YMR017W	4.60844	CUP9	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
YGR087C	4.19673	CUP9	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
YHR139C	3.32323	CUP9	YHR139C|SPS100|S000001181|Protein required for spore wall maturation; expressed during sporulation; may be a component of the spore wall
YOR100C	3.09959	CUP9	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
YMR107W	2.93463	CUP9	YMR107W|SPG4|S000004713|Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources
YGR059W	2.85859	CUP9	YGR059W|SPR3|S000003291|Sporulation-specific homolog of the yeast CDC3/10/11/12 family of bud neck microfilament genes; septin protein involved in sporulation; regulated by ABFI
YOR255W	2.61622	CUP9	YOR255W|OSW1|S000005781|Protein involved in sporulation; required for the construction of the outer spore wall layers; required for proper localization of Spo14p
YIL057C	2.54508	CUP9	YIL057C||S000001319|Putative protein of unknown function; expression induced under carbon limitation and repressed under high glucose
YFL011W	2.50741	CUP9	YFL011W|HXT10|S000001883|Putative hexose transporter, expressed at low levels and expression is repressed by glucose
YER065C	2.49656	CUP9	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
YLR307W	2.38778	CUP9	YLR307W|CDA1|S000004298|Chitin deacetylase, together with Cda2p involved in the biosynthesis ascospore wall component, chitosan; required for proper rigidity of the ascospore wall
YFL012W	2.38506	CUP9	YFL012W||S000001882|Putative protein of unknown function; transcribed during sporulation; null mutant exhibits increased resistance to rapamycin
YKL109W	2.31489	CUP9	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
YDL114W	2.30923	CUP9	YDL114W||S000002272|Putative protein of unknown function with similarity to acyl-carrier-protein reductases; YDL114W is not an essential gene
YAL062W	2.24769	CUP9	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
YMR118C	2.22727	CUP9	YMR118C||S000004724|Protein of unknown function with similarity to succinate dehydrogenase cytochrome b subunit; YMR118C is not an essential gene
YLR307C-A	2.21821	CUP9	YLR307C-A||S000028525|Putative protein of unknown function
YCL048W	2.18294	CUP9	YCL048W|SPS22|S000000553|Protein of unknown function, redundant with Sps2p for the organization of the beta-glucan layer of the spore wall
YER106W	2.15747	CUP9	YER106W|MAM1|S000000908|Monopolin, kinetochore associated protein involved in chromosome attachment to meiotic spindle
YML089C	2.14019	CUP9	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
YGL205W	2.0706	CUP9	YGL205W|POX1|S000003173|Fatty-acyl coenzyme A oxidase, involved in the fatty acid beta-oxidation pathway; localized to the peroxisomal matrix
YPL021W	2.05522	CUP9	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
YNL318C	1.84412	CUP9	YNL318C|HXT14|S000005262|Protein with similarity to hexose transporter family members, expression is induced in low glucose and repressed in high glucose; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YFR023W	1.83614	CUP9	YFR023W|PES4|S000001919|Poly(A) binding protein, suppressor of DNA polymerase epsilon mutation, similar to Mip6p
YBR180W	1.80177	CUP9	YBR180W|DTR1|S000000384|Putative dityrosine transporter, required for spore wall synthesis; expressed during sporulation; member of the major facilitator superfamily (DHA1 family) of multidrug resistance transporters
YKL177W	1.72162	CUP9	YKL177W||S000001660|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene STE3
YBR117C	1.6406	CUP9	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
YPR078C	1.63448	CUP9	YPR078C||S000006282|Putative protein of unknown function; possible role in DNA metabolism and/or in genome stability; expression is heat-inducible
YLR136C	1.61606	CUP9	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
YNL117W	1.61529	CUP9	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
YAL067C	1.56337	CUP9	YAL067C|SEO1|S000000062|Putative permease, member of the allantoate transporter subfamily of the major facilitator superfamily; mutation confers resistance to ethionine sulfoxide
YFL051C	1.53974	CUP9	YFL051C||S000001843|Putative protein of unknown function; YFL051C is not an essential gene
YAR069C	1.51984	CUP9	YAR069C||S000000092|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR218C	1.4759	CUP9	YDR218C|SPR28|S000002626|Sporulation-specific homolog of the yeast CDC3/10/11/12 family of bud neck microfilament genes; meiotic septin expressed at high levels during meiotic divisions and ascospore formation
YJR154W	1.46673	CUP9	YJR154W||S000003915|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YML090W	1.46453	CUP9	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
YAL018C	1.4643	CUP9	YAL018C||S000000016|Putative protein of unknown function
YAR070C	1.45726	CUP9	YAR070C||S000000093|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLR346C	1.44109	CUP9	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
YML091C	1.43779	CUP9	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
YAR050W	1.43068	CUP9	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
YBR051W	1.41223	CUP9	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
YDR281C	1.40895	CUP9	YDR281C|PHM6|S000002689|Protein of unknown function, expression is regulated by phosphate levels
YJR095W	1.36407	CUP9	YJR095W|SFC1|S000003856|Mitochondrial succinate-fumarate transporter, transports succinate into and fumarate out of the mitochondrion; required for ethanol and acetate utilization
YHR015W	1.36291	CUP9	YHR015W|MIP6|S000001057|Putative RNA-binding protein, interacts with Mex67p, which is a component of the nuclear pore involved in nuclear mRNA export
YAR053W	1.34345	CUP9	YAR053W||S000000085|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YCL054W	1.3308	CUP9	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
YNR062C	1.32385	CUP9	YNR062C||S000005345|Putative membrane protein of unknown function
YKR102W	1.31651	CUP9	YKR102W|FLO10|S000001810|Lectin-like protein with similarity to Flo1p, thought to be involved in flocculation
YNL183C	1.30034	CUP9	YNL183C|NPR1|S000005127|Protein kinase that stabilizes several plasma membrane amino acid transporters by antagonizing their ubiquitin-mediated degradation
YER024W	1.29678	CUP9	YER024W|YAT2|S000000826|Carnitine acetyltransferase; has similarity to Yat1p, which is a carnitine acetyltransferase associated with the mitochondrial outer membrane
YDR446W	1.28661	CUP9	YDR446W|ECM11|S000002854|Non-essential protein apparently involved in meiosis, GFP fusion protein is present in discrete clusters in the nucleus throughout mitosis; may be involved in maintaining chromatin structure
YPR169W-A	1.28102	CUP9	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
YLR308W	1.27836	CUP9	YLR308W|CDA2|S000004299|Chitin deacetylase, together with Cda1p involved in the biosynthesis ascospore wall component, chitosan; required for proper rigidity of the ascospore wall
YGR243W	1.26753	CUP9	YGR243W|FMP43|S000003475|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YJR048W	1.26382	CUP9	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
YGR088W	1.25193	CUP9	YGR088W|CTT1|S000003320|Cytosolic catalase T, has a role in protection from oxidative damage by hydrogen peroxide
YNR063W	1.23643	CUP9	YNR063W||S000005346|Putative zinc-cluster protein of unknown function
YBR144C	1.2302	CUP9	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
YDL210W	1.22941	CUP9	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
YAR047C	1.2237	CUP9	YAR047C||S000000083|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YHR048W	1.22196	CUP9	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
YDR242W	1.2209	CUP9	YDR242W|AMD2|S000002650|Putative amidase
YBR050C	1.20409	CUP9	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
YNR064C	1.19659	CUP9	YNR064C||S000005347|Epoxide hydrolase, member of the alpha/beta hydrolase fold family; may have a role in detoxification of epoxides
YAL066W	1.19226	CUP9	YAL066W||S000000061|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YGL170C	1.1657	CUP9	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
YHR145C	1.15684	CUP9	YHR145C||S000001188|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YKL178C	1.14848	CUP9	YKL178C|STE3|S000001661|Receptor for a factor receptor, transcribed in alpha cells and required for mating by alpha cells, couples to MAP kinase cascade to mediate pheromone response; ligand bound receptors are endocytosed and recycled to the plasma membrane; GPCR
YLR327C	1.12231	CUP9	YLR327C|TMA10|S000004319|Protein of unknown function that associates with ribosomes
YBR296C	1.10966	CUP9	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
YJL045W	1.10686	CUP9	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
YPR002W	1.06065	CUP9	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
YHR139C-A	1.05748	CUP9	YHR139C-A||S000003533|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YMR194C-B	1.0528	CUP9	YMR194C-B||S000028514|Putative protein of unknown function
YFL012W-A	1.05099	CUP9	YFL012W-A||S000002964|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene IES1/YFL013C
YHL040C	1.05006	CUP9	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
YOR186W	1.04344	CUP9	YOR186W||S000005712|Putative protein of unknown function; proper regulation of expression during heat stress is sphingolipid-dependent
YMR244W	1.03086	CUP9	YMR244W||S000004858|Putative protein of unknown function
YDR445C	1.02388	CUP9	YDR445C||S000002853|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGL117W	1.00397	CUP9	YGL117W||S000003085|Putative protein of unknown function
YOL052C-A	0.982034	CUP9	YOL052C-A|DDR2|S000005413|Multistress response protein, expression is activated by a variety of xenobiotic agents and environmental or physiological stresses
YFR032C-B	0.963037	CUP9	YFR032C-B||S000028630|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YEL049W	0.96164	CUP9	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
YKL161C	0.960383	CUP9	YKL161C||S000001644|Protein kinase implicated in the Slt2p mitogen-activated (MAP) kinase signaling pathway; associates with Rlm1p
YKR034W	0.959067	CUP9	YKR034W|DAL80|S000001742|Negative regulator of genes in multiple nitrogen degradation pathways; expression is regulated by nitrogen levels and by Gln3p; member of the GATA-binding family, forms homodimers and heterodimers with Deh1p
YPL092W	0.952991	CUP9	YPL092W|SSU1|S000006013|Plasma membrane sulfite pump involved in sulfite metabolism and required for efficient sulfite efflux; major facilitator superfamily protein
YGR258C	0.94817	CUP9	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
YCL018W	0.930103	CUP9	YCL018W|LEU2|S000000523|Beta-isopropylmalate dehydrogenase (IMDH), catalyzes the third step in the leucine biosynthesis pathway
YBR250W	0.926053	CUP9	YBR250W|SPO23|S000000454|Protein of unknown function; associates with meiosis-specific protein Spo1p
YPL222C-A	0.923043	CUP9	YPL222C-A||S000028722|Identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YBR179C	0.922069	CUP9	YBR179C|FZO1|S000000383|Mitochondrial integral membrane protein involved in mitochondrial fusion and maintenance of the mitochondrial genome; contains N-terminal GTPase domain
YOR237W	0.915033	CUP9	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)
YMR280C	0.914408	CUP9	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
YIL160C	0.912626	CUP9	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
YAR035W	0.908211	CUP9	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
YKR105C	0.907372	CUP9	YKR105C|VBA5|S000001813|Putative transporter of the Major Facilitator Superfamily (MFS); proposed role as a basic amino acid permease based on phylogeny
YOL082W	0.898675	CUP9	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
YHR095W	0.891345	CUP9	YHR095W||S000001137|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YBR094W	0.88849	CUP9	YBR094W|PBY1|S000000298|Putative tubulin tyrosine ligase associated with P-bodies
YMR040W	0.873363	CUP9	YMR040W|YET2|S000004643|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; homolog of human BAP31 protein
YDR042C	0.861246	CUP9	YDR042C||S000002449|Putative protein of unknown function; expression is increased in ssu72-ts69 mutant
YOL050C	0.860409	CUP9	YOL050C||S000005410|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps verified gene GAL11; deletion confers sensitivity to 4-(N-(S-glutathionylacetyl)amino) phenylarsenoxide (GSAO)
YFR029W	0.854276	CUP9	YFR029W|PTR3|S000001925|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
YPL147W	0.851057	CUP9	YPL147W|PXA1|S000006068|Subunit of a heterodimeric peroxisomal ATP-binding cassette transporter complex (Pxa1p-Pxa2p), required for import of long-chain fatty acids into peroxisomes; similarity to human adrenoleukodystrophy transporter and ALD-related proteins
YJR151C	0.843341	CUP9	YJR151C|DAN4|S000003912|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YFL013C	0.838494	CUP9	YFL013C|IES1|S000001881|Subunit of the INO80 chromatin remodeling complex
YCL069W	0.836104	CUP9	YCL069W|VBA3|S000000574|Permease of basic amino acids in the vacuolar membrane
YNL180C	0.830729	CUP9	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
YDL085W	0.830572	CUP9	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
YOL024W	0.823041	CUP9	YOL024W||S000005384|Putative protein of unknown function, predicted to have thiol-disulfide oxidoreductase active site
YDL204W	0.816557	CUP9	YDL204W|RTN2|S000002363|Protein of unknown function; has similarity to mammalian reticulon proteins; member of the RTNLA (reticulon-like A) subfamily
YBR040W	0.815249	CUP9	YBR040W|FIG1|S000000244|Integral membrane protein required for efficient mating; may participate in or regulate the low affinity Ca2+ influx system, which affects intracellular signaling and cell-cell fusion during mating
YMR090W	0.8097	CUP9	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
YHL035C	0.806559	CUP9	YHL035C|VMR1|S000001027|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; member of the ATP-binding cassette (ABC) family; potential Cdc28p substrate; detected in purified mitochondria in high-throughput studies
YPR193C	0.80547	CUP9	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
YDR043C	0.799826	CUP9	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
YNL179C	0.795362	CUP9	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
YFL030W	0.793388	CUP9	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
YML058W-A	0.790102	CUP9	YML058W-A|HUG1|S000007472|Protein involved in the Mec1p-mediated checkpoint pathway that responds to DNA damage or replication arrest, transcription is induced by DNA damage
YOR211C	0.781148	CUP9	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
YKL163W	0.780192	CUP9	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
YBR072W	0.778547	CUP9	YBR072W|HSP26|S000000276|Small heat shock protein (sHSP) with chaperone activity; forms hollow, sphere-shaped oligomers that suppress unfolded proteins aggregation; oligomer activation requires a heat-induced conformational change; not expressed in unstressed cells
YER116C	0.76029	CUP9	YER116C|SLX8|S000000918|Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate
YDR310C	0.758293	CUP9	YDR310C|SUM1|S000002718|Transcriptional repressor required for mitotic repression of middle sporulation-specific genes; involved in telomere maintenance, regulated by the pachytene checkpoint
YGL163C	0.757491	CUP9	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
YDR223W	0.754701	CUP9	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
YHR150W	0.753208	CUP9	YHR150W|PEX28|S000001193|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
YJL043W	0.751252	CUP9	YJL043W||S000003579|Putative protein of unknown function; YJL043W is a non-essential gene
YOR192C-C	0.75099	CUP9	YOR192C-C||S000028857|Putative protein of unknown function; identified by expression profiling and mass spectrometry
YER097W	0.750029	CUP9	YER097W||S000000899|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YMR195W	0.744253	CUP9	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
YDL115C	0.743175	CUP9	YDL115C|IWR1|S000002273|Protein of unknown function, deletion causes hypersensitivity to the K1 killer toxin
YGL118C	0.742935	CUP9	YGL118C||S000003086|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YIL037C	0.741348	CUP9	YIL037C|PRM2|S000001299|Pheromone-regulated protein, predicted to have 4 transmembrane segments and a coiled coil domain; regulated by Ste12p
YOR192C	0.737572	CUP9	YOR192C|THI72|S000005718|Transporter of thiamine or related compound; shares sequence similarity with Thi7p
YAR060C	0.737084	CUP9	YAR060C||S000000086|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR540C	0.722661	CUP9	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
YNL328C	0.722147	CUP9	YNL328C|MDJ2|S000005272|Constituent of the mitochondrial import motor associated with the presequence translocase; function overlaps with that of Pam18p; stimulates the ATPase activity of Ssc1p to drive mitochondrial import; contains a J domain
YBR215W	0.710869	CUP9	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
YGR110W	0.708022	CUP9	YGR110W||S000003342|Putative protein of unknown function; transcription is increased in response to genotoxic stress; plays a role in restricting Ty1 transposition
YAL063C	0.698286	CUP9	YAL063C|FLO9|S000000059|Lectin-like protein with similarity to Flo1p, thought to be expressed and involved in flocculation
YHR211W	0.694818	CUP9	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
YGR065C	0.691307	CUP9	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
YOR289W	0.689541	CUP9	YOR289W||S000005815|Putative protein of unknown function; transcription induced by the unfolded protein response; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YJR047C	0.684402	CUP9	YJR047C|ANB1|S000003808|Translation initiation factor eIF-5A, promotes formation of the first peptide bond; similar to and functionally redundant with Hyp2p; undergoes an essential hypusination modification; expressed under anaerobic conditions
YMR317W	0.676135	CUP9	YMR317W||S000004936|Putative protein of unknown function with some similarity to sialidase from Trypanosoma; YMR317W is not an essential gene
YDR528W	0.672997	CUP9	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
YKL217W	0.670225	CUP9	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
YDR259C	0.664957	CUP9	YDR259C|YAP6|S000002667|Putative basic leucine zipper (bZIP) transcription factor; overexpression increases sodium and lithium tolerance
YER014C-A	0.657136	CUP9	YER014C-A|BUD25|S000007590|Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern
YLL056C	0.654815	CUP9	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
YMR316C-B	0.651622	CUP9	YMR316C-B||S000004934|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR054C	0.648099	CUP9	YLR054C|OSW2|S000004044|Protein of unknown function proposed to be involved in the assembly of the spore wall
YOR365C	0.647531	CUP9	YOR365C||S000005892|Putative protein of unknown function; YOR365C is not an essential protein
YDR119W-A	0.637794	CUP9	YDR119W-A||S000113555|Putative protein of unknown function
YPL271W	0.637682	CUP9	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
YMR014W	0.636633	CUP9	YMR014W|BUD22|S000004616|Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern
YIR014W	0.630781	CUP9	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
YOR345C	0.624207	CUP9	YOR345C||S000005872|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene REV1; null mutant displays increased resistance to antifungal agents gliotoxin, cycloheximide and H2O2
YBR018C	0.619566	CUP9	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
YCR091W	0.61879	CUP9	YCR091W|KIN82|S000000687|Putative serine/threonine protein kinase, most similar to cyclic nucleotide-dependent protein kinase subfamily and the protein kinase C subfamily
YER098W	0.617227	CUP9	YER098W|UBP9|S000000900|Ubiquitin carboxyl-terminal hydrolase, ubiquitin-specific protease that cleaves ubiquitin-protein fusions
YKL202W	0.614009	CUP9	YKL202W||S000001685|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOR347C	0.612445	CUP9	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
YMR081C	0.612277	CUP9	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
YIR029W	0.605084	CUP9	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
YOR306C	0.604625	CUP9	YOR306C|MCH5|S000005833|Plasma membrane riboflavin transporter; facilitates the uptake of vitamin B2; required for FAD-dependent processes; sequence similarity to mammalian monocarboxylate permeases, however mutants are not deficient in monocarboxylate transport
YGR182C	0.600288	CUP9	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
YPR065W	0.599327	CUP9	YPR065W|ROX1|S000006269|Heme-dependent repressor of hypoxic genes; contains an HMG domain that is responsible for DNA bending activity
YMR013C	0.597789	CUP9	YMR013C|SEC59|S000004615|Dolichol kinase, catalyzes the terminal step in dolichyl monophosphate (Dol-P) biosynthesis; required for viability and for normal rates of lipid intermediate synthesis and protein N-glycosylation
YOR339C	0.596207	CUP9	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
YOL100W	0.59406	CUP9	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
YHR093W	0.590276	CUP9	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
YER061C	0.586171	CUP9	YER061C|CEM1|S000000863|Mitochondrial beta-keto-acyl synthase with possible role in fatty acid synthesis; required for mitochondrial respiration
YBR269C	0.584303	CUP9	YBR269C|FMP21|S000000473|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YPL018W	0.578478	CUP9	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
YHR033W	0.574403	CUP9	YHR033W||S000001075|Putative protein of unknown function; epitope-tagged protein localizes to the cytoplasm
YMR016C	0.570388	CUP9	YMR016C|SOK2|S000004618|Nuclear protein that plays a regulatory role in the cyclic AMP (cAMP)-dependent protein kinase (PKA) signal transduction pathway; negatively regulates pseudohyphal differentiation; homologous to several transcription factors
YFL003C	0.568727	CUP9	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
YML047C	0.565967	CUP9	YML047C|PRM6|S000004510|Pheromone-regulated protein, predicted to have 2 transmembrane segments; regulated by Ste12p during mating
YOR346W	0.559774	CUP9	YOR346W|REV1|S000005873|Deoxycytidyl transferase, forms a complex with the subunits of DNA polymerase zeta, Rev3p and Rev7p; involved in repair of abasic sites in damaged DNA
YPL258C	0.553526	CUP9	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
YLR369W	0.543599	CUP9	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
YGR039W	0.543472	CUP9	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
YDR542W	0.540985	CUP9	YDR542W|PAU10|S000002950|Hypothetical protein
YFR012W	0.538252	CUP9	YFR012W||S000001908|Putative protein of unknown function
YIL077C	0.53723	CUP9	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)
YDL187C	0.534864	CUP9	YDL187C||S000002346|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLL047W	0.534061	CUP9	YLL047W||S000003970|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene RNP1
YIL023C	0.531104	CUP9	YIL023C|YKE4|S000001285|Zinc transporter; localizes to the ER; null mutant is sensitive to calcofluor white, leads to zinc accumulation in cytosol; ortholog of the mouse KE4 and member of the ZIP (ZRT, IRT-like Protein) family
YJR049C	0.528166	CUP9	YJR049C|UTR1|S000003810|ATP-NADH kinase; phosphorylates both NAD and NADH; active as a hexamer; enhances the activity of ferric reductase (Fre1p)
YHR212C	0.526778	CUP9	YHR212C||S000001255|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YKR015C	0.525169	CUP9	YKR015C||S000001723|Putative protein of unknown function
YHR023W	0.524823	CUP9	YHR023W|MYO1|S000001065|Type II myosin heavy chain, required for wild-type cytokinesis and cell separation; localizes to the actomyosin ring; binds to myosin light chains Mlc1p and Mlc2p through its IQ1 and IQ2 motifs respectively
YBR147W	0.524719	CUP9	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
YMR018W	0.524041	CUP9	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
YMR141C	0.522211	CUP9	YMR141C||S000004749|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YNL052W	0.513053	CUP9	YNL052W|COX5A|S000004997|Subunit Va of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; predominantly expressed during aerobic growth while its isoform Vb (Cox5Bp) is expressed during anaerobic growth
YOR382W	0.510085	CUP9	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
YCR082W	0.507989	CUP9	YCR082W|AHC2|S000000678|Protein of unknown function, putative transcriptional regulator; proposed to be a Ada Histone acetyltransferase complex component; GFP tagged protein is localized to the cytoplasm and nucleus
YKL102C	0.506021	CUP9	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
YLR152C	0.504843	CUP9	YLR152C||S000004142|Putative protein of unknown function; YLR152C is not an essential gene
YHR184W	0.504044	CUP9	YHR184W|SSP1|S000001227|Protein involved in the control of meiotic nuclear division and coordination of meiosis with spore formation; transcription is induced midway through meiosis
YOL159C-A	0.500731	CUP9	YOL159C-A||S000007627|Putative protein of unknown function; identified by sequence comparison with hemiascomycetous yeast species
YBR060C	0.497962	CUP9	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
YMR306W	0.491028	CUP9	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
YHR206W	0.485339	CUP9	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
YLR423C	0.483962	CUP9	YLR423C|ATG17|S000004415|Scaffold protein responsible for pre-autophagosomal structure organization; regulatory subunit of an autophagy-specific complex that includes Atg1p and Atg13p; stimulates Atg1p kinase activity
YMR232W	0.483347	CUP9	YMR232W|FUS2|S000004845|Cytoplasmic protein localized to the shmoo tip; required for the alignment of parental nuclei before nuclear fusion during mating
YOR173W	0.483305	CUP9	YOR173W|DCS2|S000005699|Non-essential, stress induced regulatory protein containing a HIT (histidine triad) motif; modulates m7G-oligoribonucleotide metabolism; inhibits Dcs1p; regulated by Msn2p, Msn4p, and the Ras-cAMP-cAPK signaling pathway, similar to Dcs1p.
YDR359C	0.482803	CUP9	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
YLR304C	0.482436	CUP9	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
YHR217C	0.476553	CUP9	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.
YGL180W	0.47589	CUP9	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
YHR212W-A	0.471684	CUP9	YHR212W-A||S000028650|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YOL025W	0.470822	CUP9	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
YNL042W-B	0.469518	CUP9	YNL042W-B||S000028850|Putative protein of unknown function
YOL037C	0.465764	CUP9	YOL037C||S000005397|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YOL036W
YLR247C	0.464894	CUP9	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
YER053C	0.453669	CUP9	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
YOR221C	0.451293	CUP9	YOR221C|MCT1|S000005747|Predicted malonyl-CoA:ACP transferase, putative component of a type-II mitochondrial fatty acid synthase that produces intermediates for phospholipid remodeling
YDR178W	0.447573	CUP9	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
YDR360W	0.447528	CUP9	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.
YKL112W	0.44583	CUP9	YKL112W|ABF1|S000001595|DNA binding protein with possible chromatin-reorganizing activity involved in transcriptional activation, gene silencing, and DNA replication and repair
YAR068W	0.444352	CUP9	YAR068W||S000000091|Fungal-specific protein of unknown function; induced in respiratory-deficient cells
YFL008W	0.442565	CUP9	YFL008W|SMC1|S000001886|Subunit of the multiprotein cohesin complex, essential protein involved in chromosome segregation and in double-strand DNA break repair; SMC chromosomal ATPase family member, binds DNA with a preference for DNA with secondary structure
YBR292C	0.440954	CUP9	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
YBR301W	0.440348	CUP9	YBR301W|DAN3|S000000505|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YOL075C	0.436904	CUP9	YOL075C||S000005435|Putative ABC transporter
YGR154C	0.435743	CUP9	YGR154C|GTO1|S000003386|Omega-class glutathione transferase; induced under oxidative stress; putative peroxisomal localization
YIL150C	0.435216	CUP9	YIL150C|MCM10|S000001412|Essential chromatin-associated protein involved in the initiation of DNA replication; required for the association of the MCM2-7 complex with replication origins
YER067C-A	0.427471	CUP9	YER067C-A||S000028748|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YER067W
YLR260W	0.427374	CUP9	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
YOL036W	0.425725	CUP9	YOL036W||S000005396|Protein of unknown function; potential Cdc28p substrate
YJR004C	0.423514	CUP9	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
YCL073C	0.423288	CUP9	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
YHR146W	0.418537	CUP9	YHR146W|CRP1|S000001189|Protein that binds to cruciform DNA structures
YDL042C	0.417949	CUP9	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
YKL031W	0.416834	CUP9	YKL031W||S000001514|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species
YOL013W-B	0.414208	CUP9	YOL013W-B||S000007252|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the long terminal repeat (LTR) of a Ty1 element
YIL117C	0.41335	CUP9	YIL117C|PRM5|S000001379|Pheromone-regulated protein, predicted to have 1 transmembrane segment; induced during cell integrity signaling
YOR366W	0.410966	CUP9	YOR366W||S000005893|Hypothetical protein
YOR208W	0.410133	CUP9	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
YDR461C-A	0.409783	CUP9	YDR461C-A||S000087209|Putative protein of unknown function
YIL036W	0.408393	CUP9	YIL036W|CST6|S000001298|Basic leucine zipper (bZIP) transcription factor of the ATF/CREB family, activates transcription of genes involved in utilization of non-optimal carbon sources; involved in telomere maintenance
YGR286C	0.404485	CUP9	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
YBR076W	0.403284	CUP9	YBR076W|ECM8|S000000280|Non-essential protein of unknown function
YKL016C	0.403186	CUP9	YKL016C|ATP7|S000001499|Subunit d of the stator stalk of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis
YBR155W	0.40256	CUP9	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
YOR011W-A	0.398148	CUP9	YOR011W-A||S000028581|Putative protein of unknown function
YPL171C	0.396077	CUP9	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
YDR270W	0.394832	CUP9	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
YGL215W	0.390882	CUP9	YGL215W|CLG1|S000003183|Cyclin-like protein that interacts with Pho85p; has sequence similarity to G1 cyclins PCL1 and PCL2
YDR317W	0.389802	CUP9	YDR317W|HIM1|S000002725|Protein of unknown function involved in DNA repair
YBR157C	0.388113	CUP9	YBR157C|ICS2|S000000361|Protein of unknown function; null mutation does not confer any obvious defects in growth, spore germination, viability, or carbohydrate utilization
YNL091W	0.387277	CUP9	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
YGR043C	0.385438	CUP9	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
YLR228C	0.383573	CUP9	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
YDR034C	0.382396	CUP9	YDR034C|LYS14|S000002441|Transcriptional activator involved in regulation of genes of the lysine biosynthesis pathway; requires 2-aminoadipate semialdehyde as co-inducer
YJR152W	0.38228	CUP9	YJR152W|DAL5|S000003913|Allantoin permease; ureidosuccinate permease; expression is constitutive but sensitive to nitrogen catabolite repression
YDL227C	0.382	CUP9	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
YLR365W	0.381217	CUP9	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
YPL009C	0.380631	CUP9	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
YBL033C	0.370494	CUP9	YBL033C|RIB1|S000000129|GTP cyclohydrolase II; catalyzes the first step of the riboflavin biosynthesis pathway
YIL066C	0.369617	CUP9	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
YDR263C	0.368355	CUP9	YDR263C|DIN7|S000002671|Mitochondrial nuclease functioning in DNA repair and replication, modulates the stability of the mitochondrial genome, induced by exposure to mutagens, also induced during meiosis at a time nearly coincident with commitment to recombination
YPR036W-A	0.368323	CUP9	YPR036W-A||S000028425|Protein of unknown function; transcription is regulated by Pdr1p
YPL150W	0.368204	CUP9	YPL150W||S000006071|Putative protein kinase of unknown cellular role
YML020W	0.368054	CUP9	YML020W||S000004482|Putative protein of unknown function
YEL012W	0.364266	CUP9	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
YPR202W	0.363928	CUP9	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
YJL037W	0.36384	CUP9	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
YFL063W	0.361681	CUP9	YFL063W||S000001831|Dubious open reading frame, based on available experimental and comparative sequence data
YAR023C	0.361057	CUP9	YAR023C||S000000074|Putative integral membrane protein, member of DUP240 gene family
YGL248W	0.359229	CUP9	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
YDR171W	0.357359	CUP9	YDR171W|HSP42|S000002578|Small heat shock protein (sHSP) with chaperone activity; forms barrel-shaped oligomers that suppress unfolded protein aggregation; involved in cytoskeleton reorganization after heat shock
YKL203C	0.357036	CUP9	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
YDR285W	0.35331	CUP9	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
YKR106W	0.352944	CUP9	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
YNR001C	0.352883	CUP9	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
YGL096W	0.352171	CUP9	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
YLR176C	0.351971	CUP9	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
YDR269C	0.351216	CUP9	YDR269C||S000002677|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOR147W	0.348622	CUP9	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
YGR161C	0.347965	CUP9	YGR161C|RTS3|S000003393|Putative component of the protein phosphatase type 2A complex
YPR081C	0.347195	CUP9	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
YBR063C	0.347072	CUP9	YBR063C||S000000267|Putative protein of unknown function; YBR063C is not an essential gene
YER132C	0.345434	CUP9	YER132C|PMD1|S000000934|Protein with an N-terminal kelch-like domain, putative negative regulator of early meiotic gene expression; required, with Mds3p, for growth under alkaline conditions
YDL222C	0.344737	CUP9	YDL222C|FMP45|S000002381|Integral membrane protein localized to mitochondria (untagged protein) and eisosomes, immobile patches at the cortex associated with endocytosis; sporulation and sphingolipid content are altered in mutants; has homologs SUR7 and YNL194C
YIR028W	0.344684	CUP9	YIR028W|DAL4|S000001467|Allantoin permease; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation
YNL144C	0.344512	CUP9	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
YBR064W	0.344506	CUP9	YBR064W||S000000268|Dubious open reading frame unlikely to encode a protein; partially overlaps the uncharacterized ORF YBR063C
YML066C	0.342847	CUP9	YML066C|SMA2|S000004531|Protein of unknown function involved in the assembly of the prospore membrane during sporulation
YMR165C	0.341624	CUP9	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
YCR005C	0.341352	CUP9	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
YNL195C	0.338265	CUP9	YNL195C||S000005139|Putative protein of unknown function; shares a promoter with YNL194C; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YOR032C	0.336534	CUP9	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
YMR084W	0.336385	CUP9	YMR084W||S000004689|Putative protein of unknown function; YMR084W and adjacent ORF YMR085W are merged in related strains
YPL032C	0.331504	CUP9	YPL032C|SVL3|S000005953|Protein of unknown function, mutant phenotype suggests a potential role in vacuolar function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery, cytoplasm, bud, and bud neck
YLR425W	0.330995	CUP9	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
YMR256C	0.33041	CUP9	YMR256C|COX7|S000004869|Subunit VII of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain
YJR052W	0.329715	CUP9	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
YPL248C	0.328701	CUP9	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
YNL282W	0.3283	CUP9	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
YKL023W	0.325266	CUP9	YKL023W||S000001506|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YMR101C	0.323345	CUP9	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
YLR366W	0.322635	CUP9	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
YBR145W	0.321382	CUP9	YBR145W|ADH5|S000000349|Alcohol dehydrogenase isoenzyme V; involved in ethanol production
YHR055C	0.321202	CUP9	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
YKL028W	0.313293	CUP9	YKL028W|TFA1|S000001511|TFIIE large subunit, involved in recruitment of RNA polymerase II to the promoter, activation of TFIIH, and promoter opening
YMR164C	0.313091	CUP9	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
YHR075C	0.312862	CUP9	YHR075C|PPE1|S000001117|Protein with carboxyl methyl esterase activity that may have a role in demethylation of the phosphoprotein phosphatase catalytic subunit; also identified as a small subunit mitochondrial ribosomal protein
YJL176C	0.312028	CUP9	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
YJL112W	0.311475	CUP9	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
YHR210C	0.308882	CUP9	YHR210C||S000001253|Putative protein of unknown function; non-essential gene; highly expressed under anaeorbic conditions; sequence similarity to aldose 1-epimerases such as GAL10
YDR523C	0.307023	CUP9	YDR523C|SPS1|S000002931|Putative protein serine/threonine kinase expressed at the end of meiosis and localized to the prospore membrane, required for correct localization of enzymes involved in spore wall synthesis
YNR051C	0.306899	CUP9	YNR051C|BRE5|S000005334|Ubiquitin protease cofactor, forms deubiquitination complex with Ubp3p that coregulates anterograde and retrograde transport between the endoplasmic reticulum and Golgi compartments; null is sensitive to brefeldin A
YDR440W	0.306848	CUP9	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
YKL015W	0.304208	CUP9	YKL015W|PUT3|S000001498|Transcriptional activator of proline utilization genes, constitutively binds PUT1 and PUT2 promoter sequences and undergoes a conformational change to form the active state; has a Zn(2)-Cys(6) binuclear cluster domain
YPL223C	0.302273	CUP9	YPL223C|GRE1|S000006144|Hydrophilin of unknown function; stress induced (osmotic, ionic, oxidative, heat shock and heavy metals); regulated by the HOG pathway
YJL175W	0.302137	CUP9	YJL175W||S000003711|Dubious open reading frame unlikely to encode a functional protein; deletion confers resistance to cisplatin, hypersensitivity to 5-fluorouracil, and growth defect at high pH with high calcium; overlaps gene for SWI3 transcription factor
YPR077C	0.301017	CUP9	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
YDR329C	0.298789	CUP9	YDR329C|PEX3|S000002737|Peroxisomal membrane protein (PMP) required required for the proper localization and stability of PMPs; interacts with Pex19p
YOR313C	0.295877	CUP9	YOR313C|SPS4|S000005840|Protein whose expression is induced during sporulation; not required for sporulation; heterologous expression in E. coli induces the SOS response that senses DNA damage
YKR103W	0.293776	CUP9	YKR103W|NFT1|S000001811|Putative transporter of the multidrug resistance-associated protein (MRP) subfamily; adjacent ORFs YKR103W and YKR104W are merged in different strain backgrounds.
YHR051W	0.2937	CUP9	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
YOR031W	0.293525	CUP9	YOR031W|CRS5|S000005557|Copper-binding metallothionein, required for wild-type copper resistance
YLL005C	0.29238	CUP9	YLL005C|SPO75|S000003928|Meiosis-specific protein of unknown function, required for spore wall formation during sporulation; dispensable for both nuclear divisions during meiosis
YNL203C	0.289793	CUP9	YNL203C||S000005147|Dubious open reading frame unlikely to encode a functional protein; based on available experimental and comparative sequence data
YHR125W	0.2887	CUP9	YHR125W||S000001167|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YHR155W	0.288663	CUP9	YHR155W|YSP1|S000001198|Mitochondrial protein with a potential role in promoting mitochondrial fragmentation during programmed cell death in response to high levels of alpha-factor mating pheromone or the drug amiodarone
YDL244W	0.288512	CUP9	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
YKR039W	0.287972	CUP9	YKR039W|GAP1|S000001747|General amino acid permease; localization to the plasma membrane is regulated by nitrogen source
YEL009C-A	0.286383	CUP9	YEL009C-A||S000028741|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOR393W	0.282209	CUP9	YOR393W|ERR1|S000005920|Protein of unknown function, has similarity to enolases
YNR069C	0.282009	CUP9	YNR069C|BSC5|S000005352|Protein of unknown function, ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression
YLR205C	0.281627	CUP9	YLR205C|HMX1|S000004195|ER localized, heme-binding peroxidase involved in the degradation of heme; does not exhibit heme oxygenase activity despite similarity to heme oxygenases; expression regulated by AFT1
YKL148C	0.280632	CUP9	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
YJR094C	0.280407	CUP9	YJR094C|IME1|S000003854|Master regulator of meiosis that is active only during meiotic events, activates transcription of early meiotic genes through interaction with Ume6p, degraded by the 26S proteasome following phosphorylation by Ime2p
YPL261C	0.280229	CUP9	YPL261C||S000006182|Dubious open reading frame unlikely to encode a protein; partially overlaps the uncharacterized ORF YPL260W
YGR233C	0.279519	CUP9	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
YNL143C	0.278587	CUP9	YNL143C||S000005087|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YFL058W	0.278144	CUP9	YFL058W|THI5|S000001836|Protein involved in synthesis of the thiamine precursor hydroxymethylpyrimidine (HMP); member of a subtelomeric gene family including THI5, THI11, THI12, and THI13
YDR217C	0.277995	CUP9	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
YIL144W	0.276256	CUP9	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
YMR089C	0.275185	CUP9	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
YOR068C	0.274866	CUP9	YOR068C|VAM10|S000005594|Protein involved in vacuole morphogenesis; acts at an early step of homotypic vacuole fusion that is required for vacuole tethering
YBL078C	0.274019	CUP9	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
YGR183C	0.27211	CUP9	YGR183C|QCR9|S000003415|Subunit 9 of the ubiquinol cytochrome-c reductase complex, which is a component of the mitochondrial inner membrane electron transport chain; required for electron transfer at the ubiquinol oxidase site of the complex
YEL023C	0.267918	CUP9	YEL023C||S000000749|Putative protein of unknown function; expression is increased greatly during sporulation; YEL023C is not an essential gene
YIL161W	0.266883	CUP9	YIL161W||S000001423|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; mRNA is enriched in Scp160p-associated mRNPs; YIL161W is a non-essential gene
YLR082C	0.265939	CUP9	YLR082C|SRL2|S000004072|Protein of unknown function; overexpression suppresses the lethality caused by a rad53 null mutation
YKL041W	0.26504	CUP9	YKL041W|VPS24|S000001524|One of four subunits of the endosomal sorting complex required for transport III (ESCRT-III); forms an ESCRT-III subcomplex with Did4p; involved in the sorting of transmembrane proteins into the multivesicular body (MVB) pathway
YDR192C	0.26419	CUP9	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
YDR022C	0.263249	CUP9	YDR022C|CIS1|S000002429|Autophagy-specific protein required for autophagosome formation; may form a complex with Atg17p and Atg29p that localizes other proteins to the pre-autophagosomal structure; high-copy suppressor of CIK1 deletion
YGL187C	0.262396	CUP9	YGL187C|COX4|S000003155|Subunit IV of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; N-terminal 25 residues of precursor are cleaved during mitochondrial import; phosphorylated
YMR189W	0.262223	CUP9	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
YDR406W	0.261176	CUP9	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
YKL124W	0.259317	CUP9	YKL124W|SSH4|S000001607|Specificity factor required for Rsp5p-dependent ubiquitination and sorting of cargo proteins at the multivesicular body; identified as a high-copy suppressor of a SHR3 deletion, increasing steady-state levels of amino acid permeases
YOR152C	0.256585	CUP9	YOR152C||S000005678|Putative protein of unknown function; has no similarity to any known protein; YOR152C is not an essential gene
YPR171W	0.25605	CUP9	YPR171W|BSP1|S000006375|Adapter that links synaptojanins Inp52p and Inp53p to the cortical actin cytoskeleton
YBR200W-A	0.255455	CUP9	YBR200W-A||S000028535|Putative protein of unknown function; identified by fungal homology and RT-PCR
YIL055C	0.255082	CUP9	YIL055C||S000001317|Putative protein of unknown function
YGL230C	0.254654	CUP9	YGL230C||S000003199|Putative protein of unknown function; non-essential gene
YLR403W	0.254216	CUP9	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
YDR330W	0.253104	CUP9	YDR330W|UBX5|S000002738|UBX (ubiquitin regulatory X) domain-containing protein that interacts with Cdc48p
YKL029C	0.25208	CUP9	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
YEL050C	0.251801	CUP9	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
YML109W	0.249981	CUP9	YML109W|ZDS2|S000004577|Protein that interacts with silencing proteins at the telomere, involved in transcriptional silencing; paralog of Zds1p
YDL070W	0.248626	CUP9	YDL070W|BDF2|S000002228|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 Bdf1p
YGL062W	0.247478	CUP9	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
YOR394W	0.24723	CUP9	YOR394W|PAU21|S000005921|Hypothetical protein
YBL108W	0.247034	CUP9	YBL108W||S000000204|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YML034C-A	0.245122	CUP9	YML034C-A||S000004499|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPL250C	0.245067	CUP9	YPL250C|ICY2|S000006171|Protein of unknown function; mobilized into polysomes upon a shift from a fermentable to nonfermentable carbon source; potential Cdc28p substrate
YOR391C	0.243512	CUP9	YOR391C|HSP33|S000005918|Possible chaperone and cysteine protease with similarity to E. coli Hsp31 and S. cerevisiae Hsp31p, Hsp32p, and Sno4p; member of the DJ-1/ThiJ/PfpI superfamily, which includes human DJ-1 involved in Parkinson's disease
YJR050W	0.243446	CUP9	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
YML133C	0.242805	CUP9	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
YIR023W	0.242158	CUP9	YIR023W|DAL81|S000001462|Positive regulator of genes in multiple nitrogen degradation pathways; contains DNA binding domain but does not appear to bind the dodecanucleotide sequence present in the promoter region of many genes involved in allantoin catabolism
YPL278C	0.242156	CUP9	YPL278C||S000006199|Putative protein of unknown function; gene expression regulated by copper levels
YPL081W	0.240962	CUP9	YPL081W|RPS9A|S000006002|Protein component of the small (40S) ribosomal subunit; nearly identical to Rps9Bp and has similarity to E. coli S4 and rat S9 ribosomal proteins
YDR515W	0.240953	CUP9	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
YKL082C	0.239875	CUP9	YKL082C|RRP14|S000001565|Essential protein, constituent of 66S pre-ribosomal particles; interacts with proteins involved in ribosomal biogenesis and cell polarity; member of the SURF-6 family
YGR142W	0.239185	CUP9	YGR142W|BTN2|S000003374|v-SNARE binding protein that facilitates specific protein retrieval from a late endosome to the Golgi; modulates arginine uptake, possible role in mediating pH homeostasis between the vacuole and plasma membrane H(+)-ATPase
YPL189W	0.238675	CUP9	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
YOL160W	0.237066	CUP9	YOL160W||S000005520|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLL061W	0.235919	CUP9	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
YGR281W	0.235393	CUP9	YGR281W|YOR1|S000003513|Plasma membrane ATP-binding cassette (ABC) transporter, multidrug transporter mediates export of many different organic anions including oligomycin
YMR141W-A	0.232719	CUP9	YMR141W-A||S000028575|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene RPL13B/YMR142C
YDR381C-A	0.232185	CUP9	YDR381C-A||S000007650|Protein of unknown function, localized to the mitochondrial outer membrane
YLR402W	0.232049	CUP9	YLR402W||S000004394|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YJL074C	0.230304	CUP9	YJL074C|SMC3|S000003610|Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member
YDR490C	0.230059	CUP9	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
YER187W	0.229881	CUP9	YER187W||S000000989|Putative protein of unknown function; induced in respiratory-deficient cells
YIL048W	0.229159	CUP9	YIL048W|NEO1|S000001310|Putative aminophospholipid translocase (flippase) involved in endocytosis and vacuolar biogenesis; localizes to endosomes and the Golgi aparatus
YNL103W	0.228787	CUP9	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
YIL038C	0.227808	CUP9	YIL038C|NOT3|S000001300|Subunit of the CCR4-NOT complex, which is a global transcriptional regulator with roles in transcription initiation and elongation and in mRNA degradation
YNL325C	0.227285	CUP9	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
YDL061C	0.226106	CUP9	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
YLR394W	0.225729	CUP9	YLR394W|CST9|S000004386|SUMO E3 ligase; required for synaptonemal complex formation; localizes to synapsis initiation sites on meiotic chromosomes; potential Cdc28p substrate
YKL187C	0.224965	CUP9	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
YPL040C	0.223886	CUP9	YPL040C|ISM1|S000005961|Mitochondrial isoleucyl-tRNA synthetase, null mutant is deficient in respiratory growth
YML034W	0.223854	CUP9	YML034W|SRC1|S000004497|Inner nuclear membrane (INM) protein with a putative role in sister chromatid segregation, potentially phosphorylated by Cdc28p; contains helix-extension-helix (HEH) motif, nuclear localization signal sequence
YPL260W	0.223375	CUP9	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
YOR328W	0.223329	CUP9	YOR328W|PDR10|S000005855|ATP-binding cassette (ABC) transporter, multidrug transporter involved in the pleiotropic drug resistance network; regulated by Pdr1p and Pdr3p
YGR146C	0.222655	CUP9	YGR146C||S000003378|Putative protein of unknown function; induced by iron homeostasis transcription factor Aft2p; multicopy suppressor of a temperature sensitive hsf1 mutant; induced by treatment with 8-methoxypsoralen and UVA irradiation
YDR089W	0.221542	CUP9	YDR089W||S000002496|Protein of unknown function; deletion confers resistance to Nickel
YMR255W	0.221531	CUP9	YMR255W|GFD1|S000004868|Coiled-coiled protein of unknown function, identified as a high-copy suppressor of a dbp5 mutation
YKL121W	0.221318	CUP9	YKL121W||S000001604|Putative protein of unknown function
YER011W	0.221134	CUP9	YER011W|TIR1|S000000813|Cell wall mannoprotein of the Srp1p/Tip1p family of serine-alanine-rich proteins; expression is downregulated at acidic pH and induced by cold shock and anaerobiosis; abundance is increased in cells cultured without shaking
YGL121C	0.219546	CUP9	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
YDL223C	0.218215	CUP9	YDL223C|HBT1|S000002382|Substrate of the Hub1p ubiquitin-like protein that localizes to the shmoo tip (mating projection); mutants are defective for mating projection formation, thereby implicating Hbt1p in polarized cell morphogenesis
YEL007W	0.217893	CUP9	YEL007W||S000000733|Putative protein with sequence similarity to S. pombe gti1+ (gluconate transport inducer 1)
YLR326W	0.217888	CUP9	YLR326W||S000004318|Hypothetical protein
YDL028C	0.215024	CUP9	YDL028C|MPS1|S000002186|Dual-specificity kinase required for spindle pole body (SPB) duplication and spindle checkpoint function; substrates include SPB proteins Spc42p, Spc110p, and Spc98p, mitotic exit network protein Mob1p, and checkpoint protein Mad1p
YDL169C	0.214336	CUP9	YDL169C|UGX2|S000002328|Protein of unknown function, transcript accumulates in response to any combination of stress conditions
YAL031W-A	0.21429	CUP9	YAL031W-A||S000028731|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YCL065W	0.213416	CUP9	YCL065W||S000000570|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps HMLALPHA1
YML097C	0.213396	CUP9	YML097C|VPS9|S000004563|A guanine nucleotide exchange factor involved in vesicle-mediated vacuolar protein transport; specifically stimulates the intrinsic guanine nucleotide exchange activity of Vps21p/Rab5: similar to mammalian ras inhibitors; binds ubiquitin
YHR053C	0.213358	CUP9	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
YPL078C	0.212331	CUP9	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
YJR150C	0.21221	CUP9	YJR150C|DAN1|S000003911|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YPL035C	0.210138	CUP9	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
YHR218W	0.210044	CUP9	YHR218W||S000001261|Helicase-like protein encoded within the telomeric Y' element
YDR335W	0.209147	CUP9	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
YDR142C	0.208321	CUP9	YDR142C|PEX7|S000002549|Peroxisomal signal receptor for the N-terminal nonapeptide signal (PTS2) of peroxisomal matrix proteins; WD repeat protein; defects in human homolog cause lethal rhizomelic chondrodysplasia punctata (RCDP)
YPR013C	0.208197	CUP9	YPR013C||S000006217|Putative zinc finger protein; YPR013C is not an essential gene
YPL034W	0.206332	CUP9	YPL034W||S000005955|Putative protein of unknown function; YPL034W is not essential gene
YER076W-A	0.204761	CUP9	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
YFL064C	0.204601	CUP9	YFL064C||S000001830|Putative protein of unknown function
YNL092W	0.204145	CUP9	YNL092W||S000005036|Putative S-adenosylmethionine-dependent methyltransferase of the seven beta-strand family; YNL092W is not an essential gene
YFL055W	0.203638	CUP9	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
YCL001W-B	0.203439	CUP9	YCL001W-B||S000007596|Putative protein of unknown function; identified by homology
YML084W	0.202818	CUP9	YML084W||S000004549|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLR424W	0.202452	CUP9	YLR424W|SPP382|S000004416|Essential protein that forms a dimer with Ntr2p; also forms a trimer, with Ntr2p and Prp43p, that is involved in spliceosome disassembly; found also in a multisubunit complex with the splicing factor Clf1p; suppressor of prp38-1 mutation
YMR140W	0.202431	CUP9	YMR140W|SIP5|S000004748|Protein of unknown function; interacts with both the Reg1p/Glc7p phosphatase and the Snf1p kinase
YCR014C	0.202145	CUP9	YCR014C|POL4|S000000607|DNA polymerase IV, undergoes pair-wise interactions with Dnl4p-Lif1p and Rad27p to mediate repair of DNA double-strand breaks by non-homologous end joining (NHEJ); homologous to mammalian DNA polymerase beta
YHR054W-A	0.201929	CUP9	YHR054W-A||S000028648|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps CUP1-2
YCL001W-A	0.201893	CUP9	YCL001W-A||S000007221|Putative protein of unknown function; YCL001W-A is not an essential gene
YDL183C	0.201856	CUP9	YDL183C||S000002342|Putative protein of unknown function; YDL183C is not an essential gene
YPR186C	0.200977	CUP9	YPR186C|PZF1|S000006390|Transcription factor IIIA (TFIIIA), essential protein with nine C2H2 Zn-fingers, binds the 5S rRNA gene through the zinc finger domain and directs assembly of a multiprotein initiation complex for RNA polymerase III; also binds DNA
YPL033C	0.199894	CUP9	YPL033C||S000005954|Putative protein of unknown function; may be involved in DNA metabolism; expression is induced by Kar4p
YCR025C	0.199798	CUP9	YCR025C||S000000620|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YCR025C is not an essential gene
YJR138W	0.199391	CUP9	YJR138W|IML1|S000003899|Protein of unknown function, green fluorescent protein (GFP)-fusion protein localizes to the vacuolar membrane
YKR009C	0.199183	CUP9	YKR009C|FOX2|S000001717|Multifunctional enzyme of the peroxisomal fatty acid beta-oxidation pathway; has 3-hydroxyacyl-CoA dehydrogenase and enoyl-CoA hydratase activities
YNL125C	0.19907	CUP9	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
YDR147W	0.198586	CUP9	YDR147W|EKI1|S000002554|Ethanolamine kinase, primarily responsible for phosphatidylethanolamine synthesis via the CDP-ethanolamine pathway; exhibits some choline kinase activity, thus contributing to phosphatidylcholine synthesis via the CDP-choline pathway
YDR311W	0.198343	CUP9	YDR311W|TFB1|S000002719|Subunit of TFIIH and nucleotide excision repair factor 3 complexes, required for nucleotide excision repair, target for transcriptional activators
YDR102C	0.198248	CUP9	YDR102C||S000002509|Dubious open reading frame; homozygous diploid deletion strain exhibits high budding index
YFL059W	0.196596	CUP9	YFL059W|SNZ3|S000001835|Member of a stationary phase-induced gene family; transcription of SNZ2 is induced prior to diauxic shift, and also in the absence of thiamin in a Thi2p-dependent manner; forms a coregulated gene pair with SNO3
YKL165C-A	0.195297	CUP9	YKL165C-A||S000007617|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YNL283C	0.195153	CUP9	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
YPL282C	0.194446	CUP9	YPL282C|PAU22|S000006203|Hypothetical protein
YIL079C	0.193311	CUP9	YIL079C|AIR1|S000001341|RING finger protein that interacts with the arginine methyltransferase Hmt1p to regulate methylation of Npl3p, which modulates Npl3p function in mRNA processing and export; has similarity to Air2p
YCR007C	0.192901	CUP9	YCR007C||S000000600|Putative integral membrane protein, member of DUP240 gene family; YCR007C is not an essential gene
YHL046W-A	0.192297	CUP9	YHL046W-A||S000028775|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR259C	0.190865	CUP9	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
YFL060C	0.190344	CUP9	YFL060C|SNO3|S000001834|Protein of unknown function, nearly identical to Sno2p; expression is induced before the diauxic shift and also in the absence of thiamin
YLL010C	0.190194	CUP9	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
YNR070W	0.18886	CUP9	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
YMR158W-B	0.188582	CUP9	YMR158W-B||S000004768|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene ATG16/YMR159C
YPR106W	0.188153	CUP9	YPR106W|ISR1|S000006310|Predicted protein kinase, overexpression causes sensitivity to staurosporine, which is a potent inhibitor of protein kinase C
YDR277C	0.186219	CUP9	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
YBR039W	0.185296	CUP9	YBR039W|ATP3|S000000243|Gamma subunit of the F1 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis
YHL047C	0.18506	CUP9	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
YDR409W	0.183968	CUP9	YDR409W|SIZ1|S000002817|SUMO/Smt3 ligase that promotes the attachment of sumo (Smt3p; small ubiquitin-related modifier) to proteins; binds Ubc9p and may bind septins; specifically required for sumoylation of septins in vivo; localized to the septin ring
YDR273W	0.18276	CUP9	YDR273W|DON1|S000002681|Meiosis-specific component of the spindle pole body, part of the leading edge protein (LEP) coat, forms a ring-like structure at the leading edge of the prospore membrane during meiosis II
YDR029W	0.181931	CUP9	YDR029W||S000002436|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data
YJL219W	0.181854	CUP9	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
YNL331C	0.180077	CUP9	YNL331C|AAD14|S000005275|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role
YKR032W	0.179845	CUP9	YKR032W||S000001740|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YMR103C	0.179833	CUP9	YMR103C||S000004709|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YJL213W	0.179214	CUP9	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
YDL060W	0.178872	CUP9	YDL060W|TSR1|S000002218|Protein required for processing of 20S pre-rRNA in the cytoplasm, associates with pre-40S ribosomal particles
YBR260C	0.178493	CUP9	YBR260C|RGD1|S000000464|GTPase-activating protein (RhoGAP) for Rho3p and Rho4p, possibly involved in control of actin cytoskeleton organization
YIL107C	0.178186	CUP9	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
YDR193W	0.178075	CUP9	YDR193W||S000002601|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGL015C	0.177876	CUP9	YGL015C||S000002983|Hypothetical protein
YLR296W	0.176863	CUP9	YLR296W||S000004287|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YHR178W	0.176563	CUP9	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
YER076C	0.17585	CUP9	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
YML123C	0.175237	CUP9	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
YFL021W	0.175144	CUP9	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
YNL142W	0.174164	CUP9	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
YDR163W	0.172733	CUP9	YDR163W|CWC15|S000002570|Non-essential protein involved in pre-mRNA splicing, component of a complex containing Cef1p; has similarity to S. pombe Cwf15p
YOR235W	0.171837	CUP9	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
YBL088C	0.171199	CUP9	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
YOL055C	0.170836	CUP9	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
YNL095C	0.169858	CUP9	YNL095C||S000005039|Putative protein of unknown function predicted to contain a transmembrane domain; YNL095C is not an essential gene
YHR022C	0.169791	CUP9	YHR022C||S000001064|Putative protein of unknown function; YHR022C is not an essential gene.
YMR269W	0.169124	CUP9	YMR269W|TMA23|S000004882|Nucleolar protein of unknown function implicated in ribosome biogenesis; TMA23 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes
YDL041W	0.168143	CUP9	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
YIL125W	0.167608	CUP9	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
YDR466W	0.16725	CUP9	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
YEL041W	0.166481	CUP9	YEL041W|YEF1|S000000767|ATP-NADH kinase; phosphorylates both NAD and NADH; homooctameric structure consisting of 60-kDa subunits; sequence similarity to Utr1p and Pos5p; overexpression complements certain pos5 phenotypes
YER096W	0.166386	CUP9	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
YNR034W-A	0.166074	CUP9	YNR034W-A||S000007525|Putative protein of unknown function; expression is regulated by Msn2p/Msn4p
YNL094W	0.165881	CUP9	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
YDL156W	0.165589	CUP9	YDL156W||S000002315|Putative protein of unknown function; protein sequence contains three WD domains (WD-40 repeat); green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus
YMR253C	0.165331	CUP9	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
YGR225W	0.164982	CUP9	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
YDL053C	0.164971	CUP9	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
YMR271C	0.164736	CUP9	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
YDR422C	0.164696	CUP9	YDR422C|SIP1|S000002830|Alternate beta-subunit of the Snf1p kinase complex, may confer substrate specificity; vacuolar protein containing KIS (Kinase-Interacting Sequence) and ASC (Association with Snf1 kinase Complex) domains involved in protein interactions
YBR056W-A	0.164226	CUP9	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
YJL032W	0.163543	CUP9	YJL032W||S000003569|Dubious open reading frame unlikely to encode a functional protein; overlaps 3' end of essential BET4 gene encoding the alpha subunit of Type II geranylgeranyltransferase
YEL010W	0.163367	CUP9	YEL010W||S000000736|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YNL150W	0.16229	CUP9	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
YLR383W	0.161276	CUP9	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
YKL032C	0.161166	CUP9	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
YOR298C-A	0.160564	CUP9	YOR298C-A|MBF1|S000007253|Transcriptional coactivator that bridges the DNA-binding region of Gcn4p and TATA-binding protein Spt15p; suppressor of frameshift mutations
YHR006W	0.160212	CUP9	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
YBR295W	0.159803	CUP9	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
YKR016W	0.159609	CUP9	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
YMR086W	0.156695	CUP9	YMR086W||S000004692|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery; cAMP represses YMR086W expression
YPL039W	0.155896	CUP9	YPL039W||S000005960|Putative protein of unknown function; YPL039W is not an essential gene
YNL278W	0.154794	CUP9	YNL278W|CAF120|S000005222|Part of the evolutionarily-conserved CCR4-NOT transcriptional regulatory complex involved in controlling mRNA initiation, elongation, and degradation
YGL146C	0.154697	CUP9	YGL146C||S000003114|Putative protein of unknown function, contains two putative transmembrane spans, shows no significant homology to any other known protein sequence, YGL146C is not an essential gene
YHR185C	0.154697	CUP9	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
YPL272C	0.154607	CUP9	YPL272C||S000006193|Putative protein of unknown function; gene expression induced in response to ketoconazole; YPL272C is not an essential gene
YBR083W	0.154482	CUP9	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
YKL134C	0.152482	CUP9	YKL134C|OCT1|S000001617|Mitochondrial intermediate peptidase, cleaves N-terminal residues of a subset of proteins upon import, after their cleavage by mitochondrial processing peptidase (Mas1p-Mas2p); may contribute to mitochondrial iron homeostasis
YPL230W	0.152273	CUP9	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
YDL022C-A	0.151167	CUP9	YDL022C-A||S000028537|Dubious open reading frame unlikely to encode a protein; partially overlaps the verified gene DIA3; identified by fungal homology and RT-PCR
YDL182W	0.15097	CUP9	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
YPL190C	0.150954	CUP9	YPL190C|NAB3|S000006111|Single stranded RNA binding protein; acidic ribonucleoprotein; required for termination of non-poly(A) transcripts and efficient splicing; interacts with Nrd1p
YLR038C	0.150847	CUP9	YLR038C|COX12|S000004028|Subunit VIb of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; required for assembly of cytochrome c oxidase but not required for activity after assembly; phosphorylated
YPR054W	0.150798	CUP9	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
YPL127C	0.149395	CUP9	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
YNL036W	0.148575	CUP9	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
YBL019W	0.148133	CUP9	YBL019W|APN2|S000000115|Class II abasic (AP) endonuclease involved in repair of DNA damage; homolog of human HAP1 and E. coli exoIII
YLR165C	0.14812	CUP9	YLR165C|PUS5|S000004155|Pseudouridine synthase, catalyzes only the formation of pseudouridine (Psi)-2819 in mitochondrial 21S rRNA; not essential for viability
YDL245C	0.147559	CUP9	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
YPR192W	0.145151	CUP9	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
YPR092W	0.144555	CUP9	YPR092W||S000006296|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YNL139C	0.143845	CUP9	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
YMR188C	0.143108	CUP9	YMR188C|MRPS17|S000004800|Mitochondrial ribosomal protein of the small subunit
YKL103C	0.142978	CUP9	YKL103C|LAP4|S000001586|Vacuolar aminopeptidase, often used as a marker protein in studies of autophagy and cytosol to vacuole targeting (CVT) pathway
YMR193W	0.142493	CUP9	YMR193W|MRPL24|S000004806|Mitochondrial ribosomal protein of the large subunit
YOR392W	0.14211	CUP9	YOR392W||S000005919|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; gene expression induced by heat
YGR009C	0.141555	CUP9	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
YBR300C	0.141462	CUP9	YBR300C||S000000504|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YBR301W; YBR300C is not an essential gene
YHL024W	0.141154	CUP9	YHL024W|RIM4|S000001016|Putative RNA-binding protein required for the expression of early and middle sporulation genes
YLL060C	0.140811	CUP9	YLL060C|GTT2|S000003983|Glutathione S-transferase capable of homodimerization; functional overlap with Gtt2p, Grx1p, and Grx2p
YCR089W	0.140344	CUP9	YCR089W|FIG2|S000000685|Cell wall adhesin, expressed specifically during mating; may be involved in maintenance of cell wall integrity during mating
YGL036W	0.140089	CUP9	YGL036W||S000003004|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YGL036W is not an essential gene
YIL083C	0.140044	CUP9	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
YIR034C	0.139509	CUP9	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
YDL246C	0.139068	CUP9	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
YPL151C	0.138987	CUP9	YPL151C|PRP46|S000006072|Splicing factor that is found in the Cef1p subcomplex of the spliceosome
YHR207C	0.138377	CUP9	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
YCR105W	0.138034	CUP9	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
YML120C	0.137581	CUP9	YML120C|NDI1|S000004589|NADH:ubiquinone oxidoreductase, transfers electrons from NADH to ubiquinone in the respiratory chain but does not pump protons, in contrast to the higher eukaryotic multisubunit respiratory complex I; phosphorylated; homolog of human AMID
YAL017W	0.137156	CUP9	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
YGL177W	0.136275	CUP9	YGL177W||S000003145|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDL013W	0.135479	CUP9	YDL013W|SLX5|S000002171|Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate
YMR111C	0.135269	CUP9	YMR111C||S000004717|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; YMR111C is not an essential gene
YJR155W	0.134955	CUP9	YJR155W|AAD10|S000003916|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role
YPL005W	0.133181	CUP9	YPL005W|AEP3|S000005926|Peripheral mitochondrial inner membrane protein, located on the matrix face of the membrane; stabilizes the bicistronic AAP1-ATP6 mRNA encoding subunits 6 and 8 of the ATP synthase complex
YJR005W	0.132878	CUP9	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
YLL062C	0.132252	CUP9	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
YIR019C	0.131999	CUP9	YIR019C|MUC1|S000001458|GPI-anchored cell surface glycoprotein (flocculin) required for pseudohyphal formation, invasive growth, flocculation, and biofilms; transcriptionally regulated by the MAPK pathway (via Ste12p and Tec1p) and the cAMP pathway (via Flo8p)
YER101C	0.131897	CUP9	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
YOR193W	0.131734	CUP9	YOR193W|PEX27|S000005719|Peripheral peroxisomal membrane protein involved in controlling peroxisome size and number, interacts with homologous protein Pex25p
YNL041C	0.131684	CUP9	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
YPR075C	0.131647	CUP9	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
YMR272C	0.13115	CUP9	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
YDR473C	0.130851	CUP9	YDR473C|PRP3|S000002881|Splicing factor, component of the U4/U6-U5 snRNP complex
YPL219W	0.130195	CUP9	YPL219W|PCL8|S000006140|Cyclin, interacts with Pho85p cyclin-dependent kinase (Cdk) to phosphorylate and regulate glycogen synthase, also activates Pho85p for Glc8p phosphorylation
YMR313C	0.129667	CUP9	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
YPL008W	0.129276	CUP9	YPL008W|CHL1|S000005929|Conserved nuclear protein required to establish sister-chromatid pairing during S-phase, probable DNA helicase with similarity to human BACH1, which associates with tumor suppressor BRCA1; associates with acetyltransferase Ctf7p
YOR066W	0.129151	CUP9	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
YGL219C	0.128814	CUP9	YGL219C|MDM34|S000003187|Mitochondrial outer membrane protein, required for normal mitochondrial morphology and inheritance; localizes to dots on the mitochondrial surface near mtDNA nucleoids; interacts genetically with MDM31 and MDM32
YLR055C	0.128391	CUP9	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
YMR170C	0.128059	CUP9	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
YKR058W	0.127942	CUP9	YKR058W|GLG1|S000001766|Self-glucosylating initiator of glycogen synthesis, also glucosylates n-dodecyl-beta-D-maltoside; similar to mammalian glycogenin
YDR358W	0.127504	CUP9	YDR358W|GGA1|S000002766|Golgi-localized protein with homology to gamma-adaptin, interacts with and regulates Arf1p and Arf2p in a GTP-dependent manner in order to facilitate traffic through the late Golgi
YOR072W	0.127428	CUP9	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
YPR076W	0.126626	CUP9	YPR076W||S000006280|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR116W	0.126478	CUP9	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
YGR109C	0.126438	CUP9	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
YEL009C	0.126057	CUP9	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
YPR154W	0.125265	CUP9	YPR154W|PIN3|S000006358|Protein that induces appearance of [PIN+] prion when overproduced
YOL132W	0.125158	CUP9	YOL132W|GAS4|S000005492|1,3-beta-glucanosyltransferase, involved with Gas2p in spore wall assembly; has similarity to Gas1p; localizes to the cell wall
YDR449C	0.124349	CUP9	YDR449C|UTP6|S000002857|Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA
YNL199C	0.12427	CUP9	YNL199C|GCR2|S000005143|Transcriptional activator of genes involved in glycolysis; interacts and functions with the DNA-binding protein Gcr1p
YER004W	0.124196	CUP9	YER004W|FMP52|S000000806|Protein of unknown function, localized to the mitochondrial outer membrane; induced by treatment with 8-methoxypsoralen and UVA irradiation
YKL101W	0.123917	CUP9	YKL101W|HSL1|S000001584|Nim1p-related protein kinase that regulates the morphogenesis and septin checkpoints; associates with the assembled septin filament; required along with Hsl7p for bud neck recruitment, phosphorylation, and degradation of Swe1p
YBR217W	0.123909	CUP9	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
YDL196W	0.123378	CUP9	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
YNL088W	0.123015	CUP9	YNL088W|TOP2|S000005032|Essential type II topoisomerase, relieves torsional strain in DNA by cleaving and re-sealing the phosphodiester backbone of both positively and negatively supercoiled DNA; cleaves complementary strands; localizes to axial cores in meiosis
YIL119C	0.122945	CUP9	YIL119C|RPI1|S000001381|Putative transcriptional regulator; overexpression suppresses the heat shock sensitivity of wild-type RAS2 overexpression and also suppresses the cell lysis defect of an mpk1 mutation
YJR137C	0.122796	CUP9	YJR137C|ECM17|S000003898|Sulfite reductase beta subunit, involved in amino acid biosynthesis, transcription repressed by methionine
YPR135W	0.122792	CUP9	YPR135W|CTF4|S000006339|Chromatin-associated protein, required for sister chromatid cohesion; interacts with DNA polymerase alpha (Pol1p) and may link DNA synthesis to sister chromatid cohesion
YOL026C	0.122759	CUP9	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
YNL218W	0.121566	CUP9	YNL218W|MGS1|S000005162|Protein with DNA-dependent ATPase and ssDNA annealing activities involved in maintenance of genome; interacts functionally with DNA polymerase delta; homolog of human Werner helicase interacting protein (WHIP)
YEL011W	0.120819	CUP9	YEL011W|GLC3|S000000737|Glycogen branching enzyme, involved in glycogen accumulation; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YBR054W	0.120325	CUP9	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
YDR103W	0.120131	CUP9	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
YNL198C	0.12012	CUP9	YNL198C||S000005142|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YER145C	0.119894	CUP9	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
YDL221W	0.119439	CUP9	YDL221W||S000002380|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the 3' end of essential gene CDC13
YER176W	0.119296	CUP9	YER176W|ECM32|S000000978|DNA dependent ATPase/DNA helicase belonging to the Dna2p- and Nam7p-like family of helicases that is involved in modulating translation termination; interacts with the translation termination factors, localized to polysomes
YDR262W	0.118733	CUP9	YDR262W||S000002670|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole and is induced in response to the DNA-damaging agent MMS; gene expression increases in response to Zymoliase treatment
YOL045W	0.117954	CUP9	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)
YNL285W	0.117746	CUP9	YNL285W||S000005229|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YKL067W	0.117317	CUP9	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
YGL184C	0.116105	CUP9	YGL184C|STR3|S000003152|Cystathionine beta-lyase, converts cystathionine into homocysteine
YLL029W	0.116073	CUP9	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
YOR073W	0.116058	CUP9	YOR073W|SGO1|S000005599|Component of the spindle checkpoint, involved in sensing lack of tension on mitotic chromosomes; protects centromeric Rec8p at meiosis I; required for accurate chromosomal segregation at meiosis II and for mitotic chromosome stability
YDL021W	0.115916	CUP9	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
YDR323C	0.11513	CUP9	YDR323C|PEP7|S000002731|Multivalent adaptor protein that facilitates vesicle-mediated vacuolar protein sorting by ensuring high-fidelity vesicle docking and fusion, which are essential for targeting of vesicles to the endosome; required for vacuole inheritance
YCR032W	0.115125	CUP9	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
YOR344C	0.114084	CUP9	YOR344C|TYE7|S000005871|Serine-rich protein that contains a basic-helix-loop-helix (bHLH) DNA binding motif; binds E-boxes of glycolytic genes and contributes to their activation; may function as a transcriptional activator in Ty1-mediated gene expression
YPR014C	0.114007	CUP9	YPR014C||S000006218|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YPR014C is not an essential gene
YCL025C	0.113978	CUP9	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)
YLR115W	0.113221	CUP9	YLR115W|CFT2|S000004105|Subunit of the mRNA cleavage and polyadenlylation factor (CPF); required for pre-mRNA cleavage, polyadenylation and poly(A) site recognition, 43% similarity with the mammalian CPSF-100 protein.
YER016W	0.111758	CUP9	YER016W|BIM1|S000000818|Microtubule-binding protein that together with Kar9p makes up the cortical microtubule capture site and delays the exit from mitosis when the spindle is oriented abnormally
YKR049C	0.111634	CUP9	YKR049C|FMP46|S000001757|Putative redox protein containing a thioredoxin fold; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR389W	0.111405	CUP9	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
YFR045W	0.110344	CUP9	YFR045W||S000001941|Putative mitochondrial transport protein; null mutant is viable, exhibits decreased levels of chitin and normal resistance to calcofluor white
YLL055W	0.110276	CUP9	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
YBR109W-A	0.109816	CUP9	YBR109W-A||S000028737|Putative protein of unknown function; questionable ORF from MIPS
YLR095C	0.10959	CUP9	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
YOR177C	0.10947	CUP9	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
YBR291C	0.109049	CUP9	YBR291C|CTP1|S000000495|Mitochondrial inner membrane citrate transporter, member of the mitochondrial carrier family
YNL298W	0.108878	CUP9	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
YGR230W	0.108441	CUP9	YGR230W|BNS1|S000003462|Protein with some similarity to Spo12p; overexpression bypasses need for Spo12p, but not required for meiosis
YDR278C	0.108196	CUP9	YDR278C||S000002686|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR377C	0.107864	CUP9	YLR377C|FBP1|S000004369|Fructose-1,6-bisphosphatase, key regulatory enzyme in the gluconeogenesis pathway, required for glucose metabolism
YLR299W	0.106862	CUP9	YLR299W|ECM38|S000004290|Gamma-glutamyltranspeptidase, major glutathione-degrading enzyme; involved in detoxification of electrophilic xenobiotics; expression induced mainly by nitrogen starvation
YJR055W	0.106089	CUP9	YJR055W|HIT1|S000003816|Protein of unknown function, required for growth at high temperature
YKR031C	0.105816	CUP9	YKR031C|SPO14|S000001739|Phospholipase D, catalyzes the hydrolysis of phosphatidylcholine, producing choline and phosphatidic acid; involved in Sec14p-independent secretion; required for meiosis and spore formation; differently regulated in secretion and meiosis
YEL061C	0.105495	CUP9	YEL061C|CIN8|S000000787|Kinesin motor protein involved in mitotic spindle assembly and chromosome segregation
YPL153C	0.105468	CUP9	YPL153C|RAD53|S000006074|Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication
YPL222W	0.105041	CUP9	YPL222W|FMP40|S000006143|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YGR224W	0.10449	CUP9	YGR224W|AZR1|S000003456|Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs such as ketoconazole and fluconazole
YDR397C	0.104483	CUP9	YDR397C|NCB2|S000002805|Subunit of a heterodimeric NC2 transcription regulator complex with Bur6p; complex binds to TBP and can repress transcription by preventing preinitiation complex assembly or stimulate activated transcription; homologous to human NC2beta
YIL166C	0.10448	CUP9	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
YLR010C	0.104472	CUP9	YLR010C|TEN1|S000004000|Protein that regulates telomeric length; protects telomeric ends in a complex with Cdc13p and Stn1p
YNL086W	0.104189	CUP9	YNL086W||S000005030|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to endosomes
YKL155C	0.103912	CUP9	YKL155C|RSM22|S000001638|Mitochondrial ribosomal protein of the small subunit
YDR125C	0.103855	CUP9	YDR125C|ECM18|S000002532|Protein of unknown function, similar to Rlp24p
YCR001W	0.10359	CUP9	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
YDL197C	0.103306	CUP9	YDL197C|ASF2|S000002356|Anti-silencing protein that causes derepression of silent loci when overexpressed
YOR386W	0.10292	CUP9	YOR386W|PHR1|S000005913|DNA photolyase involved in photoreactivation, repairs pyrimidine dimers in the presence of visible light; induced by DNA damage; regulated by transcriptional repressor Rph1p
YEL072W	0.102917	CUP9	YEL072W|RMD6|S000000798|Protein required for sporulation
YOR390W	0.102597	CUP9	YOR390W||S000005917|Putative protein of unknown function
YNL054W	0.102369	CUP9	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
YLR284C	0.10138	CUP9	YLR284C|ECI1|S000004274|Peroxisomal delta3,delta2-enoyl-CoA isomerase, hexameric protein that converts 3-hexenoyl-CoA to trans-2-hexenoyl-CoA, essential for the beta-oxidation of unsaturated fatty acids, oleate-induced
YPL213W	0.101108	CUP9	YPL213W|LEA1|S000006134|Component of U2 snRNP; disruption causes reduced U2 snRNP levels; physically interacts with Msl1p; invovled in telomere maintenance; putative homolog of human U2A' snRNP protein
YGR213C	0.100334	CUP9	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
YEL059W	0.0994343	CUP9	YEL059W||S000000785|Dubious open reading frame unlikely to encode a functional protein
YLR342W	0.0984288	CUP9	YLR342W|FKS1|S000004334|Catalytic subunit of 1,3-beta-D-glucan synthase, functionally redundant with alternate catalytic subunit Gsc2p; binds to regulatory subunit Rho1p; involved in cell wall synthesis and maintenance; localizes to sites of cell wall remodeling
YGL049C	0.0982702	CUP9	YGL049C|TIF4632|S000003017|Translation initiation factor eIF4G, subunit of the mRNA cap-binding protein complex (eIF4F) that also contains eIF4E (Cdc33p); associates with the poly(A)-binding protein Pab1p, also interacts with eIF4A (Tif1p); homologous to Tif4631p
YOL047C	0.0982426	CUP9	YOL047C||S000005407|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YEL057C	0.0981752	CUP9	YEL057C||S000000783|Protein of unknown function involved in telomere maintenance; target of UME6 regulation
YDR009W	0.0979414	CUP9	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
YFR054C	0.0976536	CUP9	YFR054C||S000001950|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YKR089C	0.0971567	CUP9	YKR089C|TGL4|S000001797|Triacylglycerol lipase involved in triacylglycerol mobilization and degradation; found in lipid particles; potential Cdc28p substrate
YJL220W	0.096719	CUP9	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
YAL032C	0.0962948	CUP9	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
YIL112W	0.0962075	CUP9	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
YPL083C	0.0957075	CUP9	YPL083C|SEN54|S000006004|Subunit of the tRNA splicing endonuclease, which is composed of Sen2p, Sen15p, Sen34p, and Sen54p
YHR194W	0.095254	CUP9	YHR194W|MDM31|S000001237|Mitochondrial inner membrane protein with similarity to Mdm32p, required for normal mitochondrial morphology and inheritance; interacts genetically with MMM1, MDM10, MDM12, and MDM34
YJR160C	0.0947799	CUP9	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
YLR318W	0.0937331	CUP9	YLR318W|EST2|S000004310|Reverse transcriptase subunit of the telomerase holoenzyme, essential for telomerase core catalytic activity, involved in other aspects of telomerase assembly and function; mutations in human homolog are associated with aplastic anemia
YPL240C	0.0936655	CUP9	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
YJL070C	0.0934863	CUP9	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
YIL139C	0.0932535	CUP9	YIL139C|REV7|S000001401|Processivity subunit of DNA polymerase zeta, which is involved in DNA repair and translesion synthesis; required for mutagenesis induced by DNA damage
YOR337W	0.0928145	CUP9	YOR337W|TEA1|S000005864|Ty1 enhancer activator required for full levels of Ty enhancer-mediated transcription; C6 zinc cluster DNA-binding protein
YGL217C	0.092525	CUP9	YGL217C||S000003185|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF KIP3/YGL216W
YER064C	0.0923926	CUP9	YER064C||S000000866|Non-essential nuclear protein; null mutation has global effects on transcription
YIL022W	0.0923638	CUP9	YIL022W|TIM44|S000001284|Peripheral mitochondrial membrane protein involved in mitochondrial protein import, tethers essential chaperone Ssc1p to the translocon channel at the matrix side of the inner membrane
YDL024C	0.0921146	CUP9	YDL024C|DIA3|S000002182|Protein of unknown function, involved in invasive and pseudohyphal growth
YLR114C	0.0916772	CUP9	YLR114C|AVL9|S000004104|Conserved protein involved in exocytic transport from the Golgi; mutation is synthetically lethal with apl2 vps1 double mutation; member of a protein superfamily with orthologs in diverse organisms
YPL082C	0.0916353	CUP9	YPL082C|MOT1|S000006003|Essential abundant protein involved in regulation of transcription, removes Spt15p (TBP) from DNA via its C-terminal ATPase activity, forms a complex with TBP that binds TATA DNA with high affinity but with altered specificity
YGR260W	0.0913921	CUP9	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)
YPR018W	0.091352	CUP9	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
YAL051W	0.0909551	CUP9	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
YBR071W	0.090881	CUP9	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
YDL186W	0.0899484	CUP9	YDL186W||S000002345|Putative protein of unknown function; YDL186W is not an essential gene
YER075C	0.0898987	CUP9	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
YJL036W	0.0898445	CUP9	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
YML081C-A	0.0890742	CUP9	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
YPR195C	0.0890668	CUP9	YPR195C||S000006399|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YKL147C	0.0888728	CUP9	YKL147C||S000001630|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; partially overlaps the verified gene AVT3
YFL053W	0.0884562	CUP9	YFL053W|DAK2|S000001841|Dihydroxyacetone kinase, required for detoxification of dihydroxyacetone (DHA); involved in stress adaptation
YNL272C	0.0883367	CUP9	YNL272C|SEC2|S000005216|Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport
YDR055W	0.0881351	CUP9	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
YDR436W	0.0880388	CUP9	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
YJR005C-A	0.0880286	CUP9	YJR005C-A||S000028523|Putative protein of unknown function, originally identified as a syntenic homolog of an Ashbya gossypii gene
YKR002W	0.0871554	CUP9	YKR002W|PAP1|S000001710|Poly(A) polymerase, one of three factors required for mRNA 3'-end polyadenylation, forms multiprotein complex with polyadenylation factor I (PF I), also required for mRNA nuclear export; may also polyadenylate rRNAs
YJL221C	0.0871031	CUP9	YJL221C|FSP2|S000003757|Protein of unknown function, expression is induced during nitrogen limitation
YOR318C	0.085822	CUP9	YOR318C||S000005845|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; transcript is predicted to be spliced but there is no evidence that it is spliced in vivo
YGL216W	0.0857765	CUP9	YGL216W|KIP3|S000003184|Kinesin-related motor protein involved in mitotic spindle positioning
YLR382C	0.0850925	CUP9	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
YGL188C	0.0847736	CUP9	YGL188C||S000003156|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YHL046C	0.0845086	CUP9	YHL046C|PAU13|S000001038|Putative protein of unknown function; not an essential gene
YER166W	0.0844849	CUP9	YER166W|DNF1|S000000968|Aminophospholipid translocase (flippase) that localizes primarily to the plasma membrane; contributes to endocytosis, protein transport and cell polarity; type 4 P-type ATPase
YFR053C	0.0834061	CUP9	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
YBR226C	0.0828366	CUP9	YBR226C||S000000430|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YBR225W
YOR261C	0.0827351	CUP9	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
YML076C	0.0825722	CUP9	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
YOR203W	0.082536	CUP9	YOR203W||S000005729|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps 5' end of essential DED1 gene required for translation initiation
YKL146W	0.0821996	CUP9	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
YDL071C	0.082034	CUP9	YDL071C||S000002229|Hypothetical protein
YGL203C	0.0816704	CUP9	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
YKL071W	0.0814196	CUP9	YKL071W||S000001554|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YNL228W	0.0812975	CUP9	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
YPL113C	0.0810704	CUP9	YPL113C||S000006034|Glyoxylate reductase; acts on glyoxylate and hydroxypyruvate substrates; YPL113C is not an essential gene
YDR114C	0.0810691	CUP9	YDR114C||S000002521|Putative protein of unknown function; deletion mutant exhibits poor growth at elevated pH and calcium
YDL020C	0.0809467	CUP9	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
YHR054C	0.0805647	CUP9	YHR054C||S000001096|Putative protein of unknown function
YJL038C	0.0804029	CUP9	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
YBR027C	0.0794864	CUP9	YBR027C||S000000231|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YCR021C	0.0794796	CUP9	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
YCR027C	0.0792595	CUP9	YCR027C|RHB1|S000000622|Putative Rheb-related GTPase involved in regulating canavanine resistance and arginine uptake; member of the Ras superfamily of G-proteins
YJL164C	0.0790584	CUP9	YJL164C|TPK1|S000003700|cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p
YPR145W	0.0790248	CUP9	YPR145W|ASN1|S000006349|Asparagine synthetase, isozyme of Asn2p; catalyzes the synthesis of L-asparagine from L-aspartate in the asparagine biosynthetic pathway
YLR248W	0.0780229	CUP9	YLR248W|RCK2|S000004238|Protein kinase involved in the response to oxidative and osmotic stress; identified as suppressor of S. pombe cell cycle checkpoint mutations
YDR441C	0.0776562	CUP9	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
YGL033W	0.0776155	CUP9	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
YGR235C	0.0763665	CUP9	YGR235C||S000003467|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YHR202W	0.0763289	CUP9	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
YFR027W	0.0763019	CUP9	YFR027W|ECO1|S000001923|Acetyltransferase required for the establishment of sister chromatid cohesion during DNA replication and in response to double-strand breaks; also required for postreplicative double-strand break repair
YER041W	0.0760745	CUP9	YER041W|YEN1|S000000843|Protein of unknown function, has similarity to endonuclease Rth1p; potentially phosphorylated by Cdc28p
YDR164C	0.0756966	CUP9	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
YOR071C	0.0756145	CUP9	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
YHL036W	0.0753264	CUP9	YHL036W|MUP3|S000001028|Low affinity methionine permease, similar to Mup1p
YPL192C	0.074782	CUP9	YPL192C|PRM3|S000006113|Pheromone-regulated protein required for karyogamy; localizes to the inner membrane of the nuclear envelope
YDR036C	0.074463	CUP9	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
YOL095C	0.0741247	CUP9	YOL095C|HMI1|S000005455|Mitochondrial inner membrane localized ATP-dependent DNA helicase, required for the maintenance of the mitochondrial genome; not required for mitochondrial transcription; has homology to E. coli helicase uvrD
YLR146W-A	0.0734177	CUP9	YLR146W-A||S000113566|Putative protein of unknown function
YMR310C	0.0732132	CUP9	YMR310C||S000004927|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; YMR310C is not an essential gene
YML098W	0.0729565	CUP9	YML098W|TAF13|S000004564|TFIID subunit (19 kDa), involved in RNA polymerase II transcription initiation, similar to histone H4 with atypical histone fold motif of Spt3-like transcription factors
YIL054W	0.0727192	CUP9	YIL054W||S000001316|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YOR378W	0.0724026	CUP9	YOR378W||S000005905|Putative protein of unknown function; belongs to the DHA2 family of drug:H+ antiporters; YOR378W is not an essential gene
YHL043W	0.0723633	CUP9	YHL043W|ECM34|S000001035|Putative protein of unknown function, member of the DUP380 subfamily of conserved, often subtelomerically-encoded proteins
YML121W	0.0722664	CUP9	YML121W|GTR1|S000004590|Cytoplasmic GTP binding protein and negative regulator of the Ran/Tc4 GTPase cycle; component of GSE complex, which is required for sorting of Gap1p; involved in phosphate transport and telomeric silencing; similar to human RagA and RagB
YNL037C	0.0721881	CUP9	YNL037C|IDH1|S000004982|Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase, which catalyzes the oxidation of isocitrate to alpha-ketoglutarate in the TCA cycle
YFL041W-A	0.0717758	CUP9	YFL041W-A||S000028547|Putative protein of unknown function; identified by fungal homology and RT-PCR
YER045C	0.0717086	CUP9	YER045C|ACA1|S000000847|Basic leucine zipper (bZIP) transcription factor of the ATF/CREB family, may regulate transcription of genes involved in utilization of non-optimal carbon sources
YNL188W	0.0710533	CUP9	YNL188W|KAR1|S000005132|Essential protein involved in karyogamy during mating and in spindle pole body duplication during mitosis, localizes to the half-bridge of the spindle pole body, interacts with Spc72p during karyogamy, also interacts with Cdc31p
YDR301W	0.0703012	CUP9	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
YDR532C	0.070121	CUP9	YDR532C||S000002940|Protein of unknown function that localizes to the nuclear side of the spindle pole body and along short spindles; deletion mutants have short telomeres; forms a complex with Spc105p
YLR295C	0.0700201	CUP9	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
YER060W-A	0.0697626	CUP9	YER060W-A|FCY22|S000002958|Putative purine-cytosine permease, very similar to Fcy2p but cannot substitute for its function
YGR134W	0.0697342	CUP9	YGR134W|CAF130|S000003366|Part of the evolutionarily-conserved CCR4-NOT transcriptional regulatory complex involved in controlling mRNA initiation, elongation, and degradation
YJR107W	0.0696441	CUP9	YJR107W||S000003868|Putative protein of unknown function; has sequence or structural similarity to lipases
YOL138C	0.069585	CUP9	YOL138C|RTC1|S000005498|Putative protein of unknown function; may interact with ribosomes, based on co-purification experiments; null mutation suppresses cdc13-1 temperature sensitivity
YDR342C	0.0689434	CUP9	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
YJL147C	0.0673888	CUP9	YJL147C||S000003683|Mitochondrial protein of unknown function; homozygous diploid deletion strain has a sporulation defect characterized by elevated dityrosine in the soluble fraction; expression induced by calcium shortage; YJL147W is a non-essential gene
YCL067C	0.067278	CUP9	YCL067C|HMLALPHA2|S000000572|Silenced copy of ALPHA2 at HML; homeobox-domain protein that associates with Mcm1p in haploid cells to repress a-specific gene expression and interacts with a1p in diploid cells to repress haploid-specific gene expression
YDR520C	0.0672096	CUP9	YDR520C|URC2|S000002928|Putative transcription factor; contains the (Zn(II)2Cys6 motif; GFP-fusion protein localizes to the cytoplasm and nucleus; null mutant is viable and sensitive to caffeine; similar to the S. Kluyveri URC2 uracil catabolism gene
YOR381W	0.0668944	CUP9	YOR381W|FRE3|S000005908|Ferric reductase, reduces siderophore-bound iron prior to uptake by transporters; expression induced by low iron levels
YNL105W	0.0665956	CUP9	YNL105W||S000005049|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene INP52
YBR105C	0.0665471	CUP9	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
YBL084C	0.0662442	CUP9	YBL084C|CDC27|S000000180|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
YOL164W-A	0.0657659	CUP9	YOL164W-A||S000028580|Putative protein of unknown function; identified by fungal homology and RT-PCR
YNL240C	0.0652303	CUP9	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
YER165C-A	0.0652224	CUP9	YER165C-A||S000028762|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps the verified gene DNF1/YER166W
YLL059C	0.0652184	CUP9	YLL059C||S000003982|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YNL337W	0.0651196	CUP9	YNL337W||S000005281|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YKL197C	0.0648757	CUP9	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
YLR001C	0.064618	CUP9	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
YNR059W	0.0642348	CUP9	YNR059W|MNT4|S000005342|Putative alpha-1,3-mannosyltransferase, not required for protein O-glycosylation
YJR153W	0.0642156	CUP9	YJR153W|PGU1|S000003914|Endo-polygalacturonase, pectolytic enzyme that hydrolyzes the alpha-1,4-glycosidic bonds in the rhamnogalacturonan chains in pectins
YHL041W	0.0637899	CUP9	YHL041W||S000001033|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data
YJL146W	0.0637012	CUP9	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
YLL030C	0.0635758	CUP9	YLL030C||S000003953|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YLR368W	0.0635344	CUP9	YLR368W|MDM30|S000004360|F-box protein; physically associates with mitochondria and is required for normal mitochondrial fusion in rich medium, during sporulation, and in mating cells; promotes ubiquitin-mediated degradation of Gal4p in some strains
YGR129W	0.0633091	CUP9	YGR129W|SYF2|S000003361|Component of the spliceosome complex involved in pre-mRNA splicing; involved in regulation of cell cycle progression
YJR148W	0.0630289	CUP9	YJR148W|BAT2|S000003909|Cytosolic branched-chain amino acid aminotransferase, homolog of murine ECA39; highly expressed during stationary phase and repressed during logarithmic phase
YOR032W-A	0.0622435	CUP9	YOR032W-A||S000028710|Identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YNR060W	0.0621513	CUP9	YNR060W|FRE4|S000005343|Ferric reductase, reduces a specific subset of siderophore-bound iron prior to uptake by transporters; expression induced by low iron levels
YNL025C	0.0620961	CUP9	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
YNL322C	0.0620062	CUP9	YNL322C|KRE1|S000005266|Cell wall glycoprotein involved in beta-glucan assembly; serves as a K1 killer toxin membrane receptor
YBL104C	0.0617569	CUP9	YBL104C||S000000200|Putative protein of unknown function, promoter contains multiple GCN4 binding sites
YPL214C	0.0616637	CUP9	YPL214C|THI6|S000006135|Bifunctional enzyme with thiamine-phosphate pyrophosphorylase and 4-methyl-5-beta-hydroxyethylthiazole kinase activities, required for thiamine biosynthesis; GFP-fusion protein localizes to the cytoplasm in a punctate pattern
YOR300W	0.0616064	CUP9	YOR300W||S000005826|Dubious open reading frame, unlikely to encode a protein; overlaps with verified gene BUD7/YOR299W; mutation affects bipolar budding and bud site selection, though phenotype could be due to the mutation's effects on BUD7
YLR401C	0.0614913	CUP9	YLR401C|DUS3|S000004393|Dihydrouridine synthase, member of a widespread family of conserved proteins including Smm1p, Dus1p, and Dus4p; contains a consensus oleate response element (ORE) in its promoter region
YLR035C	0.0612151	CUP9	YLR035C|MLH2|S000004025|Protein involved in the mismatch repair of certain frameshift intermediates and involved in meiotic recombination; forms a complex with Mlh1p
YPL268W	0.0609528	CUP9	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
YCL022C	0.0608805	CUP9	YCL022C||S000000527|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps verified gene KCC4/YCL024W
YML062C	0.0608001	CUP9	YML062C|MFT1|S000004527|Subunit of the THO complex, which is a nuclear complex comprised of Hpr1p, Mft1p, Rlr1p, and Thp2p, that is involved in transcription elongation and mitotic recombination; involved in telomere maintenance
YPL279C	0.0606753	CUP9	YPL279C||S000006200|Putative protein of unknown function
YHR193C-A	0.0604296	CUP9	YHR193C-A||S000028785|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps verified ORF MDM31
YBL060W	0.0602228	CUP9	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
YCR039C	0.0601895	CUP9	YCR039C|MATALPHA2|S000000635|Homeobox-domain protein that, with Mcm1p, represses a-specific genes in haploids; acts with A1p to repress transcription of haploid-specific genes in diploids; one of two genes encoded by the MATalpha mating type cassette
YIL146C	0.060025	CUP9	YIL146C|ECM37|S000001408|Non-essential protein of unknown function
YOR128C	0.0599771	CUP9	YOR128C|ADE2|S000005654|Phosphoribosylaminoimidazole carboxylase, catalyzes a step in the 'de novo' purine nucleotide biosynthetic pathway; red pigment accumulates in mutant cells deprived of adenine
YPR145C-A	0.0599675	CUP9	YPR145C-A||S000113589|Putative protein of unknown function
YBR298C	0.0597969	CUP9	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
YER056C	0.0595582	CUP9	YER056C|FCY2|S000000858|Purine-cytosine permease, mediates purine (adenine, guanine, and hypoxanthine) and cytosine accumulation
YIR038C	0.0587651	CUP9	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
YML003W	0.0582897	CUP9	YML003W||S000004462|Putative protein of unknown function
YDR069C	0.0578779	CUP9	YDR069C|DOA4|S000002476|Ubiquitin isopeptidase, required for recycling ubiquitin from proteasome-bound ubiquitinated intermediates, acts at the late endosome/prevacuolar compartment to recover ubiquitin from ubiquitinated membrane proteins en route to the vacuole
YMR163C	0.0574855	CUP9	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
YAL039C	0.0573161	CUP9	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)
YLR024C	0.057298	CUP9	YLR024C|UBR2|S000004014|Cytoplasmic ubiquitin-protein ligase (E3)
YBR208C	0.0572128	CUP9	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
YDR423C	0.0570764	CUP9	YDR423C|CAD1|S000002831|AP-1-like bZIP transcriptional activator involved in stress responses, iron metabolism, and pleiotropic drug resistance; controls a set of genes involved in stabilizing proteins; binds consensus sequence TTACTAA; 5' UTR contains uORFs
YGR237C	0.0569725	CUP9	YGR237C||S000003469|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YDR283C	0.0569629	CUP9	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
YOR236W	0.056783	CUP9	YOR236W|DFR1|S000005762|Dihydrofolate reductase, part of the dTTP biosynthetic pathway, involved in folate metabolism, possibly required for mitochondrial function
YOR015W	0.0558402	CUP9	YOR015W||S000005541|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YOR355W	0.0555367	CUP9	YOR355W|GDS1|S000005882|Protein of unknown function, required for growth on glycerol as a carbon source; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YIL113W	0.0551868	CUP9	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
YFL042C	0.0550396	CUP9	YFL042C||S000001852|Putative protein of unknown function; YFL042C is not an essential gene
YOL158C	0.0546973	CUP9	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
YMR268C	0.0545707	CUP9	YMR268C|PRP24|S000004881|Splicing factor that reanneals U4 and U6 snRNPs during spliceosome recycling
YDR024W	0.0543065	CUP9	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
YLR270W	0.0542586	CUP9	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
YGR121C	0.0541544	CUP9	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
YCR066W	0.0537738	CUP9	YCR066W|RAD18|S000000662|Protein involved in postreplication repair; binds single-stranded DNA and has single-stranded DNA dependent ATPase activity; forms heterodimer with Rad6p; contains RING-finger motif
YOL091W	0.0537255	CUP9	YOL091W|SPO21|S000005451|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
YHL037C	0.0534082	CUP9	YHL037C||S000001029|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YER186C	0.0527821	CUP9	YER186C||S000000988|Putative protein of unknown function
YBR209W	0.0521642	CUP9	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
YKR076W	0.0520691	CUP9	YKR076W|ECM4|S000001784|Omega class glutathione transferase; not essential; similar to Ygr154cp; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YDR097C	0.0518468	CUP9	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
YHR071W	0.0518212	CUP9	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
YIL002C	0.051488	CUP9	YIL002C|INP51|S000001264|Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, synaptojanin-like protein with an N-terminal Sac1 domain, plays a role in phosphatidylinositol 4,5-bisphosphate homeostasis and in endocytosis; null mutation confers cold-tolerant growth
YPR027C	0.0514826	CUP9	YPR027C||S000006231|Putative protein of unknown function
YMR254C	0.0514444	CUP9	YMR254C||S000004867|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YMR023C	0.0512979	CUP9	YMR023C|MSS1|S000004625|Mitochondrial protein, forms a heterodimer complex with Mto1p that performs the 5-carboxymethylaminomethyl modification of the wobble uridine base in mitochondrial tRNAs; similar to human GTPBP3
YIR027C	0.0506978	CUP9	YIR027C|DAL1|S000001466|Allantoinase, converts allantoin to allantoate in the first step of allantoin degradation; expression sensitive to nitrogen catabolite repression
YLR070C	0.0505422	CUP9	YLR070C|XYL2|S000004060|Xylitol dehydrogenase, converts xylitol to D-xylulose in the endogenous xylose utilization pathway
YKL059C	0.0504882	CUP9	YKL059C|MPE1|S000001542|Essential conserved subunit of CPF (cleavage and polyadenylation factor), plays a role in 3' end formation of mRNA via the specific cleavage and polyadenylation of pre-mRNA, contains a putative RNA-binding zinc knuckle motif
YCR097W-A	0.050442	CUP9	YCR097W-A||S000007632|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; identified by homology to a hemiascomycetous yeast protein
YFR057W	0.0499535	CUP9	YFR057W||S000001953|Putative protein of unknown function
YPR172W	0.0498611	CUP9	YPR172W||S000006376|Protein of unknown function, transcriptionally activated by Yrm1p along with genes involved in multidrug resistance
YHR165W-A	0.0495917	CUP9	YHR165W-A||S000028783|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YNL187W	0.048972	CUP9	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
YKR071C	0.0487553	CUP9	YKR071C|DRE2|S000001779|Protein of unknown function required for sister chromatid cohesion; mutation displays synthetic lethal interaction with the pol3-13 allele of CDC2
YPL255W	0.0486364	CUP9	YPL255W|BBP1|S000006176|Protein required for the spindle pole body (SPB) duplication, localized at the central plaque periphery; forms a complex with a nuclear envelope protein Mps2p and SPB components Spc29p and Kar1p; required for mitotic functions of Cdc5p
YER181C	0.0484527	CUP9	YER181C||S000000983|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative data; extensively overlaps a Ty1 LTR; protein product is detected in highly purified mitochondria in high-throughput studies
YDL224C	0.0475564	CUP9	YDL224C|WHI4|S000002383|Putative RNA binding protein and partially redundant Whi3p homolog that regulates the cell size requirement for passage through Start and commitment to cell division
YOR223W	0.047326	CUP9	YOR223W||S000005749|Putative protein of unknown function
YDL044C	0.0469204	CUP9	YDL044C|MTF2|S000002202|Mitochondrial matrix protein that interacts with an N-terminal region of mitochondrial RNA polymerase (Rpo41p) and couples RNA processing and translation to transcription
YPL120W	0.0469013	CUP9	YPL120W|VPS30|S000006041|Subunit of phosphatidylinositol (PtdIns) 3-kinase complexes I and II; Complex I is essential in autophagy and Complex II is required for vacuolar protein sorting; ortholog of the higher eukaryotic gene Beclin 1
YCL017C	0.0469009	CUP9	YCL017C|NFS1|S000000522|Cysteine desulfurase involved in iron-sulfur cluster (Fe/S) biogenesis; required for the post-transcriptional thio-modification of mitochondrial and cytoplasmic tRNAs; essential protein located predominantly in mitochondria
YOL152W	0.0467238	CUP9	YOL152W|FRE7|S000005512|Putative ferric reductase with similarity to Fre2p; expression induced by low copper levels
YOR245C	0.0466038	CUP9	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
YKL020C	0.0463446	CUP9	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
YLR037C	0.0457848	CUP9	YLR037C|DAN2|S000004027|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YOR285W	0.045723	CUP9	YOR285W||S000005811|Protein of unknown function, localized to the mitochondrial outer membrane
YBR101C	0.045257	CUP9	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
YML055W	0.0449054	CUP9	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
YER127W	0.0443377	CUP9	YER127W|LCP5|S000000929|Essential protein involved in maturation of 18S rRNA; depletion leads to inhibited pre-rRNA processing and reduced polysome levels; localizes primarily to the nucleolus
YEL071W	0.0442715	CUP9	YEL071W|DLD3|S000000797|D-lactate dehydrogenase, part of the retrograde regulon which consists of genes whose expression is stimulated by damage to mitochondria and reduced in cells grown with glutamate as the sole nitrogen source, located in the cytoplasm
YPR144C	0.0441224	CUP9	YPR144C|NOC4|S000006348|Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits
YDL025C	0.0438923	CUP9	YDL025C||S000002183|Putative protein kinase, potentially phosphorylated by Cdc28p; YDL025C is not an essential gene
YBR123C	0.0432655	CUP9	YBR123C|TFC1|S000000327|One of six subunits of the RNA polymerase III transcription initiation factor complex (TFIIIC); part of the TauA globular domain of TFIIIC that binds DNA at the BoxA promoter sites of tRNA and similar genes; human homolog is TFIIIC-63
YML107C	0.0431883	CUP9	YML107C|PML39|S000004575|Protein required for nuclear retention of unspliced pre-mRNAs along with Mlp1p and Pml1p; anchored to nuclear pore complex via Mlp1p and Mlp2p; found with the subset of nuclear pores farthest from the nucleolus; may interact with ribosomes
YDL243C	0.0431288	CUP9	YDL243C|AAD4|S000002402|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase, involved in the oxidative stress response
YIR011C	0.0429847	CUP9	YIR011C|STS1|S000001450|Protein that interacts with the karyopherin Srp1p; may have a role with Srp1p in ubiquitin-mediated protein degradation
YOR093C	0.0429508	CUP9	YOR093C||S000005619|Putative protein of unknown function; deletion causes sensitivity to unfolded protein response-inducing agents
YOR017W	0.0426699	CUP9	YOR017W|PET127|S000005543|Protein with a role in 5'-end processing of mitochondrial RNAs, located in the mitochondrial membrane
YEL008W	0.0423721	CUP9	YEL008W||S000000734|Hypothetical protein predicted to be involved in metabolism
YBL080C	0.0421959	CUP9	YBL080C|PET112|S000000176|Protein required for mitochondrial translation; mutation is functionally complemented by a Bacillus subtilis ortholog
YER157W	0.042146	CUP9	YER157W|COG3|S000000959|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
YJL223C	0.0421244	CUP9	YJL223C|PAU1|S000003759|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
YPL121C	0.0417704	CUP9	YPL121C|MEI5|S000006042|Meiosis specific protein involved in DMC1-dependent meiotic recombination, forms heterodimer with Sae3p; proposed to be an assembly factor for Dmc1p
YNL324W	0.041446	CUP9	YNL324W||S000005268|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YCL066W	0.041385	CUP9	YCL066W|HMLALPHA1|S000000571|Silenced copy of ALPHA1 at HML, encoding a transcriptional coactivator involved in the regulation of mating-type alpha-specific gene expression
YBR068C	0.0411108	CUP9	YBR068C|BAP2|S000000272|High-affinity leucine permease, functions as a branched-chain amino acid permease involved in the uptake of leucine, isoleucine and valine; contains 12 predicted transmembrane domains
YBL052C	0.0408941	CUP9	YBL052C|SAS3|S000000148|Histone acetyltransferase catalytic subunit of NuA3 complex that acetylates histone H3, involved in transcriptional silencing; homolog of the mammalian MOZ proto-oncogene; sas3 gcn5 double mutation confers lethality
YIL060W	0.0408002	CUP9	YIL060W||S000001322|Putative protein of unknown function; mutant accumulates less glycogen than does wild type; YIL060W is not an essential gene
YNL196C	0.0403695	CUP9	YNL196C|SLZ1|S000005140|Sporulation-specific protein with a leucine zipper motif
YNL126W	0.0402843	CUP9	YNL126W|SPC98|S000005070|Component of the microtubule-nucleating Tub4p (gamma-tubulin) complex; interacts with Spc110p at the spindle pole body (SPB) inner plaque and with Spc72p at the SPB outer plaque
YDL215C	0.0401298	CUP9	YDL215C|GDH2|S000002374|NAD(+)-dependent glutamate dehydrogenase, degrades glutamate to ammonia and alpha-ketoglutarate; expression sensitive to nitrogen catabolite repression and intracellular ammonia levels
YOR358W	0.0400252	CUP9	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
YMR064W	0.0399402	CUP9	YMR064W|AEP1|S000004668|Protein required for expression of the mitochondrial OLI1 gene encoding subunit 9 of F1-F0 ATP synthase
YDR521W	0.0399003	CUP9	YDR521W||S000002929|Dubious ORF that overlaps YDR520C; mutant increases expression of PIS1 and RPL3 in glycerol
YPR120C	0.0398949	CUP9	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
YOR109W	0.0396411	CUP9	YOR109W|INP53|S000005635|Polyphosphatidylinositol phosphatase, dephosphorylates multiple phosphatidylinositols; involved in trans Golgi network-to-early endosome pathway; hyperosmotic stress causes translocation to actin patches; contains Sac1 and 5-ptase domains
YPL270W	0.0393836	CUP9	YPL270W|MDL2|S000006191|Mitochondrial inner membrane half-type ATP-binding cassette (ABC) transporter
YKL224C	0.0393266	CUP9	YKL224C|PAU16|S000001707|Putative protein of unknown function
YCL026C-A	0.038956	CUP9	YCL026C-A|FRM2|S000000589|Protein of unknown function, involved in the integration of lipid signaling pathways with cellular homeostasis; similar to bacterial nitroreductases
YOL140W	0.0387563	CUP9	YOL140W|ARG8|S000005500|Acetylornithine aminotransferase, catalyzes the fourth step in the biosynthesis of the arginine precursor ornithine
YDR150W	0.0387377	CUP9	YDR150W|NUM1|S000002557|Protein required for nuclear migration, localizes to the mother cell cortex and the bud tip; may mediate interactions of dynein and cytoplasmic microtubules with the cell cortex
YOR062C	0.0387006	CUP9	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
YNR044W	0.0382334	CUP9	YNR044W|AGA1|S000005327|Anchorage subunit of a-agglutinin of a-cells, highly O-glycosylated protein with N-terminal secretion signal and C-terminal signal for addition of GPI anchor to cell wall, linked to adhesion subunit Aga2p via two disulfide bonds
YBR156C	0.0381924	CUP9	YBR156C|SLI15|S000000360|Subunit of the Ipl1p-Sli15p-Bir1p complex that regulates kinetochore-microtubule attachments, activation of the spindle tension checkpoint, and mitotic spindle disassembly; regulates the activity and localization of the Ipl1p aurora kinase
YMR097C	0.0381642	CUP9	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
YPR104C	0.0375001	CUP9	YPR104C|FHL1|S000006308|Transcriptional activator with similarity to DNA-binding domain of Drosophila forkhead but unable to bind DNA in vitro; required for rRNA processing; isolated as a suppressor of splicing factor prp4
YLR297W	0.0370427	CUP9	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
YOR249C	0.0368913	CUP9	YOR249C|APC5|S000005775|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
YDR256C	0.0367819	CUP9	YDR256C|CTA1|S000002664|Catalase A, breaks down hydrogen peroxide in the peroxisomal matrix formed by acyl-CoA oxidase (Pox1p) during fatty acid beta-oxidation
YBL054W	0.0362033	CUP9	YBL054W||S000000150|Protein of unknown function involved in rRNA and ribosome biosynthesis
YGL178W	0.0360794	CUP9	YGL178W|MPT5|S000003146|Member of the Puf family of RNA-binding proteins; binds to mRNAs encoding chromatin modifiers and spindle pole body components; involved in longevity, maintenance of cell wall integrity, and sensitivity to and recovery from pheromone arrest
YGR196C	0.0360458	CUP9	YGR196C|FYV8|S000003428|Protein of unknown function, required for survival upon exposure to K1 killer toxin
YBL025W	0.0359227	CUP9	YBL025W|RRN10|S000000121|Protein involved in promoting high level transcription of rDNA, subunit of UAF (upstream activation factor) for RNA polymerase I
YBL035C	0.0357134	CUP9	YBL035C|POL12|S000000131|B subunit of DNA polymerase alpha-primase complex, required for initiation of DNA replication during mitotic and premeiotic DNA synthesis; also functions in telomere capping and length regulation
YDL110C	0.0356151	CUP9	YDL110C|TMA17|S000002268|Protein of unknown function that associates with ribosomes
YKL204W	0.0353121	CUP9	YKL204W|EAP1|S000001687|eIF4E-associated protein, binds eIF4E and inhibits cap-dependent translation, also functions independently of eIF4E to maintain genetic stability; plays a role in cell growth, implicated in the TOR signaling cascade
YNL210W	0.0351611	CUP9	YNL210W|MER1|S000005154|Protein with RNA-binding motifs required for meiosis-specific mRNA splicing; required for chromosome pairing and meiotic recombination
YPR125W	0.0350867	CUP9	YPR125W|YLH47|S000006329|Mitochondrial inner membrane protein exposed to the mitochondrial matrix, associates with mitochondrial ribosomes, NOT required for respiratory growth; homolog of human Letm1, a protein implicated in Wolf-Hirschhorn syndrome
YCR040W	0.0348436	CUP9	YCR040W|MATALPHA1|S000000636|Transcriptional co-activator involved in regulation of mating-type-specific gene expression; targets the transcription factor Mcm1p to the promoters of alpha-specific genes; one of two genes encoded by the MATalpha mating type cassette
YPL189C-A	0.0344256	CUP9	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
YIL065C	0.0343371	CUP9	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
YML041C	0.03431	CUP9	YML041C|VPS71|S000004505|Nucleosome-binding component of the SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A; required for vacuolar protein sorting
YNL047C	0.0342629	CUP9	YNL047C|SLM2|S000004992|Phosphoinositide PI4,5P(2) binding protein, forms a complex with Slm1p; acts downstream of Mss4p in a pathway regulating actin cytoskeleton organization in response to stress; subunit of and phosphorylated by the TORC2 complex
YOR160W	0.0341647	CUP9	YOR160W|MTR10|S000005686|Nuclear import receptor, mediates the nuclear localization of proteins involved in mRNA-nucleus export; promotes dissociation of mRNAs from the nucleus-cytoplasm mRNA shuttling protein Npl3p
YML081W	0.0340813	CUP9	YML081W||S000004546|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus; YML081w is not an essential gene
YDR442W	0.0339779	CUP9	YDR442W||S000002850|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YER062C	0.0338713	CUP9	YER062C|HOR2|S000000864|One of two redundant DL-glycerol-3-phosphatases (RHR2/GPP1 encodes the other) involved in glycerol biosynthesis; induced in response to hyperosmotic stress and oxidative stress, and during the diauxic transition
YPR140W	0.0337455	CUP9	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
YBR055C	0.0337255	CUP9	YBR055C|PRP6|S000000259|Splicing factor, component of the U4/U6-U5 snRNP complex
YNL321W	0.0335141	CUP9	YNL321W|VNX1|S000005265|Low affinity vacuolar membrane localized monovalent cation/H+ antiporter; member of the calcium exchanger (CAX) family; potential Cdc28p substrate
YNL106C	0.0326467	CUP9	YNL106C|INP52|S000005050|Polyphosphatidylinositol phosphatase, dephosphorylates a number of phosphatidylinositols (PIs) to PI; involved in endocytosis; hyperosmotic stress causes translocation to actin patches; synaptojanin-like protein with a Sac1 domain
YIR009W	0.0325845	CUP9	YIR009W|MSL1|S000001448|U2B component of U2 snRNP, involved in splicing, binds the U2 snRNA stem-loop IV in vitro; does not contain the conserved C-terminal RNA binding domain found in other family members
YJL222W	0.0321467	CUP9	YJL222W|VTH2|S000003758|Putative membrane glycoprotein with strong similarity to Vth1p and Pep1p/Vps10p, may be involved in vacuolar protein sorting
YFL061W	0.0319723	CUP9	YFL061W|DDI2|S000001833|Protein whose expression is induced by DNA damage
YOR190W	0.0319267	CUP9	YOR190W|SPR1|S000005716|Sporulation-specific exo-1,3-beta-glucanase; contributes to ascospore thermoresistance
YNL339C	0.0318882	CUP9	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
YMR070W	0.031826	CUP9	YMR070W|MOT3|S000004674|Nuclear transcription factor with two Cys2-His2 zinc fingers; involved in repression of a subset of hypoxic genes by Rox1p, repression of several DAN/TIR genes during aerobic growth, and repression of ergosterol biosynthetic genes
YML029W	0.0318081	CUP9	YML029W|USA1|S000004491|Protein involved in ER-associated protein degradation (ERAD); component of the Hrd1p complex; interacts with the U1 snRNP-specific protein, Snp1p
YDR028C	0.0315708	CUP9	YDR028C|REG1|S000002435|Regulatory subunit of type 1 protein phosphatase Glc7p, involved in negative regulation of glucose-repressible genes
YIL001W	0.0314381	CUP9	YIL001W||S000001263|Hypothetical protein
YJL105W	0.0313417	CUP9	YJL105W|SET4|S000003641|Protein of unknown function, contains a SET domain
YJL222W-A	0.0312132	CUP9	YJL222W-A||S000028663|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YBR021W	0.0310876	CUP9	YBR021W|FUR4|S000000225|Uracil permease, localized to the plasma membrane; expression is tightly regulated by uracil levels and environmental cues
YNL138W-A	0.030438	CUP9	YNL138W-A|YSF3|S000028509|Component of the U2 snRNP, associated with the SF3b complex; conserved in Ashbya gossypii
YBR294W	0.0302999	CUP9	YBR294W|SUL1|S000000498|High affinity sulfate permease; sulfate uptake is mediated by specific sulfate transporters Sul1p and Sul2p, which control the concentration of endogenous activated sulfate intermediates
YFL040W	0.0302885	CUP9	YFL040W||S000001854|Putative transporter, member of the sugar porter family; YFL040W is not an essential gene
YOR144C	0.0302364	CUP9	YOR144C|ELG1|S000005670|Protein required for S phase progression and telomere homeostasis, forms an alternative replication factor C complex important for DNA replication and genome integrity; involved in homologous recombination-mediated DNA repair
YOR030W	0.0301836	CUP9	YOR030W|DFG16|S000005556|Probable multiple transmembrane protein, involved in diploid invasive and pseudohyphal growth upon nitrogen starvation; required for accumulation of processed Rim101p
YPR105C	0.0301599	CUP9	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
YGL014W	0.0300396	CUP9	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
YCR081C-A	0.0299715	CUP9	YCR081C-A||S000028609|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps with SRB8/YCR081W; identified by gene-trapping, microarray expression analysis, and genome-wide homology searching
YKR050W	0.0298988	CUP9	YKR050W|TRK2|S000001758|Component of the Trk1p-Trk2p potassium transport system
YGR041W	0.0294496	CUP9	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
YDR462W	0.029221	CUP9	YDR462W|MRPL28|S000002870|Mitochondrial ribosomal protein of the large subunit
YNL027W	0.0290706	CUP9	YNL027W|CRZ1|S000004972|Transcription factor that activates transcription of genes involved in stress response; nuclear localization is positively regulated by calcineurin-mediated dephosphorylation
YHR135C	0.0289018	CUP9	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
YPR064W	0.0288675	CUP9	YPR064W||S000006268|Dubious open reading frame, unlikely to encode a functional protein; based on available experimental and comparative sequence data
YDR157W	0.0280557	CUP9	YDR157W||S000002564|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR126C	0.0278883	CUP9	YLR126C||S000004116|Putative protein of unknown function with similarity to glutamine amidotransferase proteins; has Aft1p-binding motif in the promoter; may be involved in copper and iron homeostasis; YLR126C is not an essential protein
YPL233W	0.0277499	CUP9	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
YPL228W	0.0276803	CUP9	YPL228W|CET1|S000006149|Beta (RNA 5'-triphosphatase) subunit of the mRNA capping enzyme, a heterodimer (the other subunit is CEG1, a guanylyltransferase) involved in adding the 5' cap to mRNA; the mammalian enzyme is a single bifunctional polypeptide
YKL223W	0.0268044	CUP9	YKL223W||S000001706|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR357C	0.0264955	CUP9	YDR357C||S000002765|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YIL163C	0.0263837	CUP9	YIL163C||S000001425|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGR257C	0.0262993	CUP9	YGR257C|MTM1|S000003489|Mitochondrial protein of the mitochondrial carrier family, involved in activating mitochondrial Sod2p probably by facilitating insertion of an essential manganese cofactor
YDL155W	0.0261124	CUP9	YDL155W|CLB3|S000002314|B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the G2/M transition; may be involved in DNA replication and spindle assembly; accumulates during S phase and G2, then targeted for ubiquitin-mediated degradation
YOR098C	0.0260433	CUP9	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
YFR026C	0.0259591	CUP9	YFR026C||S000001922|Putative protein of unknown function
YBL061C	0.0258154	CUP9	YBL061C|SKT5|S000000157|Activator of Chs3p (chitin synthase III), recruits Chs3p to the bud neck via interaction with Bni4p; has similarity to Shc1p, which activates Chs3p during sporulation
YDL190C	0.0256143	CUP9	YDL190C|UFD2|S000002349|Ubiquitin chain assembly factor (E4) that cooperates with a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin protein ligase (E3) to conjugate ubiquitin to substrates; also functions as an E3
YGL035C	0.025472	CUP9	YGL035C|MIG1|S000003003|Transcription factor involved in glucose repression; sequence specific DNA binding protein containing two Cys2His2 zinc finger motifs; regulated by the SNF1 kinase and the GLC7 phosphatase
YLR269C	0.0254472	CUP9	YLR269C||S000004259|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YBR110W	0.0253829	CUP9	YBR110W|ALG1|S000000314|Mannosyltransferase, involved in asparagine-linked glycosylation in the endoplasmic reticulum (ER); essential for viability, mutation is functionally complemented by human ortholog
YOR207C	0.0253707	CUP9	YOR207C|RET1|S000005733|Second-largest subunit of RNA polymerase III, which is responsible for the transcription of tRNA and 5S RNA genes, and other low molecular weight RNAs
YOR124C	0.0250365	CUP9	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
YOR204W	0.0249656	CUP9	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
YDL157C	0.0248531	CUP9	YDL157C||S000002316|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YOR262W	0.0246889	CUP9	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
YOR370C	0.024645	CUP9	YOR370C|MRS6|S000005897|Rab escort protein, forms a complex with the Ras-like small GTPase Ypt1p that is required for the prenylation of Ypt1p by protein geranylgeranyltransferase type II (Bet2p-Bet4p)
YIL070C	0.0244855	CUP9	YIL070C|MAM33|S000001332|Acidic protein of the mitochondrial matrix involved in oxidative phosphorylation; related to the human complement receptor gC1q-R
YPR022C	0.0244039	CUP9	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
YLR081W	0.0241691	CUP9	YLR081W|GAL2|S000004071|Galactose permease, required for utilization of galactose; also able to transport glucose
YBR124W	0.0240963	CUP9	YBR124W||S000000328|Putative protein of unknown function
YBR198C	0.023851	CUP9	YBR198C|TAF5|S000000402|Subunit (90 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification
YGR294W	0.0234987	CUP9	YGR294W|PAU12|S000003526|Hypothetical protein
YNL128W	0.0233093	CUP9	YNL128W|TEP1|S000005072|Homolog of human tumor suppressor gene PTEN/MMAC1/TEP1 that has lipid phosphatase activity and is linked to the phosphatidylinositol signaling pathway; plays a role in normal sporulation
YMR021C	0.0226153	CUP9	YMR021C|MAC1|S000004623|Copper-sensing transcription factor involved in regulation of genes required for high affinity copper transport
YLR134W	0.0224864	CUP9	YLR134W|PDC5|S000004124|Minor isoform of pyruvate decarboxylase, key enzyme in alcoholic fermentation, decarboxylates pyruvate to acetaldehyde, regulation is glucose- and ethanol-dependent, repressed by thiamine, involved in amino acid catabolism
YML108W	0.0222942	CUP9	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
YNL051W	0.022252	CUP9	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
YKL064W	0.0220696	CUP9	YKL064W|MNR2|S000001547|Putative magnesium transporter; has similarity to Alr1p and Alr2p, which mediate influx of Mg2+ and other divalent cations
YPL109C	0.0218461	CUP9	YPL109C||S000006030|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YNL286W	0.0212812	CUP9	YNL286W|CUS2|S000005230|Protein that binds to U2 snRNA and Prp11p, may be involved in U2 snRNA folding; contains two RNA recognition motifs (RRMs)
YOR374W	0.0211826	CUP9	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
YOR127W	0.0211433	CUP9	YOR127W|RGA1|S000005653|GTPase-activating protein for the polarity-establishment protein Cdc42p; implicated in control of septin organization, pheromone response, and haploid invasive growth
YGR010W	0.0208814	CUP9	YGR010W|NMA2|S000003242|Nicotinic acid mononucleotide adenylyltransferase, involved in de novo and salvage synthesis of NAD(+)
YLL025W	0.0208362	CUP9	YLL025W|PAU17|S000003948|Putative protein of unknown function; YLL025W is not an essential gene
YAL056W	0.020746	CUP9	YAL056W|GPB2|S000000052|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 Gpb1p
YOL137W	0.0205293	CUP9	YOL137W|BSC6|S000005497|Protein of unknown function containing 8 putative transmembrane seqments; ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression
YNL049C	0.0204766	CUP9	YNL049C|SFB2|S000004994|Probable component of COPII coated vesicles that binds to Sec23p; similar to and functionally redundant with Sec24p, but expressed at low levels; involved in ER to Golgi transport and in autophagy
YDR148C	0.0204296	CUP9	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
YHR165C	0.0199788	CUP9	YHR165C|PRP8|S000001208|Component of the U4/U6-U5 snRNP complex, involved in the second catalytic step of splicing; mutations of human Prp8 cause retinitis pigmentosa
YNL323W	0.0199562	CUP9	YNL323W|LEM3|S000005267|Membrane protein of the plasma membrane and ER, involved in translocation of phospholipids and alkylphosphocholine drugs across the plasma membrane
YBR062C	0.019602	CUP9	YBR062C||S000000266|Hypothetical protein
YDR538W	0.0194597	CUP9	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
YJR085C	0.0194346	CUP9	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
YGR097W	0.0192266	CUP9	YGR097W|ASK10|S000003329|Component of the RNA polymerase II holoenzyme, phosphorylated in response to oxidative stress; has a role in destruction of Ssn8p, which relieves repression of stress-response genes
YNL303W	0.0191249	CUP9	YNL303W||S000005247|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YCL004W	0.0190556	CUP9	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
YDL146W	0.0189999	CUP9	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
YBR200W	0.0188018	CUP9	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
YLL058W	0.0185391	CUP9	YLL058W||S000003981|Putative protein of unknown function with similarity to Str2p, which is a cystathionine gamma-synthase important in sulfur metabolism; YLL058W is not an essential gene
YDR394W	0.0182179	CUP9	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
YDR109C	0.018157	CUP9	YDR109C||S000002516|Putative kinase
YOL135C	0.0179603	CUP9	YOL135C|MED7|S000005495|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation
YCR018C-A	0.0176095	CUP9	YCR018C-A||S000007230|Putative protein of unknown function; encoded opposite a Ty1 LTR
YGR270W	0.0173477	CUP9	YGR270W|YTA7|S000003502|Protein that localizes to chromatin and has a role in regulation of histone gene expression; has a bromodomain-like region that interacts with the N-terminal tail of histone H3, and an ATPase domain; potentially phosphorylated by Cdc28p
YPR170C	0.0173335	CUP9	YPR170C||S000006374|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORFs YPR169W-A and YPR170W-B
YGR269W	0.0171408	CUP9	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
YPR072W	0.0166577	CUP9	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
YHL039W	0.0164654	CUP9	YHL039W||S000001031|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YER165W	0.016425	CUP9	YER165W|PAB1|S000000967|Poly(A) binding protein, part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G
YNL279W	0.0160917	CUP9	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
YDR162C	0.0159247	CUP9	YDR162C|NBP2|S000002569|Protein involved in the HOG (high osmolarity glycerol) pathway, negatively regulates Hog1p by recruitment of phosphatase Ptc1p the Pbs2p-Hog1p complex, found in the nucleus and cytoplasm, contains an SH3 domain that binds Pbs2p
YDR054C	0.0158559	CUP9	YDR054C|CDC34|S000002461|Ubiquitin-conjugating enzyme (E2) and catalytic subunit of SCF ubiquitin-protein ligase complex (together with Skp1p, Rbx1p, Cdc53p, and an F-box protein) that regulates cell cycle progression by targeting key substrates for degradation
YER068W	0.0158445	CUP9	YER068W|MOT2|S000000870|Component of the CCR4-NOT complex, which has multiple roles in transcription regulation, mRNA degradation, and post-transcriptional modifications; with Ubc4p, ubiquitylates subunits of the nascent polypeptide-associated complex (NAC)
YCR008W	0.015786	CUP9	YCR008W|SAT4|S000000601|Ser/Thr protein kinase involved in salt tolerance; funtions in regulation of Trk1p-Trk2p potassium transporter; partially redundant with Hal5p; has similarity to Npr1p
YBR007C	0.0153997	CUP9	YBR007C|DSF2|S000000211|Deletion suppressor of mpt5 mutation
YLR202C	0.0141205	CUP9	YLR202C||S000004192|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF YLR201C; ORF contains a putative intron
YLR316C	0.0140793	CUP9	YLR316C|TAD3|S000004308|Subunit of tRNA-specific adenosine-34 deaminase, forms a heterodimer with Tad2p that converts adenosine to inosine at the wobble position of several tRNAs
YGR193C	0.013923	CUP9	YGR193C|PDX1|S000003425|Dihydrolipoamide dehydrogenase (E3)-binding protein (E3BP) of the mitochondrial pyruvate dehydrogenase (PDH) complex, plays a structural role in the complex by binding and positioning E3 to the dihydrolipoamide acetyltransferase (E2) core
YJR093C	0.013677	CUP9	YJR093C|FIP1|S000003853|Subunit of cleavage polyadenylation factor (CPF), interacts directly with poly(A) polymerase (Pap1p) to regulate its activity
YDL168W	0.0136645	CUP9	YDL168W|SFA1|S000002327|Bifunctional enzyme containing both alcohol dehydrogenase and glutathione-dependent formaldehyde dehydrogenase activities, functions in formaldehyde detoxification and formation of long chain and complex alcohols, regulated by Hog1p-Sko1p
YOR072W-A	0.0124446	CUP9	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
YML071C	0.0123666	CUP9	YML071C|COG8|S000004536|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
YEL059C-A	0.0122385	CUP9	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
YDR113C	0.0118106	CUP9	YDR113C|PDS1|S000002520|Securin that inhibits anaphase by binding separin Esp1p, also blocks cyclin destruction and mitotic exit, essential for cell cycle arrest in mitosis in the presence of DNA damage or aberrant mitotic spindles; also present in meiotic nuclei
YOR267C	0.0117238	CUP9	YOR267C|HRK1|S000005793|Protein kinase implicated in activation of the plasma membrane H(+)-ATPase Pma1p in response to glucose metabolism; plays a role in ion homeostasis
YER155C	0.0113732	CUP9	YER155C|BEM2|S000000957|Rho GTPase activating protein (RhoGAP) involved in the control of cytoskeleton organization and cellular morphogenesis; required for bud emergence
YOR220W	0.0110251	CUP9	YOR220W|RCN2|S000005746|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
YDR118W	0.010779	CUP9	YDR118W|APC4|S000002525|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
YKL220C	0.0107729	CUP9	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
YBL071C	0.0106697	CUP9	YBL071C||S000000167|Dubious open reading frame, predicted protein contains a peroxisomal targeting signal
YOR010C	0.010485	CUP9	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
YKL092C	0.0100299	CUP9	YKL092C|BUD2|S000001575|GTPase activating factor for Rsr1p/Bud1p required for both axial and bipolar budding patterns; mutants exhibit random budding in all cell types
YML130C	0.0100011	CUP9	YML130C|ERO1|S000004599|Thiol oxidase required for oxidative protein folding in the endoplasmic reticulum
YOL054W	0.00952262	CUP9	YOL054W|PSH1|S000005415|Nuclear protein, putative RNA polymerase II elongation factor; isolated as Pob3p/Spt16p-binding protein
YML129C	0.0094913	CUP9	YML129C|COX14|S000004598|Mitochondrial membrane protein, involved in translational regulation of Cox1p and assembly of cytochrome c oxidase (complex IV); associates with complex IV assembly intermediates and complex III/complex IV supercomplexes
YBR213W	0.00916052	CUP9	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
YHL038C	0.00881161	CUP9	YHL038C|CBP2|S000001030|Mitochondrial protein required for splicing of the group I intron aI5 of the COB pre-mRNA, binds to the RNA to promote splicing; also involved in but not essential for splicing of the COB bI2 intron and the intron in the 21S rRNA gene
YNL011C	0.00877562	CUP9	YNL011C||S000004956|Putative protein of unknown function; YNL011C is not an essential gene
YMR022W	0.00854408	CUP9	YMR022W|UBC7|S000004624|Ubiquitin conjugating enzyme, involved in the ER-associated protein degradation pathway; requires Cue1p for recruitment to the ER membrane; proposed to be involved in chromatin assembly
YHL012W	0.00792021	CUP9	YHL012W||S000001004|Putative protein of unknown function, has some homology to Ugp1p, which encodes UDP-glucose pyrophosphorylase
YLR456W	0.00791414	CUP9	YLR456W||S000004448|Putative protein of unknown function; null mutant displays increased resistance to antifungal agents gliotoxin, cycloheximide and H2O2
YOR075W	0.00780489	CUP9	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
YHL045W	0.00759146	CUP9	YHL045W||S000001037|Putative protein of unknown function; not an essential gene
YML112W	0.00743178	CUP9	YML112W|CTK3|S000004580|Gamma subunit of C-terminal domain kinase I (CTDK-I), which phosphorylates the C-terminal repeated domain of the RNA polymerase II large subunit (Rpo21p) to affect both transcription and pre-mRNA 3' end processing
YJL140W	0.00734992	CUP9	YJL140W|RPB4|S000003676|RNA polymerase II subunit B32; forms two subunit dissociable complex with Rpb7p; involved recruitment of 3'-end processing factors to transcribing RNA polymerase II complex and in export of mRNA to cytoplasm under stress conditions
YBL100C	0.00705392	CUP9	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
YDR146C	0.0068601	CUP9	YDR146C|SWI5|S000002553|Transcription factor that activates transcription of genes expressed at the M/G1 phase boundary and in G1 phase; localization to the nucleus occurs during G1 and appears to be regulated by phosphorylation by Cdc28p kinase
YIR001C	0.00672169	CUP9	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
YGR268C	0.00666218	CUP9	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
YDL074C	0.00663814	CUP9	YDL074C|BRE1|S000002232|E3 ubiquitin ligase for Rad6p, required for the ubiquitination of histone H2B, recruitment of Rad6p to promoter chromatin and subsequent methylation of histone H3 (on K4 and K79), contains RING finger domain
YNR072W	0.00659785	CUP9	YNR072W|HXT17|S000005355|Hexose transporter, up-regulated in media containing raffinose and galactose at pH 7.7 versus pH 4.7, repressed by high levels of glucose
YAR007C	0.00638042	CUP9	YAR007C|RFA1|S000000065|Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination
YGR188C	0.00600007	CUP9	YGR188C|BUB1|S000003420|Protein kinase that forms a complex with Mad1p and Bub3p that is crucial in the checkpoint mechanism required to prevent cell cycle progression into anaphase in the presence of spindle damage, associates with centromere DNA via Skp1p
YOR114W	0.0059645	CUP9	YOR114W||S000005640|Putative protein of unknown function; null mutant is viable
YBR275C	0.00590576	CUP9	YBR275C|RIF1|S000000479|Protein that binds to the Rap1p C-terminus and acts synergistically with Rif2p to help control telomere length and establish telomeric silencing; deletion results in telomere elongation
YER042W	0.00588645	CUP9	YER042W|MXR1|S000000844|Peptide methionine sulfoxide reductase, reverses the oxidation of methionine residues; involved in oxidative damage repair, providing resistance to oxidative stress and regulation of lifespan
YOR307C	0.0058083	CUP9	YOR307C|SLY41|S000005834|Protein involved in ER-to-Golgi transport
YLR097C	0.00549555	CUP9	YLR097C|HRT3|S000004087|Putative SCF-ubiquitin ligase F-box protein, based on both genetic and physical interactions and sequence similarity; identified in association with Cdc53p, Skp1p and Ubi4 in large and small-scale studies
YNL335W	0.00531767	CUP9	YNL335W|DDI3|S000005279|Hypothetical protein
YAL040C	0.00511564	CUP9	YAL040C|CLN3|S000000038|G1 cyclin involved in cell cycle progression; activates Cdc28p kinase to promote the G1 to S phase transition; plays a role in regulating transcription of the other G1 cyclins, CLN1 and CLN2; regulated by phosphorylation and proteolysis
YOR050C	0.00470965	CUP9	YOR050C||S000005576|Hypothetical protein
YAL005C	0.00438653	CUP9	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
YKL210W	0.0041916	CUP9	YKL210W|UBA1|S000001693|Ubiquitin activating enzyme (E1), involved in ubiquitin-mediated protein degradation and essential for viability
YBR058C-A	0.00416004	CUP9	YBR058C-A|TSC3|S000007521|Protein that stimulates the activity of serine palmitoyltransferase (Lcb1p, Lcb2p) several-fold; involved in sphingolipid biosynthesis
YOL164W	0.00377512	CUP9	YOL164W|BDS1|S000005524|Bacterially-derived sulfatase required for use of alkyl- and aryl-sulfates as sulfur sources
YDR005C	0.00357572	CUP9	YDR005C|MAF1|S000002412|Negative regulator of RNA polymerase III; component of several signaling pathways that repress polymerase III transcription in response to changes in cellular environment; targets the initiation factor TFIIIB
YPR121W	0.00338754	CUP9	YPR121W|THI22|S000006325|Protein with similarity to hydroxymethylpyrimidine phosphate kinases; member of a gene family with THI20 and THI21; not required for thiamine biosynthesis
YFR007W	0.00324654	CUP9	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)
YOR301W	0.00324102	CUP9	YOR301W|RAX1|S000005827|Protein involved in bud site selection during bipolar budding; localization requires Rax2p; has similarity to members of the insulin-related peptide superfamily
YKL068W	0.00315027	CUP9	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
YDR477W	0.00312656	CUP9	YDR477W|SNF1|S000002885|AMP-activated serine/threonine protein kinase found in a complex containing Snf4p and members of the Sip1p/Sip2p/Gal83p family; required for transcription of glucose-repressed genes, thermotolerance, sporulation, and peroxisome biogenesis
YOR377W	0.00299322	CUP9	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
YJL073W	0.00256064	CUP9	YJL073W|JEM1|S000003609|DnaJ-like chaperone required for nuclear membrane fusion during mating, localizes to the ER membrane; exhibits genetic interactions with KAR2
YOR011W	0.00251941	CUP9	YOR011W|AUS1|S000005537|Transporter of the ATP-binding cassette family, involved in uptake of sterols and anaerobic growth
YDR295C	0.00151627	CUP9	YDR295C|HDA2|S000002703|Subunit of a possibly tetrameric trichostatin A-sensitive class II histone deacetylase complex containing an Hda1p homodimer and an Hda2p-Hda3p heterodimer; involved in telomere maintenance
YAL056C-A	0.00149569	CUP9	YAL056C-A||S000002139|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YNL259C	0.00140799	CUP9	YNL259C|ATX1|S000005203|Cytosolic copper metallochaperone that transports copper to the secretory vesicle copper transporter Ccc2p for eventual insertion into Fet3p, which is a multicopper oxidase required for high-affinity iron uptake
YPR124W	0.000771352	CUP9	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
YLR090W	0.000750485	CUP9	YLR090W|XDJ1|S000004080|Putative chaperone, homolog of E. coli DnaJ, closely related to Ydj1p; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YNL122C	0.000578666	CUP9	YNL122C||S000005066|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YNL122C is not an essential gene
YBL071W-A	0.000267686	CUP9	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
YBR219C	0.000184273	CUP9	YBR219C||S000000423|Putative protein of unknown function; YBR219C is not an essential gene
