158C||S000000960|Protein of unknown function, has similarity to Afr1p; potentially phosphorylated by Cdc28p
YDL049C	1.13837	CUP2	YDL049C|KNH1|S000002207|Protein with similarity to Kre9p, which is involved in cell wall beta 1,6-glucan synthesis; overproduction suppresses growth defects of a kre9 null mutant
YLL055W	1.1309	CUP2	YLL055W|YCT1|S000003978|High-affinity cysteine-specific transporter with similarity to the Dal5p family of transporters; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YCT1 is not an essential gene
YFR022W	1.12921	CUP2	YFR022W|ROG3|S000001918|Protein that binds to Rsp5p, which is a hect-type ubiquitin ligase, via its 2 PY motifs; has similarity to Rod1p; mutation suppresses the temperature sensitivity of an mck1 rim11 double mutant
YGR243W	1.12915	CUP2	YGR243W|FMP43|S000003475|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YPR140W	1.12892	CUP2	YPR140W|TAZ1|S000006344|Lyso-phosphatidylcholine acyltransferase, required for normal phospholipid content of mitochondrial membranes; may remodel acyl groups of cardiolipin in the inner membrane; similar to human tafazzin, which is implicated in Barth syndrome
YPL191C	1.12873	CUP2	YPL191C||S000006112|Putative protein of unknown function; diploid deletion strain exhibits high budding index; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YDR270W	1.1233	CUP2	YDR270W|CCC2|S000002678|Cu(+2)-transporting P-type ATPase, required for export of copper from the cytosol into an extracytosolic compartment; has similarity to human proteins involved in Menkes and Wilsons diseases
YCL001W-A	1.12302	CUP2	YCL001W-A||S000007221|Putative protein of unknown function; YCL001W-A is not an essential gene
YDR380W	1.12041	CUP2	YDR380W|ARO10|S000002788|Phenylpyruvate decarboxylase, catalyzes decarboxylation of phenylpyruvate to phenylacetaldehyde, which is the first specific step in the Ehrlich pathway
YPL206C	1.11921	CUP2	YPL206C|PGC1|S000006127|Phosphatidyl Glycerol phospholipase C; regulates the phosphatidylglycerol (PG) content via a phospholipase C-type degradation mechanism; contains glycerophosphodiester phosphodiesterase motifs
YKL029C	1.11284	CUP2	YKL029C|MAE1|S000001512|Mitochondrial malic enzyme, catalyzes the oxidative decarboxylation of malate to pyruvate, which is a key intermediate in sugar metabolism and a precursor for synthesis of several amino acids
YOR049C	1.11222	CUP2	YOR049C|RSB1|S000005575|Suppressor of sphingoid long chain base (LCB) sensitivity of an LCB-lyase mutation; putative integral membrane transporter or flippase that may transport LCBs from the cytoplasmic side toward the extracytoplasmic side of the membrane
YPL282C	1.10635	CUP2	YPL282C|PAU22|S000006203|Hypothetical protein
YAL002W	1.10605	CUP2	YAL002W|VPS8|S000000002|Membrane-associated protein that interacts with Vps21p to facilitate soluble vacuolar protein localization; component of the CORVET complex; required for localization and trafficking of the CPY sorting receptor; contains RING finger motif
YBR037C	1.10152	CUP2	YBR037C|SCO1|S000000241|Copper-binding protein of the mitochondrial inner membrane, required for cytochrome c oxidase activity and respiration; may function to deliver copper to cytochrome c oxidase; has similarity to thioredoxins
YPR124W	1.10026	CUP2	YPR124W|CTR1|S000006328|High-affinity copper transporter of the plasma membrane, mediates nearly all copper uptake under low copper conditions; transcriptionally induced at low copper levels and degraded at high copper levels
YJL220W	1.097	CUP2	YJL220W||S000003756|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YJL221C/FSP2
YKR095W	1.09593	CUP2	YKR095W|MLP1|S000001803|Myosin-like protein associated with the nuclear envelope, connects the nuclear pore complex with the nuclear interior; involved with Tel1p in telomere length control; involved with Pml1p and Pml39p in nuclear retention of unspliced mRNAs
YOR072W	1.09555	CUP2	YOR072W||S000005598|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data; partially overlaps the dubious gene YOR072W-A; diploid deletion strains are methotrexate, paraquat and wortmannin sensitive
YAR069C	1.09427	CUP2	YAR069C||S000000092|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDL194W	1.09383	CUP2	YDL194W|SNF3|S000002353|Plasma membrane glucose sensor that regulates glucose transport; has 12 predicted transmembrane segments; long cytoplasmic C-terminal tail is required for low glucose induction of hexose transporter genes HXT2 and HXT4
YER088C	1.08756	CUP2	YER088C|DOT6|S000000890|Protein of unknown function, involved in telomeric gene silencing and filamentation
YNR001C	1.07398	CUP2	YNR001C|CIT1|S000005284|Citrate synthase, catalyzes the condensation of acetyl coenzyme A and oxaloacetate to form citrate; the rate-limiting enzyme of the TCA cycle; nuclear encoded mitochondrial protein
YGR072W	1.07346	CUP2	YGR072W|UPF3|S000003304|Component of the nonsense-mediated mRNA decay (NMD) pathway, along with Nam7p and Nmd2p; involved in decay of mRNA containing nonsense codons; involved in telomere maintenance
YPL189C-A	1.07314	CUP2	YPL189C-A|COA2|S000028527|Putative cytochrome oxidase assembly factor; identified by homology to Ashbya gossypii; null mutation results in respiratory deficiency with specific loss of cytochrome oxidase activity
YPR120C	1.07256	CUP2	YPR120C|CLB5|S000006324|B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1 phase
YNL277W-A	1.06837	CUP2	YNL277W-A||S000028852|Putative protein of unknown function
YML131W	1.06837	CUP2	YML131W||S000004600|Putative protein of unknown function with similarity to oxidoreductases; HOG1 and SKO1-dependent mRNA expression is induced after osmotic shock; GFP-fusion protein localizes to the cytoplasm and is induced by the DNA-damaging agent MMS
YOR228C	1.06562	CUP2	YOR228C||S000005754|Protein of unknown function, localized to the mitochondrial outer membrane
YKL046C	1.0645	CUP2	YKL046C|DCW1|S000001529|Putative mannosidase, GPI-anchored membrane protein required for cell wall biosynthesis in bud formation;homologous to Dfg5p
YPL034W	1.06148	CUP2	YPL034W||S000005955|Putative protein of unknown function; YPL034W is not essential gene
YPL185W	1.06036	CUP2	YPL185W||S000006106|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene UIP4/YPL186C
YER091C-A	1.05848	CUP2	YER091C-A||S000007238|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YAR070C	1.04929	CUP2	YAR070C||S000000093|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR466W	1.04669	CUP2	YDR466W|PKH3|S000002874|Protein kinase with similarity to mammalian phosphoinositide-dependent kinase 1 (PDK1) and yeast Pkh1p and Pkh2p, two redundant upstream activators of Pkc1p; identified as a multicopy suppressor of a pkh1 pkh2 double mutant
YNL322C	1.04526	CUP2	YNL322C|KRE1|S000005266|Cell wall glycoprotein involved in beta-glucan assembly; serves as a K1 killer toxin membrane receptor
YGR032W	1.03918	CUP2	YGR032W|GSC2|S000003264|Catalytic subunit of 1,3-beta-glucan synthase, involved in formation of the inner layer of the spore wall; activity positively regulated by Rho1p and negatively by Smk1p; has similarity to an alternate catalytic subunit, Fks1p (Gsc1p)
YNL095C	1.03875	CUP2	YNL095C||S000005039|Putative protein of unknown function predicted to contain a transmembrane domain; YNL095C is not an essential gene
YHR050W	1.03481	CUP2	YHR050W|SMF2|S000001092|Divalent metal ion transporter involved in manganese homeostasis; has broad specificity for di-valent and tri-valent metals; post-translationally regulated by levels of metal ions; member of the Nramp family of metal transport proteins
YOL058W	1.02949	CUP2	YOL058W|ARG1|S000005419|Arginosuccinate synthetase, catalyzes the formation of L-argininosuccinate from citrulline and L-aspartate in the arginine biosynthesis pathway; potential Cdc28p substrate
YEL010W	1.02878	CUP2	YEL010W||S000000736|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOR066W	1.02616	CUP2	YOR066W|MSA1|S000005592|Activator of G1-specific transcription factors, MBF and SBF, that regulates both the timing of G1-specific gene transcription, and cell cycle initiation; potential Cdc28p substrate
YIL112W	1.02228	CUP2	YIL112W|HOS4|S000001374|Subunit of the Set3 complex, which is a meiotic-specific repressor of sporulation specific genes that contains deacetylase activity; potential Cdc28p substrate
YCR020C	1.02037	CUP2	YCR020C|PET18|S000000613|Protein required for respiratory growth and stability of the mitochondrial genome
YOL060C	1.01147	CUP2	YOL060C|MAM3|S000005421|Protein required for normal mitochondrial morphology, has similarity to hemolysins
YPR054W	1.00696	CUP2	YPR054W|SMK1|S000006258|Middle sporulation-specific mitogen-activated protein kinase (MAPK) required for production of the outer spore wall layers; negatively regulates activity of the glucan synthase subunit Gsc2p
YHR001W-A	0.99962	CUP2	YHR001W-A|QCR10|S000003529|Subunit of the ubiqunol-cytochrome c oxidoreductase complex which includes Cobp, Rip1p, Cyt1p, Cor1p, Qcr2p, Qcr6p, Qcr7p, Qcr8p, Qcr9p, and Qcr10p and comprises part of the mitochondrial respiratory chain
YPR123C	0.99796	CUP2	YPR123C||S000006327|Hypothetical protein
YKL148C	0.996532	CUP2	YKL148C|SDH1|S000001631|Flavoprotein subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p), which couples the oxidation of succinate to the transfer of electrons to ubiquinone
YFL063W	0.996511	CUP2	YFL063W||S000001831|Dubious open reading frame, based on available experimental and comparative sequence data
YPR106W	0.994557	CUP2	YPR106W|ISR1|S000006310|Predicted protein kinase, overexpression causes sensitivity to staurosporine, which is a potent inhibitor of protein kinase C
YIL107C	0.991371	CUP2	YIL107C|PFK26|S000001369|6-phosphofructo-2-kinase, inhibited by phosphoenolpyruvate and sn-glycerol 3-phosphate, has negligible fructose-2,6-bisphosphatase activity, transcriptional regulation involves protein kinase A
YDR036C	0.990066	CUP2	YDR036C|EHD3|S000002443|3-hydroxyisobutyryl-CoA hydrolase, member of a family of enoyl-CoA hydratase/isomerases; non-tagged protein is detected in highly purified mitochondria in high-throughput studies; phosphorylated; mutation affects fluid-phase endocytosis
YAL063C	0.989302	CUP2	YAL063C|FLO9|S000000059|Lectin-like protein with similarity to Flo1p, thought to be expressed and involved in flocculation
YBL102W	0.9791	CUP2	YBL102W|SFT2|S000000198|Non-essential tetra-spanning membrane protein found mostly in the late Golgi, can suppress some sed5 alleles; may be part of the transport machinery, but precise function is unknown; similar to mammalian syntaxin 5
YIL013C	0.978908	CUP2	YIL013C|PDR11|S000001275|ATP-binding cassette (ABC) transporter, multidrug transporter involved in multiple drug resistance; mediates sterol uptake when sterol biosynthesis is compromisedregulated by Pdr1p; required for anaerobic growth
YPL222C-A	0.976474	CUP2	YPL222C-A||S000028722|Identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YPL271W	0.975685	CUP2	YPL271W|ATP15|S000006192|Epsilon subunit of the F1 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; phosphorylated
YBR292C	0.974367	CUP2	YBR292C||S000000496|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YBR292C is not an essential gene
YDL053C	0.973845	CUP2	YDL053C|PBP4|S000002211|Pbp1p binding protein, interacts strongly with Pab1p-binding protein 1 (Pbp1p) in the yeast two-hybrid system; also interacts with Lsm12p in a copurification assay
YDL127W	0.973331	CUP2	YDL127W|PCL2|S000002285|G1 cyclin, associates with Pho85p cyclin-dependent kinase (Cdk) to contribute to entry into the mitotic cell cycle, essential for cell morphogenesis; localizes to sites of polarized cell growth
YDR391C	0.970913	CUP2	YDR391C||S000002799|Putative protein of unknown function, possibly involved in zinc homeostasis; Bdf1p-dependent transcription induced by salt stress; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YGR133W	0.968195	CUP2	YGR133W|PEX4|S000003365|Peroxisomal ubiquitin conjugating enzyme required for peroxisomal matrix protein import and peroxisome biogenesis
YBL082C	0.968016	CUP2	YBL082C|ALG3|S000000178|Dolichol-P-Man dependent alpha(1-3) mannosyltransferase, involved in the synthesis of dolichol-linked oligosaccharide donor for N-linked glycosylation of proteins
YHR151C	0.966506	CUP2	YHR151C|MTC6|S000001194|Putative protein of unknown function; YHR151C is synthetically sick with cdc13-1
YDR092W	0.965994	CUP2	YDR092W|UBC13|S000002499|Ubiquitin-conjugating enzyme involved in the error-free DNA postreplication repair pathway; interacts with Mms2p to assemble ubiquitin chains at the Ub Lys-63 residue; DNA damage triggers redistribution from the cytoplasm to the nucleus
YJR038C	0.965928	CUP2	YJR038C||S000003799|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YER010C	0.959408	CUP2	YER010C||S000000812|Protein of unknown function, forms a ring-shaped homotrimer; has similarity to members of the prokaryotic rraA family; possibly involved in a phosphotransfer reaction
YLR297W	0.959161	CUP2	YLR297W||S000004288|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; YLR297W is not an essential gene; induced by treatment with 8-methoxypsoralen and UVA irradiation
YCL035C	0.958446	CUP2	YCL035C|GRX1|S000000540|Hydroperoxide and superoxide-radical responsive heat-stable glutathione-dependent disulfide oxidoreductase with active site cysteine pair; protects cells from oxidative damage
YPL036W	0.957163	CUP2	YPL036W|PMA2|S000005957|Plasma membrane H+-ATPase, isoform of Pma1p, involved in pumping protons out of the cell; regulator of cytoplasmic pH and plasma membrane potential
YKL034W	0.955032	CUP2	YKL034W|TUL1|S000001517|Golgi-localized RING-finger ubiquitin ligase (E3), involved in ubiquitinating and sorting membrane proteins that contain polar transmembrane domains to multivesicular bodies for delivery to the vacuole for quality control purposes
YNL282W	0.953838	CUP2	YNL282W|POP3|S000005226|Subunit of both RNase MRP, which cleaves pre-rRNA, and nuclear RNase P, which cleaves tRNA precursors to generate mature 5' ends
YFL064C	0.952982	CUP2	YFL064C||S000001830|Putative protein of unknown function
YNL091W	0.951959	CUP2	YNL091W|NST1|S000005035|Protein of unknown function, mediates sensitivity to salt stress; interacts physically with the splicing factor Msl1p and also displays genetic interaction with MSL1
YBR145W	0.947292	CUP2	YBR145W|ADH5|S000000349|Alcohol dehydrogenase isoenzyme V; involved in ethanol production
YDR401W	0.946153	CUP2	YDR401W||S000002809|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YIR029W	0.945801	CUP2	YIR029W|DAL2|S000001468|Allantoicase, converts allantoate to urea and ureidoglycolate in the second step of allantoin degradation; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation
YOL055C	0.943312	CUP2	YOL055C|THI20|S000005416|Multifunctional protein with both hydroxymethylpyrimidine kinase and thiaminase activities; involved in thiamine biosynthesis and also in thiamine degradation; member of a gene family with THI21 and THI22; functionally redundant with Thi21p
YNR063W	0.941856	CUP2	YNR063W||S000005346|Putative zinc-cluster protein of unknown function
YNR069C	0.940583	CUP2	YNR069C|BSC5|S000005352|Protein of unknown function, ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression
YML017W	0.940309	CUP2	YML017W|PSP2|S000004479|Asn rich cytoplasmic protein that contains RGG motifs; high-copy suppressor of group II intron-splicing defects of a mutation in MRS2 and of a conditional mutation in POL1 (DNA polymerase alpha); possible role in mitochondrial mRNA splicing
YBR094W	0.937381	CUP2	YBR094W|PBY1|S000000298|Putative tubulin tyrosine ligase associated with P-bodies
YGR236C	0.936614	CUP2	YGR236C|SPG1|S000003468|Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YML055W	0.935442	CUP2	YML055W|SPC2|S000004519|Subunit of signal peptidase complex (Spc1p, Spc2p, Spc3p, Sec11p), which catalyzes cleavage of N-terminal signal sequences of proteins targeted to the secretory pathway; homologous to mammalian SPC25
YEL030C-A	0.934252	CUP2	YEL030C-A||S000028619|Identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YJL221C	0.932272	CUP2	YJL221C|FSP2|S000003757|Protein of unknown function, expression is induced during nitrogen limitation
YNL197C	0.929325	CUP2	YNL197C|WHI3|S000005141|RNA binding protein that sequesters CLN3 mRNA in cytoplasmic foci; cytoplasmic retention factor for Cdc28p and associated cyclins; regulates cell fate and dose-dependently regulates the critical cell size required for passage through Start
YDR406W	0.927635	CUP2	YDR406W|PDR15|S000002814|Plasma membrane ATP binding cassette (ABC) transporter, multidrug transporter and general stress response factor implicated in cellular detoxification; regulated by Pdr1p, Pdr3p and Pdr8p; promoter contains a PDR responsive element
YBR013C	0.926698	CUP2	YBR013C||S000000217|Putative protein of unknown function, haploid deletion mutant exhibits synthetic phenotype with alpha-synuclein
YPL024W	0.924566	CUP2	YPL024W|RMI1|S000005945|Involved in response to DNA damage; null mutants have increased rates of recombination and delayed S phase; interacts physically and genetically with Sgs1p (RecQ family member) and Top3p (topoisomerase III)
YDR505C	0.923772	CUP2	YDR505C|PSP1|S000002913|Asn and gln rich protein of unknown function; high-copy suppressor of POL1 (DNA polymerase alpha) and partial suppressor of CDC2 (polymerase delta) and CDC6 (pre-RC loading factor) mutations; overexpression results in growth inhibition
YFL061W	0.922663	CUP2	YFL061W|DDI2|S000001833|Protein whose expression is induced by DNA damage
YJL219W	0.922597	CUP2	YJL219W|HXT9|S000003755|Putative hexose transporter that is nearly identical to Hxt11p, has similarity to major facilitator superfamily (MFS) transporters, expression of HXT9 is regulated by transcription factors Pdr1p and Pdr3p
YDR529C	0.921286	CUP2	YDR529C|QCR7|S000002937|Subunit 7 of the ubiquinol cytochrome-c reductase complex, which is a component of the mitochondrial inner membrane electron transport chain; oriented facing the mitochondrial matrix; N-terminus appears to play a role in complex assembly
YLR251W	0.91841	CUP2	YLR251W|SYM1|S000004241|Protein required for ethanol metabolism; induced by heat shock and localized to the inner mitochondrial membrane; homologous to mammalian peroxisomal membrane protein Mpv17
YHR049C-A	0.917328	CUP2	YHR049C-A||S000003532|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YAL054C	0.913003	CUP2	YAL054C|ACS1|S000000050|Acetyl-coA synthetase isoform which, along with Acs2p, is the nuclear source of acetyl-coA for histone acetlyation; expressed during growth on nonfermentable carbon sources and under aerobic conditions
YIL134C-A	0.912291	CUP2	YIL134C-A||S000028556|Putative protein of unknown function, identified by fungal homology and RT-PCR
YIR025W	0.907548	CUP2	YIR025W|MND2|S000001464|Subunit of the anaphase-promoting complex (APC); needed for meiotic nuclear division
YMR165C	0.906234	CUP2	YMR165C|PAH1|S000004775|Mg2+-dependent phosphatidate (PA) phosphatase, catalyzes the dephosphorylation of PA to yield diacylglycerol and Pi, responsible for de novo lipid synthesis; homologous to mammalian lipin 1
YOR054C	0.905483	CUP2	YOR054C|VHS3|S000005580|Functionally redundant (see also SIS2) inhibitory subunit of Ppz1p, a PP1c-related ser/thr protein phosphatase Z isoform; synthetically lethal with sis2; putative phosphopantothenoylcysteine decarboxylase involved in coenzyme A biosynthesis
YJR148W	0.904756	CUP2	YJR148W|BAT2|S000003909|Cytosolic branched-chain amino acid aminotransferase, homolog of murine ECA39; highly expressed during stationary phase and repressed during logarithmic phase
YPL138C	0.902059	CUP2	YPL138C|SPP1|S000006059|Subunit of COMPASS (Set1C), a complex which methylates histone H3 on lysine 4 and is required in telomeric transcriptional silencing; PHD finger domain protein similar to human CGBP, an unmethylated CpG binding protein
YJR152W	0.901692	CUP2	YJR152W|DAL5|S000003913|Allantoin permease; ureidosuccinate permease; expression is constitutive but sensitive to nitrogen catabolite repression
YOR071C	0.901038	CUP2	YOR071C|NRT1|S000005597|High-affinity nicotinamide riboside transporter; also transports thiamine with low affinity; shares sequence similarity with Thi7p and Thi72p; proposed to be involved in 5-fluorocytosine sensitivity
YGL010W	0.896143	CUP2	YGL010W||S000002978|Putative protein of unknown function; YGL010W is not an essential gene
YGL006W	0.892695	CUP2	YGL006W|PMC1|S000002974|Vacuolar Ca2+ ATPase involved in depleting cytosol of Ca2+ ions; prevents growth inhibition by activation of calcineurin in the presence of elevated concentrations of calcium; similar to mammalian PMCA1a
YMR068W	0.887255	CUP2	YMR068W|AVO2|S000004672|Component of a complex containing the Tor2p kinase and other proteins, which may have a role in regulation of cell growth
YMR180C	0.88329	CUP2	YMR180C|CTL1|S000004792|RNA 5'-triphosphatase, localizes to both the nucleus and cytoplasm
YER187W	0.880552	CUP2	YER187W||S000000989|Putative protein of unknown function; induced in respiratory-deficient cells
YBL045C	0.878852	CUP2	YBL045C|COR1|S000000141|Core subunit of the ubiquinol-cytochrome c reductase complex (bc1 complex), which is a component of the mitochondrial inner membrane electron transport chain
YEL044W	0.877547	CUP2	YEL044W|IES6|S000000770|Protein that associates with the INO80 chromatin remodeling complex under low-salt conditions
YFR019W	0.876901	CUP2	YFR019W|FAB1|S000001915|1-phosphatidylinositol-3-phosphate 5-kinase; vacuolar membrane kinase that generates phosphatidylinositol (3,5)P2, which is involved in vacuolar sorting and homeostasis
YFL019C	0.876316	CUP2	YFL019C||S000001875|Dubious open reading frame unlikely to encode a protein; YFL019C is not an essential gene
YMR297W	0.875778	CUP2	YMR297W|PRC1|S000004912|Vacuolar carboxypeptidase Y (proteinase C), broad-specificity C-terminal exopeptidase involved in non-specific protein degradation in the vacuole; member of the serine carboxypeptidase family
YJR138W	0.874951	CUP2	YJR138W|IML1|S000003899|Protein of unknown function, green fluorescent protein (GFP)-fusion protein localizes to the vacuolar membrane
YGR087C	0.87427	CUP2	YGR087C|PDC6|S000003319|Minor isoform of pyruvate decarboxylase, decarboxylates pyruvate to acetaldehyde, involved in amino acid catabolism; transcription is glucose- and ethanol-dependent, and is strongly induced during sulfur limitation
YML118W	0.872445	CUP2	YML118W|NGL3|S000004587|Putative endonuclease, has a domain similar to a magnesium-dependent endonuclease motif in mRNA deadenylase Ccr4p; similar to Ngl1p and Ngl2p
YDR055W	0.869923	CUP2	YDR055W|PST1|S000002462|Cell wall protein that contains a putative GPI-attachment site; secreted by regenerating protoplasts; up-regulated by activation of the cell integrity pathway, as mediated by Rlm1p; upregulated by cell wall damage via disruption of FKS1
YDR533C	0.866971	CUP2	YDR533C|HSP31|S000002941|Possible chaperone and cysteine protease with similarity to E. coli Hsp31; member of the DJ-1/ThiJ/PfpI superfamily, which includes human DJ-1 involved in Parkinson's disease; exists as a dimer and contains a putative metal-binding site
YGR258C	0.866943	CUP2	YGR258C|RAD2|S000003490|Single-stranded DNA endonuclease, cleaves single-stranded DNA during nucleotide excision repair to excise damaged DNA; subunit of Nucleotide Excision Repair Factor 3 (NEF3); homolog of human XPG protein
YPL222W	0.866622	CUP2	YPL222W|FMP40|S000006143|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YGL227W	0.864284	CUP2	YGL227W|VID30|S000003196|Protein involved in proteasome-dependent catabolite degradation of fructose-1,6-bisphosphatase (FBPase); shifts the balance of nitrogen metabolism toward the production of glutamate; localized to the nucleus and the cytoplasm
YKR062W	0.854572	CUP2	YKR062W|TFA2|S000001770|TFIIE small subunit, involved in RNA polymerase II transcription initiation
YGR203W	0.854451	CUP2	YGR203W||S000003435|Putative protein with sequence similarity to protein tyrosine phosphatases of the CDC25-like phosphatase family; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YKL093W	0.852712	CUP2	YKL093W|MBR1|S000001576|Protein involved in mitochondrial functions and stress response; overexpression suppresses growth defects of hap2, hap3, and hap4 mutants
YPR111W	0.852318	CUP2	YPR111W|DBF20|S000006315|Ser/Thr kinase involved in late nuclear division, one of the mitotic exit network (MEN) proteins; necessary for the execution of cytokinesis
YGR121C	0.852076	CUP2	YGR121C|MEP1|S000003353|Ammonium permease; belongs to a ubiquitous family of cytoplasmic membrane proteins that transport only ammonium (NH4+); expression is under the nitrogen catabolite repression regulation
YOR328W	0.851805	CUP2	YOR328W|PDR10|S000005855|ATP-binding cassette (ABC) transporter, multidrug transporter involved in the pleiotropic drug resistance network; regulated by Pdr1p and Pdr3p
YEL006W	0.846952	CUP2	YEL006W|YEA6|S000000732|Putative mitochondrial NAD+ transporter, member of the mitochondrial carrier subfamily (see also YIA6); has putative human ortholog
YOR190W	0.846537	CUP2	YOR190W|SPR1|S000005716|Sporulation-specific exo-1,3-beta-glucanase; contributes to ascospore thermoresistance
YBR139W	0.845534	CUP2	YBR139W||S000000343|Putative serine type carboxypeptidase with a role in phytochelatin synthesis; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; expression induced by nitrogen limitation in a GLN3, GAT1-independent manner
YPL274W	0.842278	CUP2	YPL274W|SAM3|S000006195|High-affinity S-adenosylmethionine permease, required for utilization of S-adenosylmethionine as a sulfur source; has similarity to S-methylmethionine permease Mmp1p
YHR092C	0.840465	CUP2	YHR092C|HXT4|S000001134|High-affinity glucose transporter of the major facilitator superfamily, expression is induced by low levels of glucose and repressed by high levels of glucose
YLR326W	0.837751	CUP2	YLR326W||S000004318|Hypothetical protein
YIL055C	0.83575	CUP2	YIL055C||S000001317|Putative protein of unknown function
YPR160W	0.832534	CUP2	YPR160W|GPH1|S000006364|Non-essential glycogen phosphorylase required for the mobilization of glycogen, activity is regulated by cyclic AMP-mediated phosphorylation, expression is regulated by stress-response elements and by the HOG MAP kinase pathway
YJR052W	0.82863	CUP2	YJR052W|RAD7|S000003813|Protein that recognizes and binds damaged DNA in an ATP-dependent manner (with Rad16p) during nucleotide excision repair; subunit of Nucleotide Excision Repair Factor 4 (NEF4) and the Elongin-Cullin-Socs (ECS) ligase complex
YPR002W	0.817579	CUP2	YPR002W|PDH1|S000006206|Mitochondrial protein that participates in respiration, induced by diauxic shift; homologous to E. coli PrpD, may take part in the conversion of 2-methylcitrate to 2-methylisocitrate
YIL125W	0.81469	CUP2	YIL125W|KGD1|S000001387|Component of the mitochondrial alpha-ketoglutarate dehydrogenase complex, which catalyzes a key step in the tricarboxylic acid (TCA) cycle, the oxidative decarboxylation of alpha-ketoglutarate to form succinyl-CoA
YNR037C	0.811223	CUP2	YNR037C|RSM19|S000005320|Mitochondrial ribosomal protein of the small subunit, has similarity to E. coli S19 ribosomal protein
YLL005C	0.810533	CUP2	YLL005C|SPO75|S000003928|Meiosis-specific protein of unknown function, required for spore wall formation during sporulation; dispensable for both nuclear divisions during meiosis
YDR525W-A	0.809991	CUP2	YDR525W-A|SNA2|S000007236|Protein of unknown function, has similarity to Pmp3p, which is involved in cation transport; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YPR082C	0.808023	CUP2	YPR082C|DIB1|S000006286|17-kDa component of the U4/U6aU5 tri-snRNP, plays an essential role in pre-mRNA splicing, orthologue of hDIM1, the human U5-specific 15-kDa protein
YBR008C	0.80736	CUP2	YBR008C|FLR1|S000000212|Plasma membrane multidrug transporter of the major facilitator superfamily, involved in efflux of fluconazole, diazaborine, benomyl, methotrexate, and other drugs
YJR085C	0.807194	CUP2	YJR085C||S000003845|Putative protein of unknown function; GFP-fusion protein is induced in response to the DNA-damaging agent MMS; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YOR011W-A	0.803624	CUP2	YOR011W-A||S000028581|Putative protein of unknown function
YBR272C	0.803189	CUP2	YBR272C|HSM3|S000000476|Protein of unknown function, involved in DNA mismatch repair during slow growth; has weak similarity to Msh1p
YJL170C	0.799409	CUP2	YJL170C|ASG7|S000003706|Protein that regulates signaling from a G protein beta subunit Ste4p and its relocalization within the cell; specific to a-cells and induced by alpha-factor
YNL055C	0.797404	CUP2	YNL055C|POR1|S000005000|Mitochondrial porin (voltage-dependent anion channel), outer membrane protein required for the maintenance of mitochondrial osmotic stability and mitochondrial membrane permeability; phosphorylated
YBL099W	0.795273	CUP2	YBL099W|ATP1|S000000195|Alpha subunit of the F1 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; phosphorylated
YOL129W	0.793979	CUP2	YOL129W|VPS68|S000005489|Vacuolar membrane protein of unknown function involved in vacuolar protein sorting; also detected in the mitochondria
YMR147W	0.793263	CUP2	YMR147W||S000004755|Putative protein of unknown function
YPL026C	0.792456	CUP2	YPL026C|SKS1|S000005947|Putative serine/threonine protein kinase; involved in the adaptation to low concentrations of glucose independent of the SNF3 regulated pathway
YDL239C	0.791843	CUP2	YDL239C|ADY3|S000002398|Protein required for spore wall formation, thought to mediate assembly of a Don1p-containing structure at the leading edge of the prospore membrane via interaction with spindle pole body components; potentially phosphorylated by Cdc28p
YPL234C	0.791392	CUP2	YPL234C|TFP3|S000006155|Vacuolar ATPase V0 domain subunit c', involved in proton transport activity; hydrophobic integral membrane protein (proteolipid) containing four transmembrane segments; N and C termini are in the vacuolar lumen
YLR152C	0.789466	CUP2	YLR152C||S000004142|Putative protein of unknown function; YLR152C is not an essential gene
YBR060C	0.786731	CUP2	YBR060C|ORC2|S000000264|Subunit of the origin recognition complex, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; phosphorylated by Cdc28p
YDR516C	0.784139	CUP2	YDR516C|EMI2|S000002924|Non-essential protein of unknown function required for transcriptional induction of the early meiotic-specific transcription factor IME1; required for sporulation; expression is regulated by glucose-repression transcription factors Mig1/2p
YCR073W-A	0.783119	CUP2	YCR073W-A|SOL2|S000000718|Protein with a possible role in tRNA export; shows similarity to 6-phosphogluconolactonase non-catalytic domains but does not exhibit this enzymatic activity; homologous to Sol1p, Sol3p, and Sol4p
YGL248W	0.782303	CUP2	YGL248W|PDE1|S000003217|Low-affinity cyclic AMP phosphodiesterase, controls glucose and intracellular acidification-induced cAMP signaling, target of the cAMP-protein kinase A (PKA) pathway; glucose induces transcription and inhibits translation
YOR055W	0.78196	CUP2	YOR055W||S000005581|Dubious open reading frame unlikely to encode a functional protein; based on available experimental and comparative sequence data
YOR072W-A	0.780581	CUP2	YOR072W-A||S000028582|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YOR072W; originally identified by fungal homology and RT-PCR
YFL042C	0.779887	CUP2	YFL042C||S000001852|Putative protein of unknown function; YFL042C is not an essential gene
YKR046C	0.779713	CUP2	YKR046C|PET10|S000001754|Protein of unknown function that co-purifies with lipid particles; expression pattern suggests a role in respiratory growth; computational analysis of large-scale protein-protein interaction data suggests a role in ATP/ADP exchange
YBL039W-B	0.778964	CUP2	YBL039W-B||S000028517|Putative protein of unknown function
YKL004W	0.777919	CUP2	YKL004W|AUR1|S000001487|Phosphatidylinositol:ceramide phosphoinositol transferase (IPC synthase), required for sphingolipid synthesis; can mutate to confer aureobasidin A resistance
YNL215W	0.774786	CUP2	YNL215W|IES2|S000005159|Protein that associates with the INO80 chromatin remodeling complex under low-salt conditions
YGR230W	0.774196	CUP2	YGR230W|BNS1|S000003462|Protein with some similarity to Spo12p; overexpression bypasses need for Spo12p, but not required for meiosis
YPL181W	0.770882	CUP2	YPL181W|CTI6|S000006102|Protein that relieves transcriptional repression by binding to the Cyc8p-Tup1p corepressor and recruiting the SAGA complex to the repressed promoter; contains a PHD finger domain
YGR046W	0.768047	CUP2	YGR046W|TAM41|S000003278|Mitochondrial protein involved in protein import into the mitochondrial matrix; maintains the functional integrity of the TIM23 protein translocator complex; viability of null mutant is strain-dependent; mRNA is targeted to the bud
YAR068W	0.767218	CUP2	YAR068W||S000000091|Fungal-specific protein of unknown function; induced in respiratory-deficient cells
YML066C	0.765189	CUP2	YML066C|SMA2|S000004531|Protein of unknown function involved in the assembly of the prospore membrane during sporulation
YPR061C	0.763599	CUP2	YPR061C|JID1|S000006265|Probable Hsp40p co-chaperone, has a DnaJ-like domain and appears to be involved in ER-associated degradation of misfolded proteins containing a tightly folded cytoplasmic domain; inhibits replication of Brome mosaic virus in S. cerevisiae
YER066W	0.763393	CUP2	YER066W||S000000868|Putative protein of unknown function; YER066W is not an essential gene
YHR210C	0.763129	CUP2	YHR210C||S000001253|Putative protein of unknown function; non-essential gene; highly expressed under anaeorbic conditions; sequence similarity to aldose 1-epimerases such as GAL10
YHR206W	0.76123	CUP2	YHR206W|SKN7|S000001249|Nuclear response regulator and transcription factor, part of a branched two-component signaling system; required for optimal induction of heat-shock genes in response to oxidative stress; involved in osmoregulation
YIL102C-A	0.758593	CUP2	YIL102C-A||S000113587|Putative protein of unknown function, identified based on comparisons of the genome sequences of six Saccharomyces species
YGL033W	0.756505	CUP2	YGL033W|HOP2|S000003001|Meiosis-specific protein that localizes to chromosomes, preventing synapsis between nonhomologous chromosomes and ensuring synapsis between homologs; complexes with Mnd1p to promote homolog pairing and meiotic double-strand break repair
YOR376W	0.755357	CUP2	YOR376W||S000005903|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YOR376W is not an essential gene.
YLL061W	0.755107	CUP2	YLL061W|MMP1|S000003984|High-affinity S-methylmethionine permease, required for utilization of S-methylmethionine as a sulfur source; has similarity to S-adenosylmethionine permease Sam3p
YDR313C	0.754457	CUP2	YDR313C|PIB1|S000002721|RING-type ubiquitin ligase of the endosomal and vacuolar membranes, binds phosphatidylinositol(3)-phosphate; contains a FYVE finger domain
YGR239C	0.753067	CUP2	YGR239C|PEX21|S000003471|Peroxin required for targeting of peroxisomal matrix proteins containing PTS2; interacts with Pex7p; partially redundant with Pex18p
YLR259C	0.752576	CUP2	YLR259C|HSP60|S000004249|Tetradecameric mitochondrial chaperonin required for ATP-dependent folding of precursor polypeptides and complex assembly; prevents aggregation and mediates protein refolding after heat shock; role in mtDNA transmission; phosphorylated
YHR139C-A	0.751982	CUP2	YHR139C-A||S000003533|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR301W	0.750267	CUP2	YDR301W|CFT1|S000002709|RNA-binding subunit of the mRNA cleavage and polyadenylation factor; involved in poly(A) site recognition and required for both pre-mRNA cleavage and polyadenylation, 51% sequence similarity with mammalian AAUAA-binding subunit of CPSF
YIL144W	0.74863	CUP2	YIL144W|TID3|S000001406|Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); conserved coiled-coil protein involved in chromosome segregation, spindle checkpoint activity, kinetochore assembly and clustering
YPR009W	0.747198	CUP2	YPR009W|SUT2|S000006213|Putative transcription factor; multicopy suppressor of mutations that cause low activity of the cAMP/protein kinase A pathway; highly similar to Sut1p
YMR164C	0.746457	CUP2	YMR164C|MSS11|S000004774|Transcription factor involved in regulation of invasive growth and starch degradation; controls the activation of MUC1 and STA2 in response to nutritional signals
YFL054C	0.746356	CUP2	YFL054C||S000001840|Putative channel-like protein; similar to Fps1p; mediates passive diffusion of glycerol in the presence of ethanol
YDL182W	0.746034	CUP2	YDL182W|LYS20|S000002341|Homocitrate synthase isozyme, catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate, which is the first step in the lysine biosynthesis pathway; highly similar to the other isozyme, Lys21p
YGL071W	0.745488	CUP2	YGL071W|AFT1|S000003039|Transcription factor involved in iron utilization and homeostasis; binds the consensus site PyPuCACCCPu and activates the expression of target genes in response to changes in iron availability
YDL020C	0.743011	CUP2	YDL020C|RPN4|S000002178|Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses
YLR121C	0.74171	CUP2	YLR121C|YPS3|S000004111|Aspartic protease, attached to the plasma membrane via a glycosylphosphatidylinositol (GPI) anchor
YLR072W	0.741173	CUP2	YLR072W||S000004062|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; YLR072W is not an esssential gene
YIR028W	0.737939	CUP2	YIR028W|DAL4|S000001467|Allantoin permease; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation
YKL161C	0.735919	CUP2	YKL161C||S000001644|Protein kinase implicated in the Slt2p mitogen-activated (MAP) kinase signaling pathway; associates with Rlm1p
YPR064W	0.735267	CUP2	YPR064W||S000006268|Dubious open reading frame, unlikely to encode a functional protein; based on available experimental and comparative sequence data
YPL017C	0.731534	CUP2	YPL017C|IRC15|S000005938|Putative S-adenosylmethionine-dependent methyltransferase of the seven beta-strand family, required for accurate meiotic chromosome segregation; null mutant displays increased levels of spontaneous Rad52 foci
YBR063C	0.730792	CUP2	YBR063C||S000000267|Putative protein of unknown function; YBR063C is not an essential gene
YMR306C-A	0.730189	CUP2	YMR306C-A||S000004922|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOR020W-A	0.730153	CUP2	YOR020W-A||S000028526|Putative protein of unknown function, conserved in A. gossypii; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YPL035C	0.727258	CUP2	YPL035C||S000005956|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized gene YPL034W; YPL035C is not an essential gene
YDR343C	0.727033	CUP2	YDR343C|HXT6|S000002751|High-affinity glucose transporter of the major facilitator superfamily, nearly identical to Hxt7p, expressed at high basal levels relative to other HXTs, repression of expression by high glucose requires SNF3
YGR044C	0.726974	CUP2	YGR044C|RME1|S000003276|Zinc finger protein involved in control of meiosis; prevents meiosis by repressing IME1 expression and promotes mitosis by activating CLN2 expression; directly repressed by a1-a2 regulator; mediates cell type control of sporulation
YOR053W	0.725566	CUP2	YOR053W||S000005579|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene VHS3/YOR054C
YGL136C	0.724679	CUP2	YGL136C|MRM2|S000003104|Mitochondrial 2' O-ribose methyltransferase, required for methylation of U(2791) in 21S rRNA; MRM2 deletion confers thermosensitive respiration and loss of mitochondrial DNA; has similarity to Spb1p and Trm7p, and to E. coli FtsJ/RrmJ
YLR304C	0.72314	CUP2	YLR304C|ACO1|S000004295|Aconitase, required for the tricarboxylic acid (TCA) cycle and also independently required for mitochondrial genome maintenance; phosphorylated; component of the mitochondrial nucleoid; mutation leads to glutamate auxotrophy
YBL055C	0.721974	CUP2	YBL055C||S000000151|3'-->5' exonuclease and endonuclease with a possible role in apoptosis; has similarity to mammalian and C. elegans apoptotic nucleases
YBR056W	0.721548	CUP2	YBR056W||S000000260|Putative cytoplasmic protein of unknown function
YCL040W	0.721115	CUP2	YCL040W|GLK1|S000000545|Glucokinase, catalyzes the phosphorylation of glucose at C6 in the first irreversible step of glucose metabolism; one of three glucose phosphorylating enzymes; expression regulated by non-fermentable carbon sources
YIL066C	0.720946	CUP2	YIL066C|RNR3|S000001328|One of two large regulatory subunits of ribonucleotide-diphosphate reductase; the RNR complex catalyzes rate-limiting step in dNTP synthesis, regulated by DNA replication and DNA damage checkpoint pathways via localization of small subunits
YOR186C-A	0.719907	CUP2	YOR186C-A||S000028715|Identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YPL162C	0.717426	CUP2	YPL162C||S000006083|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the membrane of vacuole with cell cycle-correlated morphology
YNL125C	0.717018	CUP2	YNL125C|ESBP6|S000005069|Protein with similarity to monocarboxylate permeases, appears not to be involved in transport of monocarboxylates such as lactate, pyruvate or acetate across the plasma membrane
YBR182C	0.71654	CUP2	YBR182C|SMP1|S000000386|Putative transcription factor involved in regulating the response to osmotic stress; member of the MADS-box family of transcription factors
YPR028W	0.715701	CUP2	YPR028W|YOP1|S000006232|Membrane protein that interacts with Yip1p to mediate membrane traffic; overexpression results in cell death and accumulation of internal cell membranes; regulates vesicular traffic in stressed cells
YDL196W	0.713722	CUP2	YDL196W||S000002355|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; open reading frame is located in promoter region of essential gene SEC31
YOL035C	0.713295	CUP2	YOL035C||S000005395|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR437W	0.70997	CUP2	YDR437W|GPI19|S000002845|Subunit of GPI-GlcNAc transferase involved in synthesis of N-acetylglucosaminyl phosphatidylinositol (GlcNAc-PI), which is the first intermediate in glycosylphosphatidylinositol (GPI) anchor synthesis, shares similarity with mammalian PIG-P
YDL079C	0.709062	CUP2	YDL079C|MRK1|S000002237|Glycogen synthase kinase 3 (GSK-3) homolog; one of four GSK-3 homologs in S. cerevisiae that function to activate Msn2p-dependent transcription of stress responsive genes and that function in protein degradation
YGL056C	0.707901	CUP2	YGL056C|SDS23|S000003024|One of two S. cerevisiae homologs (Sds23p and Sds24p) of the Schizosaccharomyces pombe Sds23 protein, which genetic studies have implicated in APC/cyclosome regulation
YLR366W	0.703961	CUP2	YLR366W||S000004358|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YLR364C-A
YPL182C	0.702772	CUP2	YPL182C||S000006103|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene CTI6/YPL181W
YDR009W	0.701121	CUP2	YDR009W|GAL3|S000002416|Transcriptional regulator involved in activation of the GAL genes in response to galactose; forms a complex with Gal80p to relieve Gal80p inhibition of Gal4p; binds galactose and ATP but does not have galactokinase activity
YMR170C	0.696324	CUP2	YMR170C|ALD2|S000004780|Cytoplasmic aldehyde dehydrogenase, involved in ethanol oxidation and beta-alanine biosynthesis; uses NAD+ as the preferred coenzyme; expression is stress induced and glucose repressed; very similar to Ald3p
YDR387C	0.695481	CUP2	YDR387C||S000002795|Putative transporter, member of the sugar porter family; YDR387C is not an essential gene
YAL018C	0.691556	CUP2	YAL018C||S000000016|Putative protein of unknown function
YFL062W	0.690498	CUP2	YFL062W|COS4|S000001832|Protein of unknown function, member of the DUP380 subfamily of conserved, often subtelomerically-encoded proteins
YKL020C	0.68951	CUP2	YKL020C|SPT23|S000001503|ER membrane protein involved in regulation of OLE1 transcription, acts with homolog Mga2p; inactive ER form dimerizes and one subunit is then activated by ubiquitin/proteasome-dependent processing followed by nuclear targeting
YMR090W	0.688617	CUP2	YMR090W||S000004696|Putative protein of unknown function with similarity to DTDP-glucose 4,6-dehydratases; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YMR090W is not an essential gene
YHL024W	0.68836	CUP2	YHL024W|RIM4|S000001016|Putative RNA-binding protein required for the expression of early and middle sporulation genes
YER075C	0.688246	CUP2	YER075C|PTP3|S000000877|Phosphotyrosine-specific protein phosphatase involved in the inactivation of mitogen-activated protein kinase (MAPK) during osmolarity sensing; dephosporylates Hog1p MAPK and regulates its localization; localized to the cytoplasm
YMR216C	0.688225	CUP2	YMR216C|SKY1|S000004829|SR protein kinase (SRPK) involved in regulating proteins involved in mRNA metabolism and cation homeostasis; similar to human SRPK1
YDR001C	0.688117	CUP2	YDR001C|NTH1|S000002408|Neutral trehalase, degrades trehalose; required for thermotolerance and may mediate resistance to other cellular stresses; may be phosphorylated by Cdc28p
YJL133C-A	0.687696	CUP2	YJL133C-A||S000028805|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR463W	0.68699	CUP2	YDR463W|STP1|S000002871|Transcription factor, activated by proteolytic processing in response to signals from the SPS sensor system for external amino acids; activates transcription of amino acid permease genes and may have a role in tRNA processing
YKL067W	0.686279	CUP2	YKL067W|YNK1|S000001550|Nucleoside diphosphate kinase, catalyzes the transfer of gamma phosphates from nucleoside triphosphates, usually ATP, to nucleoside diphosphates by a mechanism that involves formation of an autophosphorylated enzyme intermediate
YHR080C	0.686032	CUP2	YHR080C||S000001122|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YBL033C	0.684884	CUP2	YBL033C|RIB1|S000000129|GTP cyclohydrolase II; catalyzes the first step of the riboflavin biosynthesis pathway
YLR327C	0.684178	CUP2	YLR327C|TMA10|S000004319|Protein of unknown function that associates with ribosomes
YPL018W	0.683157	CUP2	YPL018W|CTF19|S000005939|Outer kinetochore protein, required for accurate mitotic chromosome segregation; component of the kinetochore sub-complex COMA (Ctf19p, Okp1p, Mcm21p, Ame1p) that functions as a platform for kinetochore assembly
YPR024W	0.682466	CUP2	YPR024W|YME1|S000006228|Subunit, with Mgr1p, of the mitochondrial inner membrane i-AAA protease complex, which is responsible for degradation of unfolded or misfolded mitochondrial gene products; mutation causes an elevated rate of mitochondrial turnover
YCR079W	0.682105	CUP2	YCR079W|PTC6|S000002133|Mitochondrial protein phosphatase of type 2C with similarity to mammalian PP1Ks; involved in mitophagy; null mutant is sensitive to rapamycin and has decreased phosphorylation of the Pda1 subunit of pyruvate dehydrogenase
YGR273C	0.681717	CUP2	YGR273C||S000003505|Putative protein of unknown function; deletion mutant has no readily detectable phenotype; expression downregulated by treatment with 8-methoxypsoralen plus UVA irradiation
YJR153W	0.681507	CUP2	YJR153W|PGU1|S000003914|Endo-polygalacturonase, pectolytic enzyme that hydrolyzes the alpha-1,4-glycosidic bonds in the rhamnogalacturonan chains in pectins
YLR213C	0.67905	CUP2	YLR213C|CRR1|S000004203|Putative glycoside hydrolase of the spore wall envelope; required for normal spore wall assembly, possibly for cross-linking between the glucan and chitosan layers; expressed during sporulation
YDR296W	0.678493	CUP2	YDR296W|MHR1|S000002704|Protein involved in homologous recombination in mitochondria and in transcription regulation in nucleus; binds to activation domains of acidic activators; required for recombination-dependent mtDNA partitioning
YBR083W	0.677152	CUP2	YBR083W|TEC1|S000000287|Transcription factor required for full Ty1 epxression, Ty1-mediated gene activation, and haploid invasive and diploid pseudohyphal growth; TEA/ATTS DNA-binding domain family member
YBR064W	0.675007	CUP2	YBR064W||S000000268|Dubious open reading frame unlikely to encode a protein; partially overlaps the uncharacterized ORF YBR063C
YBR140C	0.674436	CUP2	YBR140C|IRA1|S000000344|GTPase-activating protein that negatively regulates RAS by converting it from the GTP- to the GDP-bound inactive form, required for reducing cAMP levels under nutrient limiting conditions, mediates membrane association of adenylate cyclase
YDL245C	0.674426	CUP2	YDL245C|HXT15|S000002404|Protein of unknown function with similarity to hexose transporter family members, expression is induced by low levels of glucose and repressed by high levels of glucose
YLR425W	0.673602	CUP2	YLR425W|TUS1|S000004417|Guanine nucleotide exchange factor (GEF) that functions to modulate Rho1p activity as part of the cell integrity signaling pathway; multicopy suppressor of tor2 mutation and ypk1 ypk2 double mutation; potential Cdc28p substrate
YOR186W	0.667561	CUP2	YOR186W||S000005712|Putative protein of unknown function; proper regulation of expression during heat stress is sphingolipid-dependent
YER142C	0.662674	CUP2	YER142C|MAG1|S000000944|3-methyl-adenine DNA glycosylase involved in protecting DNA against alkylating agents; initiates base excision repair by removing damaged bases to create abasic sites that are subsequently repaired
YJR137C	0.660395	CUP2	YJR137C|ECM17|S000003898|Sulfite reductase beta subunit, involved in amino acid biosynthesis, transcription repressed by methionine
YCL042W	0.654299	CUP2	YCL042W||S000000547|Putative protein of unknown function; epitope-tagged protein localizes to the cytoplasm
YBR228W	0.653212	CUP2	YBR228W|SLX1|S000000432|Subunit of a complex, with Slx4p, that hydrolyzes 5' branches from duplex DNA in response to stalled or converging replication forks; function overlaps with that of Sgs1p-Top3p
YKL005C	0.650905	CUP2	YKL005C|BYE1|S000001488|Negative regulator of transcription elongation, contains a TFIIS-like domain and a PHD finger, multicopy suppressor of temperature-sensitive ess1 mutations, probably binds RNA polymerase II large subunit
YEL030W	0.650883	CUP2	YEL030W|ECM10|S000000756|Heat shock protein of the Hsp70 family, localized in mitochondrial nucleoids, plays a role in protein translocation, interacts with Mge1p in an ATP-dependent manner; overexpression induces extensive mitochondrial DNA aggregations
YDR425W	0.650853	CUP2	YDR425W|SNX41|S000002833|Sorting nexin, involved in the retrieval of late-Golgi SNAREs from the post-Golgi endosome to the trans-Golgi network; interacts with Snx4p
YEL050W-A	0.650734	CUP2	YEL050W-A||S000028545|Dubious open reading frame unlikely to encode a functional protein, identified by fungal homology and RT-PCR
YBR214W	0.649691	CUP2	YBR214W|SDS24|S000000418|One of two S. cerevisiae homologs (Sds23p and Sds24p) of the Schizosaccharomyces pombe Sds23 protein, which genetic studies have implicated in APC/cyclosome regulation; may play an indirect role in fluid-phase endocytosis
YNL093W	0.649264	CUP2	YNL093W|YPT53|S000005037|GTPase, similar to Ypt51p and Ypt52p and to mammalian rab5; required for vacuolar protein sorting and endocytosis
YGL154C	0.646683	CUP2	YGL154C|LYS5|S000003122|Phosphopantetheinyl transferase involved in lysine biosynthesis; converts inactive apo-form of Lys2p (alpha-aminoadipate reductase) into catalytically active holo-form by posttranslational addition of phosphopantetheine
YBL106C	0.645241	CUP2	YBL106C|SRO77|S000000202|Protein with roles in exocytosis and cation homeostasis; functions in docking and fusion of post-Golgi vesicles with plasma membrane; homolog of Sro7p and Drosophila lethal giant larvae tumor suppressor; interacts with SNARE protein Sec9p
YBR132C	0.644337	CUP2	YBR132C|AGP2|S000000336|High affinity polyamine permease, preferentially uses spermidine over putrescine; expression is down-regulated by osmotic stress; plasma membrane carnitine transporter, also functions as a low-affinity amino acid permease
YBR209W	0.643708	CUP2	YBR209W||S000000413|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YBR209W is not an essential gene
YEL052W	0.639452	CUP2	YEL052W|AFG1|S000000778|Conserved protein that may act as a chaperone in the degradation of misfolded or unassembled cytochrome c oxidase subunits; localized to matrix face of the mitochondrial inner membrane; member of the AAA family but lacks a protease domain
YIL109C	0.639202	CUP2	YIL109C|SEC24|S000001371|Component of the Sec23p-Sec24p heterodimeric complex of the COPII vesicle coat; involved in ER to Golgi transport, cargo selection and autophagy; required for the binding of the Sec13 complex to ER membranes; homologous to Lst1p and Lss1p
YPL013C	0.635702	CUP2	YPL013C|MRPS16|S000005934|Mitochondrial ribosomal protein of the small subunit
YOR338W	0.633566	CUP2	YOR338W||S000005865|Putative protein of unknown function; YOR338W transcription is regulated by Azf1p and its transcript is a specific target of the G protein effector Scp160p; identified as being required for sporulation in a high-throughput mutant screen
YOR236W	0.632833	CUP2	YOR236W|DFR1|S000005762|Dihydrofolate reductase, part of the dTTP biosynthetic pathway, involved in folate metabolism, possibly required for mitochondrial function
YPL261C	0.630235	CUP2	YPL261C||S000006182|Dubious open reading frame unlikely to encode a protein; partially overlaps the uncharacterized ORF YPL260W
YGR288W	0.629886	CUP2	YGR288W|MAL13|S000003520|MAL-activator protein, part of complex locus MAL1; nonfunctional in genomic reference strain S288C
YMR311C	0.62836	CUP2	YMR311C|GLC8|S000004928|Regulatory subunit of protein phosphatase 1 (Glc7p), involved in glycogen metabolism and chromosome segregation; proposed to regulate Glc7p activity via conformational alteration; ortholog of the mammalian protein phosphatase inhibitor 2
YJR147W	0.624446	CUP2	YJR147W|HMS2|S000003908|Protein with similarity to heat shock transcription factors; overexpression suppresses the pseudohyphal filamentation defect of a diploid mep1 mep2 homozygous null mutant
YDR090C	0.622645	CUP2	YDR090C||S000002497|Putative protein of unknown function
YGL194C	0.621629	CUP2	YGL194C|HOS2|S000003162|Histone deacetylase required for gene activation via specific deacetylation of lysines in H3 and H4 histone tails; subunit of the Set3 complex, a meiotic-specific repressor of sporulation specific genes that contains deacetylase activity
YIL065C	0.621492	CUP2	YIL065C|FIS1|S000001327|Mitochondrial outer membrane protein involved in membrane fission, required for localization of Dnm1p and Mdv1p during mitochondrial division; mediates ethanol-induced apoptosis and ethanol-induced mitochondrial fragmentation
YEL074W	0.6207	CUP2	YEL074W||S000000800|Hypothetical protein
YIL143C	0.618241	CUP2	YIL143C|SSL2|S000001405|Component of the holoenzyme form of RNA polymerase transcription factor TFIIH, has DNA-dependent ATPase/helicase activity and is required, with Rad3p, for unwinding promoter DNA; involved in DNA repair; homolog of human ERCC3
YIL033C	0.617849	CUP2	YIL033C|BCY1|S000001295|Regulatory subunit of the cyclic AMP-dependent protein kinase (PKA), a component of a signaling pathway that controls a variety of cellular processes, including metabolism, cell cycle, stress response, stationary phase, and sporulation
YHR176W	0.614981	CUP2	YHR176W|FMO1|S000001219|Flavin-containing monooxygenase, localized to the cytoplasmic face of the ER membrane; catalyzes oxidation of biological thiols to maintain the ER redox buffer ratio for correct folding of disulfide-bonded proteins
YDL115C	0.614257	CUP2	YDL115C|IWR1|S000002273|Protein of unknown function, deletion causes hypersensitivity to the K1 killer toxin
YIR024C	0.613789	CUP2	YIR024C||S000001463|Protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; interacts with Arh1p, a mitochondrial oxidoreductase; deletion mutant has a respiratory growth defect
YGL180W	0.613622	CUP2	YGL180W|ATG1|S000003148|Protein serine/threonine kinase required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; structurally required for pre-autophagosome formation; during autophagy forms a complex with Atg13p and Atg17p
YDR231C	0.613551	CUP2	YDR231C|COX20|S000002639|Mitochondrial inner membrane protein, required for proteolytic processing of Cox2p and its assembly into cytochrome c oxidase
YNL305C	0.612711	CUP2	YNL305C||S000005249|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; YNL305C is not an essential gene
YNL180C	0.612158	CUP2	YNL180C|RHO5|S000005124|Non-essential small GTPase of the Rho/Rac subfamily of Ras-like proteins, likely involved in protein kinase C (Pkc1p)-dependent signal transduction pathway that controls cell integrity
YGL023C	0.611832	CUP2	YGL023C|PIB2|S000002991|Protein binding phosphatidylinositol 3-phosphate, involved in telomere-proximal repression of gene expression; similar to Fab1 and Vps27
YOR134W	0.610373	CUP2	YOR134W|BAG7|S000005660|Rho GTPase activating protein (RhoGAP), stimulates the intrinsic GTPase activity of Rho1p, which plays a role in actin cytoskeleton organization and control of cell wall synthesis; structurally and functionally related to Sac7p
YGL249W	0.607417	CUP2	YGL249W|ZIP2|S000003218|Meiosis-specific protein involved in normal synaptonemal complex formation and pairing between homologous chromosomes during meiosis
YBR293W	0.606638	CUP2	YBR293W|VBA2|S000000497|Permease of basic amino acids in the vacuolar membrane
YLR055C	0.605233	CUP2	YLR055C|SPT8|S000004045|Subunit of the SAGA transcriptional regulatory complex but not present in SAGA-like complex SLIK/SALSA, required for SAGA-mediated inhibition at some promoters
YIL089W	0.605029	CUP2	YIL089W||S000001351|Putative protein of unknown function
YBR053C	0.604862	CUP2	YBR053C||S000000257|Putative protein of unknown function; induced by cell wall perturbation
YNL012W	0.604477	CUP2	YNL012W|SPO1|S000004957|Meiosis-specific protein with similarity to phospholipase B, required for meiotic spindle pole body duplication and separation; required for spore formation
YEL049W	0.603679	CUP2	YEL049W|PAU2|S000000775|Part of 23-member seripauperin multigene family encoded mainly in subtelomeric regions, active during alcoholic fermentation, regulated by anaerobiosis, negatively regulated by oxygen, repressed by heme
YHR209W	0.603258	CUP2	YHR209W|CRG1|S000001252|Putative S-adenosylmethionine-dependent methyltransferase; mediates cantharidin resistance
YDL010W	0.601855	CUP2	YDL010W|GRX6|S000002168|Cis-golgi localized monothiol glutaredoxin that binds an iron-sulfur cluster; more similar in activity to dithiol than other monothiol glutaredoxins; involved in the oxidative stress response; functional overlap with GRX6
YAL044W-A	0.601792	CUP2	YAL044W-A||S000007586|Putative protein of unknown function; similar to S. pombe uvi31 which is a putative DNA repair protein
YHL041W	0.601282	CUP2	YHL041W||S000001033|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data
YDR347W	0.601281	CUP2	YDR347W|MRP1|S000002755|Mitochondrial ribosomal protein of the small subunit; MRP1 exhibits genetic interactions with PET122, encoding a COX3-specific translational activator, and with PET123, encoding a small subunit mitochondrial ribosomal protein
YJR117W	0.600968	CUP2	YJR117W|STE24|S000003878|Highly conserved zinc metalloprotease that functions in two steps of a-factor maturation, C-terminal CAAX proteolysis and the first step of N-terminal proteolytic processing; contains multiple transmembrane spans
YCR033W	0.598812	CUP2	YCR033W|SNT1|S000000629|Subunit of the Set3C deacetylase complex that interacts directly with the Set3C subunit, Sif2p; putative DNA-binding protein
YDR444W	0.59686	CUP2	YDR444W||S000002852|Putative protein of unknown function
YLR334C	0.596769	CUP2	YLR334C||S000004326|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps a stand-alone long terminal repeat sequence whose presence indicates a retrotransposition event occurred here
YGL236C	0.596172	CUP2	YGL236C|MTO1|S000003205|Mitochondrial protein, forms a heterodimer complex with Mss1p that performs the 5-carboxymethylaminomethyl modification of the wobble uridine base in mitochondrial tRNAs; required for respiration in paromomycin-resistant 15S rRNA mutants
YOR245C	0.59574	CUP2	YOR245C|DGA1|S000005771|Diacylglycerol acyltransferase, catalyzes the terminal step of triacylglycerol (TAG) formation, acylates diacylglycerol using acyl-CoA as an acyl donor, localized to lipid particles
YLR189C	0.593703	CUP2	YLR189C|ATG26|S000004179|UDP-glucose:sterol glucosyltransferase, conserved enzyme involved in synthesis of sterol glucoside membrane lipids; in contrast to ATG26 from P. pastoris, S. cerevisiae ATG26 is not involved in autophagy
YIL099W	0.591999	CUP2	YIL099W|SGA1|S000001361|Intracellular sporulation-specific glucoamylase involved in glycogen degradation; induced during starvation of a/a diploids late in sporulation, but dispensable for sporulation
YCR088W	0.591683	CUP2	YCR088W|ABP1|S000000684|Actin-binding protein of the cortical actin cytoskeleton, important for activation of the Arp2/3 complex that plays a key role actin in cytoskeleton organization
YOR062C	0.590386	CUP2	YOR062C||S000005588|Protein of unknown function; similar to YKR075Cp and Reg1p; expression regulated by glucose and Rgt1p; GFP-fusion protein is induced in response to the DNA-damaging agent MMS
YOR374W	0.590133	CUP2	YOR374W|ALD4|S000005901|Mitochondrial aldehyde dehydrogenase, required for growth on ethanol and conversion of acetaldehyde to acetate; phosphorylated; activity is K+ dependent; utilizes NADP+ or NAD+ equally as coenzymes; expression is glucose repressed
YLR030W	0.582976	CUP2	YLR030W||S000004020|Putative protein of unknown function
YPL048W	0.582064	CUP2	YPL048W|CAM1|S000005969|Nuclear protein required for transcription of MXR1; binds the MXR1 promoter in the presence of other nuclear factors; binds calcium and phospholipids; has similarity to translational cofactor EF-1 gamma
YGR067C	0.58099	CUP2	YGR067C||S000003299|Putative protein of unknown function; contains a zinc finger motif similar to that of Adr1p
YCR085W	0.579822	CUP2	YCR085W||S000000681|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YIL097W	0.578681	CUP2	YIL097W|FYV10|S000001359|Protein of unknown function, required for survival upon exposure to K1 killer toxin; involved in proteasome-dependent catabolite inactivation of FBPase; contains CTLH domain; plays role in anti-apoptosis
YGR232W	0.578678	CUP2	YGR232W|NAS6|S000003464|Regulatory, non-ATPase subunit of the 26S proteasome; homolog of the human oncoprotein gankyrin, which interacts with the retinoblastoma tumor suppressor (Rb) and cyclin-dependent kinase 4/6
YKL018C-A	0.577064	CUP2	YKL018C-A||S000007615|Putative protein of unknown function; identified by homology; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YGL007W	0.576346	CUP2	YGL007W|BRP1|S000002975|Dubious ORF located in the upstream region of PMA1, deletion leads to polyamine resistance due to downregulation of PMA1
YER067W	0.576208	CUP2	YER067W||S000000869|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YER067W is not an essential gene
YFR017C	0.576107	CUP2	YFR017C||S000001913|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and is induced in response to the DNA-damaging agent MMS; YFR017C is not an essential gene
YER186C	0.575349	CUP2	YER186C||S000000988|Putative protein of unknown function
YDR528W	0.574069	CUP2	YDR528W|HLR1|S000002936|Protein involved in regulation of cell wall composition and integrity and response to osmotic stress; overproduction suppresses a lysis sensitive PKC mutation; similar to Lre1p, which functions antagonistically to protein kinase A
YGL062W	0.57206	CUP2	YGL062W|PYC1|S000003030|Pyruvate carboxylase isoform, cytoplasmic enzyme that converts pyruvate to oxaloacetate; highly similar to isoform Pyc2p but differentially regulated; mutations in the human homolog are associated with lactic acidosis
YBL017C	0.571419	CUP2	YBL017C|PEP1|S000000113|Type I transmembrane sorting receptor for multiple vacuolar hydrolases; cycles between the late-Golgi and prevacuolar endosome-like compartments
YOR211C	0.570917	CUP2	YOR211C|MGM1|S000005737|Mitochondrial GTPase related to dynamin, present in a complex containing Ugo1p and Fzo1p; required for normal morphology of cristae and for stability of Tim11p; homolog of human OPA1 involved in autosomal dominant optic atrophy
YDL011C	0.569739	CUP2	YDL011C||S000002169|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the uncharacterized ORF YDL010W
YNL176C	0.568718	CUP2	YNL176C||S000005120|Cell cycle-regulated gene of unknown function, promoter bound by Fkh2p
YDR169C	0.567345	CUP2	YDR169C|STB3|S000002576|Protein that binds Sin3p in a two-hybrid assay
YBL100C	0.567132	CUP2	YBL100C||S000000196|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; almost completely overlaps the 5' end of ATP1
YDR214W	0.565399	CUP2	YDR214W|AHA1|S000002622|Co-chaperone that binds to Hsp82p and activates its ATPase activity; similar to Hch1p; expression is regulated by stresses such as heat shock
YNL042W	0.5653	CUP2	YNL042W|BOP3|S000004987|Protein of unknown function, potential Cdc28p substrate; overproduction suppresses a pam1 slv3 double null mutation and confers resistance to methylmercury
YLR315W	0.565224	CUP2	YLR315W|NKP2|S000004307|Non-essential kinetochore protein, subunit of the Ctf19 central kinetochore complex (Ctf19p-Mcm21p-Okp1p-Mcm22p-Mcm16p-Ctf3p-Chl4p-Mcm19p-Nkp1p-Nkp2p-Ame1p-Mtw1p)
YJR039W	0.563536	CUP2	YJR039W||S000003800|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YOR100C	0.563333	CUP2	YOR100C|CRC1|S000005626|Mitochondrial inner membrane carnitine transporter, required for carnitine-dependent transport of acetyl-CoA from peroxisomes to mitochondria during fatty acid beta-oxidation
YNL179C	0.562898	CUP2	YNL179C||S000005123|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; deletion in cyr1 mutant results in loss of stress resistance
YGL208W	0.561818	CUP2	YGL208W|SIP2|S000003176|One of three beta subunits of the Snf1 serine/threonine protein kinase complex involved in the response to glucose starvation; null mutants exhibit accelerated aging; N-myristoylprotein localized to the cytoplasm and the plasma membrane
YJL057C	0.560687	CUP2	YJL057C|IKS1|S000003593|Putative serine/threonine kinase; expression is induced during mild heat stress; deletion mutants are hypersensitive to copper sulphate and resistant to sorbate; interacts with an N-terminal fragment of Sst2p
YIL166C	0.558602	CUP2	YIL166C||S000001428|Putative protein with similarity to the allantoate permease (Dal5p) subfamily of the major facilitator superfamily; mRNA expression is elevated by sulfur limitation; YIL166C is a non-essential gene
YBL073W	0.557868	CUP2	YBL073W||S000000169|Hypothetical protein; open reading frame overlaps 5' end of essential AAR2 gene encoding a component of the U5 snRNP required for splicing of U3 precursors
YEL007W	0.557759	CUP2	YEL007W||S000000733|Putative protein with sequence similarity to S. pombe gti1+ (gluconate transport inducer 1)
YJL123C	0.55629	CUP2	YJL123C|MTC1|S000003659|Protein of unknown function that may interact with ribosomes; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and to COPI-coated vesicles (early Golgi); YJL123C is synthetically lethal with cdc13-1
YGL163C	0.555567	CUP2	YGL163C|RAD54|S000003131|DNA-dependent ATPase, stimulates strand exchange by modifying the topology of double-stranded DNA; involved in the recombinational repair of double-strand breaks in DNA during vegetative growth and meiosis; member of the SWI/SNF family
YDL124W	0.552944	CUP2	YDL124W||S000002282|NADPH-dependent alpha-keto amide reductase; reduces aromatic alpha-keto amides, aliphatic alpha-keto esters, and aromatic alpha-keto esters; member of the aldo-keto reductase (AKR) family
YHR021W-A	0.55099	CUP2	YHR021W-A|ECM12|S000003531|Non-essential protein of unknown function
YKL071W	0.550339	CUP2	YKL071W||S000001554|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YDR530C	0.550135	CUP2	YDR530C|APA2|S000002938|Diadenosine 5',5''-P1,P4-tetraphosphate phosphorylase II (AP4A phosphorylase), involved in catabolism of bis(5'-nucleosidyl) tetraphosphates; has similarity to Apa1p
YJL094C	0.548795	CUP2	YJL094C|KHA1|S000003630|Putative K+/H+ antiporter with a probable role in intracellular cation homeostasis, localized to Golgi vesicles and detected in highly purified mitochondria in high-throughput studies
YBL074C	0.548777	CUP2	YBL074C|AAR2|S000000170|Component of the U5 snRNP, required for splicing of U3 precursors; originally described as a splicing factor specifically required for splicing pre-mRNA of the MATa1 cistron
YLR395C	0.548282	CUP2	YLR395C|COX8|S000004387|Subunit VIII of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain
YNL335W	0.544074	CUP2	YNL335W|DDI3|S000005279|Hypothetical protein
YFL041W-A	0.543915	CUP2	YFL041W-A||S000028547|Putative protein of unknown function; identified by fungal homology and RT-PCR
YJL100W	0.543391	CUP2	YJL100W|LSB6|S000003636|Type II phosphatidylinositol 4-kinase that binds Las17p, which is a homolog of human Wiskott-Aldrich Syndrome protein involved in actin patch assembly and actin polymerization
YCL025C	0.542481	CUP2	YCL025C|AGP1|S000000530|Low-affinity amino acid permease with broad substrate range, involved in uptake of asparagine, glutamine, and other amino acids; expression is regulated by the SPS plasma membrane amino acid sensor system (Ssy1p-Ptr3p-Ssy5p)
YBL054W	0.542243	CUP2	YBL054W||S000000150|Protein of unknown function involved in rRNA and ribosome biosynthesis
YJL161W	0.54103	CUP2	YJL161W|FMP33|S000003697|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YFL020C	0.54055	CUP2	YFL020C|PAU5|S000001874|Part of 23-member seripauperin multigene family encoded mainly in subtelomeric regions, active during alcoholic fermentation, regulated by anaerobiosis, negatively regulated by oxygen, repressed by heme
YCR086W	0.538507	CUP2	YCR086W|CSM1|S000000682|Nucleolar protein that forms a complex with Lrs4p which binds Mam1p at kinetochores during meiosis I to mediate accurate chromosome segregation, may be involved in premeiotic DNA replication; possible role in telomere maintenance
YBL030C	0.535748	CUP2	YBL030C|PET9|S000000126|Major ADP/ATP carrier of the mitochondrial inner membrane, exchanges cytosolic ADP for mitochondrially synthesized ATP; phosphorylated; required for viability in many common lab strains carrying a mutation in the polymorphic SAL1 gene
YDR010C	0.534358	CUP2	YDR010C||S000002417|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YPL187W	0.532383	CUP2	YPL187W|MF(ALPHA)1|S000006108|Mating pheromone alpha-factor, made by alpha cells; interacts with mating type a cells to induce cell cycle arrest and other responses leading to mating; also encoded by MF(ALPHA)2, although MF(ALPHA)1 produces most alpha-factor
YKL175W	0.532307	CUP2	YKL175W|ZRT3|S000001658|Vacuolar membrane zinc transporter, transports zinc from storage in the vacuole to the cytoplasm when needed; transcription is induced under conditions of zinc deficiency
YFL053W	0.531649	CUP2	YFL053W|DAK2|S000001841|Dihydroxyacetone kinase, required for detoxification of dihydroxyacetone (DHA); involved in stress adaptation
YER004W	0.531618	CUP2	YER004W|FMP52|S000000806|Protein of unknown function, localized to the mitochondrial outer membrane; induced by treatment with 8-methoxypsoralen and UVA irradiation
YDR096W	0.53113	CUP2	YDR096W|GIS1|S000002503|JmjC domain-containing histone demethylase; transcription factor involved in the expression of genes during nutrient limitation; also involved in the negative regulation of DPP1 and PHR1
YLR279W	0.531086	CUP2	YLR279W||S000004269|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YEL075C	0.527415	CUP2	YEL075C||S000000801|Putative protein of unknown function
YDL197C	0.527387	CUP2	YDL197C|ASF2|S000002356|Anti-silencing protein that causes derepression of silent loci when overexpressed
YOR237W	0.52611	CUP2	YOR237W|HES1|S000005763|Protein implicated in the regulation of ergosterol biosynthesis; one of a seven member gene family with a common essential function and non-essential unique functions; similar to human oxysterol binding protein (OSBP)
YIL136W	0.52585	CUP2	YIL136W|OM45|S000001398|Protein of unknown function, major constituent of the mitochondrial outer membrane; located on the outer (cytosolic) face of the outer membrane
YPL111W	0.525288	CUP2	YPL111W|CAR1|S000006032|Arginase, responsible for arginine degradation, expression responds to both induction by arginine and nitrogen catabolite repression; disruption enhances freeze tolerance
YMR253C	0.524727	CUP2	YMR253C||S000004866|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; YMR253C is not an essential gene
YOR290C	0.523935	CUP2	YOR290C|SNF2|S000005816|Catalytic subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; contains DNA-stimulated ATPase activity; functions interdependently in transcriptional activation with Snf5p and Snf6p
YPR193C	0.522525	CUP2	YPR193C|HPA2|S000006397|Tetrameric histone acetyltransferase with similarity to Gcn5p, Hat1p, Elp3p, and Hpa3p; acetylates histones H3 and H4 in vitro and exhibits autoacetylation activity
YBL038W	0.521563	CUP2	YBL038W|MRPL16|S000000134|Mitochondrial ribosomal protein of the large subunit
YHR116W	0.521388	CUP2	YHR116W|COX23|S000001158|Mitochondrial intermembrane space protein that functions in mitochondrial copper homeostasis, essential for functional cytochrome oxidase expression; homologous to Cox17p
YLR174W	0.520456	CUP2	YLR174W|IDP2|S000004164|Cytosolic NADP-specific isocitrate dehydrogenase, catalyzes oxidation of isocitrate to alpha-ketoglutarate; levels are elevated during growth on non-fermentable carbon sources and reduced during growth on glucose
YLR094C	0.519841	CUP2	YLR094C|GIS3|S000004084|Protein of unknown function
YPL015C	0.519712	CUP2	YPL015C|HST2|S000005936|Cytoplasmic member of the silencing information regulator 2 (Sir2) family of NAD(+)-dependent protein deacetylases; modulates nucleolar (rDNA) and telomeric silencing; possesses NAD(+)-dependent histone deacetylase activity in vitro
YEL059C-A	0.518906	CUP2	YEL059C-A|SOM1|S000002954|Subunit of the mitochondrial inner membrane peptidase, which is required for maturation of mitochondrial proteins of the intermembrane space; Som1p facilitates cleavage of a subset of substrates
YOR081C	0.518639	CUP2	YOR081C|TGL5|S000005607|Triacylglycerol lipase involved in TAG mobilization; localizes to lipid particles; potential Cdc28p substrate
YFL021W	0.518374	CUP2	YFL021W|GAT1|S000001873|Transcriptional activator of genes involved in nitrogen catabolite repression; contains a GATA-1-type zinc finger DNA-binding motif; activity and localization regulated by nitrogen limitation and Ure2p
YDR379W	0.517567	CUP2	YDR379W|RGA2|S000002787|GTPase-activating protein for the polarity-establishment protein Cdc42p; implicated in control of septin organization, pheromone response, and haploid invasive growth; regulated by Pho85p and Cdc28p
YER101C	0.517265	CUP2	YER101C|AST2|S000000903|Protein that may have a role in targeting of plasma membrane [H+]ATPase (Pma1p) to the plasma membrane, as suggested by analysis of genetic interactions
YLR299W	0.51557	CUP2	YLR299W|ECM38|S000004290|Gamma-glutamyltranspeptidase, major glutathione-degrading enzyme; involved in detoxification of electrophilic xenobiotics; expression induced mainly by nitrogen starvation
YJL047C	0.515006	CUP2	YJL047C|RTT101|S000003583|Cullin subunit of a Roc1p-dependent E3 ubiquitin ligase complex; deletion phenotype suggests a role in anaphase progression; interacts with Mms22p and implicated in Mms22-dependent DNA repair; modified by the ubiquitin-like protein, Rub1p
YER175C	0.513369	CUP2	YER175C|TMT1|S000000977|Trans-aconitate methyltransferase, cytosolic enzyme that catalyzes the methyl esterification of 3-isopropylmalate, an intermediate of the leucine biosynthetic pathway, and trans-aconitate, which inhibits the citric acid cycle
YPL058C	0.513195	CUP2	YPL058C|PDR12|S000005979|Plasma membrane ATP-binding cassette (ABC) transporter, weak-acid-inducible multidrug transporter required for weak organic acid resistance; induced by sorbate and benzoate and regulated by War1p; mutants exhibit sorbate hypersensitivity
YLR399C	0.511315	CUP2	YLR399C|BDF1|S000004391|Protein involved in transcription initiation at TATA-containing promoters; associates with the basal transcription factor TFIID; contains two bromodomains; corresponds to the C-terminal region of mammalian TAF1; redundant with Bdf2p
YIL122W	0.509937	CUP2	YIL122W|POG1|S000001384|Putative transcriptional activator that promotes recovery from pheromone induced arrest; inhibits both alpha-factor induced G1 arrest and repression of CLN1 and CLN2 via SCB/MCB promoter elements; potential Cdc28p substrate; SBF regulated
YHR095W	0.509064	CUP2	YHR095W||S000001137|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPL117C	0.508836	CUP2	YPL117C|IDI1|S000006038|Isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IPP isomerase), catalyzes an essential activation step in the isoprenoid biosynthetic pathway; required for viability
YIL088C	0.508189	CUP2	YIL088C|AVT7|S000001350|Putative transporter, member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters
YGL096W	0.503582	CUP2	YGL096W|TOS8|S000003064|Homeodomain-containing transcription factor; SBF regulated target gene that in turn regulates expression of genes involved in G1/S phase events such as bud site selection, bud emergence and cell cycle progression; similarity to Cup9p
YPL184C	0.503564	CUP2	YPL184C|MRN1|S000006105|Putative RNA binding protein
YLR365W	0.502489	CUP2	YLR365W||S000004357|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps dubious gene YLR364C-A; YLR365W is not an essential gene
YOR223W	0.50221	CUP2	YOR223W||S000005749|Putative protein of unknown function
YLR312C	0.499705	CUP2	YLR312C|QNQ1|S000004303|Protein of unknown function; null mutant quiescent and non-quiescent cells exhibit reduced reproductive capacity
YOR010C	0.499315	CUP2	YOR010C|TIR2|S000005536|Putative cell wall mannoprotein of the Srp1p/Tip1p family of serine-alanine-rich proteins; transcription is induced by cold shock and anaerobiosis
YMR181C	0.499209	CUP2	YMR181C||S000004793|Protein of unknown function; mRNA transcribed as part of a bicistronic transcript with a predicted transcriptional repressor RGM1/YMR182C; mRNA is destroyed by nonsense-mediated decay (NMD); YMR181C is not an essential gene
YER054C	0.4983	CUP2	YER054C|GIP2|S000000856|Putative regulatory subunit of the protein phosphatase Glc7p, involved in glycogen metabolism; contains a conserved motif (GVNK motif) that is also found in Gac1p, Pig1p, and Pig2p
YCL048W-A	0.498204	CUP2	YCL048W-A||S000087203|Putative protein of unknown function
YCR011C	0.497039	CUP2	YCR011C|ADP1|S000000604|Putative ATP-dependent permease of the ABC transporter family of proteins
YDR479C	0.497001	CUP2	YDR479C|PEX29|S000002887|Peroxisomal integral membrane peroxin, involved in the regulation of peroxisomal size, number and distribution; genetic interactions suggest that Pex28p and Pex29p act at steps upstream of those mediated by Pex30p, Pex31p, and Pex32p
YEL039C	0.495221	CUP2	YEL039C|CYC7|S000000765|Cytochrome c isoform 2, expressed under hypoxic conditions; electron carrier of the mitochondrial intermembrane space that transfers electrons from ubiquinone-cytochrome c oxidoreductase to cytochrome c oxidase during cellular respiration
YOR215C	0.495154	CUP2	YOR215C|AIM41|S000005741|Putative protein of unknown function; the authentic protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays altered rate of mitochondrial loss and reduced growth rate in minimal glycerol media
YDL139C	0.493437	CUP2	YDL139C|SCM3|S000002298|Nonhistone component of centromeric chromatin that binds stoichiometrically to CenH3-H4 histones, required for kinetochore assembly; contains nuclear export signal (NES); required for G2/M progression and localization of Cse4p
YNL336W	0.492561	CUP2	YNL336W|COS1|S000005280|Protein of unknown function, member of the DUP380 subfamily of conserved, often subtelomerically-encoded proteins
YMR302C	0.49131	CUP2	YMR302C|YME2|S000004917|Integral inner mitochondrial membrane protein with a role in maintaining mitochondrial nucleoid structure and number; mutants exhibit an increased rate of mitochondrial DNA escape; shows some sequence similarity to exonucleases
YGR088W	0.490144	CUP2	YGR088W|CTT1|S000003320|Cytosolic catalase T, has a role in protection from oxidative damage by hydrogen peroxide
YBL071W-A	0.489471	CUP2	YBL071W-A|KTI11|S000007587|Zn-ribbon protein that co-purifies with Dph1, Dph2, Eft2 and Elongator subunits Iki3p, Elp2p, and Elp3p as a complex required for synthesis of diphthamide, a modified histidine residue, and for modification of wobble nucleosides in tRNA
YLR004C	0.487596	CUP2	YLR004C|THI73|S000003994|Putative plasma membrane permease proposed to be involved in carboxylic acid uptake and repressed by thiamine; substrate of Dbf2p/Mob1p kinase; transcription is altered if mitochondrial dysfunction occurs
YJL062W-A	0.487525	CUP2	YJL062W-A||S000007611|Putative protein of unknown function, identified based on comparison to related yeast species; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YGL066W	0.486857	CUP2	YGL066W|SGF73|S000003034|Subunit of SAGA histone acetyltransferase complex; involved in formation of the preinitiation complex assembly at promoters; null mutant displays defects in premeiotic DNA synthesis
YCL039W	0.48669	CUP2	YCL039W|GID7|S000000544|Protein of unknown function, involved in proteasome-dependent catabolite inactivation of fructose-1,6-bisphosphatase; contains six WD40 repeats; computational analysis suggests that Gid7p and Moh1p have similar functions
YNL321W	0.484733	CUP2	YNL321W|VNX1|S000005265|Low affinity vacuolar membrane localized monovalent cation/H+ antiporter; member of the calcium exchanger (CAX) family; potential Cdc28p substrate
YOR020C	0.484274	CUP2	YOR020C|HSP10|S000005546|Mitochondrial matrix co-chaperonin that inhibits the ATPase activity of Hsp60p, a mitochondrial chaperonin; involved in protein folding and sorting in the mitochondria; 10 kD heat shock protein with similarity to E. coli groES
YCR071C	0.481763	CUP2	YCR071C|IMG2|S000000667|Mitochondrial ribosomal protein of the small subunit
YPL260W	0.481347	CUP2	YPL260W||S000006181|Putative substrate of cAMP-dependent protein kinase (PKA); green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YPL260W is not an essential gene
YPR191W	0.481133	CUP2	YPR191W|QCR2|S000006395|Subunit 2 of the ubiquinol cytochrome-c reductase complex, which is a component of the mitochondrial inner membrane electron transport chain; phosphorylated; transcription is regulated by Hap1p, Hap2p/Hap3p, and heme
YCR018C-A	0.480659	CUP2	YCR018C-A||S000007230|Putative protein of unknown function; encoded opposite a Ty1 LTR
YOR156C	0.480051	CUP2	YOR156C|NFI1|S000005682|SUMO ligase, catalyzes the covalent attachment of SUMO (Smt3p) to proteins; involved in maintenance of proper telomere length
YLR131C	0.479771	CUP2	YLR131C|ACE2|S000004121|Transcription factor that activates expression of early G1-specific genes, localizes to daughter cell nuclei after cytokinesis and delays G1 progression in daughters, localization is regulated by phosphorylation; potential Cdc28p substrate
YNL077W	0.479118	CUP2	YNL077W|APJ1|S000005021|Putative chaperone of the HSP40 (DNAJ) family; overexpression interferes with propagation of the [Psi+] prion; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YJR049C	0.477878	CUP2	YJR049C|UTR1|S000003810|ATP-NADH kinase; phosphorylates both NAD and NADH; active as a hexamer; enhances the activity of ferric reductase (Fre1p)
YEL023C	0.47765	CUP2	YEL023C||S000000749|Putative protein of unknown function; expression is increased greatly during sporulation; YEL023C is not an essential gene
YOL052C	0.477225	CUP2	YOL052C|SPE2|S000005412|S-adenosylmethionine decarboxylase, required for the biosynthesis of spermidine and spermine; cells lacking Spe2p require spermine or spermidine for growth in the presence of oxygen but not when grown anaerobically
YML128C	0.476107	CUP2	YML128C|MSC1|S000004597|Protein of unknown function; mutant is defective in directing meiotic recombination events to homologous chromatids; the authentic, non-tagged protein is detected in highly purified mitochondria and is phosphorylated
YNR059W	0.475975	CUP2	YNR059W|MNT4|S000005342|Putative alpha-1,3-mannosyltransferase, not required for protein O-glycosylation
YNL250W	0.475574	CUP2	YNL250W|RAD50|S000005194|Subunit of MRX complex, with Mre11p and Xrs2p, involved in processing double-strand DNA breaks in vegetative cells, initiation of meiotic DSBs, telomere maintenance, and nonhomologous end joining
YCL030C	0.47496	CUP2	YCL030C|HIS4|S000000535|Multifunctional enzyme containing phosphoribosyl-ATP pyrophosphatase, phosphoribosyl-AMP cyclohydrolase, and histidinol dehydrogenase activities; catalyzes the second, third, ninth and tenth steps in histidine biosynthesis
YGR269W	0.474233	CUP2	YGR269W||S000003501|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF HUA1/YGR268C
YMR133W	0.473628	CUP2	YMR133W|REC114|S000004740|Protein involved in early stages of meiotic recombination; possibly involved in the coordination of recombination and meiotic division; mutations lead to premature initiation of the first meiotic division
YIL047C	0.473469	CUP2	YIL047C|SYG1|S000001309|Plasma membrane protein of unknown function; truncation and overexpression suppresses lethality of G-alpha protein deficiency
YDR350C	0.472764	CUP2	YDR350C|ATP22|S000002758|Mitochondrial inner membrane protein required for assembly of the F0 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis
YCR030C	0.472655	CUP2	YCR030C|SYP1|S000000626|Protein with a potential role in actin cytoskeletal organization; overexpression suppresses a pfy1 (profilin) null mutation
YNL033W	0.471265	CUP2	YNL033W||S000004978|Putative protein of unknown function
YBR230W-A	0.470732	CUP2	YBR230W-A||S000029722|Putative protein of unknown function
YHL025W	0.468332	CUP2	YHL025W|SNF6|S000001017|Subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; functions interdependently in transcriptional activation with Snf2p and Snf5p
YGR221C	0.46809	CUP2	YGR221C|TOS2|S000003453|Protein involved in localization of Cdc24p to the site of bud growth; may act as a membrane anchor; localizes to the bud neck and bud tip; potentially phosphorylated by Cdc28p
YDR114C	0.467767	CUP2	YDR114C||S000002521|Putative protein of unknown function; deletion mutant exhibits poor growth at elevated pH and calcium
YJL045W	0.466715	CUP2	YJL045W||S000003581|Minor succinate dehydrogenase isozyme; homologous to Sdh1p, the major isozyme reponsible for the oxidation of succinate and transfer of electrons to ubiquinone; induced during the diauxic shift in a Cat8p-dependent manner
YDR232W	0.464939	CUP2	YDR232W|HEM1|S000002640|5-aminolevulinate synthase, catalyzes the first step in the heme biosynthetic pathway; an N-terminal signal sequence is required for localization to the mitochondrial matrix; expression is regulated by Hap2p-Hap3p
YPR164W	0.46419	CUP2	YPR164W|MMS1|S000006368|Protein likely involved in protection against replication-dependent DNA damage; mutants are sensitive to methyl methanesulfonate (MMS); implicated in regulation of Ty1 transposition
YFR040W	0.463366	CUP2	YFR040W|SAP155|S000001936|Protein that forms a complex with the Sit4p protein phosphatase and is required for its function; member of a family of similar proteins including Sap4p, Sap185p, and Sap190p
YMR053C	0.462067	CUP2	YMR053C|STB2|S000004657|Protein that interacts with Sin3p in a two-hybrid assay and is part of a large protein complex with Sin3p and Stb1p
YLR369W	0.460794	CUP2	YLR369W|SSQ1|S000004361|Mitochondrial hsp70-type molecular chaperone, required for assembly of iron/sulfur clusters into proteins at a step after cluster synthesis, and for maturation of Yfh1p, which is a homolog of human frataxin implicated in Friedreich's ataxia
YBR056W-A	0.460434	CUP2	YBR056W-A||S000028736|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YBR056C-B
YMR120C	0.460226	CUP2	YMR120C|ADE17|S000004727|Enzyme of 'de novo' purine biosynthesis containing both 5-aminoimidazole-4-carboxamide ribonucleotide transformylase and inosine monophosphate cyclohydrolase activities, isozyme of Ade16p; ade16 ade17 mutants require adenine and histidine
YDR014W-A	0.457241	CUP2	YDR014W-A|HED1|S000113613|Meiosis-specific protein that down-regulates Rad51p-mediated mitotic recombination when the meiotic recombination machinery is impaired; early meiotic gene, transcribed specifically during meiotic prophase
YBR298C	0.456175	CUP2	YBR298C|MAL31|S000000502|Maltose permease, high-affinity maltose transporter (alpha-glucoside transporter); encoded in the MAL3 complex locus; member of the 12 transmembrane domain superfamily of sugar transporters; functional in genomic reference strain S288C
YEL065W	0.455504	CUP2	YEL065W|SIT1|S000000791|Ferrioxamine B transporter, member of the ARN family of transporters that specifically recognize siderophore-iron chelates; transcription is induced during iron deprivation and diauxic shift; potentially phosphorylated by Cdc28p
YLR214W	0.454806	CUP2	YLR214W|FRE1|S000004204|Ferric reductase and cupric reductase, reduces siderophore-bound iron and oxidized copper prior to uptake by transporters; expression induced by low copper and iron levels
YAL061W	0.454381	CUP2	YAL061W|BDH2|S000000057|Putative medium-chain alcohol dehydrogenase with similarity to BDH1; transcription induced by constitutively active PDR1 and PDR3; BDH2 is an essential gene
YNL240C	0.453064	CUP2	YNL240C|NAR1|S000005184|Nuclear architecture related protein; component of the cytosolic iron-sulfur (FeS) protein assembly machinery, required for maturation of cytosolic and nuclear FeS proteins; homologous to human Narf
YDR115W	0.452806	CUP2	YDR115W||S000002522|Putative mitochondrial ribosomal protein of the large subunit, has similarity to E. coli L34 ribosomal protein; required for respiratory growth, as are most mitochondrial ribosomal proteins
YLR378C	0.452399	CUP2	YLR378C|SEC61|S000004370|Essential subunit of Sec61 complex (Sec61p, Sbh1p, and Sss1p); forms a channel for SRP-dependent protein import and retrograde transport of misfolded proteins out of the ER; with Sec63 complex allows SRP-independent protein import into ER
YNL023C	0.451839	CUP2	YNL023C|FAP1|S000004968|Protein that binds to Fpr1p (FKBP12), conferring rapamycin resistance by competing with rapamycin for Fpr1p binding; has similarity to putative transcription factors, including D. melanogaster shuttle craft and human NFX1
YNR034W-A	0.450406	CUP2	YNR034W-A||S000007525|Putative protein of unknown function; expression is regulated by Msn2p/Msn4p
YDL067C	0.448149	CUP2	YDL067C|COX9|S000002225|Subunit VIIa of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain
YBR001C	0.446566	CUP2	YBR001C|NTH2|S000000205|Putative neutral trehalase, required for thermotolerance and may mediate resistance to other cellular stresses
YJL020C	0.445172	CUP2	YJL020C|BBC1|S000003557|Protein possibly involved in assembly of actin patches; interacts with an actin assembly factor Las17p and with the SH3 domains of Type I myosins Myo3p and Myo5p; localized predominantly to cortical actin patches
YBL064C	0.445154	CUP2	YBL064C|PRX1|S000000160|Mitochondrial peroxiredoxin (1-Cys Prx) with thioredoxin peroxidase activity, has a role in reduction of hydroperoxides; induced during respiratory growth and under conditions of oxidative stress; phosphorylated
YLR454W	0.4446	CUP2	YLR454W|FMP27|S000004446|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YLR431C	0.442122	CUP2	YLR431C|ATG23|S000004423|Peripheral membrane protein required for the cytoplasm-to-vacuole targeting (Cvt) pathway; cycles between the pre-autophagosome (PAS) and non-PAS locations; forms a complex with Atg9p and Atg27p
YBL101C	0.441865	CUP2	YBL101C|ECM21|S000000197|Non-essential protein of unknown function; promoter contains several Gcn4p binding elements
YKL146W	0.441614	CUP2	YKL146W|AVT3|S000001629|Vacuolar transporter, exports large neutral amino acids from the vacuole; member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters
YOR336W	0.440656	CUP2	YOR336W|KRE5|S000005863|Protein required for beta-1,6 glucan biosynthesis; mutations result in aberrant morphology and severe growth defects
YPL134C	0.439116	CUP2	YPL134C|ODC1|S000006055|Mitochondrial inner membrane transporter, exports 2-oxoadipate and 2-oxoglutarate from the mitochondrial matrix to the cytosol for lysine and glutamate biosynthesis and lysine catabolism; suppresses, in multicopy, an fmc1 null mutation
YKR089C	0.43869	CUP2	YKR089C|TGL4|S000001797|Triacylglycerol lipase involved in triacylglycerol mobilization and degradation; found in lipid particles; potential Cdc28p substrate
YDR501W	0.437678	CUP2	YDR501W|PLM2|S000002909|Protein required for partitioning of the 2-micron plasmid
YPL230W	0.436497	CUP2	YPL230W|USV1|S000006151|Putative transcription factor containing a C2H2 zinc finger; mutation affects transcriptional regulation of genes involved in protein folding, ATP binding, and cell wall biosynthesis
YLR113W	0.433098	CUP2	YLR113W|HOG1|S000004103|Mitogen-activated protein kinase involved in osmoregulation via three independent osmosensors; mediates the recruitment and activation of RNA Pol II at Hot1p-dependent promoters; localization regulated by Ptp2p and Ptp3p
YAL030W	0.4328	CUP2	YAL030W|SNC1|S000000028|Vesicle membrane receptor protein (v-SNARE) involved in the fusion between Golgi-derived secretory vesicles with the plasma membrane; proposed to be involved in endocytosis; member of the synaptobrevin/VAMP family of R-type v-SNARE proteins
YLR390W-A	0.432047	CUP2	YLR390W-A|CCW14|S000006429|Covalently linked cell wall glycoprotein, present in the inner layer of the cell wall
YNR004W	0.430313	CUP2	YNR004W||S000005287|Putative protein of unknown function; haploid disruptant exhibits slow growth rate on glucose-minimal medium at 15 C
YPL201C	0.430312	CUP2	YPL201C|YIG1|S000006122|Protein that interacts with glycerol 3-phosphatase and plays a role in anaerobic glycerol production; localizes to the nucleus and cytosol
YDL183C	0.430044	CUP2	YDL183C||S000002342|Putative protein of unknown function; YDL183C is not an essential gene
YIL101C	0.430035	CUP2	YIL101C|XBP1|S000001363|Transcriptional repressor that binds to promoter sequences of the cyclin genes, CYS3, and SMF2; expression is induced by stress or starvation during mitosis, and late in meiosis; member of the Swi4p/Mbp1p family; potential Cdc28p substrate
YNR036C	0.428826	CUP2	YNR036C||S000005319|Mitochondrial protein; may interact with ribosomes based on co-purification experiments; similar to E. coli and human mitochondrial S12 ribosomal proteins
YDR281C	0.427762	CUP2	YDR281C|PHM6|S000002689|Protein of unknown function, expression is regulated by phosphate levels
YIL115C	0.427111	CUP2	YIL115C|NUP159|S000001377|Nucleoporin, subunit of the nuclear pore complex that is found exclusively on the cytoplasmic side, forms a subcomplex with Nup82p and Nsp1p, required for mRNA export
YCR001W	0.427105	CUP2	YCR001W||S000000594|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YCR001W is not an essential gene
YBR067C	0.426602	CUP2	YBR067C|TIP1|S000000271|Major cell wall mannoprotein with possible lipase activity; transcription is induced by heat- and cold-shock; member of the Srp1p/Tip1p family of serine-alanine-rich proteins
YJL155C	0.426242	CUP2	YJL155C|FBP26|S000003691|Fructose-2,6-bisphosphatase, required for glucose metabolism
YJL152W	0.425597	CUP2	YJL152W||S000003688|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR379W	0.425087	CUP2	YLR379W||S000004371|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the essential ORF SEC61/YLR378C
YDR293C	0.425038	CUP2	YDR293C|SSD1|S000002701|Protein with a role in maintenance of cellular integrity, interacts with components of the TOR pathway; ssd1 mutant of a clinical S. cerevisiae strain displays elevated virulence
YKL147C	0.423365	CUP2	YKL147C||S000001630|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; partially overlaps the verified gene AVT3
YAL067C	0.422775	CUP2	YAL067C|SEO1|S000000062|Putative permease, member of the allantoate transporter subfamily of the major facilitator superfamily; mutation confers resistance to ethionine sulfoxide
YNL203C	0.422168	CUP2	YNL203C||S000005147|Dubious open reading frame unlikely to encode a functional protein; based on available experimental and comparative sequence data
YML047W-A	0.420735	CUP2	YML047W-A||S000004512|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YAR027W	0.420507	CUP2	YAR027W|UIP3|S000000075|Putative integral membrane protein of unknown function; interacts with Ulp1p at the nuclear periphery; member of DUP240 gene family
YPL278C	0.419329	CUP2	YPL278C||S000006199|Putative protein of unknown function; gene expression regulated by copper levels
YOR177C	0.419244	CUP2	YOR177C|MPC54|S000005703|Component of the meiotic outer plaque, a membrane-organizing center which is assembled on the cytoplasmic face of the spindle pole body during meiosis II and triggers the formation of the prospore membrane; potential Cdc28p substrate
YPL116W	0.418966	CUP2	YPL116W|HOS3|S000006037|Trichostatin A-insensitive homodimeric histone deacetylase (HDAC) with specificity in vitro for histones H3, H4, H2A, and H2B; similar to Hda1p, Rpd3p, Hos1p, and Hos2p; deletion results in increased histone acetylation at rDNA repeats
YHR006W	0.418743	CUP2	YHR006W|STP2|S000001048|Transcription factor, activated by proteolytic processing in response to signals from the SPS sensor system for external amino acids; activates transcription of amino acid permease genes
YGL166W	0.418589	CUP2	YGL166W|CUP2|S000003134|Copper-binding transcription factor; activates transcription of the metallothionein genes CUP1-1 and CUP1-2 in response to elevated copper concentrations
YNR007C	0.41812	CUP2	YNR007C|ATG3|S000005290|E2-like enzyme involved in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; plays a role in formation of Atg8p-phosphatidylethanolamine conjugates, which are involved in membrane dynamics during autophagy and Cvt
YHR159W	0.417523	CUP2	YHR159W||S000001202|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; potential Cdc28p substrate
YGL073W	0.417025	CUP2	YGL073W|HSF1|S000003041|Trimeric heat shock transcription factor, activates multiple genes in response to stresses that include hyperthermia; recognizes variable heat shock elements (HSEs) consisting of inverted NGAAN repeats; posttranslationally regulated
YAL005C	0.416334	CUP2	YAL005C|SSA1|S000000004|ATPase involved in protein folding and nuclear localization signal (NLS)-directed nuclear transport; member of heat shock protein 70 (HSP70) family; forms a chaperone complex with Ydj1p; localized to the nucleus, cytoplasm, and cell wall
YDL204W	0.41612	CUP2	YDL204W|RTN2|S000002363|Protein of unknown function; has similarity to mammalian reticulon proteins; member of the RTNLA (reticulon-like A) subfamily
YLL062C	0.415885	CUP2	YLL062C|MHT1|S000003985|S-methylmethionine-homocysteine methyltransferase, functions along with Sam4p in the conversion of S-adenosylmethionine (AdoMet) to methionine to control the methionine/AdoMet ratio
YPL109C	0.415531	CUP2	YPL109C||S000006030|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YFL029C	0.415379	CUP2	YFL029C|CAK1|S000001865|Cyclin-dependent kinase-activating kinase required for passage through the cell cycle, phosphorylates and activates Cdc28p; nucleotide-binding pocket differs significantly from those of most other protein kinases
YPL027W	0.414255	CUP2	YPL027W|SMA1|S000005948|Protein of unknown function involved in the assembly of the prospore membrane during sporulation
YML009C-A	0.413901	CUP2	YML009C-A||S000004469|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGR174C	0.41363	CUP2	YGR174C|CBP4|S000003406|Mitochondrial protein required for assembly of ubiquinol cytochrome-c reductase complex (cytochrome bc1 complex); interacts with Cbp3p and function is partially redundant with that of Cbp3p
YBR101C	0.410837	CUP2	YBR101C|FES1|S000000305|Hsp70 (Ssa1p) nucleotide exchange factor, cytosolic homolog of Sil1p, which is the nucleotide exchange factor for BiP (Kar2p) in the endoplasmic reticulum
YAL020C	0.410772	CUP2	YAL020C|ATS1|S000000018|Protein required, with Elongator complex, Kti11p, and Kti12p, for modification of wobble nucleosides in tRNA; has a potential role in regulatory interactions between microtubules and the cell cycle
YJR155W	0.410491	CUP2	YJR155W|AAD10|S000003916|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role
YOR388C	0.408977	CUP2	YOR388C|FDH1|S000005915|NAD(+)-dependent formate dehydrogenase, may protect cells from exogenous formate
YKL162C	0.408452	CUP2	YKL162C||S000001645|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the mitochondrion
YGL093W	0.407518	CUP2	YGL093W|SPC105|S000003061|Protein required for accurate chromosome segregation, localizes to the nuclear side of the spindle pole body; forms a complex with Ydr532cp
YJR048W	0.406812	CUP2	YJR048W|CYC1|S000003809|Cytochrome c, isoform 1; electron carrier of the mitochondrial intermembrane space that transfers electrons from ubiquinone-cytochrome c oxidoreductase to cytochrome c oxidase during cellular respiration
YDL129W	0.40673	CUP2	YDL129W||S000002287|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and the nucleus; YDL129W is not an essential gene
YOR378W	0.406572	CUP2	YOR378W||S000005905|Putative protein of unknown function; belongs to the DHA2 family of drug:H+ antiporters; YOR378W is not an essential gene
YIR036C	0.406537	CUP2	YIR036C|IRC24|S000001475|Putative benzil reductase;(GFP)-fusion protein localizes to the cytoplasm and is induced by the DNA-damaging agent MMS; sequence similarity with short-chain dehydrogenase/reductases; null mutant has increased spontaneous Rad52p foci
YDL214C	0.406297	CUP2	YDL214C|PRR2|S000002373|Serine/threonine protein kinase that inhibits pheromone induced signalling downstream of MAPK, possibly at the level of the Ste12p transcription factor
YBL103C	0.406254	CUP2	YBL103C|RTG3|S000000199|Basic helix-loop-helix-leucine zipper (bHLH/Zip) transcription factor that forms a complex with another bHLH/Zip protein, Rtg1p, to activate the retrograde (RTG) and TOR pathways
YGR041W	0.405694	CUP2	YGR041W|BUD9|S000003273|Protein involved in bud-site selection; diploid mutants display a unipolar budding pattern instead of the wild-type bipolar pattern, and bud at the distal pole
YER096W	0.405559	CUP2	YER096W|SHC1|S000000898|Sporulation-specific activator of Chs3p (chitin synthase III), required for the synthesis of the chitosan layer of ascospores; has similarity to Skt5p, which activates Chs3p during vegetative growth; transcriptionally induced at alkaline pH
YKR022C	0.405199	CUP2	YKR022C|NTR2|S000001730|Essential protein that forms a dimer with Ntr1p; also forms a trimer, with Ntr2p and the DExD/H-box RNA helicase Prp43p, that is involved in spliceosome disassembly
YFL055W	0.402886	CUP2	YFL055W|AGP3|S000001839|Low-affinity amino acid permease, may act to supply the cell with amino acids as nitrogen source in nitrogen-poor conditions; transcription is induced under conditions of sulfur limitation; plays a role in regulating Ty1 transposition
YLR047C	0.402776	CUP2	YLR047C|FRE8|S000004037|Protein with sequence similarity to iron/copper reductases, involved in iron homeostasis; deletion mutant has iron deficiency/accumulation growth defects; expression increased in the absence of copper-responsive transcription factor Mac1p
YFR015C	0.401195	CUP2	YFR015C|GSY1|S000001911|Glycogen synthase with similarity to Gsy2p, the more highly expressed yeast homolog; expression induced by glucose limitation, nitrogen starvation, environmental stress, and entry into stationary phase
YNR055C	0.400662	CUP2	YNR055C|HOL1|S000005338|Putative transporter in the major facilitator superfamily (DHA1 family) of multidrug resistance transporters; mutations in membrane-spanning domains permit cation and histidinol uptake
YPL190C	0.400334	CUP2	YPL190C|NAB3|S000006111|Single stranded RNA binding protein; acidic ribonucleoprotein; required for termination of non-poly(A) transcripts and efficient splicing; interacts with Nrd1p
YNL243W	0.399158	CUP2	YNL243W|SLA2|S000005187|Transmembrane actin-binding protein involved in membrane cytoskeleton assembly and cell polarization; adaptor protein that links actin to clathrin and endocytosis; present in the actin cortical patch of the emerging bud tip; dimer in vivo
YNL194C	0.398046	CUP2	YNL194C||S000005138|Integral membrane protein localized to eisosomes; sporulation and plasma membrane sphingolipid content are altered in mutants; has homologs SUR7 and FMP45; GFP-fusion protein is induced in response to the DNA-damaging agent MMS
YPR049C	0.398018	CUP2	YPR049C|ATG11|S000006253|Adapter protein for pexophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; directs receptor-bound cargo to the pro-autophagosomal structure (PAS) for packaging into vesicles; required for recruiting other proteins to the PAS
YDR151C	0.39737	CUP2	YDR151C|CTH1|S000002558|Member of the CCCH zinc finger family; has similarity to mammalian Tis11 protein, which activates transcription and also has a role in mRNA degradation; may function with Tis11p in iron homeostasis
YER056C	0.396673	CUP2	YER056C|FCY2|S000000858|Purine-cytosine permease, mediates purine (adenine, guanine, and hypoxanthine) and cytosine accumulation
YFL068W	0.396586	CUP2	YFL068W||S000001826|Putative protein of unknown function
YGL170C	0.396143	CUP2	YGL170C|SPO74|S000003138|Component of the meiotic outer plaque of the spindle pole body, involved in modifying the meiotic outer plaque that is required prior to prospore membrane formation
YGR070W	0.396109	CUP2	YGR070W|ROM1|S000003302|GDP/GTP exchange protein (GEP) for Rho1p; mutations are synthetically lethal with mutations in rom2, which also encodes a GEP
YHR180W	0.393802	CUP2	YHR180W||S000001223|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR334W	0.393576	CUP2	YDR334W|SWR1|S000002742|Swi2/Snf2-related ATPase that is the structural component of the SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A
YGR182C	0.393293	CUP2	YGR182C||S000003414|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF TIM13/YGR181W
YBR065C	0.392787	CUP2	YBR065C|ECM2|S000000269|Pre-mRNA splicing factor, facilitates the cooperative formation of U2/U6 helix II in association with stem II in the spliceosome, function may be regulated by Slu7p
YLR228C	0.392338	CUP2	YLR228C|ECM22|S000004218|Sterol regulatory element binding protein, regulates transcription of the sterol biosynthetic genes ERG2 and ERG3; member of the fungus-specific Zn[2]-Cys[6] binuclear cluster family of transcription factors; homologous to Upc2p
YLL019C	0.392173	CUP2	YLL019C|KNS1|S000003942|Nonessential putative protein kinase of unknown cellular role; member of the LAMMER family of protein kinases, which are serine/threonine kinases also capable of phosphorylating tyrosine residues
YKL151C	0.391592	CUP2	YKL151C||S000001634|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YML087C	0.388918	CUP2	YML087C|AIM33|S000004552|Putative protein of unknown function; highly conserved across species and orthologous to human CYB5R4; null mutant shows increased frequency of mitochondrial genome loss (petite formation) and severe growth defect in minimal glycerol media
YBL060W	0.388869	CUP2	YBL060W|YEL1|S000000156|Guanine nucleotide exchange factor specific for Arf3p; localized to the bud neck and tip; required for localization of Arf3p to the bud neck and tip
YDL109C	0.388524	CUP2	YDL109C||S000002267|Putative lipase; involved in lipid metabolism; YDL109C is not an essential gene
YNL254C	0.388267	CUP2	YNL254C|RTC4|S000005198|Hypothetical protein; null mutation suppresses cdc13-1 temperature sensitivity
YGL081W	0.385654	CUP2	YGL081W||S000003049|Putative protein of unknown function; non-essential gene; interacts genetically with CHS5, a gene involved in chitin biosynthesis
YGL114W	0.385291	CUP2	YGL114W||S000003082|Putative protein of unknown function; predicted member of the oligopeptide transporter (OPT) family of membrane transporters
YKL160W	0.384683	CUP2	YKL160W|ELF1|S000001643|Transcription elongation factor that contains a conserved zinc finger domain; implicated in the maintenance of proper chromatin structure in actively transcribed regions; deletion inhibits Brome mosaic virus (BMV) gene expression
YOR208W	0.384551	CUP2	YOR208W|PTP2|S000005734|Phosphotyrosine-specific protein phosphatase involved in the inactivation of mitogen-activated protein kinase (MAPK) during osmolarity sensing; dephosporylates Hog1p MAPK and regulates its localization; localized to the nucleus
YKR096W	0.384418	CUP2	YKR096W||S000001804|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; green fluorescent protein (GFP)-fusion protein localizes to the nucleus and cytoplasm; predicted to contain a PINc (PilT N terminus) domain
YGR260W	0.38435	CUP2	YGR260W|TNA1|S000003492|High affinity nicotinic acid plasma membrane permease, responsible for uptake of low levels of nicotinic acid; expression of the gene increases in the absence of extracellular nicotinic acid or para-aminobenzoate (PABA)
YBR036C	0.384285	CUP2	YBR036C|CSG2|S000000240|Endoplasmic reticulum membrane protein, required for mannosylation of inositolphosphorylceramide and for growth at high calcium concentrations
YOL157C	0.383331	CUP2	YOL157C||S000005517|Putative protein of unknown function
YDL012C	0.381072	CUP2	YDL012C||S000002170|Plasma membrane protein of unknown function; YDL012C is not an essential gene
YKR103W	0.379837	CUP2	YKR103W|NFT1|S000001811|Putative transporter of the multidrug resistance-associated protein (MRP) subfamily; adjacent ORFs YKR103W and YKR104W are merged in different strain backgrounds.
YBR218C	0.379508	CUP2	YBR218C|PYC2|S000000422|Pyruvate carboxylase isoform, cytoplasmic enzyme that converts pyruvate to oxaloacetate; highly similar to isoform Pyc1p but differentially regulated; mutations in the human homolog are associated with lactic acidosis
YDR504C	0.378581	CUP2	YDR504C|SPG3|S000002912|Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources
YLR345W	0.378033	CUP2	YLR345W||S000004337|Similar to 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase enzymes responsible for the metabolism of fructoso-2,6-bisphosphate; mRNA expression is repressed by the Rfx1p-Tup1p-Ssn6p repressor complex; YLR345W is not an essential gene
YNL339C	0.377856	CUP2	YNL339C|YRF1-6|S000005283|Helicase encoded by the Y' element of subtelomeric regions, highly expressed in the mutants lacking the telomerase component TLC1; potentially phosphorylated by Cdc28p
YDL089W	0.376998	CUP2	YDL089W||S000002247|Protein of unknown function; interacts with meiotic division protein Csm1p; green fluorescent protein (GFP)-fusion protein localizes to the nuclear periphery, potential Cdc28p substrate
YDR490C	0.376715	CUP2	YDR490C|PKH1|S000002898|Serine/threonine protein kinase involved in sphingolipid-mediated signaling pathway that controls endocytosis; activates Ypk1p and Ykr2p, components of signaling cascade required for maintenance of cell wall integrity; redundant with Pkh2p
YJL103C	0.376653	CUP2	YJL103C|GSM1|S000003639|Putative zinc cluster protein of unknown function; proposed to be involved in the regulation of energy metabolism, based on patterns of expression and sequence analysis
YDR132C	0.375631	CUP2	YDR132C||S000002539|Putative protein of unknown function
YOR075W	0.373953	CUP2	YOR075W|UFE1|S000005601|t-SNARE required for ER membrane fusion and vesicular traffic, integral membrane protein that constitutes with Sec20p and Use1p the trimeric acceptor for R/v-SNAREs on Golgi-derived vesicles at the ER; part of Dsl1p complex
YJL127C-B	0.372706	CUP2	YJL127C-B||S000028522|Putative protein of unknown function; identified based on homology to the filamentous fungus, Ashbya gossypii
YGR057C	0.370584	CUP2	YGR057C|LST7|S000003289|Protein possibly involved in a post-Golgi secretory pathway; required for the transport of nitrogen-regulated amino acid permease Gap1p from the Golgi to the cell surface
YNL276C	0.369401	CUP2	YNL276C||S000005220|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene MET2/YNL277W
YFL024C	0.367883	CUP2	YFL024C|EPL1|S000001870|Component of NuA4, which is an essential histone H4/H2A acetyltransferase complex; homologous to Drosophila Enhancer of Polycomb
YOR227W	0.367679	CUP2	YOR227W||S000005753|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YPL006W	0.367541	CUP2	YPL006W|NCR1|S000005927|Vacuolar membrane protein that transits through the biosynthetic vacuolar protein sorting pathway, involved in sphingolipid metabolism; glycoprotein and functional orthologue of human Niemann Pick C1 (NPC1) protein
YNL019C	0.36536	CUP2	YNL019C||S000004964|Putative protein of unknown function
YPR096C	0.364961	CUP2	YPR096C||S000006300|Protein of unknown function that may interact with ribosomes, based on co-purification experiments
YBL071C	0.364746	CUP2	YBL071C||S000000167|Dubious open reading frame, predicted protein contains a peroxisomal targeting signal
YOL156W	0.364667	CUP2	YOL156W|HXT11|S000005516|Putative hexose transporter that is nearly identical to Hxt9p, has similarity to major facilitator superfamily (MFS) transporters and is involved in pleiotropic drug resistance
YLR001C	0.364505	CUP2	YLR001C||S000003991|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YLR001C is not an essential gene
YLR294C	0.363346	CUP2	YLR294C||S000004285|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene ATP14
YDR290W	0.362931	CUP2	YDR290W||S000002698|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF RTT103
YCR067C	0.360634	CUP2	YCR067C|SED4|S000000663|Integral endoplasmic reticulum membrane protein, functions as a positive regulator of Sar1p probably through inhibition of GTPase activation by Sec23p; binds Sec16p, participates in vesicle formation, similar to Sec12p
YCR037C	0.360425	CUP2	YCR037C|PHO87|S000000633|Low-affinity inorganic phosphate (Pi) transporter, involved in activation of PHO pathway; expression is independent of Pi concentration and Pho4p activity; contains 12 membrane-spanning segments
YDL227C	0.359536	CUP2	YDL227C|HO|S000002386|Site-specific endonuclease required for gene conversion at the MAT locus (homothallic switching) through the generation of a ds DNA break; expression restricted to mother cells in late G1 as controlled by Swi4p-Swi6p, Swi5p and Ash1p
YML029W	0.35924	CUP2	YML029W|USA1|S000004491|Protein involved in ER-associated protein degradation (ERAD); component of the Hrd1p complex; interacts with the U1 snRNP-specific protein, Snp1p
YOR363C	0.359039	CUP2	YOR363C|PIP2|S000005890|Autoregulatory oleate-specific transcriptional activator of peroxisome proliferation, contains Zn(2)-Cys(6) cluster domain, forms heterodimer with Oaf1p, binds oleate response elements (OREs), activates beta-oxidation genes
YOR291W	0.357739	CUP2	YOR291W||S000005817|Putative protein of unknown function; shares sequence similarity with the type V P-type ATPase Spf1p; YOR291W is not an essential protein
YNL164C	0.357444	CUP2	YNL164C|IBD2|S000005108|Component of the BUB2-dependent spindle checkpoint pathway, interacts with Bfa1p and functions upstream of Bub2p and Bfa1p
YBL078C	0.356648	CUP2	YBL078C|ATG8|S000000174|Conserved protein that is a component of autophagosomes and Cvt vesicles; undergoes C-terminal conjugation to phosphatidylethanolamine (PE), Atg8p-PE is anchored to membranes and may mediate membrane fusion during autophagosome formation
YKL170W	0.356598	CUP2	YKL170W|MRPL38|S000001653|Mitochondrial ribosomal protein of the large subunit; appears as two protein spots (YmL34 and YmL38) on two-dimensional SDS gels
YMR008C	0.35606	CUP2	YMR008C|PLB1|S000004610|Phospholipase B (lysophospholipase) involved in lipid metabolism, required for deacylation of phosphatidylcholine and phosphatidylethanolamine but not phosphatidylinositol
YIR037W	0.355338	CUP2	YIR037W|HYR1|S000001476|Thiol peroxidase that functions as a hydroperoxide receptor to sense intracellular hydroperoxide levels and transduce a redox signal to the Yap1p transcription factor
YMR042W	0.354434	CUP2	YMR042W|ARG80|S000004645|Transcription factor involved in regulation of arginine-responsive genes; acts with Arg81p and Arg82p
YOR371C	0.353311	CUP2	YOR371C|GPB1|S000005898|Multistep regulator of cAMP-PKA signaling; inhibits PKA downstream of Gpa2p and Cyr1p, thereby increasing cAMP dependency; inhibits Ras activity through direct interactions with Ira1p/2p; regulated by G-alpha protein Gpa2p; homolog of Gpb2p
YJL084C	0.353159	CUP2	YJL084C|ALY2|S000003620|Cytoplasmic protein of unknown function that interacts with the cyclin Pcl7p; phosphorylated in vitro by the cyclin-CDK complex, Pcl7p-Pho85p; identified as a potential Cdc28p substrate; mRNA is cell cycle regulated, peaking in M phase
YMR092C	0.35239	CUP2	YMR092C|AIP1|S000004698|Actin cortical patch component, interacts with the actin depolymerizing factor cofilin; required to restrict cofilin localization to cortical patches; contains WD repeats
YGR213C	0.350911	CUP2	YGR213C|RTA1|S000003445|Protein involved in 7-aminocholesterol resistance; has seven potential membrane-spanning regions; expression is induced under both low-heme and low-oxygen conditions
YGL191W	0.35033	CUP2	YGL191W|COX13|S000003159|Subunit VIa of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; not essential for cytochrome c oxidase activity but may modulate activity in response to ATP
YPL061W	0.349545	CUP2	YPL061W|ALD6|S000005982|Cytosolic aldehyde dehydrogenase, activated by Mg2+ and utilizes NADP+ as the preferred coenzyme; required for conversion of acetaldehyde to acetate; constitutively expressed; locates to the mitochondrial outer surface upon oxidative stress
YAL019W-A	0.349435	CUP2	YAL019W-A||S000028729|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YOL044W	0.349048	CUP2	YOL044W|PEX15|S000005404|Phosphorylated tail-anchored type II integral peroxisomal membrane protein required for peroxisome biogenesis, cells lacking Pex15p mislocalize peroxisomal matrix proteins to cytosol, overexpression results in impaired peroxisome assembly
YKL121W	0.348459	CUP2	YKL121W||S000001604|Putative protein of unknown function
YLR332W	0.347713	CUP2	YLR332W|MID2|S000004324|O-glycosylated plasma membrane protein that acts as a sensor for cell wall integrity signaling and activates the pathway; interacts with Rom2p, a guanine nucleotide exchange factor for Rho1p, and with cell integrity pathway protein Zeo1p
YER015W	0.347631	CUP2	YER015W|FAA2|S000000817|Long chain fatty acyl-CoA synthetase; accepts a wider range of acyl chain lengths than Faa1p, preferring C9:0-C13:0; involved in the activation of endogenous pools of fatty acids
YBR021W	0.346418	CUP2	YBR021W|FUR4|S000000225|Uracil permease, localized to the plasma membrane; expression is tightly regulated by uracil levels and environmental cues
YNL165W	0.345672	CUP2	YNL165W||S000005109|Putative protein of unknown function; YNL165W is not an essential gene
YDR319C	0.345651	CUP2	YDR319C|YFT2|S000002727|Putative protein of unknown function, identified as an ortholog of the highly conserved FIT family of proteins involved in triglyceride droplet biosynthesis; interacts with Sst2p and Hsp82p in high-throughput two-hybrid screens
YBL047C	0.344975	CUP2	YBL047C|EDE1|S000000143|Key endocytic protein involved in a network of interactions with other endocytic proteins, binds membranes in a ubiquitin-dependent manner, may also bind ubiquitinated membrane-associated proteins
YDR247W	0.344625	CUP2	YDR247W|VHS1|S000002655|Cytoplasmic serine/threonine protein kinase; identified as a high-copy suppressor of the synthetic lethality of a sis2 sit4 double mutant, suggesting a role in G1/S phase progression; homolog of Sks1p
YDL147W	0.344406	CUP2	YDL147W|RPN5|S000002306|Essential, non-ATPase regulatory subunit of the 26S proteasome lid, similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p
YPR077C	0.343893	CUP2	YPR077C||S000006281|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data; expression increased by deletion of NAP1
YMR018W	0.343588	CUP2	YMR018W||S000004620|Putative protein of unknown function with similarity to human PEX5Rp (peroxin protein 5 related protein); transcription increases during colony development similar to genes involved in peroxisome biogenesis; YMR018W is not an essential gene
YDR178W	0.343414	CUP2	YDR178W|SDH4|S000002585|Membrane anchor subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p), which couples the oxidation of succinate to the transfer of electrons to ubiquinone
YFL067W	0.343302	CUP2	YFL067W||S000001827|Protein of unknown function, down-regulated at low calcium levels
YER085C	0.342261	CUP2	YER085C||S000000887|Putative protein of unknown function
YGL095C	0.342049	CUP2	YGL095C|VPS45|S000003063|Protein of the Sec1p/Munc-18 family, essential for vacuolar protein sorting; required for the function of Pep12p and the early endosome/late Golgi SNARE Tlg2p; essential for fusion of Golgi-derived vesicles with the prevacuolar compartment
YER164W	0.340995	CUP2	YER164W|CHD1|S000000966|Nucleosome remodeling factor that functions in regulation of transcription elongation; contains a chromo domain, a helicase domain and a DNA-binding domain; component of both the SAGA and SLIK complexes
YBR018C	0.34015	CUP2	YBR018C|GAL7|S000000222|Galactose-1-phosphate uridyl transferase, synthesizes glucose-1-phosphate and UDP-galactose from UDP-D-glucose and alpha-D-galactose-1-phosphate in the second step of galactose catabolism
YLR331C	0.340136	CUP2	YLR331C|JIP3|S000004323|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; 98% of ORF overlaps the verified gene MID2
YLR320W	0.339901	CUP2	YLR320W|MMS22|S000004312|Protein that acts with Mms1p in a repair pathway that may be involved in resolving replication intermediates or preventing the damage caused by blocked replication forks; required for accurate meiotic chromosome segregation
YLL030C	0.339163	CUP2	YLL030C||S000003953|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR097C	0.336927	CUP2	YDR097C|MSH6|S000002504|Protein required for mismatch repair in mitosis and meiosis, forms a complex with Msh2p to repair both single-base & insertion-deletion mispairs; potentially phosphorylated by Cdc28p
YPR117W	0.333562	CUP2	YPR117W||S000006321|Putative protein of unknown function
YOR381W	0.332723	CUP2	YOR381W|FRE3|S000005908|Ferric reductase, reduces siderophore-bound iron prior to uptake by transporters; expression induced by low iron levels
YHR009C	0.332335	CUP2	YHR009C||S000001051|Putative protein of unknown function; not an essential gene
YGR066C	0.330983	CUP2	YGR066C||S000003298|Putative protein of unknown function
YFR057W	0.330906	CUP2	YFR057W||S000001953|Putative protein of unknown function
YJR005W	0.330562	CUP2	YJR005W|APL1|S000003765|Beta-adaptin, large subunit of the clathrin associated protein complex (AP-2); involved in vesicle mediated transport; similar to mammalian beta-chain of the clathrin associated protein complex
YKL115C	0.33011	CUP2	YKL115C||S000001598|Dubious open reading frame, unlikely to encode a protein; partially overlaps the verified gene PRR1
YFR034C	0.329299	CUP2	YFR034C|PHO4|S000001930|Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability
YIR038C	0.329294	CUP2	YIR038C|GTT1|S000001477|ER associated glutathione S-transferase capable of homodimerization; expression induced during the diauxic shift and throughout stationary phase; functional overlap with Gtt2p, Grx1p, and Grx2p
YOR064C	0.327881	CUP2	YOR064C|YNG1|S000005590|Subunit of the NuA3 histone acetyltransferase complex that acetylates histone H3; contains PHD finger domain that interacts with methylated histone H3, has similarity to the human tumor suppressor ING1
YDR166C	0.327552	CUP2	YDR166C|SEC5|S000002573|Essential 107kDa subunit of the exocyst complex (Sec3p, Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, Exo70p, and Exo84p), which has the essential function of mediating polarized targeting of secretory vesicles to active sites of exocytosis
YBL067C	0.327149	CUP2	YBL067C|UBP13|S000000163|Putative ubiquitin carboxyl-terminal hydrolase, ubiquitin-specific protease that cleaves ubiquitin-protein fusions
YOR125C	0.326228	CUP2	YOR125C|CAT5|S000005651|Protein required for ubiquinone (Coenzyme Q) biosynthesis; localizes to the matrix face of the mitochondrial inner membrane in a large complex with ubiquinone biosynthetic enzymes; required for gluconeogenic gene activation
YPL250C	0.325809	CUP2	YPL250C|ICY2|S000006171|Protein of unknown function; mobilized into polysomes upon a shift from a fermentable to nonfermentable carbon source; potential Cdc28p substrate
YLR153C	0.325302	CUP2	YLR153C|ACS2|S000004143|Acetyl-coA synthetase isoform which, along with Acs1p, is the nuclear source of acetyl-coA for histone acetylation; mutants affect global transcription; required for growth on glucose; expressed under anaerobic conditions
YOR113W	0.325157	CUP2	YOR113W|AZF1|S000005639|Zinc-finger transcription factor, involved in induction of CLN3 transcription in response to glucose; genetic and physical interactions indicate a possible role in mitochondrial transcription or genome maintenance
YCL016C	0.325046	CUP2	YCL016C|DCC1|S000000521|Subunit of a complex with Ctf8p and Ctf18p that shares some components with Replication Factor C, required for sister chromatid cohesion and telomere length maintenance
YPR093C	0.324499	CUP2	YPR093C|ASR1|S000006297|Protein involved in a putative alcohol-responsive signaling pathway; accumulates in the nucleus under alcohol stress; contains a Ring/PHD finger domain
YBR295W	0.323604	CUP2	YBR295W|PCA1|S000000499|Cadmium transporting P-type ATPase; may also have a role in copper and iron homeostasis; S288C and most other lab strains contain a G970R mutation which eliminates normal cadmium transport function
YMR145C	0.322835	CUP2	YMR145C|NDE1|S000004753|Mitochondrial external NADH dehydrogenase, a type II NAD(P)H:quinone oxidoreductase that catalyzes the oxidation of cytosolic NADH; Nde1p and Nde2p provide cytosolic NADH to the mitochondrial respiratory chain
YDL174C	0.322217	CUP2	YDL174C|DLD1|S000002333|D-lactate dehydrogenase, oxidizes D-lactate to pyruvate, transcription is heme-dependent, repressed by glucose, and derepressed in ethanol or lactate; located in the mitochondrial inner membrane
YOL053W	0.321904	CUP2	YOL053W|AIM39|S000005414|Putative protein of unknown function; YOL053W is not an essential gene; null mutant displays decreased frequency of mitochondrial genome loss (petite formation)
YLR080W	0.321897	CUP2	YLR080W|EMP46|S000004070|Integral membrane component of endoplasmic reticulum-derived COPII-coated vesicles, which function in ER to Golgi transport
YDL097C	0.321523	CUP2	YDL097C|RPN6|S000002255|Essential, non-ATPase regulatory subunit of the 26S proteasome lid required for the assembly and activity of the 26S proteasome; the human homolog (S9 protein) partially rescues Rpn6p depletion
YOL099C	0.320938	CUP2	YOL099C||S000005459|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene PKH2/YOL100W; may interact with ribosomes
YOL160W	0.319455	CUP2	YOL160W||S000005520|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YBR085C-A	0.31929	CUP2	YBR085C-A||S000007522|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and to the nucleus
YPR076W	0.319085	CUP2	YPR076W||S000006280|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOL110W	0.318722	CUP2	YOL110W|SHR5|S000005470|Subunit of a palmitoyltransferase, composed of Shr5p and Erf2p, that adds a palmitoyl lipid moiety to heterolipidated substrates such as Ras1p and Ras2p through a thioester linkage; palmitoylation is required for Ras2p membrane localization
YPL189W	0.316957	CUP2	YPL189W|GUP2|S000006110|Probable membrane protein with a possible role in proton symport of glycerol; member of the MBOAT family of putative membrane-bound O-acyltransferases; Gup1p homolog
YFR012W	0.315992	CUP2	YFR012W||S000001908|Putative protein of unknown function
YDR024W	0.315703	CUP2	YDR024W|FYV1|S000002431|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; mutation decreases survival upon exposure to K1 killer toxin
YLR040C	0.315573	CUP2	YLR040C||S000004030|Putative protein of unknown function; localizes to the cell wall; predicted to be a GPI-attached protein; upregulated by Mcm1p-Alpha1p transcription factor; partially overlaps the dubious ORF YLR041W; YLR040C is not essential
YBR220C	0.315545	CUP2	YBR220C||S000000424|Putative protein of unknown function; YBR220C is not an essential gene
YGR011W	0.315235	CUP2	YGR011W||S000003243|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR440W	0.315216	CUP2	YDR440W|DOT1|S000002848|Nucleosomal histone H3-Lys79 methylase, associates with transcriptionally active genes, functions in gene silencing at telomeres, most likely by directly modulating chromatin structure and Sir protein localization
YMR041C	0.313556	CUP2	YMR041C|ARA2|S000004644|NAD-dependent arabinose dehydrogenase, involved in biosynthesis of erythroascorbic acid; similar to plant L-galactose dehydrogenase
YBR133C	0.313285	CUP2	YBR133C|HSL7|S000000337|Protein arginine N-methyltransferase that exhibits septin and Hsl1p-dependent bud neck localization and periodic Hsl1p-dependent phosphorylation; required along with Hsl1p for bud neck recruitment, phosphorylation, and degradation of Swe1p
YPR075C	0.31306	CUP2	YPR075C|OPY2|S000006279|Integral membrane protein that functions in the signaling branch of the high-osmolarity glycerol (HOG) pathway; interacts with Ste50p; overproduction blocks cell cycle arrest in the presence of mating pheromone
YCL065W	0.312854	CUP2	YCL065W||S000000570|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps HMLALPHA1
YBR051W	0.312402	CUP2	YBR051W||S000000255|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partiallly overlaps the REG2/YBR050C regulatory subunit of the Glc7p type-1 protein phosphatase
YLR247C	0.31226	CUP2	YLR247C|IRC20|S000004237|Putative helicase; localizes to the mitochondrion and the nucleus; YLR247C is not an essential gene; null mutant displays increased levels of spontaneous Rad52p foci
YLR278C	0.311486	CUP2	YLR278C||S000004268|Zinc-cluster protein; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; mutant shows moderate growth defect on caffeine; YLR278C is not an essential gene
YHR022C	0.311306	CUP2	YHR022C||S000001064|Putative protein of unknown function; YHR022C is not an essential gene.
YOR147W	0.309958	CUP2	YOR147W|MDM32|S000005673|Mitochondrial inner membrane protein with similarity to Mdm31p, required for normal mitochondrial morphology and inheritance; interacts genetically with MMM1, MDM10, MDM12, and MDM34
YJL142C	0.309189	CUP2	YJL142C|IRC9|S000003678|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene YJL141C; null mutant displays increased levels of spontaneous Rad52p foci
YML081W	0.308861	CUP2	YML081W||S000004546|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; YML081w is not an essential gene
YGL156W	0.308194	CUP2	YGL156W|AMS1|S000003124|Vacuolar alpha mannosidase, involved in free oligosaccharide (fOS) degradation; delivered to the vacuole in a novel pathway separate from the secretory pathway
YJR036C	0.308185	CUP2	YJR036C|HUL4|S000003797|Protein with similarity to hect domain E3 ubiquitin-protein ligases, not essential for viability
YKL202W	0.307856	CUP2	YKL202W||S000001685|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPR095C	0.30748	CUP2	YPR095C|SYT1|S000006299|Guanine nucleotide exchange factor (GEF) for Arf proteins; involved in vesicular transport; suppressor of ypt3 mutations; member of the Sec7-domain family
YJR050W	0.306391	CUP2	YJR050W|ISY1|S000003811|Component of the spliceosome complex involved in pre-mRNA splicing, auxiliary splicing factor that may modulate Syf1p activity and help optimize splicing; isy1 syf2 double mutation activates the spindle checkpoint, causing cell cycle arrest
YPL089C	0.306256	CUP2	YPL089C|RLM1|S000006010|MADS-box transcription factor, component of the protein kinase C-mediated MAP kinase pathway involved in the maintenance of cell integrity; phosphorylated and activated by the MAP-kinase Slt2p
YER103W	0.304474	CUP2	YER103W|SSA4|S000000905|Heat shock protein that is highly induced upon stress; plays a role in SRP-dependent cotranslational protein-membrane targeting and translocation; member of the HSP70 family; cytoplasmic protein that concentrates in nuclei upon starvation
YAL017W	0.303465	CUP2	YAL017W|PSK1|S000000015|One of two (see also PSK2) PAS domain containing S/T protein kinases; coordinately regulates protein synthesis and carbohydrate metabolism and storage in response to a unknown metabolite that reflects nutritional status
YBR050C	0.302655	CUP2	YBR050C|REG2|S000000254|Regulatory subunit of the Glc7p type-1 protein phosphatase; involved with Reg1p, Glc7p, and Snf1p in regulation of glucose-repressible genes, also involved in glucose-induced proteolysis of maltose permease
YML070W	0.302137	CUP2	YML070W|DAK1|S000004535|Dihydroxyacetone kinase, required for detoxification of dihydroxyacetone (DHA); involved in stress adaptation
YLR309C	0.301504	CUP2	YLR309C|IMH1|S000004300|Protein involved in vesicular transport, mediates transport between an endosomal compartment and the Golgi, contains a Golgi-localization (GRIP) domain that interacts with activated Arl1p-GTP to localize Imh1p to the Golgi
YML009W-B	0.301147	CUP2	YML009W-B||S000004471|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data; deletion mutation confers an increase in Ty1 transposition
YHL016C	0.299997	CUP2	YHL016C|DUR3|S000001008|Plasma membrane transporter for both urea and polyamines, expression is highly sensitive to nitrogen catabolite repression and induced by allophanate, the last intermediate of the allantoin degradative pathway
YBR134W	0.298336	CUP2	YBR134W||S000000338|Dubious open reading frame, unlikely to encode a functional protein; based on available experimental and comparative sequence data
YLR041W	0.297167	CUP2	YLR041W||S000004031|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YLR040C
YBR071W	0.297057	CUP2	YBR071W||S000000275|Putative protein of unknown function; (GFP)-fusion and epitope-tagged proteins localize to the cytoplasm; mRNA expression may be regulated by the cell cycle and/or cell wall stress
YNL104C	0.295377	CUP2	YNL104C|LEU4|S000005048|Alpha-isopropylmalate synthase (2-isopropylmalate synthase); the main isozyme responsible for the first step in the leucine biosynthesis pathway
YBR270C	0.294767	CUP2	YBR270C|BIT2|S000000474|Hypothetical protein
YOR032C	0.294146	CUP2	YOR032C|HMS1|S000005558|Basic helix-loop-helix (bHLH) protein with similarity to myc-family transcription factors; overexpression confers hyperfilamentous growth and suppresses the pseudohyphal filamentation defect of a diploid mep1 mep2 homozygous null mutant
YNL326C	0.293731	CUP2	YNL326C|PFA3|S000005270|Palmitoyltransferase for Vac8p, required for vacuolar membrane fusion; contains an Asp-His-His-Cys-cysteine rich (DHHC-CRD) domain; autoacylates; required for vacuolar integrity under stress conditions
YPL224C	0.291774	CUP2	YPL224C|MMT2|S000006145|Putative metal transporter involved in mitochondrial iron accumulation; closely related to Mmt1p
YIR034C	0.291568	CUP2	YIR034C|LYS1|S000001473|Saccharopine dehydrogenase (NAD+, L-lysine-forming), catalyzes the conversion of saccharopine to L-lysine, which is the final step in the lysine biosynthesis pathway
YBR144C	0.291429	CUP2	YBR144C||S000000348|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YBR144C is not an essential gene
YNL036W	0.291411	CUP2	YNL036W|NCE103|S000004981|Carbonic anhydrase; poorly transcribed under aerobic conditions and at an undetectable level under anaerobic conditions; involved in non-classical protein export pathway
YLR255C	0.291037	CUP2	YLR255C||S000004245|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YER119C	0.291026	CUP2	YER119C|AVT6|S000000921|Vacuolar amino acid transporter, exports aspartate and glutamate from the vacuole; member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters
YLR267W	0.290778	CUP2	YLR267W|BOP2|S000004257|Protein of unknown function, overproduction suppresses a pam1 slv3 double null mutation
YDL128W	0.290707	CUP2	YDL128W|VCX1|S000002286|Vacuolar H+/Ca2+ exchanger involved in control of cytosolic Ca2+ concentration; has similarity to sodium/calcium exchangers, including the bovine Na+/Ca2+,K+ antiporter
YBR136W	0.289564	CUP2	YBR136W|MEC1|S000000340|Genome integrity checkpoint protein and PI kinase superfamily member; signal transducer required for cell cycle arrest and transcriptional responses prompted by damaged or unreplicated DNA; monitors and participates in meiotic recombination
YDR392W	0.289057	CUP2	YDR392W|SPT3|S000002800|Subunit of the SAGA and SAGA-like transcriptional regulatory complexes, interacts with Spt15p to activate transcription of some RNA polymerase II-dependent genes, also functions to inhibit transcription at some promoters
YDR246W	0.288846	CUP2	YDR246W|TRS23|S000002654|One of 10 subunits of the transport protein particle (TRAPP) complex of the cis-Golgi which mediates vesicle docking and fusion; involved in endoplasmic reticulum (ER) to Golgi membrane traffic; human homolog is TRAPPC4
YBL001C	0.288485	CUP2	YBL001C|ECM15|S000000097|Non-essential protein of unknown function, likely exists as tetramer, may be regulated by the binding of small-molecule ligands (possibly sulfate ions), may have a role in yeast cell-wall biogenesis
YNL054W	0.288122	CUP2	YNL054W|VAC7|S000004999|Integral vacuolar membrane protein involved in vacuole inheritance and morphology; activates Fab1p kinase activity under basal conditions and also after hyperosmotic shock
YER069W	0.287628	CUP2	YER069W|ARG5,6|S000000871|Protein that is processed in the mitochondrion to yield acetylglutamate kinase and N-acetyl-gamma-glutamyl-phosphate reductase, which catalyze the 2nd and 3rd steps in arginine biosynthesis; enzymes form a complex with Arg2p
YPL040C	0.286895	CUP2	YPL040C|ISM1|S000005961|Mitochondrial isoleucyl-tRNA synthetase, null mutant is deficient in respiratory growth
YGL109W	0.286037	CUP2	YGL109W||S000003077|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the uncharacterized gene YGL108C
YJL043W	0.283118	CUP2	YJL043W||S000003579|Putative protein of unknown function; YJL043W is a non-essential gene
YER068C-A	0.28254	CUP2	YER068C-A||S000028749|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR289C	0.282116	CUP2	YDR289C|RTT103|S000002697|Protein that interacts with exonuclease Rat1p and Rai1p and plays a role in transcription termination by RNA polymerase II, has an RPR domain (carboxy-terminal domain interacting domain); also involved in regulation of Ty1 transposition
YML061C	0.280662	CUP2	YML061C|PIF1|S000004526|DNA helicase involved in telomere formation and elongation; acts as a catalytic inhibitor of telomerase; also plays a role in repair and recombination of mitochondrial DNA
YFL036W	0.280596	CUP2	YFL036W|RPO41|S000001858|Mitochondrial RNA polymerase; single subunit enzyme similar to those of T3 and T7 bacteriophages; requires a specificity subunit encoded by MTF1 for promoter recognition
YPL272C	0.279619	CUP2	YPL272C||S000006193|Putative protein of unknown function; gene expression induced in response to ketoconazole; YPL272C is not an essential gene
YOL084W	0.278904	CUP2	YOL084W|PHM7|S000005444|Protein of unknown function, expression is regulated by phosphate levels; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery and vacuole
YER039C	0.278849	CUP2	YER039C|HVG1|S000000841|Protein of unknown function, has homology to Vrg4p
YOR244W	0.278758	CUP2	YOR244W|ESA1|S000005770|Histone acetyltransferase catalytic subunit of the native multisubunit complex (NuA4) that acetylates four conserved internal lysines of histone H4 N-terminal tail; required for cell cycle progression
YDR333C	0.277893	CUP2	YDR333C||S000002741|Putative protein of unknown function
YNL139C	0.277639	CUP2	YNL139C|THO2|S000005083|Subunit of the THO complex, which is required for efficient transcription elongation and involved in transcriptional elongation-associated recombination; required for LacZ RNA expression from certain plasmids
YOR034C	0.277481	CUP2	YOR034C|AKR2|S000005560|Ankyrin repeat-containing protein similar to Akr1p; member of a family of putative palmitoyltransferases containing an Asp-His-His-Cys-cysteine rich (DHHC-CRD) domain; possibly involved in constitutive endocytosis of Ste3p
YHR087W	0.277076	CUP2	YHR087W|RTC3|S000001129|Protein of unknown function involved in RNA metabolism; has structural similarity to SBDS, the human protein mutated in Shwachman-Diamond Syndrome (the yeast SBDS ortholog = SDO1); null mutation suppresses cdc13-1 temperature sensitivity
YJR080C	0.2762	CUP2	YJR080C|AIM24|S000003841|Protein of unknown function; non-tagged protein is detected in purified mitochondria in high-throughput studies; null mutant displays increased frequency of mitochondrial genome loss and reduced growth rate in minimal glycerol media
YDR148C	0.27604	CUP2	YDR148C|KGD2|S000002555|Dihydrolipoyl transsuccinylase, component of the mitochondrial alpha-ketoglutarate dehydrogenase complex, which catalyzes the oxidative decarboxylation of alpha-ketoglutarate to succinyl-CoA in the TCA cycle; phosphorylated
YLR387C	0.275957	CUP2	YLR387C|REH1|S000004379|Protein of unknown function, similar to Rei1p but not involved in bud growth; contains dispersed C2H2 zinc finger domains
YJL093C	0.275298	CUP2	YJL093C|TOK1|S000003629|Outward-rectifier potassium channel of the plasma membrane with two pore domains in tandem, each of which forms a functional channel permeable to potassium; carboxy tail functions to prevent inner gate closures; target of K1 toxin
YOL159C-A	0.275294	CUP2	YOL159C-A||S000007627|Putative protein of unknown function; identified by sequence comparison with hemiascomycetous yeast species
YIR017C	0.273792	CUP2	YIR017C|MET28|S000001456|Transcriptional activator in the Cbf1p-Met4p-Met28p complex, participates in the regulation of sulfur metabolism
YHR132W-A	0.273762	CUP2	YHR132W-A|IGO2|S000007496|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus
YER175W-A	0.273007	CUP2	YER175W-A||S000028625|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YJR120W	0.271963	CUP2	YJR120W||S000003881|Protein of unknown function; essential for growth under anaerobic conditions; mutation causes decreased expression of ATP2, impaired respiration, defective sterol uptake, and altered levels/localization of ABC transporters Aus1p and Pdr11p
YNL121C	0.271443	CUP2	YNL121C|TOM70|S000005065|Component (70 kDa) of the TOM (translocase of outer membrane) complex responsible for recognition and initial import steps for all mitochondrially directed proteins; acts as a receptor for incoming precursor proteins
YPL200W	0.271141	CUP2	YPL200W|CSM4|S000006121|Protein required for accurate chromosome segregation during meiosis
YIL032C	0.270375	CUP2	YIL032C||S000001294|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YHL026C	0.269771	CUP2	YHL026C||S000001018|Putative protein of unknown function; YHL026C is not an essential gene; in 2005 the start site was moved 141 nt upstream (see Locus History)
YOL158C	0.269292	CUP2	YOL158C|ENB1|S000005518|Endosomal ferric enterobactin transporter, expressed under conditions of iron deprivation; member of the major facilitator superfamily; expression is regulated by Rcs1p and affected by chloroquine treatment
YDR377W	0.268741	CUP2	YDR377W|ATP17|S000002785|Subunit f of the F0 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis
YIL100C-A	0.268489	CUP2	YIL100C-A||S000028794|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YMR169C	0.267375	CUP2	YMR169C|ALD3|S000004779|Cytoplasmic aldehyde dehydrogenase, involved in beta-alanine synthesis; uses NAD+ as the preferred coenzyme; very similar to Ald2p; expression is induced by stress and repressed by glucose
YBR291C	0.266413	CUP2	YBR291C|CTP1|S000000495|Mitochondrial inner membrane citrate transporter, member of the mitochondrial carrier family
YKR015C	0.266333	CUP2	YKR015C||S000001723|Putative protein of unknown function
YMR193W	0.265174	CUP2	YMR193W|MRPL24|S000004806|Mitochondrial ribosomal protein of the large subunit
YBR099C	0.264889	CUP2	YBR099C||S000000303|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the verified gene MMS4
YPL025C	0.264844	CUP2	YPL025C||S000005946|Hypothetical protein
YMR007W	0.264196	CUP2	YMR007W||S000004609|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YGR058W	0.263563	CUP2	YGR058W|PEF1|S000003290|Penta-EF-hand protein required for polar bud growth and cell wall abscission; binds calcium and zinc with different affinity; localizes to bud site in G1, bud neck in G2
YGL229C	0.263447	CUP2	YGL229C|SAP4|S000003198|Protein required for function of the Sit4p protein phosphatase, member of a family of similar proteins that form complexes with Sit4p, including Sap155p, Sap185p, and Sap190p
YLL059C	0.263168	CUP2	YLL059C||S000003982|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YGL256W	0.263012	CUP2	YGL256W|ADH4|S000003225|Alcohol dehydrogenase isoenzyme type IV, dimeric enzyme demonstrated to be zinc-dependent despite sequence similarity to iron-activated alcohol dehydrogenases; transcription is induced in response to zinc deficiency
YOL073C	0.26256	CUP2	YOL073C||S000005434|Putative protein of unknown function
YPL059W	0.262483	CUP2	YPL059W|GRX5|S000005980|Hydroperoxide and superoxide-radical responsive glutathione-dependent oxidoreductase; mitochondrial matrix protein involved in the synthesis/assembly of iron-sulfur centers; monothiol glutaredoxin subfamily member along with Grx3p and Grx4p
YNL201C	0.262142	CUP2	YNL201C|PSY2|S000005145|Putative subunit of an evolutionarily conserved protein phosphatase complex containing the catalytic subunit Pph3p and the regulatory subunit Psy4p; required for cisplatin and oxaliplatin resistance; localizes to nucleus
YER111C	0.261743	CUP2	YER111C|SWI4|S000000913|DNA binding component of the SBF complex (Swi4p-Swi6p), a transcriptional activator that in concert with MBF (Mbp1-Swi6p) regulates late G1-specific transcription of targets including cyclins and genes required for DNA synthesis and repair
YPR202W	0.260537	CUP2	YPR202W||S000006406|Putative protein of unknown function with similarity to telomere-encoded helicases; YPR202W is not an essential gene; transcript is predicted to be spliced but there is no evidence that it is spliced in vivo
YDR524C	0.260488	CUP2	YDR524C|AGE1|S000002932|ADP-ribosylation factor (ARF) GTPase activating protein (GAP) effector, involved in the secretory and endocytic pathways; contains C2C2H2 cysteine/histidine motif
YMR141C	0.25992	CUP2	YMR141C||S000004749|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLL026W	0.259845	CUP2	YLL026W|HSP104|S000003949|Heat shock protein that cooperates with Ydj1p (Hsp40) and Ssa1p (Hsp70) to refold and reactivate previously denatured, aggregated proteins; responsive to stresses including: heat, ethanol, and sodium arsenite; involved in [PSI+] propagation
YHL046W-A	0.259241	CUP2	YHL046W-A||S000028775|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YER188C-A	0.258965	CUP2	YER188C-A||S000028764|Putative protein of unknown function
YGR053C	0.25859	CUP2	YGR053C||S000003285|Putative protein of unknown function
YML012C-A	0.25825	CUP2	YML012C-A||S000004474|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene SEL1
YGL074C	0.257233	CUP2	YGL074C||S000003042|Dubious open reading frame unlikely to encode a functional protein; overlaps 5' end of essential HSF1 gene encoding heat shock transcription factor
YMR052W	0.255198	CUP2	YMR052W|FAR3|S000004656|Protein involved in G1 cell cycle arrest in response to pheromone, in a pathway different from the Far1p-dependent pathway; interacts with Far7p, Far8p, Far9p, Far10p, and Far11p
YGR211W	0.254988	CUP2	YGR211W|ZPR1|S000003443|Essential protein with two zinc fingers, present in the nucleus of growing cells but relocates to the cytoplasm in starved cells via a process mediated by Cpr1p; binds to translation elongation factor eEF-1 (Tef1p)
YHR165W-A	0.254279	CUP2	YHR165W-A||S000028783|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YBL081W	0.25367	CUP2	YBL081W||S000000177|Non-essential protein of unknown function
YKR098C	0.253263	CUP2	YKR098C|UBP11|S000001806|Ubiquitin-specific protease that cleaves ubiquitin from ubiquitinated proteins
YJL019W	0.252901	CUP2	YJL019W|MPS3|S000003556|Essential integral membrane protein required for spindle pole body duplication and for nuclear fusion, localizes to the spindle pole body half bridge, interacts with DnaJ-like chaperone Jem1p and with centrin homolog Cdc31p
YPL233W	0.252668	CUP2	YPL233W|NSL1|S000006154|Essential component of the MIND kinetochore complex (Mtw1p Including Nnf1p-Nsl1p-Dsn1p) which joins kinetochore subunits contacting DNA to those contacting microtubules; required for accurate chromosome segregation
YMR312W	0.252105	CUP2	YMR312W|ELP6|S000004929|Subunit of Elongator complex, which is required for modification of wobble nucleosides in tRNA; required for Elongator structural integrity
YKL197C	0.252021	CUP2	YKL197C|PEX1|S000001680|AAA-peroxin that heterodimerizes with AAA-peroxin Pex6p and participates in the recycling of peroxisomal signal receptor Pex5p from the peroxisomal membrane to the cystosol; induced by oleic acid and upregulated during anaerobiosis
YDL142C	0.250754	CUP2	YDL142C|CRD1|S000002301|Cardiolipin synthase; produces cardiolipin, which is an important constituent of mitochondrial membranes; required for normal mitochondrial membrane potential and function
YGR284C	0.250559	CUP2	YGR284C|ERV29|S000003516|Protein localized to COPII-coated vesicles, involved in vesicle formation and incorporation of specific secretory cargo
YDR014W	0.250097	CUP2	YDR014W|RAD61|S000002421|Protein of unknown function; mutation confers radiation sensitivity
YLL042C	0.249998	CUP2	YLL042C|ATG10|S000003965|E2-like conjugating enzyme that mediates formation of the Atg12p-Atg5p conjugate, which is a critical step in autophagy
YER076C	0.249866	CUP2	YER076C||S000000878|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; analysis of HA-tagged protein suggests a membrane localization
YIL120W	0.249569	CUP2	YIL120W|QDR1|S000001382|Multidrug transporter of the major facilitator superfamily, required for resistance to quinidine, ketoconazole, fluconazole, and barban
YER180C	0.249419	CUP2	YER180C|ISC10|S000000982|Protein required for sporulation, transcript is induced 7.5 hours after induction of meiosis, expected to play significant role in the formation of reproductive cells
YGL041C	0.246778	CUP2	YGL041C||S000003009|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YHR164C	0.246552	CUP2	YHR164C|DNA2|S000001207|Essential tripartite DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, and helicase activities; required for Okazaki fragment processing; involved in DNA repair pathways; potential Cdc28p substrate
YGR286C	0.246156	CUP2	YGR286C|BIO2|S000003518|Biotin synthase, catalyzes the conversion of dethiobiotin to biotin, which is the last step of the biotin biosynthesis pathway; complements E. coli bioB mutant
YOL043C	0.245998	CUP2	YOL043C|NTG2|S000005403|DNA N-glycosylase and apurinic/apyrimidinic (AP) lyase involved in base excision repair, localizes to the nucleus
YMR257C	0.245416	CUP2	YMR257C|PET111|S000004870|Mitochondrial translational activator specific for the COX2 mRNA; located in the mitochondrial inner membrane
YGL205W	0.245288	CUP2	YGL205W|POX1|S000003173|Fatty-acyl coenzyme A oxidase, involved in the fatty acid beta-oxidation pathway; localized to the peroxisomal matrix
YBR219C	0.245251	CUP2	YBR219C||S000000423|Putative protein of unknown function; YBR219C is not an essential gene
YIR036W-A	0.244954	CUP2	YIR036W-A||S000028803|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YHR199C-A	0.2449	CUP2	YHR199C-A||S000029704|Putative protein of unknown function; transcribed sequence appears to contain an intron
YHR175W	0.244781	CUP2	YHR175W|CTR2|S000001218|Putative low-affinity copper transporter of the vacuolar membrane; mutation confers resistance to toxic copper concentrations, while overexpression confers resistance to copper starvation
YPR019W	0.243296	CUP2	YPR019W|MCM4|S000006223|Essential helicase component of heterohexameric MCM2-7 complexes which bind pre-replication complexes on DNA and melt the DNA prior to replication; accumulates in the nucleus in G1; homolog of S. pombe Cdc21p
YOR188W	0.243207	CUP2	YOR188W|MSB1|S000005714|Protein involved in positive regulation of both 1,3-beta-glucan synthesis and the Pkc1p-MAPK pathway, potential Cdc28p substrate; multicopy suppressor of temperature-sensitive mutations in CDC24 and CDC42, and of mutations in BEM4
YER189W	0.242549	CUP2	YER189W||S000000991|Putative protein of unknown function
YNL074C	0.242237	CUP2	YNL074C|MLF3|S000005018|Serine-rich protein of unknown function; overproduction suppresses the growth inhibition caused by exposure to the immunosuppressant leflunomide
YKL019W	0.242218	CUP2	YKL019W|RAM2|S000001502|Alpha subunit of both the farnesyltransferase and type I geranylgeranyltransferase that catalyze prenylation of proteins containing a CAAX consensus motif; essential protein required for membrane localization of Ras proteins and a-factor
YJL102W	0.241319	CUP2	YJL102W|MEF2|S000003638|Mitochondrial elongation factor involved in translational elongation
YHR185C	0.24034	CUP2	YHR185C|PFS1|S000001228|Sporulation protein required for prospore membrane formation at selected spindle poles, ensures functionality of all four spindle pole bodies during meiosis II; not required for meiotic recombination or meiotic chromosome segregation
YDL170W	0.240129	CUP2	YDL170W|UGA3|S000002329|Transcriptional activator necessary for gamma-aminobutyrate (GABA)-dependent induction of GABA genes (such as UGA1, UGA2, UGA4); zinc-finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type; localized to the nucleus
YHR115C	0.239156	CUP2	YHR115C|DMA1|S000001157|Protein involved in ubiquitin ligation; plays a role in regulating spindle position and orientation; functionally redundant with Dma2p; orthologous to human RNF8 protein, also has sequence similarity to human Chfr.
YER076W-A	0.238209	CUP2	YER076W-A||S000028750|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YER076C
YGR226C	0.237965	CUP2	YGR226C||S000003458|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; overlaps significantly with a verified ORF, AMA1/YGR225W
YPL258C	0.237403	CUP2	YPL258C|THI21|S000006179|Hydroxymethylpyrimidine phosphate kinase, involved in the last steps in thiamine biosynthesis; member of a gene family with THI20 and THI22; functionally redundant with Thi20p
YDR271C	0.237364	CUP2	YDR271C||S000002679|Hypothetical protein
YJL121C	0.236554	CUP2	YJL121C|RPE1|S000003657|D-ribulose-5-phosphate 3-epimerase, catalyzes a reaction in the non-oxidative part of the pentose-phosphate pathway; mutants are sensitive to oxidative stress
YML095C	0.236478	CUP2	YML095C|RAD10|S000004560|Single-stranded DNA endonuclease (with Rad1p), cleaves single-stranded DNA during nucleotide excision repair and double-strand break repair; subunit of Nucleotide Excision Repair Factor 1 (NEF1); homolog of human ERCC1 protein
YHL047C	0.234202	CUP2	YHL047C|ARN2|S000001039|Transporter, member of the ARN family of transporters that specifically recognize siderophore-iron chelates; responsible for uptake of iron bound to the siderophore triacetylfusarinine C
YOR381W-A	0.233982	CUP2	YOR381W-A||S000028587|Putative protein of unknown function; identified by fungal homology and RT-PCR
YGR069W	0.23391	CUP2	YGR069W||S000003301|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YMR255W	0.233538	CUP2	YMR255W|GFD1|S000004868|Coiled-coiled protein of unknown function, identified as a high-copy suppressor of a dbp5 mutation
YGL094C	0.232957	CUP2	YGL094C|PAN2|S000003062|Essential subunit of the Pan2p-Pan3p poly(A)-ribonuclease complex, which acts to control poly(A) tail length and regulate the stoichiometry and activity of postreplication repair complexes
YLR035C	0.232621	CUP2	YLR035C|MLH2|S000004025|Protein involved in the mismatch repair of certain frameshift intermediates and involved in meiotic recombination; forms a complex with Mlh1p
YJR021C	0.232428	CUP2	YJR021C|REC107|S000003782|Protein involved in early stages of meiotic recombination; involved in coordination between the initiation of recombination and the first division of meiosis; part of a complex (Rec107p-Mei4p-Rec114p) required for ds break formation
YKR058W	0.232274	CUP2	YKR058W|GLG1|S000001766|Self-glucosylating initiator of glycogen synthesis, also glucosylates n-dodecyl-beta-D-maltoside; similar to mammalian glycogenin
YMR272C	0.231256	CUP2	YMR272C|SCS7|S000004885|Sphingolipid alpha-hydroxylase, functions in the alpha-hydroxylation of sphingolipid-associated very long chain fatty acids, has both cytochrome b5-like and hydroxylase/desaturase domains, not essential for growth
YLR270W	0.230658	CUP2	YLR270W|DCS1|S000004260|Non-essential hydrolase involved in mRNA decapping, may function in a feedback mechanism to regulate deadenylation, contains pyrophosphatase activity and a HIT (histidine triad) motif; interacts with neutral trehalase Nth1p
YGL188C	0.229702	CUP2	YGL188C||S000003156|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR043C	0.229469	CUP2	YDR043C|NRG1|S000002450|Transcriptional repressor that recruits the Cyc8p-Tup1p complex to promoters; mediates glucose repression and negatively regulates a variety of processes including filamentous growth and alkaline pH response
YFR049W	0.229465	CUP2	YFR049W|YMR31|S000001945|Mitochondrial ribosomal protein of the small subunit, has similarity to human mitochondrial ribosomal protein MRP-S36
YJL036W	0.229186	CUP2	YJL036W|SNX4|S000003573|Sorting nexin, involved in the retrieval of late-Golgi SNAREs from the post-Golgi endosome to the trans-Golgi network and in cytoplasm to vacuole transport; contains a PX domain; forms complexes with Snx41p and with Atg20p
YJL101C	0.229142	CUP2	YJL101C|GSH1|S000003637|Gamma glutamylcysteine synthetase catalyzes the first step in glutathione (GSH) biosynthesis; expression induced by oxidants, cadmium, and mercury
YBR251W	0.228933	CUP2	YBR251W|MRPS5|S000000455|Mitochondrial ribosomal protein of the small subunit
YDL054C	0.228616	CUP2	YDL054C|MCH1|S000002212|Protein with similarity to mammalian monocarboxylate permeases, which are involved in transport of monocarboxylic acids across the plasma membrane; mutant is not deficient in monocarboxylate transport
YKL187C	0.228588	CUP2	YKL187C||S000001670|Putative protein of unknown function; the authentic, non-tagged protein is detected in a phosphorylated state in highly purified mitochondria in high-throughput studies
YKL108W	0.228387	CUP2	YKL108W|SLD2|S000001591|Protein required for DNA replication, phosphorylated in S phase by S-phase cyclin-dependent kinases (Cdks), phosphorylation is essential for DNA replication and for complex formation with Dpb11p; potential Cdc28p substrate
YKR025W	0.228215	CUP2	YKR025W|RPC37|S000001733|RNA polymerase III subunit C37
YPL127C	0.228123	CUP2	YPL127C|HHO1|S000006048|Histone H1, a linker histone required for nucleosome packaging at restricted sites; suppresses DNA repair involving homologous recombination; not required for telomeric silencing, basal transcriptional repression, or efficient sporulation
YNL015W	0.227868	CUP2	YNL015W|PBI2|S000004960|Cytosolic inhibitor of vacuolar proteinase B, required for efficient vacuole inheritance; with thioredoxin forms protein complex LMA1, which assists in priming SNARE molecules and promotes vacuole fusion
YPL133C	0.226649	CUP2	YPL133C|RDS2|S000006054|Zinc cluster transcriptional activator involved in conferring resistance to ketoconazole
YDR192C	0.226513	CUP2	YDR192C|NUP42|S000002600|Subunit of the nuclear pore complex (NPC) that localizes exclusively to the cytoplasmic side; involved in RNA export, most likely at a terminal step; interacts with Gle1p
YDR404C	0.226508	CUP2	YDR404C|RPB7|S000002812|RNA polymerase II subunit B16; forms two subunit dissociable complex with Rpb4p
YCL056C	0.226093	CUP2	YCL056C||S000000561|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YGR013W	0.225434	CUP2	YGR013W|SNU71|S000003245|Component of U1 snRNP required for mRNA splicing via spliceosome; yeast specific, no metazoan counterpart
YEL005C	0.225333	CUP2	YEL005C|VAB2|S000000731|Protein with a potential role in vacuolar function, as suggested by its ability to bind Vac8p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YJR112W-A	0.224248	CUP2	YJR112W-A||S000028513|Putative protein of unknown function; identified based on homology to Ashbya gossypii
YDR511W	0.223954	CUP2	YDR511W|ACN9|S000002919|Protein of the mitochondrial intermembrane space, required for acetate utilization and gluconeogenesis; has orthologs in higher eukaryotes
YEL072W	0.223799	CUP2	YEL072W|RMD6|S000000798|Protein required for sporulation
YPR153W	0.223614	CUP2	YPR153W||S000006357|Putative protein of unknown function
YDR441C	0.222998	CUP2	YDR441C|APT2|S000002849|Apparent pseudogene, not transcribed or translated under normal conditions; encodes a protein with similarity to adenine phosphoribosyltransferase, but artificially expressed protein exhibits no enzymatic activity
YPL083C	0.222025	CUP2	YPL083C|SEN54|S000006004|Subunit of the tRNA splicing endonuclease, which is composed of Sen2p, Sen15p, Sen34p, and Sen54p
YDL162C	0.221732	CUP2	YDL162C||S000002321|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps ENT1/YDL161W, a verified gene involved in endocytosis and actin cortical patch assembly
YPL088W	0.221259	CUP2	YPL088W||S000006009|Putative aryl alcohol dehydrogenase; transcription is activated by paralogous transcription factors Yrm1p and Yrr1p along with genes involved in multidrug resistance
YPL067C	0.220582	CUP2	YPL067C||S000005988|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YPL067C is not an essential gene
YGR194C	0.219787	CUP2	YGR194C|XKS1|S000003426|Xylulokinase, converts D-xylulose and ATP to xylulose 5-phosphate and ADP; rate limiting step in fermentation of xylulose; required for xylose fermentation by recombinant S. cerevisiae strains
YOR213C	0.219674	CUP2	YOR213C|SAS5|S000005739|Subunit of the SAS complex (Sas2p, Sas4p, Sas5p), which acetylates free histones and nucleosomes and regulates transcriptional silencing; stimulates Sas2p HAT activity
YDR527W	0.217861	CUP2	YDR527W|RBA50|S000002935|Protein involved in transcription; interacts with RNA polymerase II subunits Rpb2p, Rpb3, and Rpb11p; has similarity to human RPAP1
YHR102W	0.216205	CUP2	YHR102W|KIC1|S000001144|Protein kinase of the PAK/Ste20 kinase family, required for cell integrity possibly through regulating 1,6-beta-glucan levels in the wall; physically interacts with Cdc31p (centrin), which is a component of the spindle pole body
YKL210W	0.215809	CUP2	YKL210W|UBA1|S000001693|Ubiquitin activating enzyme (E1), involved in ubiquitin-mediated protein degradation and essential for viability
YJR106W	0.214866	CUP2	YJR106W|ECM27|S000003867|Non-essential protein of unknown function
YLL039C	0.214615	CUP2	YLL039C|UBI4|S000003962|Ubiquitin, becomes conjugated to proteins, marking them for selective degradation via the ubiquitin-26S proteasome system; essential for the cellular stress response; encoded as a polyubiquitin precursor comprised of 5 head-to-tail repeats
YAL031C	0.214582	CUP2	YAL031C|GIP4|S000000029|Cytoplasmic Glc7-interacting protein whose overexpression relocalizes Glc7p from the nucleus and prevents chromosome segregation; potential Cdc28p substrate
YMR122C	0.214521	CUP2	YMR122C||S000004729|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDL021W	0.214513	CUP2	YDL021W|GPM2|S000002179|Homolog of Gpm1p phosphoglycerate mutase which converts 3-phosphoglycerate to 2-phosphoglycerate in glycolysis; may be non-functional derivative of a gene duplication event
YDR164C	0.214061	CUP2	YDR164C|SEC1|S000002571|Sm-like protein involved in docking and fusion of exocytic vesicles through binding to assembled SNARE complexes at the membrane; localization to sites of secretion (bud neck and bud tip) is dependent on SNARE function
YLR071C	0.213928	CUP2	YLR071C|RGR1|S000004061|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; required for glucose repression, HO repression, RME1 repression and sporulation
YGL041C-B	0.213898	CUP2	YGL041C-B||S000028548|Putative protein of unknown function; identified by fungal homology and RT-PCR
YER084W-A	0.21375	CUP2	YER084W-A||S000028752|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR310C	0.213719	CUP2	YDR310C|SUM1|S000002718|Transcriptional repressor required for mitotic repression of middle sporulation-specific genes; involved in telomere maintenance, regulated by the pachytene checkpoint
YLL025W	0.213702	CUP2	YLL025W|PAU17|S000003948|Putative protein of unknown function; YLL025W is not an essential gene
YPR071W	0.213591	CUP2	YPR071W||S000006275|Putative membrane protein; YPR071W is not an essential gene
YGR282C	0.213224	CUP2	YGR282C|BGL2|S000003514|Endo-beta-1,3-glucanase, major protein of the cell wall, involved in cell wall maintenance
YLL040C	0.213157	CUP2	YLL040C|VPS13|S000003963|Protein of unknown function; heterooligomeric or homooligomeric complex; peripherally associated with membranes; homologous to human COH1; involved in sporulation, vacuolar protein sorting and protein-Golgi retention
YOR268C	0.212931	CUP2	YOR268C||S000005794|Putative protein of unknown function; sporulation is abnormal in homozygous diploid; YOR268C is not an essential gene
YHL036W	0.212892	CUP2	YHL036W|MUP3|S000001028|Low affinity methionine permease, similar to Mup1p
YMR284W	0.212844	CUP2	YMR284W|YKU70|S000004897|Subunit of the telomeric Ku complex (Yku70p-Yku80p), involved in telomere length maintenance, structure and telomere position effect; relocates to sites of double-strand cleavage to promote nonhomologous end joining during DSB repair
YJL156W-A	0.212743	CUP2	YJL156W-A||S000007613|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YER053C	0.211484	CUP2	YER053C|PIC2|S000000855|Mitochondrial phosphate carrier, imports inorganic phosphate into mitochondria; functionally redundant with Mir1p but less abundant than Mir1p under normal conditions; expression is induced at high temperature
YKL220C	0.211016	CUP2	YKL220C|FRE2|S000001703|Ferric reductase and cupric reductase, reduces siderophore-bound iron and oxidized copper prior to uptake by transporters; expression induced by low iron levels but not by low copper levels
YMR104C	0.211001	CUP2	YMR104C|YPK2|S000004710|Protein kinase with similarityto serine/threonine protein kinase Ypk1p; functionally redundant with YPK1 at the genetic level; participates in a signaling pathway required for optimal cell wall integrity; homolog of mammalian kinase SGK
YOL025W	0.210601	CUP2	YOL025W|LAG2|S000005385|Protein involved in determination of longevity; LAG2 gene is preferentially expressed in young cells; overexpression extends the mean and maximum life span of cells
YGR132C	0.2105	CUP2	YGR132C|PHB1|S000003364|Subunit of the prohibitin complex (Phb1p-Phb2p), a 1.2 MDa ring-shaped inner mitochondrial membrane chaperone that stabilizes newly synthesized proteins; determinant of replicative life span; involved in mitochondrial segregation
YDR236C	0.210492	CUP2	YDR236C|FMN1|S000002644|Riboflavin kinase, phosphorylates riboflavin to form riboflavin monophosphate (FMN), which is a necessary cofactor for many enzymes; localizes to microsomes and to the mitochondrial inner membrane
YDR359C	0.210327	CUP2	YDR359C|EAF1|S000002767|Component of the NuA4 histone acetyltransferase complex; required for initiation of pre-meiotic DNA replication, probably due to its requirement for significant expression of IME1
YOR040W	0.210008	CUP2	YOR040W|GLO4|S000005566|Mitochondrial glyoxalase II, catalyzes the hydrolysis of S-D-lactoylglutathione into glutathione and D-lactate
YER158W-A	0.208976	CUP2	YER158W-A||S000028624|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YNL295W	0.208898	CUP2	YNL295W||S000005239|Putative protein of unknown function
YOL083W	0.208859	CUP2	YOL083W||S000005443|Hypothetical protein
YDR057W	0.208776	CUP2	YDR057W|YOS9|S000002464|ER quality-control lectin; integral subunit of the HRD ligase; serves as a receptor for misfolded N-glycosylated proteins, participates in their targeting to ERAD; member of the OS-9 protein family
YLR219W	0.20871	CUP2	YLR219W|MSC3|S000004209|Protein of unknown function, green fluorescent protein (GFP)-fusion protein localizes to the cell periphery; msc3 mutants are defective in directing meiotic recombination events to homologous chromatids; potential Cdc28p substrate
YIL147C	0.208462	CUP2	YIL147C|SLN1|S000001409|Histidine kinase osmosensor that regulates a MAP kinase cascade; transmembrane protein with an intracellular kinase domain that signals to Ypd1p and Ssk1p, thereby forming a phosphorelay system similar to bacterial two-component regulators
YDR360W	0.207962	CUP2	YDR360W|OPI7|S000002768|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene VID21/YDR359C.
YDR317W	0.207525	CUP2	YDR317W|HIM1|S000002725|Protein of unknown function involved in DNA repair
YOL018C	0.207387	CUP2	YOL018C|TLG2|S000005378|Syntaxin-like t-SNARE that forms a complex with Tlg1p and Vti1p and mediates fusion of endosome-derived vesicles with the late Golgi; binds Vps45p, which prevents Tlg2p degradation and also facilitates t-SNARE complex formation
YNL285W	0.206958	CUP2	YNL285W||S000005229|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YER093C-A	0.206948	CUP2	YER093C-A|AIM11|S000002960|Putative protein of unknown function; YER093C-A contains an intron; null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YJR122W	0.206154	CUP2	YJR122W|IBA57|S000003883|Mitochondrial matrix protein involved in the incorporation of iron-sulfur clusters into mitochondrial aconitase-type proteins; activates the radical-SAM family members Bio2p and Lip5p; interacts with Ccr4p in the two-hybrid system
YDL007C-A	0.206033	CUP2	YDL007C-A||S000113557|Putative protein of unknown function
YIL146C	0.205461	CUP2	YIL146C|ECM37|S000001408|Non-essential protein of unknown function
YJR044C	0.205128	CUP2	YJR044C|VPS55|S000003805|Late endosomal protein involved in late endosome to vacuole trafficking; functional homolog of human obesity receptor gene-related protein (OB-RGRP)
YOR389W	0.203193	CUP2	YOR389W||S000005916|Putative protein of unknown function; expression regulated by copper levels
YBR255C-A	0.20304	CUP2	YBR255C-A||S000007649|Putative protein of unknown function; identified by sequence comparison with hemiascomycetous yeast species
YLR402W	0.202806	CUP2	YLR402W||S000004394|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YGR254W	0.202787	CUP2	YGR254W|ENO1|S000003486|Enolase I, a phosphopyruvate hydratase that catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate during glycolysis and the reverse reaction during gluconeogenesis; expression is repressed in response to glucose
YEL046C	0.202607	CUP2	YEL046C|GLY1|S000000772|Threonine aldolase, catalyzes the cleavage of L-allo-threonine and L-threonine to glycine; involved in glycine biosynthesis
YFR047C	0.202348	CUP2	YFR047C|BNA6|S000001943|Quinolinate phosphoribosyl transferase, required for the de novo biosynthesis of NAD from tryptophan via kynurenine; expression regulated by Hst1p
YDR186C	0.201993	CUP2	YDR186C||S000002594|Putative protein of unknown function; may interact with ribosomes, based on co-purification experiments; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YFL025C	0.201909	CUP2	YFL025C|BST1|S000001869|GPI inositol deacylase of the ER that negatively regulates COPII vesicle formation, prevents production of vesicles with defective subunits, required for proper discrimination between resident ER proteins and Golgi-bound cargo molecules
YKL159C	0.20173	CUP2	YKL159C|RCN1|S000001642|Protein involved in calcineurin regulation during calcium signaling; has similarity to H. sapiens DSCR1 which is found in the Down Syndrome candidate region
YBR082C	0.201167	CUP2	YBR082C|UBC4|S000000286|Ubiquitin-conjugating enzyme (E2), mediates degradation of short-lived and abnormal proteins; interacts with E3-CaM in ubiquitinating calmodulin; interacts with many SCF ubiquitin protein ligases; component of the cellular stress response
YAL046C	0.200236	CUP2	YAL046C|AIM1|S000000044|Putative protein of unknown function; null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YGR033C	0.200193	CUP2	YGR033C|TIM21|S000003265|Constituent of the mitochondrial inner membrane presequence translocase (TIM23 complex); may regulate protein import by binding to both the translocase of the outer membrane (TOM) and presequence-associated motor (PAM) complexes
YOR204W	0.19968	CUP2	YOR204W|DED1|S000005730|ATP-dependent DEAD (Asp-Glu-Ala-Asp)-box RNA helicase, required for translation initiation of all yeast mRNAs; mutations in human DEAD-box DBY are a frequent cause of male infertility
YLR403W	0.19905	CUP2	YLR403W|SFP1|S000004395|Transcription factor that controls expression of many ribosome biogenesis genes in response to nutrients and stress, regulates G2/M transitions during mitotic cell cycle and DNA-damage response, involved in cell size modulation
YDL120W	0.198838	CUP2	YDL120W|YFH1|S000002278|Frataxin, regulates mitochondrial iron accumulation; interacts with Isu1p which promotes Fe-S cluster assembly; interacts with electron transport chain components and may influence respiration; human homolog involved in Friedrich's ataxia
YDL061C	0.198374	CUP2	YDL061C|RPS29B|S000002219|Protein component of the small (40S) ribosomal subunit; nearly identical to Rps29Ap and has similarity to rat S29 and E. coli S14 ribosomal proteins
YJR068W	0.198199	CUP2	YJR068W|RFC2|S000003829|Subunit of heteropentameric Replication factor C (RF-C), which is a DNA binding protein and ATPase that acts as a clamp loader of the proliferating cell nuclear antigen (PCNA) processivity factor for DNA polymerases delta and epsilon
YJL046W	0.196626	CUP2	YJL046W|AIM22|S000003582|Putative lipoate-protein ligase A family member; null mutant displays respiratory growth defect, decreased frequency of mitochondrial genome loss (petite formation) and severe growth defect in minimal glycerol media
YLR271W	0.196522	CUP2	YLR271W||S000004261|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and the nucleus and is induced in response to the DNA-damaging agent MMS
YDL035C	0.194026	CUP2	YDL035C|GPR1|S000002193|Plasma membrane G protein coupled receptor (GPCR) that interacts with the heterotrimeric G protein alpha subunit, Gpa2p, and with Plc1p; sensor that integrates nutritional signals with the modulation of cell fate via PKA and cAMP synthesis
YPL236C	0.193652	CUP2	YPL236C||S000006157|Putative protein kinase that exhibits Akr1p-dependent palmitoylation
YLR116W	0.193325	CUP2	YLR116W|MSL5|S000004106|Component of the commitment complex, which defines the first step in the splicing pathway; essential protein that interacts with Mud2p and Prp40p, forming a bridge between the intron ends; also involved in nuclear retention of pre-mRNA
YGR039W	0.193292	CUP2	YGR039W||S000003271|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the Autonomously Replicating Sequence ARS722
YJL135W	0.193041	CUP2	YJL135W||S000003671|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified genes YJL134W/LCB3
YER125W	0.192904	CUP2	YER125W|RSP5|S000000927|Ubiquitin-protein ligase involved in ubiquitin-mediated protein degradation; functions in multivesicular body sorting, heat shock response and ubiquitylation of arrested RNAPII; contains a hect (homologous to E6-AP carboxyl terminus) domain
YDR193W	0.192503	CUP2	YDR193W||S000002601|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOL132W	0.192146	CUP2	YOL132W|GAS4|S000005492|1,3-beta-glucanosyltransferase, involved with Gas2p in spore wall assembly; has similarity to Gas1p; localizes to the cell wall
YAL031W-A	0.191454	CUP2	YAL031W-A||S000028731|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YJR019C	0.190911	CUP2	YJR019C|TES1|S000003780|Peroxisomal acyl-CoA thioesterase likely to be involved in fatty acid oxidation rather than fatty acid synthesis; conserved protein also found in human peroxisomes; TES1 mRNA levels increase during growth on fatty acids
YFR016C	0.19059	CUP2	YFR016C||S000001912|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and bud; interacts with Spa2p; YFL016C is not an essential gene
YPR169W-A	0.19055	CUP2	YPR169W-A||S000028591|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps two other dubious ORFs: YPR170C and YPR170W-B
YAR031W	0.190429	CUP2	YAR031W|PRM9|S000000078|Pheromone-regulated protein with 3 predicted transmembrane segments and an FF sequence, a motif involved in COPII binding; member of DUP240 gene family
YPR022C	0.190275	CUP2	YPR022C||S000006226|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus and is induced in response to the DNA-damaging agent MMS
YPR103W	0.189938	CUP2	YPR103W|PRE2|S000006307|Beta 5 subunit of the 20S proteasome, responsible for the chymotryptic activity of the proteasome
YKL150W	0.189267	CUP2	YKL150W|MCR1|S000001633|Mitochondrial NADH-cytochrome b5 reductase, involved in ergosterol biosynthesis
YDL243C	0.18864	CUP2	YDL243C|AAD4|S000002402|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase, involved in the oxidative stress response
YDR393W	0.188602	CUP2	YDR393W|SHE9|S000002801|Mitochondrial inner membrane protein required for normal mitochondrial morphology, may be involved in fission of the inner membrane; forms a homo-oligomeric complex
YBR287W	0.188161	CUP2	YBR287W||S000000491|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the ER; YBR287W is not an essential gene
YFL018C	0.187634	CUP2	YFL018C|LPD1|S000001876|Dihydrolipoamide dehydrogenase, the lipoamide dehydrogenase component (E3) of the pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase multi-enzyme complexes
YLL051C	0.187349	CUP2	YLL051C|FRE6|S000003974|Putative ferric reductase with similarity to Fre2p; expression induced by low iron levels
YIR002C	0.186594	CUP2	YIR002C|MPH1|S000001441|Member of the DEAH family of helicases, functions in an error-free DNA damage bypass pathway that involves homologous recombination, mutations confer a mutator phenotype
YMR157C	0.185929	CUP2	YMR157C|AIM36|S000004766|Protein of unknown function; non-tagged protein is detected in purified mitochondria in high-throughput studies; null mutant displays increased frequency of mitochondrial genome loss and reduced growth rate in minimal glycerol media
YKL039W	0.185409	CUP2	YKL039W|PTM1|S000001522|Protein of unknown function, copurifies with late Golgi vesicles containing the v-SNARE Tlg2p
YCL041C	0.185402	CUP2	YCL041C||S000000546|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps both the verified gene PDI1/YCL043C and the uncharacterized gene YCL042W
YMR088C	0.185327	CUP2	YMR088C|VBA1|S000004694|Permease of basic amino acids in the vacuolar membrane
YDL057W	0.185219	CUP2	YDL057W||S000002215|Putative protein of unknown function; YDL057W is not an essential gene
YDR306C	0.185121	CUP2	YDR306C||S000002714|F-box protein of unknown function; interacts with Sgt1p via a Leucine-Rich Repeat (LRR) domain
YGL160W	0.184836	CUP2	YGL160W|AIM14|S000003128|Putative protein of unknown function; similar to iron/copper reductases (FRE1-8), possibly involved in iron homeostasis; may interact with ribosomes, null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YOR279C	0.184468	CUP2	YOR279C|RFM1|S000005805|DNA-binding protein required for vegetative repression of middle sporulation genes; specificity factor that directs the Hst1p histone deacetylase to some of the promoters regulated by Sum1p; involved in telomere maintenance
YOL001W	0.184209	CUP2	YOL001W|PHO80|S000005361|Cyclin, negatively regulates phosphate metabolism; Pho80p-Pho85p (cyclin-CDK complex) phosphorylates Pho4p and Swi5p; deletion of PHO80 leads to aminoglycoside supersensitivity; truncated form of PHO80 affects vacuole inheritance
YDR403W	0.183249	CUP2	YDR403W|DIT1|S000002811|Sporulation-specific enzyme required for spore wall maturation, involved in the production of a soluble LL-dityrosine-containing precursor of the spore wall; transcripts accumulate at the time of prospore enclosure
YPR147C	0.182847	CUP2	YPR147C||S000006351|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and is induced in response to the DNA-damaging agent MMS
YML110C	0.18281	CUP2	YML110C|COQ5|S000004578|2-hexaprenyl-6-methoxy-1,4-benzoquinone methyltransferase, involved in ubiquinone (Coenzyme Q) biosynthesis; localizes to the matrix face of the mitochondrial inner membrane in a large complex with other ubiquinone biosynthetic enzymes
YFL034W	0.182765	CUP2	YFL034W||S000001860|Putative integral membrane protein that interacts with Rpp0p, which is a component of the ribosomal stalk
YAR019C	0.182246	CUP2	YAR019C|CDC15|S000000072|Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p
YGL167C	0.181708	CUP2	YGL167C|PMR1|S000003135|High affinity Ca2+/Mn2+ P-type ATPase required for Ca2+ and Mn2+ transport into Golgi; involved in Ca2+ dependent protein sorting and processing; mutations in human homolog ATP2C1 cause acantholytic skin condition Hailey-Hailey disease
YMR148W	0.181495	CUP2	YMR148W||S000004756|Putative protein of unknown function; predicted to contain a transmembrane domain; YMR148W is not an essential gene
YNL298W	0.181236	CUP2	YNL298W|CLA4|S000005242|Cdc42p activated signal transducing kinase of the PAK (p21-activated kinase) family, involved in septin ring assembly and cytokinesis; directly phosphorylates septins Cdc3p and Cdc10p; other yeast PAK family members are Ste20p and Skm1p
YEL050C	0.180641	CUP2	YEL050C|RML2|S000000776|Mitochondrial ribosomal protein of the large subunit, has similarity to E. coli L2 ribosomal protein; fat21 mutant allele causes inability to utilize oleate and may interfere with activity of the Adr1p transcription factor
YGR233C	0.180419	CUP2	YGR233C|PHO81|S000003465|Cyclin-dependent kinase (CDK) inhibitor, regulates Pho80p-Pho85p and Pcl7p-Pho85p cyclin-CDK complexes in response to phosphate levels; inhibitory activity for Pho80p-Pho85p requires myo-D-inositol heptakisphosphate (IP7) generated by Vip1p
YNL331C	0.179684	CUP2	YNL331C|AAD14|S000005275|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role
YMR179W	0.179162	CUP2	YMR179W|SPT21|S000004791|Protein required for normal transcription at several loci including HTA2-HTB2 and HHF2-HHT2, but not required at the other histone loci; functionally related to Spt10p; involved in telomere maintenance
YMR254C	0.178389	CUP2	YMR254C||S000004867|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YNR019W	0.178311	CUP2	YNR019W|ARE2|S000005302|Acyl-CoA:sterol acyltransferase, isozyme of Are1p; endoplasmic reticulum enzyme that contributes the major sterol esterification activity in the presence of oxygen
YDR526C	0.17829	CUP2	YDR526C||S000002934|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOR098C	0.177969	CUP2	YOR098C|NUP1|S000005624|Nuclear pore complex (NPC) subunit, involved in protein import/export and in export of RNAs, possible karyopherin release factor that accelerates release of karyopherin-cargo complexes after transport across NPC; potential Cdc28p substrate
YLR310C	0.177669	CUP2	YLR310C|CDC25|S000004301|Membrane bound guanine nucleotide exchange factor (GEF or GDP-release factor); indirectly regulates adenylate cyclase through activation of Ras1p and Ras2p by stimulating the exchange of GDP for GTP; required for progression through G1
YJR129C	0.177168	CUP2	YJR129C||S000003890|Putative protein of unknown function; predicted S-adenosylmethionine-dependent methyltransferase of the seven beta-strand family; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YJL112W	0.176421	CUP2	YJL112W|MDV1|S000003648|Peripheral protein of the cytosolic face of the mitochondrial outer membrane, required for mitochondrial fission; interacts with Fis1p and with the dynamin-related GTPase Dnm1p; contains WD repeats
YEL064C	0.176348	CUP2	YEL064C|AVT2|S000000790|Putative transporter, member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters
YIR018W	0.175856	CUP2	YIR018W|YAP5|S000001457|Basic leucine zipper (bZIP) transcription factor
YHL012W	0.175633	CUP2	YHL012W||S000001004|Putative protein of unknown function, has some homology to Ugp1p, which encodes UDP-glucose pyrophosphorylase
YJR037W	0.175319	CUP2	YJR037W||S000003798|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene HUL4/YJR036C; YJR037W is not an essential gene.
YHR057C	0.174962	CUP2	YHR057C|CPR2|S000001099|Peptidyl-prolyl cis-trans isomerase (cyclophilin), catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; has a potential role in the secretory pathway
YLR046C	0.174386	CUP2	YLR046C||S000004036|Putative membrane protein, transcription is activated by paralogous transcription factors Yrm1p and Yrr1p along with genes involved in multidrug resistance
YGL204C	0.174259	CUP2	YGL204C||S000003172|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPR176C	0.174098	CUP2	YPR176C|BET2|S000006380|Beta subunit of Type II geranylgeranyltransferase required for vesicular transport between the endoplasmic reticulum and the Golgi; provides a membrane attachment moiety to Rab-like proteins Ypt1p and Sec4p
YLR107W	0.173963	CUP2	YLR107W|REX3|S000004097|RNA exonuclease; required for maturation of the RNA component of RNase MRP; functions redundantly with Rnh70p and Rex2p in processing of U5 snRNA and RNase P RNA; member of RNase D family of exonucleases
YIL154C	0.173915	CUP2	YIL154C|IMP2'|S000001416|Transcriptional activator involved in maintenance of ion homeostasis and protection against DNA damage caused by bleomycin and other oxidants, contains a C-terminal leucine-rich repeat
YPR097W	0.173794	CUP2	YPR097W||S000006301|Protein that contains a Phox homology (PX) domain and binds phosphoinositides; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YFL007W	0.173519	CUP2	YFL007W|BLM10|S000001887|Proteosome activator subunit; found in association with core particles, with and without the 19S regulatory particle; required for resistance to bleomycin, may be involved in protecting against oxidative damage; similar to mammalian PA200
YKL094W	0.173483	CUP2	YKL094W|YJU3|S000001577|Serine hydrolase with sequence similarity to monoglyceride lipase (MGL), localizes to lipid particles
YML109W	0.173345	CUP2	YML109W|ZDS2|S000004577|Protein that interacts with silencing proteins at the telomere, involved in transcriptional silencing; paralog of Zds1p
YCR026C	0.173273	CUP2	YCR026C|NPP1|S000000621|Nucleotide pyrophosphatase/phosphodiesterase family member; mediates extracellular nucleotide phosphate hydrolysis along with Npp2p and Pho5p; activity and expression enhanced during conditions of phosphate starvation
YDR275W	0.173005	CUP2	YDR275W|BSC2|S000002683|Protein of unknown function, ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression
YKR016W	0.172883	CUP2	YKR016W|AIM28|S000001724|Protein of unknown function; non-tagged protein is detected in purified mitochondria in high-throughput studies; null mutant displays decreased frequency of mitochondrial genome loss and severe growth defect in minimal glycerol media
YER013W	0.172537	CUP2	YER013W|PRP22|S000000815|DEAH-box RNA-dependent ATPase/ATP-dependent RNA helicase, associates with lariat intermediates before the second catalytic step of splicing; mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes
YLR235C	0.172522	CUP2	YLR235C||S000004225|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene TOP3
YDL158C	0.172385	CUP2	YDL158C||S000002317|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data
YPL248C	0.172368	CUP2	YPL248C|GAL4|S000006169|DNA-binding transcription factor required for the activation of the GAL genes in response to galactose; repressed by Gal80p and activated by Gal3p
YJR020W	0.172176	CUP2	YJR020W||S000003781|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPL039W	0.1721	CUP2	YPL039W||S000005960|Putative protein of unknown function; YPL039W is not an essential gene
YFR030W	0.172004	CUP2	YFR030W|MET10|S000001926|Subunit alpha of assimilatory sulfite reductase, which is responsible for the conversion of sulfite into sulfide
YPL078C	0.17169	CUP2	YPL078C|ATP4|S000005999|Subunit b of the stator stalk of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; phosphorylated
YMR139W	0.171319	CUP2	YMR139W|RIM11|S000004747|Protein kinase required for signal transduction during entry into meiosis; promotes the formation of the Ime1p-Ume6p complex by phosphorylating Ime1p and Ume6p; shares similarity with mammalian glycogen synthase kinase 3-beta
YIL100W	0.171311	CUP2	YIL100W||S000001362|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the dubious ORF YIL100C-A
YDR453C	0.171219	CUP2	YDR453C|TSA2|S000002861|Stress inducible cytoplasmic thioredoxin peroxidase; cooperates with Tsa1p in the removal of reactive oxygen, nitrogen and sulfur species using thioredoxin as hydrogen donor; deletion enhances the mutator phenotype of tsa1 mutants
YEL019C	0.171007	CUP2	YEL019C|MMS21|S000000745|SUMO ligase involved in chromosomal organization and DNA repair; essential subunit of the Mms21-Smc5-Smc6 complex; mutants are sensitive to methyl methanesulfonate and show increased spontaneous mutation and mitotic recombination
YGR009C	0.170981	CUP2	YGR009C|SEC9|S000003241|t-SNARE protein important for fusion of secretory vesicles with the plasma membrane; similar to but not functionally redundant with Spo20p; SNAP-25 homolog
YOR187W	0.170859	CUP2	YOR187W|TUF1|S000005713|Mitochondrial translation elongation factor Tu; comprises both GTPase and guanine nucleotide exchange factor activities, while these activities are found in separate proteins in S. pombe and humans
YHR082C	0.170741	CUP2	YHR082C|KSP1|S000001124|Nonessential putative serine/threonine protein kinase of unknown cellular role; overproduction causes allele-specific suppression of the prp20-10 mutation
YAR019W-A	0.170018	CUP2	YAR019W-A||S000028735|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLR436C	0.169798	CUP2	YLR436C|ECM30|S000004428|Non-essential protein of unknown function
YER080W	0.169199	CUP2	YER080W|AIM9|S000000882|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays decreased frequency of mitochondrial genome loss (petite formation)
YBR095C	0.169195	CUP2	YBR095C|RXT2|S000000299|Subunit of the histone deacetylase Rpd3L complex; possibly involved in cell fusion and invasive growth
YMR155W	0.16911	CUP2	YMR155W||S000004764|Putative protein of unknown function; identified as interacting with Hsp82p in a high-throughput two-hybrid screen
YNL011C	0.168449	CUP2	YNL011C||S000004956|Putative protein of unknown function; YNL011C is not an essential gene
YNR039C	0.168428	CUP2	YNR039C|ZRG17|S000005322|Endoplasmic reticulum protein of unknown function, transcription is induced under conditions of zinc deficiency; mutant phenotype suggests a role in uptake of zinc
YJR046W	0.168013	CUP2	YJR046W|TAH11|S000003807|DNA replication licensing factor, required for pre-replication complex assembly
YJL149W	0.167641	CUP2	YJL149W|DAS1|S000003685|Putative SCF ubiquitin ligase F-box protein; interacts physically with both Cdc53p and Skp1 and genetically with CDC34; similar to putative F-box protein YDR131C; null mutant suppresses dst1delta sensitivity for 6-azauracil
YFR034W-A	0.167223	CUP2	YFR034W-A||S000028631|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps YFR035C; identified by gene-trapping, microarray expression analysis, and genome-wide homology searching
YOR364W	0.167209	CUP2	YOR364W||S000005891|Hypothetical protein
YOR023C	0.166891	CUP2	YOR023C|AHC1|S000005549|Subunit of the Ada histone acetyltransferase complex, required for structural integrity of the complex
YHL023C	0.166707	CUP2	YHL023C|RMD11|S000001015|Protein required for meiosis
YFL041W	0.166045	CUP2	YFL041W|FET5|S000001853|Multicopper oxidase, integral membrane protein with similarity to Fet3p; may have a role in iron transport
YBR070C	0.165889	CUP2	YBR070C|ALG14|S000000274|Component of UDP-GlcNAc transferase required for the second step of dolichyl-linked oligosaccharide synthesis; anchors the catalytic subunit Alg13p to the ER membrane; similar to bacterial and human glycosyltransferases
YNR062C	0.165866	CUP2	YNR062C||S000005345|Putative membrane protein of unknown function
YOR017W	0.165389	CUP2	YOR017W|PET127|S000005543|Protein with a role in 5'-end processing of mitochondrial RNAs, located in the mitochondrial membrane
YKL203C	0.165082	CUP2	YKL203C|TOR2|S000001686|PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis
YKL157W	0.165013	CUP2	YKL157W|APE2|S000001640|Zinc-dependent metallopeptidase yscII, may have a role in obtaining leucine from dipeptide substrates; sequence coordinates have changed since RT-PCR analysis showed that the adjacent ORF YKL158W comprises the 5' exon of APE2/YKL157W
YNL187W	0.164757	CUP2	YNL187W||S000005131|Putative protein of unknown function; contains a consensus nuclear export signal (NES) sequence similar to the consensus sequence recognized by Crm1p; may interact with or be fuctionally redundant with Prp40p
YKL171W	0.164204	CUP2	YKL171W||S000001654|Putative protein of unknown function; predicted protein kinase; implicated in proteasome function; epitope-tagged protein localizes to the cytoplasm
YOL078W	0.164178	CUP2	YOL078W|AVO1|S000005438|Component of a membrane-bound complex containing the Tor2p kinase and other proteins, which may have a role in regulation of cell growth
YOR068C	0.164147	CUP2	YOR068C|VAM10|S000005594|Protein involved in vacuole morphogenesis; acts at an early step of homotypic vacuole fusion that is required for vacuole tethering
YNL241C	0.163941	CUP2	YNL241C|ZWF1|S000005185|Glucose-6-phosphate dehydrogenase (G6PD), catalyzes the first step of the pentose phosphate pathway; involved in adapting to oxidatve stress; homolog of the human G6PD which is deficient in patients with hemolytic anemia
YNL037C	0.163606	CUP2	YNL037C|IDH1|S000004982|Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase, which catalyzes the oxidation of isocitrate to alpha-ketoglutarate in the TCA cycle
YLR237W	0.163435	CUP2	YLR237W|THI7|S000004227|Plasma membrane transporter responsible for the uptake of thiamine, member of the major facilitator superfamily of transporters; mutation of human ortholog causes thiamine-responsive megaloblastic anemia
YHL027W	0.162705	CUP2	YHL027W|RIM101|S000001019|Transcriptional repressor involved in response to pH and in cell wall construction; required for alkaline pH-stimulated haploid invasive growth and sporulation; activated by proteolytic processing; similar to A. nidulans PacC
YDR239C	0.162058	CUP2	YDR239C||S000002647|Protein of unknown function that may interact with ribosomes, based on co-purification experiments
YNL177C	0.16183	CUP2	YNL177C|MRPL22|S000005121|Mitochondrial ribosomal protein of the large subunit
YLR073C	0.161735	CUP2	YLR073C||S000004063|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to endosomes; YLR073C is not an esssential gene
YGR257C	0.161271	CUP2	YGR257C|MTM1|S000003489|Mitochondrial protein of the mitochondrial carrier family, involved in activating mitochondrial Sod2p probably by facilitating insertion of an essential manganese cofactor
YDR248C	0.160967	CUP2	YDR248C||S000002656|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YOL077W-A	0.159943	CUP2	YOL077W-A|ATP19|S000007339|Subunit k of the mitochondrial F1F0 ATP synthase, which is a large enzyme complex required for ATP synthesis; associated only with the dimeric form of ATP synthase
YHR071W	0.159643	CUP2	YHR071W|PCL5|S000001113|Cyclin, interacts with Pho85p cyclin-dependent kinase (Cdk), induced by Gcn4p at level of transcription, specifically required for Gcn4p degradation, may be sensor of cellular protein biosynthetic capacity
YOL100W	0.159492	CUP2	YOL100W|PKH2|S000005460|Serine/threonine protein kinase involved in sphingolipid-mediated signaling pathway that controls endocytosis; activates Ypk1p and Ykr2p, components of signaling cascade required for maintenance of cell wall integrity; redundant with Pkh1p
YIL083C	0.158151	CUP2	YIL083C||S000001345|Putative phosphopantothenoylcysteine synthetase (PPCS) that catalyzes the second step in the biosynthesis of coenzyme A from pantothenate; conserved in bacteria, humans, and plants; essential for viability
YLR034C	0.157747	CUP2	YLR034C|SMF3|S000004024|Putative divalent metal ion transporter involved in iron homeostasis; transcriptionally regulated by metal ions; member of the Nramp family of metal transport proteins
YDR378C	0.157731	CUP2	YDR378C|LSM6|S000002786|Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA
YHR024C	0.15739	CUP2	YHR024C|MAS2|S000001066|Larger subunit of the mitochondrial processing protease (MPP), essential processing enzyme that cleaves the N-terminal targeting sequences from mitochondrially imported proteins
YGL215W	0.157293	CUP2	YGL215W|CLG1|S000003183|Cyclin-like protein that interacts with Pho85p; has sequence similarity to G1 cyclins PCL1 and PCL2
YNL329C	0.157026	CUP2	YNL329C|PEX6|S000005273|AAA-peroxin that heterodimerizes with AAA-peroxin Pex1p and participates in the recycling of peroxisomal signal receptor Pex5p from the peroxisomal membrane to the cystosol
YGR235C	0.156542	CUP2	YGR235C||S000003467|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YLR450W	0.156408	CUP2	YLR450W|HMG2|S000004442|One of two isozymes of HMG-CoA reductase that convert HMG-CoA to mevalonate, a rate-limiting step in sterol biosynthesis; overproduction induces assembly of peripheral ER membrane arrays and short nuclear-associated membrane stacks
YBR208C	0.15568	CUP2	YBR208C|DUR1,2|S000000412|Urea amidolyase, contains both urea carboxylase and allophanate hydrolase activities, degrades urea to CO2 and NH3; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation
YIL054W	0.155608	CUP2	YIL054W||S000001316|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YNL082W	0.154761	CUP2	YNL082W|PMS1|S000005026|ATP-binding protein required for mismatch repair in mitosis and meiosis; functions as a heterodimer with Mlh1p, binds double- and single-stranded DNA via its N-terminal domain, similar to E. coli MutL
YNR047W	0.154041	CUP2	YNR047W||S000005330|Putative protein kinase that, when overexpressed, interferes with pheromone-induced growth arrest; localizes to the cytoplasm; potential Cdc28p substrate
YKL112W	0.153519	CUP2	YKL112W|ABF1|S000001595|DNA binding protein with possible chromatin-reorganizing activity involved in transcriptional activation, gene silencing, and DNA replication and repair
YML076C	0.153249	CUP2	YML076C|WAR1|S000004541|Homodimeric Zn2Cys6 zinc finger transcription factor; binds to a weak acid response element to induce transcription of PDR12 and FUN34, encoding an acid transporter and a putative ammonia transporter, respectively
YGL015C	0.153221	CUP2	YGL015C||S000002983|Hypothetical protein
YJL119C	0.153092	CUP2	YJL119C||S000003655|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YJR091C	0.153021	CUP2	YJR091C|JSN1|S000003851|Member of the Puf family of RNA-binding proteins, interacts with mRNAs encoding membrane-associated proteins; overexpression suppresses a tub2-150 mutation and causes increased sensitivity to benomyl in wild-type cells
YDR160W	0.153014	CUP2	YDR160W|SSY1|S000002567|Component of the SPS plasma membrane amino acid sensor system (Ssy1p-Ptr3p-Ssy5p), which senses external amino acid concentration and transmits intracellular signals that result in regulation of expression of amino acid permease genes
YNL025C	0.152901	CUP2	YNL025C|SSN8|S000004970|Cyclin-like component of the RNA polymerase II holoenzyme, involved in phosphorylation of the RNA polymerase II C-terminal domain; involved in glucose repression and telomere maintenance
YER147C	0.152831	CUP2	YER147C|SCC4|S000000949|Subunit of cohesin loading factor (Scc2p-Scc4p), a complex required for the loading of cohesin complexes onto chromosomes; involved in establishing sister chromatid cohesion during double-strand break repair via phosphorylated histone H2AX
YLR176C	0.152326	CUP2	YLR176C|RFX1|S000004166|Major transcriptional repressor of DNA-damage-regulated genes, recruits repressors Tup1p and Cyc8p to their promoters; involved in DNA damage and replication checkpoint pathway; similar to a family of mammalian DNA binding RFX1-4 proteins
YOR032W-A	0.152301	CUP2	YOR032W-A||S000028710|Identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YDR272W	0.152293	CUP2	YDR272W|GLO2|S000002680|Cytoplasmic glyoxalase II, catalyzes the hydrolysis of S-D-lactoylglutathione into glutathione and D-lactate
YKR019C	0.152254	CUP2	YKR019C|IRS4|S000001727|EH domain-containing protein involved in regulating phosphatidylinositol 4,5-bisphosphate levels and autophagy; Irs4p and Tax4p bind and activate the PtdIns phosphatase Inp51p; Irs4p and Tax4p are involved in localizing Atg17p to the PAS
YEL057C	0.152106	CUP2	YEL057C||S000000783|Protein of unknown function involved in telomere maintenance; target of UME6 regulation
YLR354C	0.151896	CUP2	YLR354C|TAL1|S000004346|Transaldolase, enzyme in the non-oxidative pentose phosphate pathway; converts sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate to erythrose 4-phosphate and fructose 6-phosphate
YKL123W	0.151754	CUP2	YKL123W||S000001606|Dubious open reading frame, unlikely to encode a protein; partially overlaps the verified gene SSH4
YEL017W	0.151316	CUP2	YEL017W|GTT3|S000000743|Protein of unknown function with a possible role in glutathione metabolism, as suggested by computational analysis of large-scale protein-protein interaction data; GFP-fusion protein localizes to the nuclear periphery
YLR095C	0.151218	CUP2	YLR095C|IOC2|S000004085|Member of a complex (Isw1b) with Isw1p and Ioc4p that exhibits nucleosome-stimulated ATPase activity and acts within coding regions to coordinate transcription elongation with termination and processing, contains a PHD finger motif
YJR079W	0.150866	CUP2	YJR079W||S000003840|Putative protein of unknown function; mutation results in impaired mitochondrial respiration
YPR003C	0.15078	CUP2	YPR003C||S000006207|Putative sulfate permease; physically interacts with Hsp82p; green fluorescent protein (GFP)-fusion protein localizes to the ER; YPR003C is not an essential gene
YKL176C	0.150678	CUP2	YKL176C|LST4|S000001659|Protein possibly involved in a post-Golgi secretory pathway; required for the transport of nitrogen-regulated amino acid permease Gap1p from the Golgi to the cell surface
YCL052C	0.150512	CUP2	YCL052C|PBN1|S000000557|Essential component of glycosylphosphatidylinositol-mannosyltransferase I, required for the autocatalytic post-translational processing of the protease B precursor Prb1p, localizes to ER in lumenal orientation; homolog of mammalian PIG-X
YJR025C	0.149761	CUP2	YJR025C|BNA1|S000003786|3-hydroxyanthranilic acid dioxygenase, required for the de novo biosynthesis of NAD from tryptophan via kynurenine; expression regulated by Hst1p
YDR205W	0.149723	CUP2	YDR205W|MSC2|S000002613|Member of the cation diffusion facilitator family, localizes to the endoplasmic reticulum and nucleus; mutations affect the cellular distribution of zinc and also confer defects in meiotic recombination between homologous chromatids
YNL293W	0.149181	CUP2	YNL293W|MSB3|S000005237|GTPase-activating protein for Sec4p and several other Rab GTPases, regulates exocytosis via its action on Sec4p, also required for proper actin organization; similar to Msb4p; both Msb3p and Msb4p localize to sites of polarized growth
YJR067C	0.148931	CUP2	YJR067C|YAE1|S000003828|Essential protein of unknown function
YKL165C-A	0.148557	CUP2	YKL165C-A||S000007617|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YGL043W	0.147311	CUP2	YGL043W|DST1|S000003011|General transcription elongation factor TFIIS, enables RNA polymerase II to read through blocks to elongation by stimulating cleavage of nascent transcripts stalled at transcription arrest sites
YGL041W-A	0.146427	CUP2	YGL041W-A||S000028826|Putative protein of unknown function, conserved in fungi; identified by expression profiling and mass spectrometry
YHR101C	0.146342	CUP2	YHR101C|BIG1|S000001143|Integral membrane protein of the endoplasmic reticulum, required for normal content of cell wall beta-1,6-glucan
YPL033C	0.145677	CUP2	YPL033C||S000005954|Putative protein of unknown function; may be involved in DNA metabolism; expression is induced by Kar4p
YAL066W	0.14563	CUP2	YAL066W||S000000061|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLR184W	0.145181	CUP2	YLR184W||S000004174|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YNL150W	0.144776	CUP2	YNL150W||S000005094|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; extensive overlap with PGA2/YNL149C, an uncharacterized gene with a proposed role in protein trafficking
YOL085W-A	0.144705	CUP2	YOL085W-A||S000028708|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YOL085C
YNL245C	0.144467	CUP2	YNL245C|CWC25|S000005189|Component of a complex containing Cef1p, involved in pre-mRNA splicing; has similarity to S. pombe Cwf25p
YML004C	0.144466	CUP2	YML004C|GLO1|S000004463|Monomeric glyoxalase I, catalyzes the detoxification of methylglyoxal (a by-product of glycolysis) via condensation with glutathione to produce S-D-lactoylglutathione; expression regulated by methylglyoxal levels and osmotic stress
YNL018C	0.14413	CUP2	YNL018C||S000004963|Putative protein of unknown function
YDL246C	0.143766	CUP2	YDL246C|SOR2|S000002405|Protein of unknown function, computational analysis of large-scale protein-protein interaction data suggests a possible role in fructose or mannose metabolism
YNL337W	0.143665	CUP2	YNL337W||S000005281|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YJR151C	0.143226	CUP2	YJR151C|DAN4|S000003912|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YJR128W	0.143225	CUP2	YJR128W||S000003889|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF RSF2
YLR236C	0.142421	CUP2	YLR236C||S000004226|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YBR197C	0.142419	CUP2	YBR197C||S000000401|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YBR197C is not an essential gene
YDR376W	0.142159	CUP2	YDR376W|ARH1|S000002784|Oxidoreductase of the mitochondrial inner membrane, involved in cytoplasmic and mitochondrial iron homeostasis and required for activity of Fe-S cluster-containing enzymes; one of the few mitochondrial proteins essential for viability
YGL044C	0.14082	CUP2	YGL044C|RNA15|S000003012|Cleavage and polyadenylation factor I (CF I) component involved in cleavage and polyadenylation of mRNA 3' ends; interacts with the A-rich polyadenylation signal in complex with Rna14p and Hrp1p
YBL096C	0.14069	CUP2	YBL096C||S000000192|Non-essential protein of unknown function
YDL060W	0.140413	CUP2	YDL060W|TSR1|S000002218|Protein required for processing of 20S pre-rRNA in the cytoplasm, associates with pre-40S ribosomal particles
YDR351W	0.140392	CUP2	YDR351W|SBE2|S000002759|Protein involved in the transport of cell wall components from the Golgi to the cell surface; required for bud growth
YGR109C	0.139016	CUP2	YGR109C|CLB6|S000003341|B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1
YKR021W	0.138891	CUP2	YKR021W|ALY1|S000001729|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YLL057C	0.138661	CUP2	YLL057C|JLP1|S000003980|Fe(II)-dependent sulfonate/alpha-ketoglutarate dioxygenase, involved in sulfonate catabolism for use as a sulfur source, contains sequence that closely resembles a J domain (typified by the E. coli DnaJ protein)
YDL146W	0.138132	CUP2	YDL146W|LDB17|S000002305|Protein of unknown function; GFP-fusion protein localizes to the cell periphery, cytoplasm, bud, and bud neck; null mutant shows a reduced affinity for the alcian blue dye suggesting a decreased net negative charge of the cell surface
YIL092W	0.13765	CUP2	YIL092W||S000001354|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and to the nucleus
YPL031C	0.13761	CUP2	YPL031C|PHO85|S000005952|Cyclin-dependent kinase, with ten cyclin partners; involved in regulating the cellular response to nutrient levels and environmental conditions and progression through the cell cycle
YIR003W	0.137288	CUP2	YIR003W|AIM21|S000001442|Protein of unknown function; may interact with ribosomes; GFP-fusion protein colocalizes with Sac1p to the actin cytoskeleton; null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YNL296W	0.137225	CUP2	YNL296W||S000005240|Dubious open reading frame unlikely to encode a functional protein; deletion adversely affects sporulation; deletion mutant exhibits synthetic phenotype under expression of mutant huntingtin fragment, but gene does not have human ortholog
YPL114W	0.136012	CUP2	YPL114W||S000006035|Dubious open reading frame, unlikely to encode a functional protein; largely overlaps ORF YPL113C; diploid deletion in BY4743 strain background exhibits high budding index
YDR168W	0.135965	CUP2	YDR168W|CDC37|S000002575|Essential Hsp90p co-chaperone; necessary for passage through the START phase of the cell cycle; stabilizes protein kinase nascent chains and participates along with Hsp90p in their folding
YJR045C	0.135547	CUP2	YJR045C|SSC1|S000003806|Mitochondrial matrix ATPase, subunit of the presequence translocase-associated protein import motor (PAM) and of SceI endonuclease; involved in protein folding and translocation into the matrix; phosphorylated; member of HSP70 family
YBL042C	0.13528	CUP2	YBL042C|FUI1|S000000138|High affinity uridine permease, localized to the plasma membrane; not involved in uracil transport
YBR290W	0.134975	CUP2	YBR290W|BSD2|S000000494|Heavy metal ion homeostasis protein, facilitates trafficking of Smf1p and Smf2p metal transporters to the vacuole where they are degraded, controls metal ion transport, prevents metal hyperaccumulation, functions in copper detoxification
YBL095W	0.134959	CUP2	YBL095W||S000000191|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YML083C	0.134247	CUP2	YML083C||S000004548|Putative protein of unknown function; strong increase in transcript abundance during anaerobic growth compared to aerobic growth; cells deleted for YML083C do not exhibit growth defects in anerobic or anaerobic conditions
YPL126W	0.134071	CUP2	YPL126W|NAN1|S000006047|U3 snoRNP protein, component of the small (ribosomal) subunit (SSU) processosome containing U3 snoRNA; required for the biogenesis of18S rRNA
YLL010C	0.133874	CUP2	YLL010C|PSR1|S000003933|Plasma membrane associated protein phosphatase involved in the general stress response; required along with binding partner Whi2p for full activation of STRE-mediated gene expression, possibly through dephosphorylation of Msn2p
YDR522C	0.133589	CUP2	YDR522C|SPS2|S000002930|Protein expressed during sporulation, redundant with Sps22p for organization of the beta-glucan layer of the spore wall; S. pombe ortholog is a spore wall component
YPL264C	0.133464	CUP2	YPL264C||S000006185|Putative membrane protein of unknown function; physically interacts with Hsp82p; YPL264C is not an essential gene
YEL004W	0.133177	CUP2	YEL004W|YEA4|S000000730|Uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) transporter required for cell wall chitin synthesis; localized to the ER
YER145C	0.132255	CUP2	YER145C|FTR1|S000000947|High affinity iron permease involved in the transport of iron across the plasma membrane; forms complex with Fet3p; expression is regulated by iron
YIL084C	0.132247	CUP2	YIL084C|SDS3|S000001346|Component of the Rpd3p/Sin3p deacetylase complex required for its structural integrity and catalytic activity, involved in transcriptional silencing and required for sporulation; cells defective in SDS3 display pleiotropic phenotypes
YOR360C	0.132084	CUP2	YOR360C|PDE2|S000005887|High-affinity cyclic AMP phosphodiesterase, component of the cAMP-dependent protein kinase signaling system, protects the cell from extracellular cAMP, contains readthrough motif surrounding termination codon
YJR051W	0.131734	CUP2	YJR051W|OSM1|S000003812|Fumarate reductase, catalyzes the reduction of fumarate to succinate, required for the reoxidation of intracellular NADH under anaerobic conditions; mutations cause osmotic sensitivity
YMR089C	0.131641	CUP2	YMR089C|YTA12|S000004695|Component, with Afg3p, of the mitochondrial inner membrane m-AAA protease that mediates degradation of misfolded or unassembled proteins and is also required for correct assembly of mitochondrial enzyme complexes
YPR109W	0.131566	CUP2	YPR109W||S000006313|Predicted membrane protein; dipoid deletion strain has high budding index
YPL257W	0.131259	CUP2	YPL257W||S000006178|Putative protein of unknown function;; homozygous diploid deletion strain exhibits low budding index; physically interacts with Hsp82p; YPL257W is not an essential gene
YKL098W	0.130893	CUP2	YKL098W|MTC2|S000001581|Putative protein of unknown function; YKL098W is synthetically sick with cdc13-1
YCR096C	0.130589	CUP2	YCR096C|HMRA2|S000000692|Silenced copy of a2 at HMR; similarity to Alpha2p; required along with a1p for inhibiting expression of the HO endonuclease in a/alpha HO/HO diploid cells with an active mating-type interconversion system
YLR064W	0.130211	CUP2	YLR064W||S000004054|Putative protein of unknown function; highly conserved across species and orthologous to human TMEM33; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YLR064W is not an essential gene
YAL032C	0.13018	CUP2	YAL032C|PRP45|S000000030|Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene
YLR248W	0.129999	CUP2	YLR248W|RCK2|S000004238|Protein kinase involved in the response to oxidative and osmotic stress; identified as suppressor of S. pombe cell cycle checkpoint mutations
YDR419W	0.129481	CUP2	YDR419W|RAD30|S000002827|DNA polymerase eta, involved in the predominantly error-free bypass replication of DNA lesions, catalyzes the efficient and accurate synthesis of DNA opposite cyclobutane pyrimidine dimers; homolog of human POLH and bacterial DinB proteins
YBR033W	0.129459	CUP2	YBR033W|EDS1|S000000237|Putative zinc cluster protein; YBR033W is not an essential gene
YDR442W	0.129159	CUP2	YDR442W||S000002850|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGL162W	0.128885	CUP2	YGL162W|SUT1|S000003130|Transcription factor of the Zn[II]2Cys6 family involved in sterol uptake; involved in induction of hypoxic gene expression
YDR311W	0.12861	CUP2	YDR311W|TFB1|S000002719|Subunit of TFIIH and nucleotide excision repair factor 3 complexes, required for nucleotide excision repair, target for transcriptional activators
YGR210C	0.128504	CUP2	YGR210C||S000003442|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YER098W	0.128477	CUP2	YER098W|UBP9|S000000900|Ubiquitin carboxyl-terminal hydrolase, ubiquitin-specific protease that cleaves ubiquitin-protein fusions
YLR015W	0.128464	CUP2	YLR015W|BRE2|S000004005|Subunit of the COMPASS (Set1C) complex, which methylates histone H3 on lysine 4 and is required in transcriptional silencing near telomeres; involved in telomere maintenance; similar to trithorax-group protein ASH2L
YCL069W	0.12843	CUP2	YCL069W|VBA3|S000000574|Permease of basic amino acids in the vacuolar membrane
YGL150C	0.128019	CUP2	YGL150C|INO80|S000003118|ATPase that forms a large complex, containing actin and several actin-related proteins, that has chromatin remodeling activity and 3' to 5' DNA helicase activity in vitro; shows similarity to the Snf2p family of ATPases
YER190W	0.127978	CUP2	YER190W|YRF1-2|S000000992|Helicase encoded by the Y' element of subtelomeric regions, highly expressed in the mutants lacking the telomerase component TLC1; potentially phosphorylated by Cdc28p; induced by treatment with 8-methoxypsoralen and UVA irradiation
YPR081C	0.127943	CUP2	YPR081C|GRS2|S000006285|Protein with sequence similarity to Grs1p, which is a glycyl-tRNA synthetase; cannot substitute for Grs1p; possible pseudogene that is expressed at very low levels
YDR237W	0.126619	CUP2	YDR237W|MRPL7|S000002645|Mitochondrial ribosomal protein of the large subunit
YBR131W	0.126285	CUP2	YBR131W|CCZ1|S000000335|Protein involved in vacuolar assembly, essential for autophagy and the cytoplasm-to-vacuole pathway
YGL090W	0.126279	CUP2	YGL090W|LIF1|S000003058|Component of the DNA ligase IV complex that mediates nonhomologous end joining in DNA double-strand break repair; physically interacts with Dnl4p and Nej1p; homologous to mammalian XRCC4 protein
YMR213W	0.12598	CUP2	YMR213W|CEF1|S000004826|Essential splicing factor; associated with Prp19p and the spliceosome, contains an N-terminal c-Myb DNA binding motif necessary for cell viability but not for Prp19p association, evolutionarily conserved and homologous to S. pombe Cdc5p
YOR171C	0.125663	CUP2	YOR171C|LCB4|S000005697|Sphingoid long-chain base kinase, responsible for synthesis of long-chain base phosphates, which function as signaling molecules, regulates synthesis of ceramide from exogenous long-chain bases, localizes to the Golgi and late endosomes
YMR162C	0.125418	CUP2	YMR162C|DNF3|S000004772|Aminophospholipid translocase (flippase) that maintains membrane lipid asymmetry in post-Golgi secretory vessicles; localizes to the trans-Golgi network; likely involved in protein transport; type 4 P-type ATPase
YKL167C	0.125188	CUP2	YKL167C|MRP49|S000001650|Mitochondrial ribosomal protein of the large subunit, not essential for mitochondrial translation
YCR028C	0.125043	CUP2	YCR028C|FEN2|S000000623|Plasma membrane H+-pantothenate symporter; confers sensitivity to the antifungal agent fenpropimorph
YDL026W	0.124911	CUP2	YDL026W||S000002184|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data
YMR027W	0.124686	CUP2	YMR027W||S000004629|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus and cytoplasm; YMR027W is not an essential gene
YCR048W	0.12438	CUP2	YCR048W|ARE1|S000000644|Acyl-CoA:sterol acyltransferase, isozyme of Are2p; endoplasmic reticulum enzyme that contributes the major sterol esterification activity in the absence of oxygen
YDR473C	0.124115	CUP2	YDR473C|PRP3|S000002881|Splicing factor, component of the U4/U6-U5 snRNP complex
YPL174C	0.122737	CUP2	YPL174C|NIP100|S000006095|Large subunit of the dynactin complex, which is involved in partitioning the mitotic spindle between mother and daughter cells; putative ortholog of mammalian p150(glued)
YOR246C	0.122712	CUP2	YOR246C||S000005772|Protein with similarity to oxidoreductases, found in lipid particles; required for replication of Brome mosaic virus in S. cerevisiae, which is a model system for studying replication of positive-strand RNA viruses in their natural hosts
YHR156C	0.122641	CUP2	YHR156C|LIN1|S000001199|Non-essential component of U5 snRNP; nuclear protein; physically interacts with Irr1p of cohesin complex; may link together proteins involved in chromosome segregation, mRNA splicing and DNA replication
YLR059C	0.122283	CUP2	YLR059C|REX2|S000004049|RNA exonuclease, required for U4 snRNA maturation; functions redundantly with Rnh70p in 5.8S rRNA maturation, and with Rnh70p and Rex3p in processing of U5 snRNA and RNase P RNA; member of RNase D family of exonucleases
YOR016C	0.122093	CUP2	YOR016C|ERP4|S000005542|Protein with similarity to Emp24p and Erv25p, member of the p24 family involved in ER to Golgi transport
YKR042W	0.122071	CUP2	YKR042W|UTH1|S000001750|Mitochondrial outer membrane and cell wall localized SUN family member required for mitochondrial autophagy; involved in the oxidative stress response, life span during starvation, mitochondrial biogenesis, and cell death
YGR127W	0.12177	CUP2	YGR127W||S000003359|Putative protein of unknown function; expression is regulated by Msn2p/Msn4p, indicating a possible role in stress response
YJL070C	0.121571	CUP2	YJL070C||S000003606|Putative protein of unknown function with similarity to AMP deaminases; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YJL070C is a non-essential gene
YMR294W	0.121373	CUP2	YMR294W|JNM1|S000004908|Component of the yeast dynactin complex, consisting of Nip100p, Jnm1p, and Arp1p; required for proper nuclear migration and spindle partitioning during mitotic anaphase B
YCR097W	0.121226	CUP2	YCR097W|HMRA1|S000000694|Silenced copy of a1 at HMR; homeobox corepressor that interacts with Alpha2p to repress haploid-specific gene transcription in diploid cells
YHR104W	0.121042	CUP2	YHR104W|GRE3|S000001146|Aldose reductase involved in methylglyoxal, d-xylose and arabinose metabolism; stress induced (osmotic, ionic, oxidative, heat shock, starvation and heavy metals); regulated by the HOG pathway
YDR285W	0.120976	CUP2	YDR285W|ZIP1|S000002693|Transverse filament protein of the synaptonemal complex; required for normal levels of meiotic recombination and pairing between homologous chromosome during meiosis; potential Cdc28p substrate
YLR350W	0.120397	CUP2	YLR350W|ORM2|S000004342|Evolutionarily conserved protein with similarity to Orm1p, required for resistance to agents that induce the unfolded protein response; human ortholog is located in the endoplasmic reticulum
YGL176C	0.120248	CUP2	YGL176C||S000003144|Putative protein of unknown function; deletion mutant is viable and has no detectable phenotype
YDR242W	0.120083	CUP2	YDR242W|AMD2|S000002650|Putative amidase
YGL254W	0.119562	CUP2	YGL254W|FZF1|S000003223|Transcription factor involved in sulfite metabolism, sole identified regulatory target is SSU1, overexpression suppresses sulfite-sensitivity of many unrelated mutants due to hyperactivation of SSU1, contains five zinc fingers
YIL090W	0.11948	CUP2	YIL090W|ICE2|S000001352|Integral ER membrane protein with type-III transmembrane domains; mutations cause defects in cortical ER morphology in both the mother and daughter cells
YLR231C	0.119109	CUP2	YLR231C|BNA5|S000004221|Kynureninase, required for the de novo biosynthesis of NAD from tryptophan via kynurenine; expression regulated by Hst1p
YDR459C	0.117915	CUP2	YDR459C|PFA5|S000002867|Palmitoyltransferase with autoacylation activity; likely functions in pathway(s) outside Ras; member of a family of putative palmitoyltransferases containing an Asp-His-His-Cys-cysteine rich (DHHC-CRD) domain
YOR350C	0.116874	CUP2	YOR350C|MNE1|S000005877|Mitochondrial protein similar to Lucilia illustris mitochondrial cytochrome oxidase
YNL053W	0.116686	CUP2	YNL053W|MSG5|S000004998|Dual-specificity protein phosphatase required for maintenance of a low level of signaling through the cell integrity pathway; regulates and is regulated by Slt2p; dephosphorylates Fus3p; required for adaptive response to pheromone
YDL027C	0.116588	CUP2	YDL027C||S000002185|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YDL027C is not an essential gene
YOR200W	0.115828	CUP2	YOR200W||S000005726|Hypothetical protein
YNL288W	0.115727	CUP2	YNL288W|CAF40|S000005232|Evolutionarily conserved subunit of the CCR4-NOT complex involved in controlling mRNA initiation, elongation and degradation; binds Cdc39p
YBL086C	0.115656	CUP2	YBL086C||S000000182|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery
YCR073C	0.115641	CUP2	YCR073C|SSK22|S000000669|MAP kinase kinase kinase of the HOG1 mitogen-activated signaling pathway; functionally redundant with, and homologous to, Ssk2p; interacts with and is activated by Ssk1p; phosphorylates Pbs2p
YEL069C	0.11512	CUP2	YEL069C|HXT13|S000000795|Hexose transporter, induced in the presence of non-fermentable carbon sources, induced by low levels of glucose, repressed by high levels of glucose
YGR259C	0.114592	CUP2	YGR259C||S000003491|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps almost completely with the verified ORF TNA1/YGR260W
YLR415C	0.114399	CUP2	YLR415C||S000004407|Putative protein of unknown function; YLR415C is not an essential gene
YGR220C	0.114129	CUP2	YGR220C|MRPL9|S000003452|Mitochondrial ribosomal protein of the large subunit
YHR166C	0.114081	CUP2	YHR166C|CDC23|S000001209|Subunit of the anaphase-promoting complex/cyclosome (APC/C), which is a ubiquitin-protein ligase required for degradation of anaphase inhibitors, including mitotic cyclins, during the metaphase/anaphase transition
YNL042W-B	0.113826	CUP2	YNL042W-B||S000028850|Putative protein of unknown function
YKR077W	0.113023	CUP2	YKR077W|MSA2|S000001785|Putative transcriptional activator, that interacts with G1-specific transcription factor, MBF and G1-specific promoters; ortholog of Msa2p, an MBF and SBF activator that regulates G1-specific transcription and cell cycle initiation
YDR011W	0.112998	CUP2	YDR011W|SNQ2|S000002418|Plasma membrane ATP-binding cassette (ABC) transporter, multidrug transporter involved in multidrug resistance and resistance to singlet oxygen species
YDR375C	0.112763	CUP2	YDR375C|BCS1|S000002783|Protein of the mitochondrial inner membrane that functions as an ATP-dependent chaperone, required for the incorporation of the Rip1p and Qcr10p subunits into the cytochrome bc(1) complex; member of the CDC48/PAS1/SEC18 ATPase family
YDL086W	0.112591	CUP2	YDL086W||S000002244|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YDL086W is not an essential gene
YOR024W	0.112286	CUP2	YOR024W||S000005550|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR220C	0.11214	CUP2	YDR220C||S000002628|Dubious open reading frame, null mutant exhibits synthetic phenotype with alpha-synuclein
YNL308C	0.111369	CUP2	YNL308C|KRI1|S000005252|Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p
YGL087C	0.111324	CUP2	YGL087C|MMS2|S000003055|Protein involved in error-free postreplication DNA repair; forms a heteromeric complex with Ubc13p that has a ubiquitin-conjugating activity; cooperates with chromatin-associated RING finger proteins, Rad18p and Rad5p
YDL104C	0.111211	CUP2	YDL104C|QRI7|S000002262|Putative metalloprotease, similar to O-sialoglycoprotein metallopeptidase from P. haemolytica; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YGL112C	0.109372	CUP2	YGL112C|TAF6|S000003080|Subunit (60 kDa) of TFIID and SAGA complexes, involved in transcription initiation of RNA polymerase II and in chromatin modification, similar to histone H4
YMR154C	0.109212	CUP2	YMR154C|RIM13|S000004763|Calpain-like cysteine protease involved in proteolytic activation of Rim101p in response to alkaline pH; has similarity to A. nidulans palB
YOL151W	0.109062	CUP2	YOL151W|GRE2|S000005511|3-methylbutanal reductase and NADPH-dependent methylglyoxal reductase (D-lactaldehyde dehydrogenase); stress induced (osmotic, ionic, oxidative, heat shock and heavy metals); regulated by the HOG pathway
YDR464W	0.108337	CUP2	YDR464W|SPP41|S000002872|Protein involved in negative regulation of expression of spliceosome components PRP4 and PRP3
YKR086W	0.107282	CUP2	YKR086W|PRP16|S000001794|RNA helicase in the DEAH-box family involved in the second catalytic step of splicing, exhibits ATP-dependent RNA unwinding activity
YOL026C	0.106979	CUP2	YOL026C|MIM1|S000005386|Mitochondrial outer membrane protein, required for assembly of the translocase of the outer membrane (TOM) complex and thereby for mitochondrial protein import; N terminus is exposed to the cytosol: transmembrane segment is highly conserved
YMR151W	0.106418	CUP2	YMR151W|YIM2|S000004759|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; 5% of ORF overlaps the verified gene IMP1
YLR207W	0.105734	CUP2	YLR207W|HRD3|S000004197|Resident protein of the ER membrane that plays a central role in ER-associated protein degradation (ERAD), forms HRD complex with Hrd1p and ERAD determinants that engages in lumen to cytosol communication and coordination of ERAD events
YLR382C	0.105487	CUP2	YLR382C|NAM2|S000004374|Mitochondrial leucyl-tRNA synthetase, also has a direct role in splicing of several mitochondrial group I introns; indirectly required for mitochondrial genome maintenance
YDR335W	0.105309	CUP2	YDR335W|MSN5|S000002743|Karyopherin involved in nuclear import and export; shown to be responsible for nuclear import of replication protein A and for export of several proteins including Swi6p, Far1p, and Pho4p; cargo dissociation involves binding to RanGTP
YGR048W	0.104819	CUP2	YGR048W|UFD1|S000003280|Protein that interacts with Cdc48p and Npl4p, involved in recognition of polyubiquitinated proteins and their presentation to the 26S proteasome for degradation; involved in transporting proteins from the ER to the cytosol
YJR083C	0.104504	CUP2	YJR083C|ACF4|S000003843|Protein of unknown function, computational analysis of large-scale protein-protein interaction data suggests a possible role in actin cytoskeleton organization; potential Cdc28p substrate
YNL080C	0.104383	CUP2	YNL080C|EOS1|S000005024|Protein involved in N-glycosylation; deletion mutation confers sensitivity to exidative stress and shows synthetic lethality with mutations in the spindle checkpoint genes BUB3 and MAD1; YNL080C is not an essential gene
YHR118C	0.104315	CUP2	YHR118C|ORC6|S000001160|Subunit of the origin recognition complex, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; phosphorylated by Cdc28p
YDR217C	0.103679	CUP2	YDR217C|RAD9|S000002625|DNA damage-dependent checkpoint protein, required for cell-cycle arrest in G1/S, intra-S, and G2/M; transmits checkpoint signal by activating Rad53p and Chk1p; hyperphosphorylated by Mec1p and Tel1p; potential Cdc28p substrate
YOR037W	0.103348	CUP2	YOR037W|CYC2|S000005563|Mitochondrial peripheral inner membrane protein, contains a FAD cofactor in a domain exposed in the intermembrane space; exhibits redox activity in vitro; likely participates in ligation of heme to acytochromes c and c1 (Cyc1p and Cyt1p)
YIL105C	0.103212	CUP2	YIL105C|SLM1|S000001367|Phosphoinositide PI4,5P(2) binding protein, forms a complex with Slm2p; acts downstream of Mss4p in a pathway regulating actin cytoskeleton organization in response to stress; subunit of and phosphorylated by the TORC2 complex
YGR010W	0.103098	CUP2	YGR010W|NMA2|S000003242|Nicotinic acid mononucleotide adenylyltransferase, involved in de novo and salvage synthesis of NAD(+)
YOR231W	0.102847	CUP2	YOR231W|MKK1|S000005757|Mitogen-activated kinase kinase involved in protein kinase C signaling pathway that controls cell integrity; upon activation by Bck1p phosphorylates downstream target, Slt2p; functionally redundant with Mkk2p
YLR281C	0.102164	CUP2	YLR281C||S000004271|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YLR281C is not an essential gene
YKL105C	0.102124	CUP2	YKL105C||S000001588|Putative protein of unknown function
YDR388W	0.101966	CUP2	YDR388W|RVS167|S000002796|Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin
YPR066W	0.101951	CUP2	YPR066W|UBA3|S000006270|Protein that acts together with Ula1p to activate Rub1p before its conjugation to proteins (neddylation), which may play a role in protein degradation; GFP-fusion protein localizes to the cytoplasm in a punctate pattern
YNL103W	0.101944	CUP2	YNL103W|MET4|S000005047|Leucine-zipper transcriptional activator, responsible for the regulation of the sulfur amino acid pathway, requires different combinations of the auxiliary factors Cbf1p, Met28p, Met31p and Met32p
YDR338C	0.101829	CUP2	YDR338C||S000002746|Hypothetical protein
YIL048W	0.100794	CUP2	YIL048W|NEO1|S000001310|Putative aminophospholipid translocase (flippase) involved in endocytosis and vacuolar biogenesis; localizes to endosomes and the Golgi aparatus
YMR291W	0.100652	CUP2	YMR291W||S000004905|Putative kinase of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YMR291W is not an essential gene
YLL031C	0.100447	CUP2	YLL031C|GPI13|S000003954|ER membrane localized phosphoryltransferase that adds phosphoethanolamine onto the third mannose residue of the glycosylphosphatidylinositol (GPI) anchor precursor; similar to human PIG-O protein
YLR280C	0.100287	CUP2	YLR280C||S000004270|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YFL050C	0.0999803	CUP2	YFL050C|ALR2|S000001844|Probable Mg(2+) transporter; overexpression confers increased tolerance to Al(3+) and Ga(3+) ions; plays a role in regulating Ty1 transposition
YBR239C	0.0999498	CUP2	YBR239C|ERT1|S000000443|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; plays a role in restricting Ty1 transposition
YKL100C	0.09969	CUP2	YKL100C||S000001583|Putative protein of unknown function with similarity to a human minor histocompatibility antigen; YKL100C is not an essential gene
YMR189W	0.0996334	CUP2	YMR189W|GCV2|S000004801|P subunit of the mitochondrial glycine decarboxylase complex, required for the catabolism of glycine to 5,10-methylene-THF; expression is regulated by levels of 5,10-methylene-THF in the cytoplasm
YBR213W	0.098378	CUP2	YBR213W|MET8|S000000417|Bifunctional dehydrogenase and ferrochelatase, involved in the biosynthesis of siroheme, a prosthetic group used by sulfite reductase; required for sulfate assimilation and methionine biosynthesis
YKL095W	0.0982463	CUP2	YKL095W|YJU2|S000001578|Essential protein required for pre-mRNA splicing; associates transiently with the spliceosomal NTC ("nineteen complex") and acts after Prp2p to promote the first catalytic reaction of splicing
YPL268W	0.097963	CUP2	YPL268W|PLC1|S000006189|Phospholipase C, hydrolyzes phosphatidylinositol 4,5-biphosphate (PIP2) to generate the signaling molecules inositol 1,4,5-triphosphate (IP3) and 1,2-diacylglycerol (DAG); involved in regulating many cellular processes
YNR040W	0.0978402	CUP2	YNR040W||S000005323|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YPR017C	0.0976707	CUP2	YPR017C|DSS4|S000006221|Guanine nucleotide dissociation stimulator for Sec4p, functions in the post-Golgi secretory pathway; binds zinc, found both on membranes and in the cytosol
YLL054C	0.0975268	CUP2	YLL054C||S000003977|Putative protein of unknown function with similarity to Pip2p, an oleate-specific transcriptional activator of peroxisome proliferation; YLL054C is not an essential gene
YNL009W	0.0972186	CUP2	YNL009W|IDP3|S000004954|Peroxisomal NADP-dependent isocitrate dehydrogenase, catalyzes oxidation of isocitrate to alpha-ketoglutarate with the formation of NADP(H+), required for growth on unsaturated fatty acids
YPR138C	0.0970348	CUP2	YPR138C|MEP3|S000006342|Ammonium permease of high capacity and low affinity; belongs to a ubiquitous family of cytoplasmic membrane proteins that transport only ammonium (NH4+); expression is under the nitrogen catabolite repression regulation ammonia permease
YBL088C	0.0967779	CUP2	YBL088C|TEL1|S000000184|Protein kinase primarily involved in telomere length regulation; contributes to cell cycle checkpoint control in response to DNA damage; functionally redundant with Mec1p; homolog of human ataxia telangiectasia (ATM) gene
YKL061W	0.0967285	CUP2	YKL061W||S000001544|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endosome
YPR018W	0.0966772	CUP2	YPR018W|RLF2|S000006222|Largest subunit (p90) of the Chromatin Assembly Complex (CAF-1) with Cac2p and Msi1p that assembles newly synthesized histones onto recently replicated DNA; involved in the maintenance of transcriptionally silent chromatin
YJL159W	0.0962494	CUP2	YJL159W|HSP150|S000003695|O-mannosylated heat shock protein that is secreted and covalently attached to the cell wall via beta-1,3-glucan and disulfide bridges; required for cell wall stability; induced by heat shock, oxidative stress, and nitrogen limitation
YER041W	0.0962145	CUP2	YER041W|YEN1|S000000843|Protein of unknown function, has similarity to endonuclease Rth1p; potentially phosphorylated by Cdc28p
YDR234W	0.0959487	CUP2	YDR234W|LYS4|S000002642|Homoaconitase, catalyzes the conversion of homocitrate to homoisocitrate, which is a step in the lysine biosynthesis pathway
YDR340W	0.0951457	CUP2	YDR340W||S000002748|Putative protein of unknown function
YMR077C	0.0949618	CUP2	YMR077C|VPS20|S000004682|Myristoylated subunit of ESCRTIII, the endosomal sorting complex required for transport of transmembrane proteins into the multivesicular body pathway to the lysosomal/vacuolar lumen; cytoplasmic protein recruited to endosomal membranes
YLR104W	0.0948643	CUP2	YLR104W||S000004094|Putative protein of unknown function; mutant is deficient in amounts of cell wall mannosylphosphate
YGR222W	0.0948285	CUP2	YGR222W|PET54|S000003454|Mitochondrial inner membrane protein that binds to the 5' UTR of the COX3 mRNA to activate its translation together with Pet122p and Pet494p; also binds to the COX1 Group I intron AI5 beta to facilitate exon ligation during splicing
YOL164W	0.094716	CUP2	YOL164W|BDS1|S000005524|Bacterially-derived sulfatase required for use of alkyl- and aryl-sulfates as sulfur sources
YHL044W	0.0946488	CUP2	YHL044W||S000001036|Putative integral membrane protein, member of DUP240 gene family; green fluorescent protein (GFP)-fusion protein localizes to the plasma membrane in a punctate pattern
YDR204W	0.0935812	CUP2	YDR204W|COQ4|S000002612|Protein with a role in ubiquinone (Coenzyme Q) biosynthesis, possibly functioning in stabilization of Coq7p; located on the matrix face of the mitochondrial inner membrane; component of a mitochondrial ubiquinone-synthesizing complex
YIL098C	0.0934733	CUP2	YIL098C|FMC1|S000001360|Mitochondrial matrix protein, required for assembly or stability at high temperature of the F1 sector of mitochondrial F1F0 ATP synthase; null mutant temperature sensitive growth on glycerol is suppressed by multicopy expression of Odc1p
YDR436W	0.0934707	CUP2	YDR436W|PPZ2|S000002844|Serine/threonine protein phosphatase Z, isoform of Ppz1p; involved in regulation of potassium transport, which affects osmotic stability, cell cycle progression, and halotolerance
YMR188C	0.0933868	CUP2	YMR188C|MRPS17|S000004800|Mitochondrial ribosomal protein of the small subunit
YPL168W	0.0933863	CUP2	YPL168W||S000006089|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the mitochondrion; expression may be cell cycle-regulated
YMR087W	0.0933596	CUP2	YMR087W||S000004693|Putative ADP-ribose-1''-monophosphatase that converts ADP-ribose-1''-monophosphate to ADP-ribose; may have a role in tRNA splicing; contains an A1pp domain
YKR076W	0.0928512	CUP2	YKR076W|ECM4|S000001784|Omega class glutathione transferase; not essential; similar to Ygr154cp; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YNL156C	0.0928511	CUP2	YNL156C|NSG2|S000005100|Protein involved in regulation of sterol biosynthesis; specifically stabilizes Hmg2p, one of two HMG-CoA isoenzymes that catalyze the rate-limiting step in sterol biosynthesis; homolog of mammalian INSIG proteins
YDR079W	0.0927015	CUP2	YDR079W|PET100|S000002486|Chaperone that specifically facilitates the assembly of cytochrome c oxidase, integral to the mitochondrial inner membrane; interacts with a subcomplex of subunits VII, VIIa, and VIII (Cox7p, Cox9p, and Cox8p) but not with the holoenzyme
YDR077W	0.0926273	CUP2	YDR077W|SED1|S000002484|Major stress-induced structural GPI-cell wall glycoprotein in stationary-phase cells, associates with translating ribosomes, possible role in mitochondrial genome maintenance; ORF contains two distinct variable minisatellites
YFR007W	0.0925127	CUP2	YFR007W|YFH7|S000001903|Putative kinase with similarity to the phosphoribulokinase/uridine kinase/bacterial pantothenate kinase (PRK/URK/PANK) subfamily of P-loop kinases; null mutant displays decreased frequency of mitochondrial genome loss (petite formation)
YNR060W	0.0922989	CUP2	YNR060W|FRE4|S000005343|Ferric reductase, reduces a specific subset of siderophore-bound iron prior to uptake by transporters; expression induced by low iron levels
YOR242C	0.0911642	CUP2	YOR242C|SSP2|S000005768|Sporulation specific protein that localizes to the spore wall; required for sporulation at a point after meiosis II and during spore wall formation; SSP2 expression is induced midway in meiosis
YJR084W	0.0911213	CUP2	YJR084W|CSN12|S000003844|Subunit of the Cop9 signalosome, which is required for deneddylation, or removal of the ubiquitin-like protein Rub1p from Cdc53p (cullin); involved in adaptation to pheromone signaling
YMR075W	0.0910954	CUP2	YMR075W|RCO1|S000004680|Essential subunit of the histone deacetylase Rpd3S complex; interacts with Eaf3p
YKR044W	0.0908746	CUP2	YKR044W|UIP5|S000001752|Protein of unknown function that interacts with Ulp1p, a Ubl (ubiquitin-like protein)-specific protease for Smt3p protein conjugates
YGR250C	0.0903006	CUP2	YGR250C||S000003482|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YGR231C	0.090082	CUP2	YGR231C|PHB2|S000003463|Subunit of the prohibitin complex (Phb1p-Phb2p), a 1.2 MDa ring-shaped inner mitochondrial membrane chaperone that stabilizes newly synthesized proteins; determinant of replicative life span; involved in mitochondrial segregation
YGL002W	0.0900141	CUP2	YGL002W|ERP6|S000002970|Protein with similarity to Emp24p and Erv25p, member of the p24 family involved in ER to Golgi transport; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR068W	0.0896817	CUP2	YDR068W|DOS2|S000002475|Protein of unknown function, green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YDL024C	0.089592	CUP2	YDL024C|DIA3|S000002182|Protein of unknown function, involved in invasive and pseudohyphal growth
YAL047C	0.0893168	CUP2	YAL047C|SPC72|S000000045|Component of the cytoplasmic Tub4p (gamma-tubulin) complex, binds spindle pole bodies and links them to microtubules; has roles in astral microtubule formation and stabilization
YOR205C	0.0886211	CUP2	YOR205C|LRC5|S000005731|Protein of unknown function; non-tagged protein is detected in purified mitochondria in high-throughput studies; null mutant displays decreased frequency of mitochondrial genome loss and severe growth defect in minimal glycerol media
YFR042W	0.0883628	CUP2	YFR042W|KEG1|S000001938|Integral membrane protein of the ER; physically interacts with Kre6p; has a role in the synthesis of beta-1,6-glucan in the cell wall; required for cell viability
YOR292C	0.0882413	CUP2	YOR292C||S000005818|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; YOR292C is not an essential gene
YOR172W	0.0875021	CUP2	YOR172W|YRM1|S000005698|Zn2-Cys6 zinc-finger transcription factor that activates genes involved in multidrug resistance; paralog of Yrr1p, acting on an overlapping set of target genes
YBR231C	0.0872095	CUP2	YBR231C|SWC5|S000000435|Protein of unknown function, component of the SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A
YDR131C	0.0869857	CUP2	YDR131C||S000002538|F-box protein, substrate-specific adaptor subunit that recruits substrates to a core ubiquitination complex
YNL239W	0.0868137	CUP2	YNL239W|LAP3|S000005183|Cysteine aminopeptidase with homocysteine-thiolactonase activity; protects cells against homocysteine toxicity; has bleomycin hydrolase activity in vitro; transcription is regulated by galactose via Gal4p; orthologous to human BLMH
YDR485C	0.0865662	CUP2	YDR485C|VPS72|S000002893|Htz1p-binding component of the SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A; required for vacuolar protein sorting
YLR091W	0.0861771	CUP2	YLR091W||S000004081|Protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; YLR091W is not an esssential gene
YCR046C	0.0860866	CUP2	YCR046C|IMG1|S000000642|Mitochondrial ribosomal protein of the large subunit, required for respiration and for maintenance of the mitochondrial genome
YHR093W	0.0857818	CUP2	YHR093W|AHT1|S000001135|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; multicopy suppressor of glucose transport defects, likely due to the presence of an HXT4 regulatory element in the region
YOR006C	0.0852874	CUP2	YOR006C|TSR3|S000005532|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus; Null mutant accumulates 20S pre-rRNA
YHR056C	0.0849796	CUP2	YHR056C|RSC30|S000001098|Component of the RSC chromatin remodeling complex; non-essential gene required for regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc3p; null mutants are osmosensitive
YIL093C	0.0846573	CUP2	YIL093C|RSM25|S000001355|Mitochondrial ribosomal protein of the small subunit
YGL143C	0.0843503	CUP2	YGL143C|MRF1|S000003111|Mitochondrial translation release factor, involved in stop codon recognition and hydrolysis of the peptidyl-tRNA bond during mitochondrial translation; lack of MRF1 causes mitochondrial genome instability
YGL237C	0.0843189	CUP2	YGL237C|HAP2|S000003206|Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression; contains sequences sufficient for both complex assembly and DNA binding
YLL047W	0.084051	CUP2	YLL047W||S000003970|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene RNP1
YNL173C	0.0838288	CUP2	YNL173C|MDG1|S000005117|Plasma membrane protein involved in G-protein mediated pheromone signaling pathway; overproduction suppresses bem1 mutations
YDR282C	0.083819	CUP2	YDR282C||S000002690|Putative protein of unknown function
YPR116W	0.0836097	CUP2	YPR116W||S000006320|Putative protein of unknown function
YKL075C	0.0831464	CUP2	YKL075C||S000001558|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; proposed to be involved in resistance to streptozotocin and camptothecin
YLR027C	0.0830074	CUP2	YLR027C|AAT2|S000004017|Cytosolic aspartate aminotransferase, involved in nitrogen metabolism; localizes to peroxisomes in oleate-grown cells
YML020W	0.0828969	CUP2	YML020W||S000004482|Putative protein of unknown function
YHR182W	0.082595	CUP2	YHR182W||S000001225|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery and cytoplasm
YAL016W	0.0823375	CUP2	YAL016W|TPD3|S000000014|Regulatory subunit A of the heterotrimeric protein phosphatase 2A, which also contains regulatory subunit Cdc55p and either catalytic subunit Pph21p or Pph22p; required for cell morphogenesis and for transcription by RNA polymerase III
YNR048W	0.0822887	CUP2	YNR048W||S000005331|Protein proposed to interact with phospholipid translocases, shares similarity to Cdc50p
YGL053W	0.0820233	CUP2	YGL053W|PRM8|S000003021|Pheromone-regulated protein with 2 predicted transmembrane segments and an FF sequence, a motif involved in COPII binding; forms a complex with Prp9p in the ER; member of DUP240 gene family
YKL045W	0.0819703	CUP2	YKL045W|PRI2|S000001528|Subunit of DNA primase, which is required for DNA synthesis and double-strand break repair
YJL151C	0.08102	CUP2	YJL151C|SNA3|S000003687|Integral membrane protein localized to vacuolar intralumenal vesicles, computational analysis of large-scale protein-protein interaction data suggests a possible role in either cell wall synthesis or protein-vacuolar targeting
YOR003W	0.0809825	CUP2	YOR003W|YSP3|S000005529|Putative precursor to the subtilisin-like protease III
YMR097C	0.0808819	CUP2	YMR097C|MTG1|S000004703|Peripheral GTPase of the mitochondrial inner membrane, essential for respiratory competence, likely functions in assembly of the large ribosomal subunit, has homologs in plants and animals
YHR205W	0.0805188	CUP2	YHR205W|SCH9|S000001248|Protein kinase involved in transcriptional activation of osmostress-responsive genes; regulates G1 progression, cAPK activity, nitrogen activation of the FGM pathway; involved in life span regulation; homologous to mammalian Akt/PKB
YLR347C	0.0800742	CUP2	YLR347C|KAP95|S000004339|Karyopherin beta, forms a dimeric complex with Srp1p (Kap60p) that mediates nuclear import of cargo proteins via a nuclear localization signal (NLS), interacts with nucleoporins to guide transport across the nuclear pore complex
YDR029W	0.0800173	CUP2	YDR029W||S000002436|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data
YHR124W	0.0798328	CUP2	YHR124W|NDT80|S000001166|Meiosis-specific transcription factor required for exit from pachytene and for full meiotic recombination; activates middle sporulation genes; competes with Sum1p for binding to promoters containing middle sporulation elements (MSE)
YBR178W	0.0798078	CUP2	YBR178W||S000000382|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YBR177C
YDL009C	0.0796403	CUP2	YDL009C||S000002167|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YDL010W; YDL009C is not an essential gene
YBR114W	0.0793705	CUP2	YBR114W|RAD16|S000000318|Protein that recognizes and binds damaged DNA in an ATP-dependent manner (with Rad7p) during nucleotide excision repair; subunit of Nucleotide Excision Repair Factor 4 (NEF4) and the Elongin-Cullin-Socs (ECS) ligase complex
YNL325C	0.0789158	CUP2	YNL325C|FIG4|S000005269|Polyphosphatidylinositol phosphatase involved in the metabolism of phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2); required for efficient mating; physically associates with and regulated by Vac14p; contains a SAC1-like domain
YBR203W	0.0788761	CUP2	YBR203W|COS111|S000000407|Protein required for resistance to the antifungal drug ciclopirox olamine; not related to the subtelomerically-encoded COS family; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YJR130C	0.0784997	CUP2	YJR130C|STR2|S000003891|Cystathionine gamma-synthase, converts cysteine into cystathionine
YMR278W	0.0784548	CUP2	YMR278W|PGM3|S000004891|Phosphoglucomutase, catalyzes interconversion of glucose-1-phosphate and glucose-6-phospate; transcription induced in response to stress; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; non-essential
YMR171C	0.0784431	CUP2	YMR171C|EAR1|S000004781|Specificity factor required for Rsp5p-dependent ubiquitination and sorting of specific cargo proteins at the multivesicular body; mRNA is targeted to the bud via the mRNA transport system involving She2p: YMR171C is not an essential gene
YNL198C	0.0780294	CUP2	YNL198C||S000005142|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YPL103C	0.0779792	CUP2	YPL103C|FMP30|S000006024|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR314C	0.0779785	CUP2	YDR314C|RAD34|S000002722|Protein involved in nucleotide excision repair (NER); homologous to RAD4
YKR106W	0.0778322	CUP2	YKR106W||S000001814|Protein of unconfirmed function; displays a topology characteristic of the Major Facilitators Superfamily of membrane proteins; coding sequence 98% identical to that of YCL073C
YCR105W	0.0778019	CUP2	YCR105W|ADH7|S000000702|NADPH-dependent medium chain alcohol dehydrogenase with broad substrate specificity; member of the cinnamyl family of alcohol dehydrogenases; may be involved in fusel alcohol synthesis or in aldehyde tolerance
YOR124C	0.0776762	CUP2	YOR124C|UBP2|S000005650|Ubiquitin-specific protease that removes ubiquitin from ubiquitinated proteins, cleaves at the C terminus of ubiquitin fusions; capable of cleaving polyubiquitin and possesses isopeptidase activity
YMR172W	0.0775552	CUP2	YMR172W|HOT1|S000004783|Transcription factor required for the transient induction of glycerol biosynthetic genes GPD1 and GPP2 in response to high osmolarity; targets Hog1p to osmostress responsive promoters; has similarity to Msn1p and Gcr1p
YAL016C-B	0.0770578	CUP2	YAL016C-B||S000028528|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YKR071C	0.0768038	CUP2	YKR071C|DRE2|S000001779|Protein of unknown function required for sister chromatid cohesion; mutation displays synthetic lethal interaction with the pol3-13 allele of CDC2
YBR115C	0.0766987	CUP2	YBR115C|LYS2|S000000319|Alpha aminoadipate reductase, catalyzes the reduction of alpha-aminoadipate to alpha-aminoadipate 6-semialdehyde, which is the fifth step in biosynthesis of lysine; activation requires posttranslational phosphopantetheinylation by Lys5p
YDL088C	0.076436	CUP2	YDL088C|ASM4|S000002246|Nuclear pore complex subunit, part of a subcomplex also containing Nup53p, Nup170p, and Pse1p
YPR161C	0.0763005	CUP2	YPR161C|SGV1|S000006365|Cyclin (Bur2p)-dependent protein kinase that functions in transcriptional regulation; phosphorylates the carboxy-terminal domain of Rpo21p, which is the largest subunit of RNA polymerase II; regulated by Cak1p
YLR383W	0.0762523	CUP2	YLR383W|SMC6|S000004375|Protein involved in structural maintenance of chromosomes; essential subunit of Mms21-Smc5-Smc6 complex; required for growth, DNA repair, interchromosomal and sister chromatid recombination; homologous to S. pombe rad18
YLR352W	0.0761094	CUP2	YLR352W||S000004344|Putative protein of unknown function with similarity to F-box proteins; interacts with Skp1p and Cdc53p; YLR352W is not an essential gene
YML117W	0.0758949	CUP2	YML117W|NAB6|S000004585|Putative RNA-binding protein, based on computational analysis of large-scale protein-protein interaction data
YOL150C	0.0757909	CUP2	YOL150C||S000005510|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YJL133W	0.0752462	CUP2	YJL133W|MRS3|S000003669|Mitochondrial iron transporter of the mitochondrial carrier family (MCF), very similar to and functionally redundant with Mrs4p; functions under low-iron conditions; may transport other cations in addition to iron
YNL297C	0.0752232	CUP2	YNL297C|MON2|S000005241|Peripheral membrane protein with a role in endocytosis and vacuole integrity, interacts with Arl1p and localizes to the endosome; member of the Sec7p family of proteins
YDR438W	0.0746532	CUP2	YDR438W|THI74|S000002846|Mitochondrial transporter repressible by thiamine
YHR079C	0.0745448	CUP2	YHR079C|IRE1|S000001121|Serine-threonine kinase and endoribonuclease; transmembrane protein that mediates the unfolded protein response (UPR) by regulating Hac1p synthesis through HAC1 mRNA splicing; Kar2p binds inactive Ire1p and releases from it upon ER stress
YOL034W	0.0745061	CUP2	YOL034W|SMC5|S000005394|Structural maintenance of chromosomes (SMC) protein; essential subunit of the Mms21-Smc5-Smc6 complex; required for growth and DNA repair; S. pombe homolog forms a heterodimer with S. pombe Rad18p that is involved in DNA repair
YAL045C	0.0743466	CUP2	YAL045C||S000000043|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; almost completely overlaps YAL044W-A
YML047C	0.0743149	CUP2	YML047C|PRM6|S000004510|Pheromone-regulated protein, predicted to have 2 transmembrane segments; regulated by Ste12p during mating
YDR291W	0.0738509	CUP2	YDR291W|HRQ1|S000002699|Putative DNA helicase
YML003W	0.0738228	CUP2	YML003W||S000004462|Putative protein of unknown function
YKL174C	0.073605	CUP2	YKL174C|TPO5|S000001657|Protein involved in excretion of putrescine and spermidine; putative polyamine transporter in the Golgi or post-Golgi vesicles
YIR014W	0.0735025	CUP2	YIR014W||S000001453|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; expression directly regulated by the metabolic and meiotic transcriptional regulator Ume6p; YIR014W is a non-essential gene
YHR119W	0.0733381	CUP2	YHR119W|SET1|S000001161|Histone methyltransferase, subunit of the COMPASS (Set1C) complex which methylates histone H3 on lysine 4; required in transcriptional silencing near telomeres and at the silent mating type loci; contains a SET domain
YPL096C-A	0.0733201	CUP2	YPL096C-A|ERI1|S000028423|Endoplasmic reticulum membrane protein that binds to and inhibits GTP-bound Ras2p at the ER; component of the GPI-GnT complex which catalyzes the first step in GPI-anchor biosynthesis; probable homolog of mammalian PIG-Y protein
YMR163C	0.0731111	CUP2	YMR163C|INP2|S000004773|Peroxisome-specific receptor important for peroxisome inheritance; co-fractionates with peroxisome membranes and co-localizes with peroxisomes in vivo; physically interacts with the myosin V motor Myo2p; INP2 is not an essential gene
YLR430W	0.073041	CUP2	YLR430W|SEN1|S000004422|Presumed helicase required for RNA polymerase II transcription termination and processing of RNAs; homolog of Senataxin which causes Ataxia-Oculomotor Apraxia 2 and a dominant form of amyotrophic lateral sclerosis
YMR295C	0.0729263	CUP2	YMR295C||S000004910|Protein of unknown function that associates with ribosomes; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery and bud; YMR295C is not an essential gene
YAL001C	0.0729204	CUP2	YAL001C|TFC3|S000000001|Largest of six subunits of the RNA polymerase III transcription initiation factor complex (TFIIIC); part of the TauB domain of TFIIIC that binds DNA at the BoxB promoter sites of tRNA and similar genes; cooperates with Tfc6p in DNA binding
YKL088W	0.0727066	CUP2	YKL088W||S000001571|Predicted phosphopantothenoylcysteine decarboxylase, may be involved in coenzyme A biosynthesis; interacts with Sis2p and Vhs3p
YPL046C	0.0725863	CUP2	YPL046C|ELC1|S000005967|Elongin C, forms heterodimer with Ela1p that participates in transcription elongation; required for ubiquitin-dependent degradation of the RNA Polymerase II subunit RPO21; expression dramatically upregulated during sporulation
YLR086W	0.0725852	CUP2	YLR086W|SMC4|S000004076|Subunit of the condensin complex, which reorganizes chromosomes during cell division, forms a stable complex with Smc2p that has ATP-hydrolyzing and DNA-binding activity and promotes knotting of circular DNA; potential Cdc28p substrate
YNL230C	0.0725489	CUP2	YNL230C|ELA1|S000005174|Elongin A, F-box protein that forms a heterodimer with Elc1p and is required for ubiquitin-dependent degredation of the RNA Polymerase II subunit RPO21; subunit of the Elongin-Cullin-Socs (ECS) ligase complex
YNL249C	0.0715081	CUP2	YNL249C|MPA43|S000005193|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YNL138W-A	0.0712347	CUP2	YNL138W-A|YSF3|S000028509|Component of the U2 snRNP, associated with the SF3b complex; conserved in Ashbya gossypii
YGL014W	0.0710698	CUP2	YGL014W|PUF4|S000002982|Member of the PUF protein family, which is defined by the presence of Pumilio homology domains that confer RNA binding activity; preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors
YOR351C	0.0709021	CUP2	YOR351C|MEK1|S000005878|Meiosis-specific serine/threonine protein kinase, functions in meiotic checkpoint, promotes recombination between homologous chromosomes by suppressing double strand break repair between sister chromatids
YIL075C	0.0704445	CUP2	YIL075C|RPN2|S000001337|Subunit of the 26S proteasome, substrate of the N-acetyltransferase Nat1p
YIL073C	0.0701232	CUP2	YIL073C|SPO22|S000001335|Meiosis-specific protein essential for chromosome synapsis, involved in completion of nuclear divisions during meiosis; induced early in meiosis
YDL186W	0.0700716	CUP2	YDL186W||S000002345|Putative protein of unknown function; YDL186W is not an essential gene
YNR010W	0.0695878	CUP2	YNR010W|CSE2|S000005293|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; component of the Med9/10 module; required for regulation of RNA polymerase II activity
YOR007C	0.0694931	CUP2	YOR007C|SGT2|S000005533|Glutamine-rich cytoplasmic protein of unknown function; contains tetratricopeptide (TPR) repeats, which often mediate protein-protein interactions; has similarity to human SGT, which is a cochaperone that negatively regulates Hsp70
YDL042C	0.0692504	CUP2	YDL042C|SIR2|S000002200|Conserved NAD+ dependent histone deacetylase of the Sirtuin family involved in regulation of lifespan; plays roles in silencing at HML, HMR, telomeres, and the rDNA locus; negatively regulates initiation of DNA replication
YIL082W	0.069198	CUP2	YIL082W||S000001344|Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag
YJL079C	0.0690372	CUP2	YJL079C|PRY1|S000003615|Protein of unknown function, has similarity to Pry2p and Pry3p and to the plant PR-1 class of pathogen related proteins
YDR179C	0.0689539	CUP2	YDR179C|CSN9|S000002586|Subunit of the Cop9 signalosome, which is required for deneddylation, or removal of the ubiquitin-like protein Rub1p from Cdc53p (cullin); involved in adaptation to pheromone signaling
YJL214W	0.0688169	CUP2	YJL214W|HXT8|S000003750|Protein of unknown function with similarity to hexose transporter family members, expression is induced by low levels of glucose and repressed by high levels of glucose
YDL066W	0.0688016	CUP2	YDL066W|IDP1|S000002224|Mitochondrial NADP-specific isocitrate dehydrogenase, catalyzes the oxidation of isocitrate to alpha-ketoglutarate; not required for mitochondrial respiration and may function to divert alpha-ketoglutarate to biosynthetic processes
YNL294C	0.0683098	CUP2	YNL294C|RIM21|S000005238|Component of the RIM101 pathway, has a role in cell wall construction and alkaline pH response; has similarity to A. nidulans PalH
YER020W	0.0682635	CUP2	YER020W|GPA2|S000000822|Nucleotide binding alpha subunit of the heterotrimeric G protein that interacts with the receptor Gpr1p, has signaling role in response to nutrients; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery
YER078W-A	0.0680303	CUP2	YER078W-A||S000028546|Putative protein of unknown function; identified by fungal homology and RT-PCR
YCR027C	0.0679186	CUP2	YCR027C|RHB1|S000000622|Putative Rheb-related GTPase involved in regulating canavanine resistance and arginine uptake; member of the Ras superfamily of G-proteins
YLR269C	0.0670393	CUP2	YLR269C||S000004259|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YFR011C	0.0670205	CUP2	YFR011C|AIM13|S000001907|Putative protein of unknown function; non-tagged protein is detected in highly purified mitochondria; null mutant displays increased frequency of mitochondrial genome loss (petite formation) and reduced growth rate in minimal glycerol media
YER137W-A	0.0668532	CUP2	YER137W-A||S000028757|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YNL244C	0.0667882	CUP2	YNL244C|SUI1|S000005188|Translation initiation factor eIF1; component of a complex involved in recognition of the initiator codon; modulates translation accuracy at the initiation phase
YNL020C	0.0667484	CUP2	YNL020C|ARK1|S000004965|Serine/threonine protein kinase involved in regulation of the cortical actin cytoskeleton; involved in control of endocytosis
YDR104C	0.0666227	CUP2	YDR104C|SPO71|S000002511|Meiosis-specific protein of unknown function, required for spore wall formation during sporulation; dispensable for both nuclear divisions during meiosis
YDR460W	0.0665276	CUP2	YDR460W|TFB3|S000002868|Subunit of TFIIH and nucleotide excision repair factor 3 complexes, involved in transcription initiation, required for nucleotide excision repair; ring finger protein similar to mammalian CAK and TFIIH subunit
YCL002C	0.0659696	CUP2	YCL002C||S000000508|Putative protein of unknown function; YCL002C is not an essential gene
YPL020C	0.0656342	CUP2	YPL020C|ULP1|S000005941|Ubl (ubiquitin-like protein)-specific protease that cleaves Smt3p protein conjugates; specifically required for cell cycle progression; associates with nucleoporins and may interact with septin rings during telophase
YBL020W	0.0656296	CUP2	YBL020W|RFT1|S000000116|Flippase, essential integral membrane protein that is required for translocation of Man5GlcNac2-PP-Dol from the cytoplasmic side to the lumenal side of the ER membrane; mutation is suppressed by expression human p53 protein
YGR100W	0.0652491	CUP2	YGR100W|MDR1|S000003332|Cytoplasmic GTPase-activating protein for Ypt/Rab transport GTPases Ypt6p, Ypt31p and Sec4p; involved in recycling of internalized proteins and regulation of Golgi secretory function
YML108W	0.0645005	CUP2	YML108W||S000004576|Putative protein of unknown function whose structure defines a new subfamily of the split beta-alpha-beta sandwiches; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YML108W is not an essential gene
YLR456W	0.0643975	CUP2	YLR456W||S000004448|Putative protein of unknown function; null mutant displays increased resistance to antifungal agents gliotoxin, cycloheximide and H2O2
YMR078C	0.0642997	CUP2	YMR078C|CTF18|S000004683|Subunit of a complex with Ctf8p that shares some subunits with Replication Factor C and is required for sister chromatid cohesion; may have overlapping functions with Rad24p in the DNA damage replication checkpoint
YAL037W	0.0641677	CUP2	YAL037W||S000000035|Putative protein of unknown function
YMR134W	0.0641425	CUP2	YMR134W|ERG29|S000004741|Protein that binds to and regulates Erg25p; localized to the ER; null mutant is viable in a respiratory defective background; synthetic lethal with mmt1 and mmt2 mutations; highly conserved in ascomycetes
YER179W	0.0638144	CUP2	YER179W|DMC1|S000000981|Meiosis-specific protein required for repair of double-strand breaks and pairing between homologous chromosomes; homolog of Rad51p and the bacterial RecA protein
YGR263C	0.0634185	CUP2	YGR263C|SAY1|S000003495|Sterol deacetylase; component of the sterol acetylation/deacetylation cycle along with Atf2p; integral membrane protein with active site in the ER lumen; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum
YNL017C	0.063392	CUP2	YNL017C||S000004962|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the tRNA ORF tI(AAU)N2
YOL045W	0.0630922	CUP2	YOL045W|PSK2|S000005405|One of two (see also PSK1) PAS domain containing S/T protein kinases; regulates sugar flux and translation in response to an unknown metabolite by phosphorylating Ugp1p and Gsy2p (sugar flux) and Caf20p, Tif11p and Sro9p (translation)
YJL120W	0.062391	CUP2	YJL120W||S000003656|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YJL121C/RPE1; deletion confers sensitivity to GSAO
YHR040W	0.0622822	CUP2	YHR040W|BCD1|S000001082|Essential protein required for the accumulation of box C/D snoRNA
YGL153W	0.0621205	CUP2	YGL153W|PEX14|S000003121|Peroxisomal membrane peroxin that is a central component of the peroxisomal protein import machinery; interacts with both PTS1 (Pex5p) and PTS2 (Pex7p), peroxisomal matrix protein signal recognition factors and membrane receptor Pex13p
YGL139W	0.0620789	CUP2	YGL139W|FLC3|S000003107|Putative FAD transporter, similar to Flc1p and Flc2p; localized to the ER
YNL034W	0.0618989	CUP2	YNL034W||S000004979|Putative protein of unknown function; YNL034W is not an essential gene
YAR003W	0.0617781	CUP2	YAR003W|SWD1|S000000064|Subunit of the COMPASS (Set1C) complex, which methylates histone H3 on lysine 4 and is required in transcriptional silencing near telomeres; WD40 beta propeller superfamily member with similarity to mammalian Rbbp7
YKR087C	0.0617626	CUP2	YKR087C|OMA1|S000001795|Metalloendopeptidase of the mitochondrial inner membrane, involved in turnover of membrane-embedded proteins; member of a family of predicted membrane-bound metallopeptidases in prokaryotes and higher eukaryotes
YNR066C	0.0616974	CUP2	YNR066C||S000005349|Putative membrane-localized protein of unknown function
YPR016W-A	0.0615538	CUP2	YPR016W-A||S000007630|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YAL051W	0.0613637	CUP2	YAL051W|OAF1|S000000048|Oleate-activated transcription factor, acts alone and as a heterodimer with Pip2p; activates genes involved in beta-oxidation of fatty acids and peroxisome organization and biogenesis
YGL140C	0.0612834	CUP2	YGL140C||S000003108|Putative protein of unknown function; non-essential gene; contains multiple predicted transmembrane domains
YAL049C	0.0609873	CUP2	YAL049C|AIM2|S000000047|Cytoplasmic protein of unknown function, potential Hsp82p interactor; null mutant displays decreased frequency of mitochondrial genome loss (petite formation)
YNL220W	0.0609819	CUP2	YNL220W|ADE12|S000005164|Adenylosuccinate synthase, catalyzes the first step in synthesis of adenosine monophosphate from inosine 5'monophosphate during purine nucleotide biosynthesis; exhibits binding to single-stranded autonomously replicating (ARS) core sequence
YPL125W	0.0607871	CUP2	YPL125W|KAP120|S000006046|Karyopherin with a role in the assembly or export of 60S ribosomal subunits
YOL063C	0.0606059	CUP2	YOL063C|CRT10|S000005424|Protein involved in transcriptional regulation of RNR2 and RNR3; expression of the gene is induced by DNA damage and null mutations confer increased resistance to hydroxyurea; N-terminal region has a leucine repeat and a WD40 repeat
YFL023W	0.0603336	CUP2	YFL023W|BUD27|S000001871|Protein involved in bud-site selection, nutrient signaling, and gene expression controlled by TOR kinase; diploid mutants show a random budding pattern rather than the wild-type bipolar pattern; plays a role in regulating Ty1 transposition
YHR050W-A	0.0601344	CUP2	YHR050W-A||S000028832|Protein of unknown function; identified by expression profiling and mass spectrometry
YNL311C	0.0600973	CUP2	YNL311C||S000005255|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; putative F-box protein; analysis of integrated high-throughput datasets predicts involvement in ubiquitin-dependent protein catabolism
YLR232W	0.0599745	CUP2	YLR232W||S000004222|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene BNA5
YDR004W	0.0598748	CUP2	YDR004W|RAD57|S000002411|Protein that stimulates strand exchange by stabilizing the binding of Rad51p to single-stranded DNA; involved in the recombinational repair of double-strand breaks in DNA during vegetative growth and meiosis; forms heterodimer with Rad55p
YOR250C	0.0596807	CUP2	YOR250C|CLP1|S000005776|Subunit of cleavage factor I (CFI), involved in both the endonucleolyitc cleavage and polyadenylation steps of mRNA 3'-end maturation
YER099C	0.0596102	CUP2	YER099C|PRS2|S000000901|5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase, synthesizes PRPP, which is required for nucleotide, histidine, and tryptophan biosynthesis; one of five related enzymes, which are active as heteromultimeric complexes
YMR084W	0.0594596	CUP2	YMR084W||S000004689|Putative protein of unknown function; YMR084W and adjacent ORF YMR085W are merged in related strains
YGL003C	0.0591784	CUP2	YGL003C|CDH1|S000002971|Cell-cycle regulated activator of the anaphase-promoting complex/cyclosome (APC/C), which directs ubiquitination of cyclins resulting in mitotic exit; targets the APC/C to specific substrates including CDC20, ASE1, CIN8 and FIN1
YPL106C	0.0589966	CUP2	YPL106C|SSE1|S000006027|ATPase that is a component of the heat shock protein Hsp90 chaperone complex; binds unfolded proteins; member of the heat shock protein 70 (HSP70) family; localized to the cytoplasm
YOL003C	0.0586471	CUP2	YOL003C|PFA4|S000005363|Palmitoyltransferase with autoacylation activity, required for palmitoylation of amino acid permeases containing a C-terminal Phe-Trp-Cys site; required for modification of Chs3p; member of the DHHC family of putative palmitoyltransferases
YLR256W	0.0583856	CUP2	YLR256W|HAP1|S000004246|Zinc finger transcription factor involved in the complex regulation of gene expression in response to levels of heme and oxygen; the S288C sequence differs from other strain backgrounds due to a Ty1 insertion in the carboxy terminus
YER143W	0.0578528	CUP2	YER143W|DDI1|S000000945|DNA damage-inducible v-SNARE binding protein, contains a ubiquitin-associated (UBA) domain, may act as a negative regulator of constitutive exocytosis, may play a role in S-phase checkpoint control
YJL051W	0.0577803	CUP2	YJL051W|IRC8|S000003587|Bud tip localized protein of unknown function; mRNA is targeted to the bud by a She2p dependent transport system; mRNA is cell cycle regulated via Fkh2p, peaking in G2/M phase; null mutant displays increased levels of spontaneous Rad52p foc
YOR261C	0.0575247	CUP2	YOR261C|RPN8|S000005787|Essential, non-ATPase regulatory subunit of the 26S proteasome; has similarity to the human p40 proteasomal subunit and to another S. cerevisiae regulatory subunit, Rpn11p
YGR112W	0.0571739	CUP2	YGR112W|SHY1|S000003344|Mitochondrial inner membrane protein required for assembly of cytochrome c oxidase (complex IV); associates with complex IV assembly intermediates and complex III/complex IV supercomplexes; similar to human SURF1 involved in Leigh Syndrome
YNL124W	0.0568764	CUP2	YNL124W|NAF1|S000005068|Protein required for the assembly of box H/ACA snoRNPs and for pre-rRNA processing, forms a complex with Shq1p and interacts with H/ACA snoRNP components Nhp2p and Cbf5p; has similarity to Gar1p and other RNA-binding proteins
YCL073C	0.0564785	CUP2	YCL073C||S000000575|Protein of unconfirmed function; displays a topology characteristic of the Major Facilitators Superfamily of membrane proteins; coding sequence 98% identical to that of YKR106W
YLR218C	0.0562334	CUP2	YLR218C||S000004208|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YLR218C is not essential; mutants exhibit glycogen storage defects and growth defects on a non-fermentable carbon source
YNL167C	0.0559961	CUP2	YNL167C|SKO1|S000005111|Basic leucine zipper (bZIP) transcription factor of the ATF/CREB family, forms a complex with Tup1p and Ssn6p to both activate and repress transcription; cytosolic and nuclear protein involved in osmotic and oxidative stress responses
YDL013W	0.0559178	CUP2	YDL013W|SLX5|S000002171|Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate
YJR119C	0.0557554	CUP2	YJR119C|JHD2|S000003880|JmjC domain family histone demethylase specific for H3-K4 (lysine at position 4 of the histone H3 protein); removes methyl groups specifically added by Set1p methyltransferase
YNR033W	0.0557258	CUP2	YNR033W|ABZ1|S000005316|Para-aminobenzoate (PABA) synthase, has similarity to Escherichia coli PABA synthase components PabA and PabB
YJR030C	0.0555968	CUP2	YJR030C||S000003791|Putative protein of unknown function; expression repressed in carbon limited vs carbon replete chemostat cultures; YJR030C is a non-essential gene
YJL110C	0.0554503	CUP2	YJL110C|GZF3|S000003646|GATA zinc finger protein and Dal80p homolog that negatively regulates nitrogen catabolic gene expression by competing with Gat1p for GATA site binding; function requires a repressive carbon source; dimerizes with Dal80p and binds to Tor1p
YBR215W	0.0552046	CUP2	YBR215W|HPC2|S000000419|Subunit of the HIR complex, a nucleosome assembly complex involved in regulation of histone gene transcription; mutants display synthetic defects with subunits of FACT, a complex that allows passage of RNA Pol II through nucleosomes
YER172C-A	0.0550911	CUP2	YER172C-A||S000028763|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGL063W	0.0548746	CUP2	YGL063W|PUS2|S000003031|Mitochondrial tRNA:pseudouridine synthase; acts at positions 27 and 28, but not at position 72; efficiently and rapidly targeted to mitochondria, specifically dedicated to mitochondrial tRNA modification
YPL002C	0.0548722	CUP2	YPL002C|SNF8|S000005923|Component of the ESCRT-II complex, which is involved in ubiquitin-dependent sorting of proteins into the endosome; appears to be functionally related to SNF7; involved in glucose derepression
YLR005W	0.0546245	CUP2	YLR005W|SSL1|S000003995|Component of the core form of RNA polymerase transcription factor TFIIH, which has both protein kinase and DNA-dependent ATPase/helicase activities and is essential for transcription and nucleotide excision repair; interacts with Tfb4p
YGL075C	0.0546012	CUP2	YGL075C|MPS2|S000003043|Essential membrane protein localized at the nuclear envelope and spindle pole body (SPB), required for insertion of the newly duplicated SPB into the nuclear envelope; potentially phosphorylated by Cdc28p
YNL161W	0.0544224	CUP2	YNL161W|CBK1|S000005105|Serine/threonine protein kinase that regulates cell morphogenesis pathways; involved in cell wall biosynthesis, apical growth, proper mating projection morphology, bipolar bud site selection in diploid cells, and cell separation
YNR071C	0.0541089	CUP2	YNR071C||S000005354|Putative protein of unknown function
YDR307W	0.0537812	CUP2	YDR307W||S000002715|Putative protein of unknown function
YER079C-A	0.0537078	CUP2	YER079C-A||S000028751|Dubious open reading frame unlikely to encode a protein, partially overlaps uncharacterized ORF YER080W
YAL024C	0.0535747	CUP2	YAL024C|LTE1|S000000022|Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP
YDL034W	0.0535351	CUP2	YDL034W||S000002192|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps with verified gene GPR1/YDL035C; YDL034W is not an essential gene
YNL199C	0.0535059	CUP2	YNL199C|GCR2|S000005143|Transcriptional activator of genes involved in glycolysis; interacts and functions with the DNA-binding protein Gcr1p
YIR016W	0.0534755	CUP2	YIR016W||S000001455|Putative protein of unknown function; expression directly regulated by the metabolic and meiotic transcriptional regulator Ume6p; YIR016W is a non-essential gene
YDR078C	0.0533857	CUP2	YDR078C|SHU2|S000002485|Protein of unassigned function involved in mutation suppression, important for error-free repair of spontaneous and induced DNA lesions to protect the genome from mutation; associates with Shu1p, Psy3p, and Csm2p
YAL016C-A	0.053377	CUP2	YAL016C-A||S000028728|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YBR165W	0.053332	CUP2	YBR165W|UBS1|S000000369|Ubiquitin-conjugating enzyme suppressor that functions as a general positive regulator of Cdc34p activity; nuclear protein that may represent a link between nucleocytoplasmic transport and ubiquitin ligase activity
YDL025C	0.0528998	CUP2	YDL025C||S000002183|Putative protein kinase, potentially phosphorylated by Cdc28p; YDL025C is not an essential gene
YOR097C	0.0528874	CUP2	YOR097C||S000005623|Putative protein of unknown function; identified as interacting with Hsp82p in a high-throughput two-hybrid screen; YOR097C is not an essential gene
YBR148W	0.0528847	CUP2	YBR148W|YSW1|S000000352|Protein expressed specifically in spores
YMR200W	0.052505	CUP2	YMR200W|ROT1|S000004813|Essential ER membrane protein; may be involved in protein folding; mutation causes defects in cell wall synthesis and in lysis of autophagic bodies, suppresses tor2 mutations, and is synthetically lethal with kar2-1 and with rot2 mutations
YER172C	0.0524875	CUP2	YER172C|BRR2|S000000974|RNA-dependent ATPase RNA helicase (DEIH box); required for disruption of U4/U6 base-pairing in native snRNPs to activate the spliceosome for catalysis; homologous to human U5-200kD
YAL067W-A	0.052479	CUP2	YAL067W-A||S000028593|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YDR229W	0.0524028	CUP2	YDR229W|IVY1|S000002637|Phospholipid-binding protein that interacts with both Ypt7p and Vps33p, may partially counteract the action of Vps33p and vice versa, localizes to the rim of the vacuole as cells approach stationary phase
YGR150C	0.0523988	CUP2	YGR150C|DMR1|S000003382|Protein of unknown function, contains PPR motifs; mutant has growth defects on both non-fermentable carbon sources and rich medium; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR402C	0.0517995	CUP2	YDR402C|DIT2|S000002810|N-formyltyrosine oxidase, sporulation-specific microsomal enzyme involved in the production of N,N-bisformyl dityrosine required for spore wall maturation, homologous to cytochrome P-450s
YER093C	0.0517614	CUP2	YER093C|TSC11|S000000895|Subunit of TORC2 (Tor2p-Lst8p-Avo1-Avo2-Tsc11p-Bit61p), a membrane-associated complex that regulates actin cytoskeletal dynamics during polarized growth and cell wall integrity; involved in sphingolipid metabolism; contains a RasGEFN domain
YOL126C	0.0516222	CUP2	YOL126C|MDH2|S000005486|Cytoplasmic malate dehydrogenase, one of three isozymes that catalyze interconversion of malate and oxaloacetate; involved in the glyoxylate cycle and gluconeogenesis during growth on two-carbon compounds; interacts with Pck1p and Fbp1
YNR032C-A	0.0516049	CUP2	YNR032C-A|HUB1|S000007251|Ubiquitin-like protein modifier, may function in modification of Sph1p and Hbt1p, functionally complemented by the human or S. pombe ortholog; mechanism of Hub1p adduct formation not yet clear
YHR186C	0.0514529	CUP2	YHR186C|KOG1|S000001229|Subunit of TORC1, a rapamycin-sensitive complex involved in growth control that contains Tor1p or Tor2p, Lst8p and Tco89p; contains four HEAT repeats and seven WD-40 repeats; may act as a scaffold protein to couple TOR and its effectors
YDR475C	0.0512982	CUP2	YDR475C|JIP4|S000002883|Protein of unknown function; previously annotated as two separate ORFs, YDR474C and YDR475C, which were merged as a result of corrections to the systematic reference sequence
YOL059W	0.0510745	CUP2	YOL059W|GPD2|S000005420|NAD-dependent glycerol 3-phosphate dehydrogenase, homolog of Gpd1p, expression is controlled by an oxygen-independent signaling pathway required to regulate metabolism under anoxic conditions; located in cytosol and mitochondria
YDR431W	0.0509588	CUP2	YDR431W||S000002839|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YJR127C	0.0508289	CUP2	YJR127C|RSF2|S000003888|Zinc-finger protein involved in transcriptional control of both nuclear and mitochondrial genes, many of which specify products required for glycerol-based growth, respiration, and other functions
YCR084C	0.0507123	CUP2	YCR084C|TUP1|S000000680|General repressor of transcription, forms complex with Cyc8p, involved in the establishment of repressive chromatin structure through interactions with histones H3 and H4, appears to enhance expression of some genes
YPL009C	0.0503454	CUP2	YPL009C||S000005930|Protein of unknown function; may interact with ribosomes, based on co-purification experiments; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YPL009C is not an essential gene
YKL224C	0.0501759	CUP2	YKL224C|PAU16|S000001707|Putative protein of unknown function
YDL141W	0.0500225	CUP2	YDL141W|BPL1|S000002300|Biotin:apoprotein ligase, covalently modifies proteins with the addition of biotin, required for acetyl-CoA carboxylase (Acc1p) holoenzyme formation
YOL145C	0.0494251	CUP2	YOL145C|CTR9|S000005505|Component of the Paf1p complex, which is a large complex that binds to and modulates the activity of RNA polymerase II and is required for expression of a subset of genes, including cyclin genes; contains TPR repeats
YDL087C	0.0489098	CUP2	YDL087C|LUC7|S000002245|Essential protein associated with the U1 snRNP complex; splicing factor involved in recognition of 5' splice site; contains two zinc finger motifs; N-terminal zinc finger binds pre-mRNA
YLR199C	0.0486098	CUP2	YLR199C|PBA1|S000004189|Protein involved in 20S proteasome assembly; forms a heterodimer with Add66p that binds to proteasome precursors; similar to human PAC1 constituent of the PAC1-PAC2 complex involved in proteasome assembly
YDR155C	0.0482489	CUP2	YDR155C|CPR1|S000002562|Cytoplasmic peptidyl-prolyl cis-trans isomerase (cyclophilin), catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; binds the drug cyclosporin A
YMR101C	0.0476639	CUP2	YMR101C|SRT1|S000004707|Cis-prenyltransferase involved in synthesis of long-chain dolichols (19-22 isoprene units; as opposed to Rer2p which synthesizes shorter-chain dolichols); localizes to lipid bodies; transcription is induced during stationary phase
YOR114W	0.0475395	CUP2	YOR114W||S000005640|Putative protein of unknown function; null mutant is viable
YNL192W	0.0472723	CUP2	YNL192W|CHS1|S000005136|Chitin synthase I, requires activation from zymogenic form in order to catalyze the transfer of N-acetylglucosamine (GlcNAc) to chitin; required for repairing the chitin septum during cytokinesis; transcription activated by mating factor
YGR062C	0.0471236	CUP2	YGR062C|COX18|S000003294|Mitochondrial integral inner membrane protein required for membrane insertion of C-terminus of Cox2p; interacts genetically and physically with Mss2p and Pnt1p; similar to S. cerevisiae Oxa1, N. crassa Oxa2p, and E. coli YidC
YMR313C	0.0470792	CUP2	YMR313C|TGL3|S000004930|Triacylglycerol lipase of the lipid particle, responsible for all the TAG lipase activity of the lipid particle; contains the consensus sequence motif GXSXG, which is found in lipolytic enzymes
YGL203C	0.0470369	CUP2	YGL203C|KEX1|S000003171|Protease involved in the processing of killer toxin and alpha factor precursor; cleaves Lys and Arg residues from the C-terminus of peptides and proteins
YKR105C	0.0469655	CUP2	YKR105C|VBA5|S000001813|Putative transporter of the Major Facilitator Superfamily (MFS); proposed role as a basic amino acid permease based on phylogeny
YCL004W	0.0468262	CUP2	YCL004W|PGS1|S000000510|Phosphatidylglycerolphosphate synthase, catalyzes the synthesis of phosphatidylglycerolphosphate from CDP-diacylglycerol and sn-glycerol 3-phosphate in the first committed and rate-limiting step of cardiolipin biosynthesis
YKR082W	0.0467837	CUP2	YKR082W|NUP133|S000001790|Subunit of the Nup84p subcomplex of the nuclear pore complex (NPC), localizes to both sides of the NPC, required to establish a normal nucleocytoplasmic concentration gradient of the GTPase Gsp1p
YIL153W	0.0464853	CUP2	YIL153W|RRD1|S000001415|Peptidyl-prolyl cis/trans-isomerase, activator of the phosphotyrosyl phosphatase activity of PP2A; involved in G1 phase progression, microtubule dynamics, bud morphogenesis and DNA repair; subunit of the Tap42p-Sit4p-Rrd1p complex
YHR028C	0.045997	CUP2	YHR028C|DAP2|S000001070|Dipeptidyl aminopeptidase, synthesized as a glycosylated precursor; localizes to the vacuolar membrane; similar to Ste13p
YHR028W-A	0.0458969	CUP2	YHR028W-A||S000028776|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR260W	0.0454862	CUP2	YLR260W|LCB5|S000004250|Minor sphingoid long-chain base kinase, paralog of Lcb4p responsible for few percent of the total activity, possibly involved in synthesis of long-chain base phosphates, which function as signaling molecules
YOR247W	0.0452203	CUP2	YOR247W|SRL1|S000005773|Mannoprotein that exhibits a tight association with the cell wall, required for cell wall stability in the absence of GPI-anchored mannoproteins; has a high serine-threonine content; expression is induced in cell wall mutants
YJL174W	0.0451241	CUP2	YJL174W|KRE9|S000003710|Glycoprotein involved in cell wall beta-glucan assembly; null mutation leads to severe growth defects, aberrant multibudded morphology, and mating defects
YDR389W	0.0450524	CUP2	YDR389W|SAC7|S000002797|GTPase activating protein (GAP) for Rho1p, involved in signaling to the actin cytoskeleton, null mutations suppress tor2 mutations and temperature sensitive mutations in actin; potential Cdc28p substrate
YGR031W	0.0448978	CUP2	YGR031W||S000003263|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YHL037C	0.0445976	CUP2	YHL037C||S000001029|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YHL046C	0.0437278	CUP2	YHL046C|PAU13|S000001038|Putative protein of unknown function; not an essential gene
YJL096W	0.0434891	CUP2	YJL096W|MRPL49|S000003632|Mitochondrial ribosomal protein of the large subunit
YKL185W	0.0433425	CUP2	YKL185W|ASH1|S000001668|Zinc-finger inhibitor of HO transcription; mRNA is localized and translated in the distal tip of anaphase cells, resulting in accumulation of Ash1p in daughter cell nuclei and inhibition of HO expression; potential Cdc28p substrate
YHL006W-A	0.0431755	CUP2	YHL006W-A||S000028771|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPR072W	0.0430794	CUP2	YPR072W|NOT5|S000006276|Subunit of the CCR4-NOT complex, which is a global transcriptional regulator with roles in transcription initiation and elongation and in mRNA degradation
YMR227C	0.041351	CUP2	YMR227C|TAF7|S000004840|TFIID subunit (67 kDa), involved in RNA polymerase II transcription initiation
YOR095C	0.0413459	CUP2	YOR095C|RKI1|S000005621|Ribose-5-phosphate ketol-isomerase, catalyzes the interconversion of ribose 5-phosphate and ribulose 5-phosphate in the pentose phosphate pathway; participates in pyridoxine biosynthesis
YDL001W	0.0412671	CUP2	YDL001W|RMD1|S000002159|Cytoplasmic protein required for sporulation
YPR152C	0.0409492	CUP2	YPR152C|URN1|S000006356|Pre-mRNA splicing factor associated with the U2-U5-U6 snRNPs, the RES complex, and the Prp19-associated complex (NTC); null mutation displays synthetic genetic interactions with mutations affecting U2 snRNA and pre-mRNA splicing factors
YMR126C	0.0406701	CUP2	YMR126C|DLT1|S000004733|Protein of unknown function, mutant sensitive to 6-azauracil (6AU) and mycophenolic acid (MPA)
YGL064C	0.040513	CUP2	YGL064C|MRH4|S000003032|Mitochondrial ATP-dependent RNA helicase of the DEAD-box family, plays an essential role in mitochondrial function
YFR045W	0.0404252	CUP2	YFR045W||S000001941|Putative mitochondrial transport protein; null mutant is viable, exhibits decreased levels of chitin and normal resistance to calcofluor white
YKL104C	0.039548	CUP2	YKL104C|GFA1|S000001587|Glutamine-fructose-6-phosphate amidotransferase, catalyzes the formation of glucosamine-6-P and glutamate from fructose-6-P and glutamine in the first step of chitin biosynthesis
YHL045W	0.0393858	CUP2	YHL045W||S000001037|Putative protein of unknown function; not an essential gene
YGL260W	0.0393779	CUP2	YGL260W||S000003229|Putative protein of unknown function; transcription is significantly increased in a NAP1 deletion background; deletion mutant has increased accumulation of nickel and selenium
YOR296W	0.0393657	CUP2	YOR296W||S000005822|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; expressed during copper starvation; YOR296W is not an essential gene
YBR240C	0.0390621	CUP2	YBR240C|THI2|S000000444|Zinc finger protein of the Zn(II)2Cys6 type, probable transcriptional activator of thiamine biosynthetic genes
YPL154C	0.0388879	CUP2	YPL154C|PEP4|S000006075|Vacuolar aspartyl protease (proteinase A), required for the posttranslational precursor maturation of vacuolar proteinases; important for protein turnover after oxidative damage; synthesized as a zymogen, self-activates
YHR207C	0.038569	CUP2	YHR207C|SET5|S000001250|Zinc-finger protein of unknown function, contains one canonical and two unusual fingers in unusual arrangements; deletion enhances replication of positive-strand RNA virus
YGL091C	0.038221	CUP2	YGL091C|NBP35|S000003059|Essential iron-sulfur cluster binding protein localized in the cytoplasm; forms a complex with Cfd1p that is involved in iron-sulfur protein assembly in the cytosol; similar to P-loop NTPases
YPL071C	0.037978	CUP2	YPL071C||S000005992|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YPR032W	0.0376623	CUP2	YPR032W|SRO7|S000006236|Effector of Rab GTPase Sec4p, forms a complex with Sec4p and t-SNARE Sec9p; involved in exocytosis and docking and fusion of post-Golgi vesicles with plasma membrane; homolog of Sro77p and Drosophila lgl tumor suppressor
YMR019W	0.0373585	CUP2	YMR019W|STB4|S000004621|Protein that binds Sin3p in a two-hybrid assay; contains a Zn(II)2Cys6 zinc finger domain characteristic of DNA-binding proteins
YNR049C	0.0371774	CUP2	YNR049C|MSO1|S000005332|Probable component of the secretory vesicle docking complex, acts at a late step in secretion; shows genetic and physical interactions with Sec1p and is enriched in microsomal membrane fractions; required for sporulation
YDL185W	0.0367212	CUP2	YDL185W|TFP1|S000002344|Vacuolar ATPase V1 domain subunit A containing the catalytic nucleotide binding sites; protein precursor undergoes self-catalyzed splicing to yield the extein Tfp1p and the intein Vde (PI-SceI), which is a site-specific endonuclease
YHR178W	0.0365778	CUP2	YHR178W|STB5|S000001221|Activator of multidrug resistance genes, forms a heterodimer with Pdr1p; contains a Zn(II)2Cys6 zinc finger domain that interacts with a PDRE (pleotropic drug resistance element) in vitro; binds Sin3p in a two-hybrid assay
YJL146W	0.036394	CUP2	YJL146W|IDS2|S000003682|Protein involved in modulation of Ime2p activity during meiosis, appears to act indirectly to promote Ime2p-mediated late meiotic functions; found in growing cells and degraded during sporulation
YCR032W	0.0363219	CUP2	YCR032W|BPH1|S000000628|PProtein homologous to human Chediak-Higashi syndrome and murine Beige proteins, which are implicated in disease syndromes due to defective lysosomal trafficking; mutant phenotype and genetic interactions suggest a role in protein sorting
YPR115W	0.0362473	CUP2	YPR115W|GCA1|S000006319|Pleckstrin homology domain containing protein proposed to function as a glycerol channel activator; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YNL262W	0.0354717	CUP2	YNL262W|POL2|S000005206|Catalytic subunit of DNA polymerase (II) epsilon, one of the major chromosomal DNA replication polymerases characterized by processivity and proofreading exonuclease activity; also involved in DNA synthesis during DNA repair
YPR141C	0.0354096	CUP2	YPR141C|KAR3|S000006345|Minus-end-directed microtubule motor that functions in mitosis and meiosis, localizes to the spindle pole body and localization is dependent on functional Cik1p, required for nuclear fusion during mating; potential Cdc28p substrate
YGL261C	0.0351697	CUP2	YGL261C|PAU11|S000003230|Putative protein of unknown function; mRNA expression appears to be regulated by SUT1 and UPC2
YPR002C-A	0.0347799	CUP2	YPR002C-A||S000007254|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the Ty1 long terminal repeat, YPRWdelta12
YGR068C	0.0338972	CUP2	YGR068C||S000003300|Putative protein of unknown function; YGR068C is not an essential gene.
YLR077W	0.0338837	CUP2	YLR077W|FMP25|S000004067|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YIL145C	0.0334555	CUP2	YIL145C|PAN6|S000001407|Pantothenate synthase, also known as pantoate-beta-alanine ligase, required for pantothenic acid biosynthesis, deletion causes pantothenic acid auxotrophy, homologous to E. coli panC
YDR515W	0.03315	CUP2	YDR515W|SLF1|S000002923|RNA binding protein that associates with polysomes; proposed to be involved in regulating mRNA translation; involved in the copper-dependent mineralization of copper sulfide complexes on cell surface in cells cultured in copper salts
YLR008C	0.032637	CUP2	YLR008C|PAM18|S000003998|J-protein co-chaperone of the mitochondrial import motor associated with the presequence translocase, with Ssc1p, Tim44p, Mge1p, and Pam16p; stimulates ATPase activity of Ssc1p to drive mitochondrial import; activity is inhibited by Pam16p
YKL223W	0.0326163	CUP2	YKL223W||S000001706|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR116C	0.0316918	CUP2	YDR116C|MRPL1|S000002523|Mitochondrial ribosomal protein of the large subunit
YHR042W	0.0316874	CUP2	YHR042W|NCP1|S000001084|NADP-cytochrome P450 reductase; involved in ergosterol biosynthesis; associated and coordinately regulated with Erg11p
YPL158C	0.0312454	CUP2	YPL158C|AIM44|S000006079|Protein of unknown function; null mutant displays increased frequency of mitochondrial genome loss (petite formation) and reduced growth rate in minimal glycerol media
YGR154C	0.0308902	CUP2	YGR154C|GTO1|S000003386|Omega-class glutathione transferase; induced under oxidative stress; putative peroxisomal localization
YLR014C	0.0307573	CUP2	YLR014C|PPR1|S000004004|Zinc finger transcription factor containing a Zn(2)-Cys(6) binuclear cluster domain, positively regulates transcription of genes involved in uracil biosynthesis; activity may be modulated by interaction with Tup1p
YLR106C	0.0305911	CUP2	YLR106C|MDN1|S000004096|Huge dynein-related AAA-type ATPase (midasin), forms extended pre-60S particle with the Rix1 complex (Rix1p-Ipi1p-Ipi3p), may mediate ATP-dependent remodeling of 60S subunits and subsequent export from nucleoplasm to cytoplasm
YBR262C	0.0304815	CUP2	YBR262C|AIM5|S000000466|Protein of unknown function; non-tagged protein is detected in purified mitochondria in high-throughput studies; null mutant displays decreased frequency of mitochondrial genome loss and reduced growth rate in minimal glycerol media
YBL029C-A	0.0301303	CUP2	YBL029C-A||S000007591|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery; has potential orthologs in Saccharomyces species and in Yarrowia lipolytica
YDL195W	0.0299504	CUP2	YDL195W|SEC31|S000002354|Essential phosphoprotein component (p150) of the COPII coat of secretory pathway vesicles, in complex with Sec13p; required for ER-derived transport vesicle formation
YMR186W	0.0299428	CUP2	YMR186W|HSC82|S000004798|Cytoplasmic chaperone of the Hsp90 family, redundant in function and nearly identical with Hsp82p, and together they are essential; expressed constitutively at 10-fold higher basal levels than HSP82 and induced 2-3 fold by heat shock
YBR155W	0.0298502	CUP2	YBR155W|CNS1|S000000359|TPR-containing co-chaperone; binds both Hsp82p (Hsp90) and Ssa1p (Hsp70) and stimulates the ATPase activity of SSA1, ts mutants reduce Hsp82p function while over expression suppresses the phenotypes of an HSP82 ts allele and a cpr7 deletion
YBR120C	0.0298416	CUP2	YBR120C|CBP6|S000000324|Mitochondrial translational activator of the COB mRNA; phosphorylated
YOR136W	0.0297597	CUP2	YOR136W|IDH2|S000005662|Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase, which catalyzes the oxidation of isocitrate to alpha-ketoglutarate in the TCA cycle; phosphorylated
YPL104W	0.0296064	CUP2	YPL104W|MSD1|S000006025|Mitochondrial aspartyl-tRNA synthetase, required for acylation of aspartyl-tRNA; yeast and bacterial aspartyl-, asparaginyl-, and lysyl-tRNA synthetases contain regions with high sequence similarity, suggesting a common ancestral gene
YBR150C	0.0295583	CUP2	YBR150C|TBS1|S000000354|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YNR070W	0.0294018	CUP2	YNR070W||S000005353|Putative transporter of the ATP-binding cassette (ABC) family, implicated in pleiotropic drug resistance; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YGR143W	0.0288659	CUP2	YGR143W|SKN1|S000003375|Protein involved in sphingolipid biosynthesis; type II membrane protein with similarity to Kre6p
YML099W-A	0.0283126	CUP2	YML099W-A||S000004567|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF ARG81/YML099C
YGL197W	0.0282015	CUP2	YGL197W|MDS3|S000003165|Protein with an N-terminal kelch-like domain, putative negative regulator of early meiotic gene expression; required, with Pmd1p, for growth under alkaline conditions
YNL219C	0.0277491	CUP2	YNL219C|ALG9|S000005163|Mannosyltransferase, involved in N-linked glycosylation; catalyzes the transfer of mannose from Dol-P-Man to lipid-linked oligosaccharides; mutation of the human ortholog causes type 1 congenital disorders of glycosylation
YER097W	0.0276876	CUP2	YER097W||S000000899|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR221W	0.0276648	CUP2	YDR221W|GTB1|S000002629|Glucosidase II beta subunit, forms a complex with alpha subunit Rot2p, involved in removal of two glucose residues from N-linked glycans during glycoprotein biogenesis in the ER
YBL005W	0.0276379	CUP2	YBL005W|PDR3|S000000101|Transcriptional activator of the pleiotropic drug resistance network, regulates expression of ATP-binding cassette (ABC) transporters through binding to cis-acting sites known as PDREs (PDR responsive elements)
YNL109W	0.027543	CUP2	YNL109W||S000005053|Hypothetical protein
YJL063C	0.0275216	CUP2	YJL063C|MRPL8|S000003599|Mitochondrial ribosomal protein of the large subunit
YNL181W	0.0273805	CUP2	YNL181W||S000005125|Putative oxidoreductase; required for cell viability
YJL092W	0.0270286	CUP2	YJL092W|SRS2|S000003628|DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination
YDR325W	0.0266871	CUP2	YDR325W|YCG1|S000002733|Non-SMC subunit of the condensin complex (Smc2p-Smc4p-Ycs4p-Brn1p-Ycg1p); required for establishment and maintenance of chromosome condensation, chromosome segregation and for chromatin binding of the condensin complex
YHR135C	0.0266794	CUP2	YHR135C|YCK1|S000001177|Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p
YCR049C	0.0265429	CUP2	YCR049C||S000000645|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLR056W	0.0264993	CUP2	YLR056W|ERG3|S000004046|C-5 sterol desaturase, catalyzes the introduction of a C-5(6) double bond into episterol, a precursor in ergosterol biosynthesis; mutants are viable, but cannot grow on non-fermentable carbon sources
YLR146W-A	0.0264113	CUP2	YLR146W-A||S000113566|Putative protein of unknown function
YMR026C	0.0263795	CUP2	YMR026C|PEX12|S000004628|C3HC4-type RING-finger peroxisomal membrane peroxin required for peroxisome biogenesis and peroxisomal matrix protein import; forms translocation subcomplex with Pex2p and Pex10p; mutations in human homolog cause peroxisomal disorders
YOR135C	0.0263759	CUP2	YOR135C|IRC14|S000005661|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YOR136W; null mutant displays increased levels of spontaneous Rad52 foci
YDR394W	0.0262713	CUP2	YDR394W|RPT3|S000002802|One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; substrate of N-acetyltransferase B
YNL232W	0.0262441	CUP2	YNL232W|CSL4|S000005176|Subunit of the exosome, which is an essential complex present in both nucleus and cytoplasm that mediates RNA processing and degradation
YMR086C-A	0.0259421	CUP2	YMR086C-A||S000004691|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOR358W	0.0256966	CUP2	YOR358W|HAP5|S000005885|Subunit of the heme-activated, glucose-repressed Hap2/3/4/5 CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression; required for assembly and DNA binding activity of the complex
YDR457W	0.0253301	CUP2	YDR457W|TOM1|S000002865|E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators
YOL116W	0.0252698	CUP2	YOL116W|MSN1|S000005476|Transcriptional activator involved in regulation of invertase and glucoamylase expression, invasive growth and pseudohyphal differentiation, iron uptake, chromium accumulation, and response to osmotic stress; localizes to the nucleus
YER112W	0.0252033	CUP2	YER112W|LSM4|S000000914|Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA
YJL186W	0.0247529	CUP2	YJL186W|MNN5|S000003722|Alpha-1,2-mannosyltransferase, responsible for addition of the second alpha-1,2-linked mannose of the branches on the mannan backbone of oligosaccharides, localizes to an early Golgi compartment
YLR360W	0.0246626	CUP2	YLR360W|VPS38|S000004352|Part of a Vps34p phosphatidylinositol 3-kinase complex that functions in carboxypeptidase Y (CPY) sorting; binds Vps30p and Vps34p to promote production of phosphatidylinositol 3-phosphate (PtdIns3P) which stimulates kinase activity
YNL306W	0.0245908	CUP2	YNL306W|MRPS18|S000005250|Mitochondrial ribosomal protein of the small subunit; essential for viability, unlike most other mitoribosomal proteins
YOR278W	0.0245711	CUP2	YOR278W|HEM4|S000005804|Uroporphyrinogen III synthase, catalyzes the conversion of hydroxymethylbilane to uroporphyrinogen III, the fourth step in the heme biosynthetic pathway
YBR229C	0.024283	CUP2	YBR229C|ROT2|S000000433|Glucosidase II catalytic subunit required for normal cell wall synthesis; mutations in rot2 suppress tor2 mutations, and are synthetically lethal with rot1 mutations
YBR188C	0.0241116	CUP2	YBR188C|NTC20|S000000392|Member of a complex, including Prp19p, that binds to the spliceosome; required for pre-mRNA splicing
YJL172W	0.0237846	CUP2	YJL172W|CPS1|S000003708|Vacuolar carboxypeptidase yscS; expression is induced under low-nitrogen conditions
YDL131W	0.0237485	CUP2	YDL131W|LYS21|S000002289|Homocitrate synthase isozyme, catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate, which is the first step in the lysine biosynthesis pathway; highly similar to the other isozyme, Lys20p
YOL141W	0.0233505	CUP2	YOL141W|PPM2|S000005501|tRNA methyltransferase required for the synthesis of wybutosine, a modified guanosine found at the 3'-position adjacent to the anticodon of phe-tRNA; similar to Ppm1p carboxymethyltransferase
YNL070W	0.0233172	CUP2	YNL070W|TOM7|S000005014|Component of the TOM (translocase of outer membrane) complex responsible for recognition and initial import steps for all mitochondrially directed proteins; promotes assembly and stability of the TOM complex
YOR044W	0.0229001	CUP2	YOR044W|IRC23|S000005570|Putative protein of unknown function; green fluorescent protein (GFP)-fusion localizes to the ER; null mutant displays increased levels of spontaneous Rad52p foci
YDR048C	0.0228688	CUP2	YDR048C||S000002455|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGL098W	0.0228048	CUP2	YGL098W|USE1|S000003066|Essential SNARE protein localized to the ER, involved in retrograde traffic from the Golgi to the ER; forms a complex with the SNAREs Sec22p, Sec20p and Ufe1p
YML114C	0.0228007	CUP2	YML114C|TAF8|S000004582|TFIID subunit (65 kDa), involved in RNA polymerase II transcription initiation
YMR074C	0.0225922	CUP2	YMR074C||S000004678|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus and cytoplasm; YMR074C is not an essential gene
YGR008C	0.0225887	CUP2	YGR008C|STF2|S000003240|Protein involved in regulation of the mitochondrial F1F0-ATP synthase; Stf1p and Stf2p may act as stabilizing factors that enhance inhibitory action of the Inh1p protein
YEL073C	0.0225755	CUP2	YEL073C||S000000799|Putative protein of unknown function; located adjacent to ARS503 and the telomere on the left arm of chromosome V; regulated by inositol/choline
YFR014C	0.0224877	CUP2	YFR014C|CMK1|S000001910|Calmodulin-dependent protein kinase; may play a role in stress response, many CA++/calmodulan dependent phosphorylation substrates demonstrated in vitro, amino acid sequence similar to Cmk2p and mammalian Cam Kinase II
YMR004W	0.0224652	CUP2	YMR004W|MVP1|S000004606|Protein required for sorting proteins to the vacuole; overproduction of Mvp1p suppresses several dominant VPS1 mutations; Mvp1p and Vps1p act in concert to promote membrane traffic to the vacuole
YLR118C	0.0223119	CUP2	YLR118C||S000004108|Acyl-protein thioesterase responsible for depalmitoylation of Gpa1p; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and nucleus and is induced in response to the DNA-damaging agent MMS
YPL070W	0.022296	CUP2	YPL070W|MUK1|S000005991|Cytoplasmic protein of unknown function; computational analysis of large-scale protein-protein interaction data suggests a possible role in transcriptional regulation
YKL222C	0.0221311	CUP2	YKL222C||S000001705|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; similar to transcriptional regulators from the zinc cluster (binuclear cluster) family; null mutant is sensitive to caffeine
YOR199W	0.0220887	CUP2	YOR199W||S000005725|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR159W	0.0220056	CUP2	YDR159W|SAC3|S000002566|Nuclear pore-associated protein, forms a complex with Thp1p that is involved in transcription and in mRNA export from the nucleus
YGL164C	0.0219547	CUP2	YGL164C|YRB30|S000003132|RanGTP-binding protein, inhibits RanGAP1 (Rna1p)-mediated GTP hydrolysis of RanGTP (Gsp1p); shares similarity to proteins in other fungi but not in higher eukaryotes
YER060W	0.0215678	CUP2	YER060W|FCY21|S000000862|Putative purine-cytosine permease, very similar to Fcy2p but cannot substitute for its function
YGR246C	0.0214343	CUP2	YGR246C|BRF1|S000003478|TFIIIB B-related factor, one of three subunits of RNA polymerase III transcription initiation factor TFIIIB, binds TFIIIC and TBP and recruits RNA pol III to promoters, amino-terminal half is homologous to TFIIB
YHL007C	0.020931	CUP2	YHL007C|STE20|S000000999|Signal transducing kinase of the PAK (p21-activated kinase) family, involved in pheromone response and pseudohyphal/invasive growth pathways, activated by Cdc42p; binds Ste4p at a GBB motif present in noncatalytic domains of PAK kinases
YJR134C	0.0204198	CUP2	YJR134C|SGM1|S000003895|Protein of unknown function, required for wild-type growth rate on galactose and mannose; localizes to COPI coated vesicles and the Golgi apparatus
YPL100W	0.0203232	CUP2	YPL100W|ATG21|S000006021|Phosphoinositide binding protein required for vesicle formation in the cytoplasm-to-vacuole targeting (Cvt) pathway; binds both phosphatidylinositol (3,5)-bisphosphate and phosphatidylinositol 3-phosphate; WD-40 repeat protein
YNL160W	0.0192183	CUP2	YNL160W|YGP1|S000005104|Cell wall-related secretory glycoprotein; induced by nutrient deprivation-associated growth arrest and upon entry into stationary phase; may be involved in adaptation prior to stationary phase entry; has similarity to Sps100p
YML123C	0.0191765	CUP2	YML123C|PHO84|S000004592|High-affinity inorganic phosphate (Pi) transporter and low-affinity manganese transporter; regulated by Pho4p and Spt7p; mutation confers resistance to arsenate; exit from the ER during maturation requires Pho86p
YMR030W	0.0191652	CUP2	YMR030W|RSF1|S000004632|Protein required for respiratory growth; localized to both the nucleus and mitochondrion; mutant displays decreased transcription of specific nuclear and mitochondrial genes whose products are involved in respiratory growth
YML057W	0.0190676	CUP2	YML057W|CMP2|S000004521|Calcineurin A; one isoform (the other is CNA1) of the catalytic subunit of calcineurin, a Ca++/calmodulin-regulated protein phosphatase which regulates Crz1p (a stress-response transcription factor), the other calcineurin subunit is CNB1
YDL041W	0.0190274	CUP2	YDL041W||S000002199|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene SIR2/YDL042C
YOL111C	0.0190128	CUP2	YOL111C|MDY2|S000005471|Protein required for efficient mating; involved in shmoo formation and nuclear migration in the pre-zygote; associates with ribosomes and interacts with YOR164C; contains a ubiquitin-like (UBL) domain
YHR131W-A	0.0187922	CUP2	YHR131W-A||S000028782|Dubious open reading frame unlikely to encode a protein; partially overlaps the uncharacterized ORF YHR131C
YHR200W	0.0186713	CUP2	YHR200W|RPN10|S000001243|Non-ATPase base subunit of the 19S regulatory particle (RP) of the 26S proteasome; N-terminus plays a role in maintaining the structural integrity of the RP; binds selectively to polyubiquitin chains; homolog of the mammalian S5a protein
YEL018C-A	0.01858	CUP2	YEL018C-A||S000028742|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YFL049W	0.0182408	CUP2	YFL049W|SWP82|S000001845|Member of the SWI/SNF chromatin remodeling complex in which it plays an as yet unidentified role; has identifiable counterparts in closely related yeast species; abundantly expressed in many growth conditions; paralog of Npl6p
YDR183W	0.0175096	CUP2	YDR183W|PLP1|S000002591|Protein with a possible role in folding of beta-tubulin; has weak similarity to phosducins, which are G-protein regulators
YBL105C	0.0171977	CUP2	YBL105C|PKC1|S000000201|Protein serine/threonine kinase essential for cell wall remodeling during growth; localized to sites of polarized growth and the mother-daughter bud neck; homolog of the alpha, beta, and gamma isoforms of mammalian protein kinase C (PKC)
YPR105C	0.0171853	CUP2	YPR105C|COG4|S000006309|Essential component of the conserved oligomeric Golgi complex (Cog1p through Cog8p), a cytosolic tethering complex that functions in protein trafficking to mediate fusion of transport vesicles to Golgi compartments
YOR117W	0.0167862	CUP2	YOR117W|RPT5|S000005643|One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; recruited to the GAL1-10 promoter region upon induction of transcription
YOR262W	0.0166366	CUP2	YOR262W||S000005788|Protein of unknown function required for establishment of sister chromatid cohesion; contains an ATP/GTP binding site motif; similar to YLR243W and is highly conserved across species and homologous to human gene GPN2/ATPBD1B
YHR014W	0.0161488	CUP2	YHR014W|SPO13|S000001056|Meiosis-specific protein, involved in maintaining sister chromatid cohesion during meiosis I as well as promoting proper attachment of kinetochores to the spindle during meiosis I and meiosis II
YDR006C	0.0160884	CUP2	YDR006C|SOK1|S000002413|Protein whose overexpression suppresses the growth defect of mutants lacking protein kinase A activity; involved in cAMP-mediated signaling; localized to the nucleus; similar to the mouse testis-specific protein PBS13
YBR259W	0.0160166	CUP2	YBR259W||S000000463|Putative protein of unknown function; YBR259W is not an essential gene
YNL324W	0.0157936	CUP2	YNL324W||S000005268|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YIL068W-A	0.0157241	CUP2	YIL068W-A||S000028792|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDR233C	0.0156669	CUP2	YDR233C|RTN1|S000002641|ER membrane protein that interacts with exocyst subunit Sec6p and with Yip3p; also interacts with Sbh1p; null mutant has an altered (mostly cisternal) ER morphology; member of the RTNLA (reticulon-like A) subfamily
YJL099W	0.0156324	CUP2	YJL099W|CHS6|S000003635|Member of the ChAPs family of proteins (Chs5p-Arf1p-binding proteins: Bch1p, Bch2p, Bud7p, Chs6p), that forms the exomer complex with Chs5p to mediate export of specific cargo proteins, including Chs3p, from the Golgi to the plasma membrane
YLR044C	0.0152764	CUP2	YLR044C|PDC1|S000004034|Major of three pyruvate decarboxylase isozymes, key enzyme in alcoholic fermentation, decarboxylates pyruvate to acetaldehyde; subject to glucose-, ethanol-, and autoregulation; involved in amino acid catabolism
YLR396C	0.014672	CUP2	YLR396C|VPS33|S000004388|ATP-binding protein that is a subunit of the HOPS complex and the CORVET tethering complex; essential for membrane docking and fusion at both the Golgi-to-endosome and endosome-to-vacuole stages of protein transport
YLR390W	0.0144967	CUP2	YLR390W|ECM19|S000004382|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YBR258C	0.014458	CUP2	YBR258C|SHG1|S000000462|Subunit of the COMPASS (Set1C) complex, which methylates histone H3 on lysine 4 and is required in transcriptional silencing near telomeres
YIR001C	0.0140849	CUP2	YIR001C|SGN1|S000001440|Cytoplasmic RNA-binding protein, contains an RNA recognition motif (RRM); may have a role in mRNA translation, as suggested by genetic interactions with genes encoding proteins involved in translational initiation
YOR304W	0.0138799	CUP2	YOR304W|ISW2|S000005831|Member of the imitation-switch (ISWI) class of ATP-dependent chromatin remodeling complexes; ATPase component that, with Itc1p, forms a complex required for repression of a-specific genes, INO1, and early meiotic genes during mitotic growth
YKL027W	0.0136175	CUP2	YKL027W||S000001510|Protein of unknown function, localized to the mitochondrial outer membrane
YDR222W	0.0134704	CUP2	YDR222W||S000002630|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YHR132C	0.0131969	CUP2	YHR132C|ECM14|S000001174|Putative metalloprotease with similarity to the zinc carboxypeptidase family, required for normal cell wall assembly
YNL205C	0.012935	CUP2	YNL205C||S000005149|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YBR301W	0.0126052	CUP2	YBR301W|DAN3|S000000505|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YPL110C	0.0124807	CUP2	YPL110C|GDE1|S000006031|Glycerophosphocholine (GroPCho) phosphodiesterase; hydrolyzes GroPCho to choline and glycerolphosphate, for use as a phosphate source and as a precursor for phosphocholine synthesis; may interact with ribosomes
YLR223C	0.0122972	CUP2	YLR223C|IFH1|S000004213|Essential protein with a highly acidic N-terminal domain; IFH1 exhibits genetic interactions with FHL1, overexpression interferes with silencing at telomeres and HM loci; potential Cdc28p substrate
YAL041W	0.0122884	CUP2	YAL041W|CDC24|S000000039|Guanine nucleotide exchange factor (GEF or GDP-release factor) for Cdc42p; required for polarity establishment and maintenance, and mutants have morphological defects in bud formation and shmooing
YDR141C	0.0116983	CUP2	YDR141C|DOP1|S000002548|Protein of unknown function, essential for viability, involved in establishing cellular polarity and morphogenesis; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDL185C-A	0.0115386	CUP2	YDL185C-A||S000007600|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YDL185W; identified by homology with hemiascomycetous yeast species
YBR016W	0.0114827	CUP2	YBR016W||S000000220|Plasma membrane protein of unknown function; has similarity to hydrophilins, which are hydrophilic, glycine-rich proteins involved in the adaptive response to hyperosmotic conditions
YML122C	0.0113675	CUP2	YML122C||S000004591|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YNL279W	0.0113172	CUP2	YNL279W|PRM1|S000005223|Pheromone-regulated multispanning membrane protein involved in membrane fusion during mating; predicted to have 5 transmembrane segments and a coiled coil domain; localizes to the shmoo tip; regulated by Ste12p
YDR219C	0.0113	CUP2	YDR219C|MFB1|S000002627|Mitochondria-associated F-box protein involved in maintenance of normal mitochondrial morphology; interacts with Skp1p through the F-box motif; preferentially localizes to the mother cell during budding
YPL102C	0.0109858	CUP2	YPL102C||S000006023|Dubious open reading frame, not conserved in closely related Saccharomyces species; deletion mutation enhances replication of Brome mosaic virus in S. cerevisiae, but this is likely due to effects on the overlapping gene ELP4
YPL101W	0.0109419	CUP2	YPL101W|ELP4|S000006022|Subunit of Elongator complex, which is required for modification of wobble nucleosides in tRNA; required for Elongator structural integrity
YIR041W	0.0109105	CUP2	YIR041W|PAU15|S000001480|Hypothetical protein
YJL001W	0.0106021	CUP2	YJL001W|PRE3|S000003538|Beta 1 subunit of the 20S proteasome, responsible for cleavage after acidic residues in peptides
YJL176C	0.00879192	CUP2	YJL176C|SWI3|S000003712|Subunit of the SWI/SNF chromatin remodeling complex, which regulates transcription by remodeling chromosomes; required for transcription of many genes, including ADH1, ADH2, GAL1, HO, INO1 and SUC2
YCL010C	0.00866601	CUP2	YCL010C|SGF29|S000000516|SaGa associated Factor 29kDa; Probable 29kKDa Subunit of SAGA histone acetyltransferase complex
YIL026C	0.00861806	CUP2	YIL026C|IRR1|S000001288|Subunit of the cohesin complex, which is required for sister chromatid cohesion during mitosis and meiosis and interacts with centromeres and chromosome arms, essential for viability
YLR007W	0.00858428	CUP2	YLR007W|NSE1|S000003997|Essential subunit of the Mms21-Smc5-Smc6 complex; nuclear protein required for DNA repair and growth; has a nonstructural role in the maintenance of chromosomes
YJL118W	0.00856637	CUP2	YJL118W||S000003654|Putative protein of unknown function; may interact with ribosomes, based on co-purification experiments; YJL18W is a non-essential gene; deletion enhances the toxicity of heterologously expressed human alpha-synuclein
YDL203C	0.00856316	CUP2	YDL203C|ACK1|S000002362|Putative protein of unknown function; GFP-fusion protein expression is induced in response to the DNA-damaging agent MMS; the authentic, non-tagged protein is detected in purified mitochondria
YMR150C	0.00814269	CUP2	YMR150C|IMP1|S000004758|Catalytic subunit of the mitochondrial inner membrane peptidase complex, required for maturation of mitochondrial proteins of the intermembrane space; complex contains Imp1p and Imp2p (both catalytic subunits), and Som1p
YEL045C	0.00798863	CUP2	YEL045C||S000000771|Dubious open reading frame unlikely to encode a protein based on available experimental and comparative sequence data; deletion gives MMS sensitivity, growth defect under alkaline conditions, less than optimal growth upon citric acid stress
YDL178W	0.00767708	CUP2	YDL178W|DLD2|S000002337|D-lactate dehydrogenase, located in the mitochondrial matrix
YNL051W	0.00767183	CUP2	YNL051W|COG5|S000004996|Component of the conserved oligomeric Golgi complex (Cog1p through Cog8p), a cytosolic tethering complex that functions in protein trafficking to mediate fusion of transport vesicles to Golgi compartments
YPR047W	0.00755776	CUP2	YPR047W|MSF1|S000006251|Mitochondrial phenylalanyl-tRNA synthetase alpha subunit, active as a monomer, unlike the cytoplasmic subunit which is active as a dimer complexed to a beta subunit dimer; similar to the alpha subunit of E. coli phenylalanyl-tRNA synthetase
YNL041C	0.00702941	CUP2	YNL041C|COG6|S000004986|Component of the conserved oligomeric Golgi complex (Cog1p through Cog8p), a cytosolic tethering complex that functions in protein trafficking to mediate fusion of transport vesicles to Golgi compartments
YNL003C	0.00687042	CUP2	YNL003C|PET8|S000004948|S-adenosylmethionine transporter of the mitochondrial inner membrane, member of the mitochondrial carrier family; required for biotin biosynthesis and respiratory growth
YNL228W	0.00667777	CUP2	YNL228W||S000005172|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data; almost completely overlaps ORF YNL227C/JJJ1
YDR320C	0.00653299	CUP2	YDR320C|SWA2|S000002728|Auxilin-like protein involved in vesicular transport; clathrin-binding protein required for uncoating of clathrin-coated vesicles
YKR088C	0.00579879	CUP2	YKR088C|TVP38|S000001796|Integral membrane protein localized to late Golgi vesicles along with the v-SNARE Tlg2p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YER074W-A	0.00570998	CUP2	YER074W-A|YOS1|S000007651|Integral membrane protein required for ER to Golgi transport; localized to the Golgi, the ER, and COPII vesicles; interacts with Yip1p and Yif1p
YKR017C	0.00549956	CUP2	YKR017C||S000001725|Putative protein of unknown function; contains a RING finger motif
YLR024C	0.00537957	CUP2	YLR024C|UBR2|S000004014|Cytoplasmic ubiquitin-protein ligase (E3)
YPR162C	0.00505476	CUP2	YPR162C|ORC4|S000006366|Subunit of the origin recognition complex, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing
YOR116C	0.00493352	CUP2	YOR116C|RPO31|S000005642|RNA polymerase III subunit C160, part of core enzyme; similar to bacterial beta-prime subunit
YPR094W	0.00480037	CUP2	YPR094W|RDS3|S000006298|Zinc cluster protein involved in pre-mRNA splicing and cycloheximide resistance
YBR135W	0.00459309	CUP2	YBR135W|CKS1|S000000339|Cyclin-dependent protein kinase regulatory subunit and adaptor; modulates proteolysis of M-phase targets through interactions with the proteasome; role in transcriptional regulation, recruiting proteasomal subunits to target gene promoters
YLR010C	0.0045246	CUP2	YLR010C|TEN1|S000004000|Protein that regulates telomeric length; protects telomeric ends in a complex with Cdc13p and Stn1p
YNL258C	0.0040335	CUP2	YNL258C|DSL1|S000005202|Peripheral membrane protein required for Golgi-to-ER retrograde traffic; component of the ER target site that interacts with coatomer, the major component of the COPI vesicle protein coat; also interacts with Cin5p and Sec39p
YDL045W-A	0.00369103	CUP2	YDL045W-A|MRP10|S000006430|Mitochondrial ribosomal protein of the small subunit
YBR217W	0.00367228	CUP2	YBR217W|ATG12|S000000421|Conserved ubiquitin-like modifier involved in autophagy and the Cvt pathway; conjugated to Atg5p to form a complex involved in Atg8p lipidation; Atg12p-Atg5p also forms a complex with Atg16p that is required for autophagosome formation
YER173W	0.00362721	CUP2	YER173W|RAD24|S000000975|Checkpoint protein, involved in the activation of the DNA damage and meiotic pachytene checkpoints; subunit of a clamp loader that loads Rad17p-Mec3p-Ddc1p onto DNA; homolog of human and S. pombe Rad17 protein
YKR005C	0.00344442	CUP2	YKR005C||S000001713|Putative protein of unknown function
YIR020W-A	0.00332533	CUP2	YIR020W-A||S000007241|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data
YBR200W	0.00331355	CUP2	YBR200W|BEM1|S000000404|Protein containing SH3-domains, involved in establishing cell polarity and morphogenesis; functions as a scaffold protein for complexes that include Cdc24p, Ste5p, Ste20p, and Rsr1p
YPR166C	0.00322837	CUP2	YPR166C|MRP2|S000006370|Mitochondrial ribosomal protein of the small subunit
YNL186W	0.00316614	CUP2	YNL186W|UBP10|S000005130|Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus
YGR171C	0.00311753	CUP2	YGR171C|MSM1|S000003403|Mitochondrial methionyl-tRNA synthetase (MetRS), functions as a monomer in mitochondrial protein synthesis; functions similarly to cytoplasmic MetRS although the cytoplasmic form contains a zinc-binding domain not found in Msm1p
YOL105C	0.00287185	CUP2	YOL105C|WSC3|S000005465|Partially redundant sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway involved in maintenance of cell wall integrity; involved in the response to heat shock and other stressors; regulates 1,3-beta-glucan synthesis
YDR327W	0.00240414	CUP2	YDR327W||S000002735|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data; partially overlaps the verified gene SKP1
YCR093W	0.00238548	CUP2	YCR093W|CDC39|S000000689|Component of the CCR4-NOT complex, which has multiple roles in regulating mRNA levels including regulation of transcription and destabilizing mRNAs by deadenylation; basal transcription factor
YJR090C	0.00230655	CUP2	YJR090C|GRR1|S000003850|F-box protein component of the SCF ubiquitin-ligase complex; involved in carbon catabolite repression, glucose-dependent divalent cation transport, high-affinity glucose transport, morphogenesis, and sulfite detoxification
YPR149W	0.00177107	CUP2	YPR149W|NCE102|S000006353|Protein of unknown function; contains transmembrane domains; involved in secretion of proteins that lack classical secretory signal sequences; component of the detergent-insoluble glycolipid-enriched complexes (DIGs)
YOL004W	0.00171036	CUP2	YOL004W|SIN3|S000005364|Component of the Sin3p-Rpd3p histone deacetylase complex, involved in transcriptional repression and activation of diverse processes, including mating-type switching and meiosis; involved in the maintenance of chromosomal integrity
YDR283C	0.00156517	CUP2	YDR283C|GCN2|S000002691|Protein kinase, phosphorylates the alpha-subunit of translation initiation factor eIF2 (Sui2p) in response to starvation; activated by uncharged tRNAs and the Gcn1p-Gcn20p complex
YCR106W	0.00128849	CUP2	YCR106W|RDS1|S000000703|Zinc cluster transcription factor involved in conferring resistance to cycloheximide
YKL068W	0.000925203	CUP2	YKL068W|NUP100|S000001551|Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup116p
YIR006C	0.000751112	CUP2	YIR006C|PAN1|S000001445|Part of actin cytoskeleton-regulatory complex Pan1p-Sla1p-End3p, associates with actin patches on the cell cortex; promotes protein-protein interactions essential for endocytosis; previously thought to be a subunit of poly(A) ribonuclease
YPR089W	0.000411665	CUP2	YPR089W||S000006293|Protein of unknown function; exhibits genetic interaction with ERG11 and protein-protein interaction with Hsp82p
YLR263W	0.000218846	CUP2	YLR263W|RED1|S000004253|Protein component of the axial elements of the synaptonemal complex, involved in chromosome segregation during the first meiotic division; interacts with Hop1p; required for wild-type levels of Mek1p kinase activity
YBL008W-A	0.000198552	CUP2	YBL008W-A||S000028529|Putative protein of unknown function; identified by fungal homology and RT-PCR
YKR080W	0.00010154	CUP2	YKR080W|MTD1|S000001788|NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase, plays a catalytic role in oxidation of cytoplasmic one-carbon units; expression is regulated by Bas1p and Bas2p, repressed by adenine, and may be induced by inositol and choline
