YMR107W	57.8547	RPH1	YMR107W|SPG4|S000004713|Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources
YHR096C	54.2712	RPH1	YHR096C|HXT5|S000001138|Hexose transporter with moderate affinity for glucose, induced in the presence of non-fermentable carbon sources, induced by a decrease in growth rate, contains an extended N-terminal domain relative to other HXTs
YBR072W	53.23	RPH1	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
YMR175W	48.9029	RPH1	YMR175W|SIP18|S000004787|Protein of unknown function whose expression is induced by osmotic stress
YGR087C	47.017	RPH1	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
YNR034W-A	41.2004	RPH1	YNR034W-A||S000007525|Putative protein of unknown function; expression is regulated by Msn2p/Msn4p
YKL065W-A	40.5045	RPH1	YKL065W-A||S000113563|Putative protein of unknown function
YGR256W	34.0504	RPH1	YGR256W|GND2|S000003488|6-phosphogluconate dehydrogenase (decarboxylating), catalyzes an NADPH regenerating reaction in the pentose phosphate pathway; required for growth on D-glucono-delta-lactone
YFR017C	33.7761	RPH1	YFR017C||S000001913|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and is induced in response to the DNA-damaging agent MMS; YFR017C is not an essential gene
YHR139C	32.913	RPH1	YHR139C|SPS100|S000001181|Protein required for spore wall maturation; expressed during sporulation; may be a component of the spore wall
YOL052C-A	32.5401	RPH1	YOL052C-A|DDR2|S000005413|Multistress response protein, expression is activated by a variety of xenobiotic agents and environmental or physiological stresses
YKL217W	31.9476	RPH1	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
YOR393W	31.8653	RPH1	YOR393W|ERR1|S000005920|Protein of unknown function, has similarity to enolases
YAL062W	30.9663	RPH1	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
YAL054C	30.5442	RPH1	YAL054C|ACS1|S000000050|Acetyl-coA synthetase isoform which, along with Acs2p, is the nuclear source of acetyl-coA for histone acetlyation; expressed during growth on nonfermentable carbon sources and under aerobic conditions
YDR277C	29.2994	RPH1	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
YNL117W	28.7374	RPH1	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
YPL223C	27.8782	RPH1	YPL223C|GRE1|S000006144|Hydrophilin of unknown function; stress induced (osmotic, ionic, oxidative, heat shock and heavy metals); regulated by the HOG pathway
YIL136W	27.1321	RPH1	YIL136W|OM45|S000001398|Protein of unknown function, major constituent of the mitochondrial outer membrane; located on the outer (cytosolic) face of the outer membrane
YGR088W	26.108	RPH1	YGR088W|CTT1|S000003320|Cytosolic catalase T, has a role in protection from oxidative damage by hydrogen peroxide
YFR053C	24.1114	RPH1	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
YPL036W	23.7243	RPH1	YPL036W|PMA2|S000005957|Plasma membrane H+-ATPase, isoform of Pma1p, involved in pumping protons out of the cell; regulator of cytoplasmic pH and plasma membrane potential
YPL054W	22.9724	RPH1	YPL054W|LEE1|S000005975|Zinc-finger protein of unknown function
YKL107W	22.4683	RPH1	YKL107W||S000001590|Putative protein of unknown function
YPR010C-A	21.9947	RPH1	YPR010C-A||S000122558|Putative protein of unknown function; conserved among Saccharomyces sensu stricto species
YFL011W	21.8025	RPH1	YFL011W|HXT10|S000001883|Putative hexose transporter, expressed at low levels and expression is repressed by glucose
YLR312C	21.7862	RPH1	YLR312C|QNQ1|S000004303|Protein of unknown function; null mutant quiescent and non-quiescent cells exhibit reduced reproductive capacity
YBR241C	21.4011	RPH1	YBR241C||S000000445|Putative transporter, member of the sugar porter family; green fluorescent protein (GFP)-fusion protein localizes to the vacuolar membrane; YBR241C is not an essential gene
YMR081C	21.4004	RPH1	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
YGR043C	21.2553	RPH1	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
YOR391C	21.0311	RPH1	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
YIL099W	20.1583	RPH1	YIL099W|SGA1|S000001361|Intracellular sporulation-specific glucoamylase involved in glycogen degradation; induced during starvation of a/a diploids late in sporulation, but dispensable for sporulation
YDR070C	20.0459	RPH1	YDR070C|FMP16|S000002477|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YBL049W	19.8909	RPH1	YBL049W|MOH1|S000000145|Protein of unknown function, has homology to kinase Snf7p; not required for growth on nonfermentable carbon sources; essential for viability in stationary phase
YMR174C	19.8044	RPH1	YMR174C|PAI3|S000004786|Cytoplasmic proteinase A (Pep4p) inhibitor, dependent on Pbs2p and Hog1p protein kinases for osmotic induction; intrinsically unstructured, N-terminal half becomes ordered in the active site of proteinase A upon contact
YMR105C	19.5296	RPH1	YMR105C|PGM2|S000004711|Phosphoglucomutase, catalyzes the conversion from glucose-1-phosphate to glucose-6-phosphate, which is a key step in hexose metabolism; functions as the acceptor for a Glc-phosphotransferase
YOR186W	18.6689	RPH1	YOR186W||S000005712|Putative protein of unknown function; proper regulation of expression during heat stress is sphingolipid-dependent
YDL085W	18.3797	RPH1	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
YPR030W	18.3543	RPH1	YPR030W|CSR2|S000006234|Nuclear protein with a potential regulatory role in utilization of galactose and nonfermentable carbon sources; overproduction suppresses the lethality at high temperature of a chs5 spa2 double null mutation; potential Cdc28p substrate
YKL103C	18.3097	RPH1	YKL103C|LAP4|S000001586|Vacuolar aminopeptidase, often used as a marker protein in studies of autophagy and cytosol to vacuole targeting (CVT) pathway
YER067W	17.8128	RPH1	YER067W||S000000869|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YER067W is not an essential gene
YKL163W	17.7872	RPH1	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
YBL075C	17.3533	RPH1	YBL075C|SSA3|S000000171|ATPase involved in protein folding and the response to stress; plays a role in SRP-dependent cotranslational protein-membrane targeting and translocation; member of the heat shock protein 70 (HSP70) family; localized to the cytoplasm
YKL148C	17.1906	RPH1	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
YAL034C	17.156	RPH1	YAL034C|FUN19|S000002134|Non-essential protein of unknown function
YEL039C	17.0134	RPH1	YEL039C|CYC7|S000000765|Cytochrome c isoform 2, expressed under hypoxic conditions; electron carrier of the mitochondrial intermembrane space that transfers electrons from ubiquinone-cytochrome c oxidoreductase to cytochrome c oxidase during cellular respiration
YDL222C	16.6495	RPH1	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
YHL040C	16.5771	RPH1	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
YNR001C	16.5529	RPH1	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
YBR117C	16.5473	RPH1	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
YKL102C	16.1745	RPH1	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
YOR031W	16.1488	RPH1	YOR031W|CRS5|S000005557|Copper-binding metallothionein, required for wild-type copper resistance
YDL204W	16.0736	RPH1	YDL204W|RTN2|S000002363|Protein of unknown function; has similarity to mammalian reticulon proteins; member of the RTNLA (reticulon-like A) subfamily
YDL130W-A	15.946	RPH1	YDL130W-A|STF1|S000007232|Protein involved in regulation of the mitochondrial F1F0-ATP synthase; Stf1p and Stf2p may act as stabilizing factors that enhance inhibitory action of the Inh1p protein
YDR343C	15.6827	RPH1	YDR343C|HXT6|S000002751|High-affinity glucose transporter of the major facilitator superfamily, nearly identical to Hxt7p, expressed at high basal levels relative to other HXTs, repression of expression by high glucose requires SNF3
YIL101C	15.5796	RPH1	YIL101C|XBP1|S000001363|Transcriptional repressor that binds to promoter sequences of the cyclin genes, CYS3, and SMF2; expression is induced by stress or starvation during mitosis, and late in meiosis; member of the Swi4p/Mbp1p family; potential Cdc28p substrate
YFL058W	15.5535	RPH1	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
YJL116C	15.4058	RPH1	YJL116C|NCA3|S000003652|Protein that functions with Nca2p to regulate mitochondrial expression of subunits 6 (Atp6p) and 8 (Atp8p ) of the Fo-F1 ATP synthase; member of the SUN family
YAR053W	15.3263	RPH1	YAR053W||S000000085|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDL210W	15.2663	RPH1	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
YGR067C	15.226	RPH1	YGR067C||S000003299|Putative protein of unknown function; contains a zinc finger motif similar to that of Adr1p
YLR327C	14.6042	RPH1	YLR327C|TMA10|S000004319|Protein of unknown function that associates with ribosomes
YER103W	14.5356	RPH1	YER103W|SSA4|S000000905|Heat shock protein that is highly induced upon stress; plays a role in SRP-dependent cotranslational protein-membrane targeting and translocation; member of the HSP70 family; cytoplasmic protein that concentrates in nuclei upon starvation
YGR243W	14.2663	RPH1	YGR243W|FMP43|S000003475|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YMR250W	13.939	RPH1	YMR250W|GAD1|S000004862|Glutamate decarboxylase, converts glutamate into gamma-aminobutyric acid (GABA) during glutamate catabolism; involved in response to oxidative stress
YBR214W	13.8232	RPH1	YBR214W|SDS24|S000000418|One of two S. cerevisiae homologs (Sds23p and Sds24p) of the Schizosaccharomyces pombe Sds23 protein, which genetic studies have implicated in APC/cyclosome regulation; may play an indirect role in fluid-phase endocytosis
YNL014W	13.8046	RPH1	YNL014W|HEF3|S000004959|Translational elongation factor EF-3; paralog of YEF3 and member of the ABC superfamily; stimulates EF-1 alpha-dependent binding of aminoacyl-tRNA by the ribosome; normally expressed in zinc deficient cells
YHR033W	13.6437	RPH1	YHR033W||S000001075|Putative protein of unknown function; epitope-tagged protein localizes to the cytoplasm
YLR377C	13.5776	RPH1	YLR377C|FBP1|S000004369|Fructose-1,6-bisphosphatase, key regulatory enzyme in the gluconeogenesis pathway, required for glucose metabolism
YML089C	13.5393	RPH1	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
YLR356W	13.4466	RPH1	YLR356W||S000004348|Putative protein of unknown function with similarity to SCM4; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YLR356W is not an essential gene
YOR348C	13.3255	RPH1	YOR348C|PUT4|S000005875|Proline permease, required for high-affinity transport of proline; also transports the toxic proline analog azetidine-2-carboxylate (AzC); PUT4 transcription is repressed in ammonia-grown cells
YGR201C	13.3059	RPH1	YGR201C||S000003433|Putative protein of unknown function
YPL240C	13.2321	RPH1	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
YDL218W	12.8996	RPH1	YDL218W||S000002377|Putative protein of unknown function; YDL218W transcription is regulated by Azf1p and induced by starvation and aerobic conditions
YOR374W	12.8504	RPH1	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
YMR251W	12.5519	RPH1	YMR251W|GTO3|S000004863|Omega class glutathione transferase; putative cytosolic localization
YDR258C	12.5005	RPH1	YDR258C|HSP78|S000002666|Oligomeric mitochondrial matrix chaperone that cooperates with Ssc1p in mitochondrial thermotolerance after heat shock; prevents the aggregation of misfolded matrix proteins; component of the mitochondrial proteolysis system
YML131W	12.0749	RPH1	YML131W||S000004600|Putative protein of unknown function with similarity to oxidoreductases; HOG1 and SKO1-dependent mRNA expression is induced after osmotic shock; GFP-fusion protein localizes to the cytoplasm and is induced by the DNA-damaging agent MMS
YNL194C	11.855	RPH1	YNL194C||S000005138|Integral membrane protein localized to eisosomes; sporulation and plasma membrane sphingolipid content are altered in mutants; has homologs SUR7 and FMP45; GFP-fusion protein is induced in response to the DNA-damaging agent MMS
YEL070W	11.8462	RPH1	YEL070W|DSF1|S000000796|Deletion suppressor of mpt5 mutation
YOR346W	11.7172	RPH1	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
YGR144W	11.5235	RPH1	YGR144W|THI4|S000003376|Thiazole synthase, catalyzes formation of the thiazole moiety of thiamin pyrophosphate; required for thiamine biosynthesis and for mitochondrial genome stability
YOR392W	11.4472	RPH1	YOR392W||S000005919|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; gene expression induced by heat
YPL222W	11.2927	RPH1	YPL222W|FMP40|S000006143|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YOR100C	11.2142	RPH1	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
YAR060C	11.1058	RPH1	YAR060C||S000000086|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YPR127W	10.9908	RPH1	YPR127W||S000006331|Putative protein of unknown function; expression is activated by transcription factor YRM1/YOR172W; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YOR345C	10.8744	RPH1	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
YMR206W	10.872	RPH1	YMR206W||S000004819|Putative protein of unknown function; YMR206W is not an essential gene
YIL107C	10.8466	RPH1	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
YLR149C	10.8115	RPH1	YLR149C||S000004139|Putative protein of unknown function; YLR149C is not an essential gene
YIL086C	10.7285	RPH1	YIL086C||S000001348|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPR192W	10.6711	RPH1	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
YKL050C	10.4295	RPH1	YKL050C||S000001533|Protein of unknown function; the YKL050W protein is a target of the SCFCdc4 ubiquitin ligase complex and YKL050W transcription is regulated by Azf1p
YDL214C	10.3475	RPH1	YDL214C|PRR2|S000002373|Serine/threonine protein kinase that inhibits pheromone induced signalling downstream of MAPK, possibly at the level of the Ste12p transcription factor
YPL186C	10.248	RPH1	YPL186C|UIP4|S000006107|Protein that interacts with Ulp1p, a Ubl (ubiquitin-like protein)-specific protease for Smt3p protein conjugates; detected in a phosphorylated state in the mitochondrial outer membrane; also detected in ER and nuclear envelope
YMR181C	10.2445	RPH1	YMR181C||S000004793|Protein of unknown function; mRNA transcribed as part of a bicistronic transcript with a predicted transcriptional repressor RGM1/YMR182C; mRNA is destroyed by nonsense-mediated decay (NMD); YMR181C is not an essential gene
YJR154W	10.2257	RPH1	YJR154W||S000003915|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YER096W	10.0796	RPH1	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
YDR342C	10.0319	RPH1	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
YEL009C-A	9.97695	RPH1	YEL009C-A||S000028741|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGL156W	9.97212	RPH1	YGL156W|AMS1|S000003124|Vacuolar alpha mannosidase, involved in free oligosaccharide (fOS) degradation; delivered to the vacuole in a novel pathway separate from the secretory pathway
YOR173W	9.93548	RPH1	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.
YNL332W	9.87904	RPH1	YNL332W|THI12|S000005276|Protein involved in synthesis of the thiamine precursor hydroxymethylpyrimidine (HMP); member of a subtelomeric gene family including THI5, THI11, THI12, and THI13
YOL118C	9.78362	RPH1	YOL118C||S000005478|Dubious open reading frame, unlikely to encode a functional protein; based on available experimental and comparative sequence data
YAL061W	9.72842	RPH1	YAL061W|BDH2|S000000057|Putative medium-chain alcohol dehydrogenase with similarity to BDH1; transcription induced by constitutively active PDR1 and PDR3; BDH2 is an essential gene
YPR184W	9.61202	RPH1	YPR184W|GDB1|S000006388|Glycogen debranching enzyme containing glucanotranferase and alpha-1,6-amyloglucosidase activities, required for glycogen degradation; phosphorylated in mitochondria
YAL005C	9.56185	RPH1	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
YLR164W	9.54738	RPH1	YLR164W||S000004154|Mitochondrial inner membrane of unknown function; similar to Tim18p and Sdh4p; expression induced by nitrogen limitation in a GLN3, GAT1-dependent manner
YNL115C	9.46712	RPH1	YNL115C||S000005059|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to mitochondria; YNL115C is not an essential gene
YJR115W	9.4489	RPH1	YJR115W||S000003876|Putative protein of unknown function
YGL096W	9.44357	RPH1	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
YIL055C	9.38967	RPH1	YIL055C||S000001317|Putative protein of unknown function
YJL089W	9.36786	RPH1	YJL089W|SIP4|S000003625|C6 zinc cluster transcriptional activator that binds to the carbon source-responsive element (CSRE) of gluconeogenic genes; involved in the positive regulation of gluconeogenesis; regulated by Snf1p protein kinase; localized to the nucleus
YIR039C	9.35301	RPH1	YIR039C|YPS6|S000001478|Putative GPI-anchored aspartic protease
YHR139C-A	9.33903	RPH1	YHR139C-A||S000003533|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YAL063C	9.31049	RPH1	YAL063C|FLO9|S000000059|Lectin-like protein with similarity to Flo1p, thought to be expressed and involved in flocculation
YKL066W	9.30953	RPH1	YKL066W||S000001549|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; partially overlaps the verified gene YNK1
YMR196W	9.2221	RPH1	YMR196W||S000004809|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YMR196W is not an essential gene
YDR533C	8.966	RPH1	YDR533C|HSP31|S000002941|Possible chaperone and cysteine protease with similarity to E. coli Hsp31; member of the DJ-1/ThiJ/PfpI superfamily, which includes human DJ-1 involved in Parkinson's disease; exists as a dimer and contains a putative metal-binding site
YLR326W	8.96108	RPH1	YLR326W||S000004318|Hypothetical protein
YOL083W	8.95619	RPH1	YOL083W||S000005443|Hypothetical protein
YPL185W	8.94022	RPH1	YPL185W||S000006106|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene UIP4/YPL186C
YMR194C-B	8.84161	RPH1	YMR194C-B||S000028514|Putative protein of unknown function
YNL092W	8.83567	RPH1	YNL092W||S000005036|Putative S-adenosylmethionine-dependent methyltransferase of the seven beta-strand family; YNL092W is not an essential gene
YMR169C	8.80712	RPH1	YMR169C|ALD3|S000004779|Cytoplasmic aldehyde dehydrogenase, involved in beta-alanine synthesis; uses NAD+ as the preferred coenzyme; very similar to Ald2p; expression is induced by stress and repressed by glucose
YBR201C-A	8.74754	RPH1	YBR201C-A||S000087085|Putative protein of unknown function
YLL041C	8.73553	RPH1	YLL041C|SDH2|S000003964|Iron-sulfur protein subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p), which couples the oxidation of succinate to the transfer of electrons to ubiquinone
YMR053C	8.59289	RPH1	YMR053C|STB2|S000004657|Protein that interacts with Sin3p in a two-hybrid assay and is part of a large protein complex with Sin3p and Stb1p
YIL100C-A	8.58976	RPH1	YIL100C-A||S000028794|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR267W	8.57328	RPH1	YLR267W|BOP2|S000004257|Protein of unknown function, overproduction suppresses a pam1 slv3 double null mutation
YNL180C	8.5253	RPH1	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
YDL181W	8.49603	RPH1	YDL181W|INH1|S000002340|Protein that inhibits ATP hydrolysis by the F1F0-ATP synthase; inhibitory function is enhanced by stabilizing proteins Stf1p and Stf2p; has similarity to Stf1p; has a calmodulin-binding motif and binds calmodulin in vitro
YML120C	8.49423	RPH1	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
YHR087W	8.46516	RPH1	YHR087W|RTC3|S000001129|Protein of unknown function involved in RNA metabolism; has structural similarity to SBDS, the human protein mutated in Shwachman-Diamond Syndrome (the yeast SBDS ortholog = SDO1); null mutation suppresses cdc13-1 temperature sensitivity
YPL271W	8.45746	RPH1	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
YML118W	8.44622	RPH1	YML118W|NGL3|S000004587|Putative endonuclease, has a domain similar to a magnesium-dependent endonuclease motif in mRNA deadenylase Ccr4p; similar to Ngl1p and Ngl2p
YHR212C	8.41486	RPH1	YHR212C||S000001255|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YBR054W	8.35669	RPH1	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
YEL011W	8.34112	RPH1	YEL011W|GLC3|S000000737|Glycogen branching enzyme, involved in glycogen accumulation; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YBR280C	8.2739	RPH1	YBR280C|SAF1|S000000484|F-Box protein involved in proteasome-dependent degradation of Aah1p during entry of cells into quiescence; interacts with Skp1
YDR505C	8.27307	RPH1	YDR505C|PSP1|S000002913|Asn and gln rich protein of unknown function; high-copy suppressor of POL1 (DNA polymerase alpha) and partial suppressor of CDC2 (polymerase delta) and CDC6 (pre-RC loading factor) mutations; overexpression results in growth inhibition
YLR080W	8.27247	RPH1	YLR080W|EMP46|S000004070|Integral membrane component of endoplasmic reticulum-derived COPII-coated vesicles, which function in ER to Golgi transport
YPL119C	8.26082	RPH1	YPL119C|DBP1|S000006040|Putative ATP-dependent RNA helicase of the DEAD-box protein family; mutants show reduced stability of the 40S ribosomal subunit scanning through 5' untranslated regions of mRNAs
YML090W	8.25088	RPH1	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
YIL087C	8.15611	RPH1	YIL087C|LRC2|S000001349|Putative protein of unknown function; protein is detected in purified mitochondria in high-throughput studies; null mutant displays decreased mitochondrial genome loss (petite formation) and severe growth defect in minimal glycerol media
YJR150C	8.10279	RPH1	YJR150C|DAN1|S000003911|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YFL019C	7.94797	RPH1	YFL019C||S000001875|Dubious open reading frame unlikely to encode a protein; YFL019C is not an essential gene
YBR203W	7.9411	RPH1	YBR203W|COS111|S000000407|Protein required for resistance to the antifungal drug ciclopirox olamine; not related to the subtelomerically-encoded COS family; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YNL077W	7.883	RPH1	YNL077W|APJ1|S000005021|Putative chaperone of the HSP40 (DNAJ) family; overexpression interferes with propagation of the [Psi+] prion; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YNL179C	7.84073	RPH1	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
YBR132C	7.83049	RPH1	YBR132C|AGP2|S000000336|High affinity polyamine permease, preferentially uses spermidine over putrescine; expression is down-regulated by osmotic stress; plasma membrane carnitine transporter, also functions as a low-affinity amino acid permease
YKL031W	7.79823	RPH1	YKL031W||S000001514|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species
YPR117W	7.78458	RPH1	YPR117W||S000006321|Putative protein of unknown function
YIL100W	7.74566	RPH1	YIL100W||S000001362|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the dubious ORF YIL100C-A
YPL230W	7.71172	RPH1	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
YHL021C	7.66839	RPH1	YHL021C|AIM17|S000001013|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays decreased frequency of mitochondrial genome loss (petite formation)
YER065C	7.63222	RPH1	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
YJL144W	7.61109	RPH1	YJL144W||S000003680|Cytoplasmic hydrophilin of unknown function, possibly involved in the dessication response; expression induced by osmotic stress, starvation and during stationary phase; GFP-fusion protein is induced by the DNA-damaging agent MMS
YPR027C	7.60739	RPH1	YPR027C||S000006231|Putative protein of unknown function
YKR033C	7.59612	RPH1	YKR033C||S000001741|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene DAL80
YHR212W-A	7.58784	RPH1	YHR212W-A||S000028650|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YKL109W	7.53409	RPH1	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
YAL028W	7.50881	RPH1	YAL028W|FRT2|S000000026|Tail-anchored endoplasmic reticulum membrane protein, interacts with homolog Frt1p but is not a substrate of calcineurin (unlike Frt1p), promotes growth in conditions of high Na+, alkaline pH, or cell wall stress; potential Cdc28p substrate
YAL067C	7.43689	RPH1	YAL067C|SEO1|S000000062|Putative permease, member of the allantoate transporter subfamily of the major facilitator superfamily; mutation confers resistance to ethionine sulfoxide
YMR103C	7.36702	RPH1	YMR103C||S000004709|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YBR077C	7.3659	RPH1	YBR077C|SLM4|S000000281|Component of the EGO complex, which is involved in the regulation of microautophagy, and of the GSE complex, which is required for proper sorting of amino acid permease Gap1p; gene exhibits synthetic genetic interaction with MSS4
YEL010W	7.31385	RPH1	YEL010W||S000000736|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YMR118C	7.25377	RPH1	YMR118C||S000004724|Protein of unknown function with similarity to succinate dehydrogenase cytochrome b subunit; YMR118C is not an essential gene
YPL282C	7.09217	RPH1	YPL282C|PAU22|S000006203|Hypothetical protein
YPL017C	7.05114	RPH1	YPL017C|IRC15|S000005938|Putative S-adenosylmethionine-dependent methyltransferase of the seven beta-strand family, required for accurate meiotic chromosome segregation; null mutant displays increased levels of spontaneous Rad52 foci
YDR043C	7.02224	RPH1	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
YJL020C	7.01918	RPH1	YJL020C|BBC1|S000003557|Protein possibly involved in assembly of actin patches; interacts with an actin assembly factor Las17p and with the SH3 domains of Type I myosins Myo3p and Myo5p; localized predominantly to cortical actin patches
YMR256C	7.00728	RPH1	YMR256C|COX7|S000004869|Subunit VII of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain
YJR149W	6.97372	RPH1	YJR149W||S000003910|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YJL103C	6.97134	RPH1	YJL103C|GSM1|S000003639|Putative zinc cluster protein of unknown function; proposed to be involved in the regulation of energy metabolism, based on patterns of expression and sequence analysis
YAR050W	6.96545	RPH1	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
YLR337C	6.95707	RPH1	YLR337C|VRP1|S000004329|Proline-rich actin-associated protein involved in cytoskeletal organization and cytokinesis; related to mammalian Wiskott-Aldrich syndrome protein (WASP)-interacting protein (WIP)
YKL146W	6.94785	RPH1	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
YOL047C	6.94667	RPH1	YOL047C||S000005407|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YPR160W	6.93592	RPH1	YPR160W|GPH1|S000006364|Non-essential glycogen phosphorylase required for the mobilization of glycogen, activity is regulated by cyclic AMP-mediated phosphorylation, expression is regulated by stress-response elements and by the HOG MAP kinase pathway
YCR010C	6.90678	RPH1	YCR010C|ADY2|S000000603|Acetate transporter required for normal sporulation; phosphorylated in mitochondria
YMR170C	6.87255	RPH1	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
YHR138C	6.82697	RPH1	YHR138C||S000001180|Putative protein of unknown function; has similarity to Pbi2p; double null mutant lacking Pbi2p and Yhr138p exhibits highly fragmented vacuoles
YCR025C	6.80127	RPH1	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
YKL147C	6.73499	RPH1	YKL147C||S000001630|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; partially overlaps the verified gene AVT3
YJL161W	6.73088	RPH1	YJL161W|FMP33|S000003697|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YGR248W	6.69641	RPH1	YGR248W|SOL4|S000003480|6-phosphogluconolactonase with similarity to Sol3p
YAL039C	6.67619	RPH1	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)
YOR065W	6.67083	RPH1	YOR065W|CYT1|S000005591|Cytochrome c1, component of the mitochondrial respiratory chain; expression is regulated by the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex
YDR322C-A	6.6396	RPH1	YDR322C-A|TIM11|S000007255|Subunit e of mitochondrial F1F0-ATPase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; essential for the dimeric and oligomeric state of ATP synthase
YEL030C-A	6.61513	RPH1	YEL030C-A||S000028619|Identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YML091C	6.60296	RPH1	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
YLR136C	6.58337	RPH1	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
YDR446W	6.55622	RPH1	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
YMR084W	6.54723	RPH1	YMR084W||S000004689|Putative protein of unknown function; YMR084W and adjacent ORF YMR085W are merged in related strains
YEL008W	6.51656	RPH1	YEL008W||S000000734|Hypothetical protein predicted to be involved in metabolism
YPR061C	6.51625	RPH1	YPR061C|JID1|S000006265|Probable Hsp40p co-chaperone, has a DnaJ-like domain and appears to be involved in ER-associated degradation of misfolded proteins containing a tightly folded cytoplasmic domain; inhibits replication of Brome mosaic virus in S. cerevisiae
YPR002W	6.49706	RPH1	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
YKR015C	6.48351	RPH1	YKR015C||S000001723|Putative protein of unknown function
YMR304W	6.47462	RPH1	YMR304W|UBP15|S000004920|Ubiquitin-specific protease that may play a role in ubiquitin precursor processing
YOL119C	6.40168	RPH1	YOL119C|MCH4|S000005479|Protein with similarity to mammalian monocarboxylate permeases, which are involved in transport of monocarboxylic acids across the plasma membrane; mutant is not deficient in monocarboxylate transport
YPL206C	6.4015	RPH1	YPL206C|PGC1|S000006127|Phosphatidyl Glycerol phospholipase C; regulates the phosphatidylglycerol (PG) content via a phospholipase C-type degradation mechanism; contains glycerophosphodiester phosphodiesterase motifs
YLR178C	6.39837	RPH1	YLR178C|TFS1|S000004168|Carboxypeptidase Y inhibitor, function requires acetylation by the NatB N-terminal acetyltransferase; phosphatidylethanolamine-binding protein involved in protein kinase A signaling pathway
YNR047W	6.34738	RPH1	YNR047W||S000005330|Putative protein kinase that, when overexpressed, interferes with pheromone-induced growth arrest; localizes to the cytoplasm; potential Cdc28p substrate
YLR053C	6.33291	RPH1	YLR053C||S000004043|Putative protein of unknown function
YKR011C	6.33085	RPH1	YKR011C||S000001719|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the nucleus
YJL070C	6.2049	RPH1	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
YOR394W	6.19794	RPH1	YOR394W|PAU21|S000005921|Hypothetical protein
YEL009C	6.19164	RPH1	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
YLL056C	6.13723	RPH1	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
YDR504C	6.07534	RPH1	YDR504C|SPG3|S000002912|Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources
YOR178C	6.05039	RPH1	YOR178C|GAC1|S000005704|Regulatory subunit for Glc7p type-1 protein phosphatase (PP1), tethers Glc7p to Gsy2p glycogen synthase, binds Hsf1p heat shock transcription factor, required for induction of some HSF-regulated genes under heat shock
YOL082W	6.02606	RPH1	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
YBR006W	5.99472	RPH1	YBR006W|UGA2|S000000210|Succinate semialdehyde dehydrogenase involved in the utilization of gamma-aminobutyrate (GABA) as a nitrogen source; part of the 4-aminobutyrate and glutamate degradation pathways; localized to the cytoplasm
YGR149W	5.96984	RPH1	YGR149W||S000003381|Putative protein of unknown function; predicted to be an integal membrane protein
YPR145C-A	5.93546	RPH1	YPR145C-A||S000113589|Putative protein of unknown function
YOR285W	5.87337	RPH1	YOR285W||S000005811|Protein of unknown function, localized to the mitochondrial outer membrane
YGR066C	5.87136	RPH1	YGR066C||S000003298|Putative protein of unknown function
YDR216W	5.85955	RPH1	YDR216W|ADR1|S000002624|Carbon source-responsive zinc-finger transcription factor, required for transcription of the glucose-repressed gene ADH2, of peroxisomal protein genes, and of genes required for ethanol, glycerol, and fatty acid utilization
YBL078C	5.71966	RPH1	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
YDR255C	5.70931	RPH1	YDR255C|RMD5|S000002663|Cytosolic protein required for sporulation; also required for the ubiquitination of the gluconeogenetic enzyme fructose-1,6-bisphosphatase, which is degraded rapidly after the switch from gluconeogenesis to glycolysis
YJL045W	5.69892	RPH1	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
YMR280C	5.6876	RPH1	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
YHR097C	5.68391	RPH1	YHR097C||S000001139|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and the nucleus
YDR403W	5.64906	RPH1	YDR403W|DIT1|S000002811|Sporulation-specific enzyme required for spore wall maturation, involved in the production of a soluble LL-dityrosine-containing precursor of the spore wall; transcripts accumulate at the time of prospore enclosure
YCL025C	5.64181	RPH1	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)
YAR047C	5.60903	RPH1	YAR047C||S000000083|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YFL054C	5.58369	RPH1	YFL054C||S000001840|Putative channel-like protein; similar to Fps1p; mediates passive diffusion of glycerol in the presence of ethanol
YGL170C	5.57273	RPH1	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
YBR051W	5.55179	RPH1	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
YPR193C	5.52988	RPH1	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
YHR150W	5.45374	RPH1	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
YPL147W	5.4433	RPH1	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
YGL010W	5.42741	RPH1	YGL010W||S000002978|Putative protein of unknown function; YGL010W is not an essential gene
YOL154W	5.39523	RPH1	YOL154W|ZPS1|S000005514|Putative GPI-anchored protein; transcription is induced under low-zinc conditions, as mediated by the Zap1p transcription factor, and at alkaline pH
YHR001W-A	5.37651	RPH1	YHR001W-A|QCR10|S000003529|Subunit of the ubiqunol-cytochrome c oxidoreductase complex which includes Cobp, Rip1p, Cyt1p, Cor1p, Qcr2p, Qcr6p, Qcr7p, Qcr8p, Qcr9p, and Qcr10p and comprises part of the mitochondrial respiratory chain
YDR119W-A	5.37389	RPH1	YDR119W-A||S000113555|Putative protein of unknown function
YER035W	5.36908	RPH1	YER035W|EDC2|S000000837|RNA-binding protein, activates mRNA decapping directly by binding to the mRNA substrate and enhancing the activity of the decapping proteins Dcp1p and Dcp2p
YGR268C	5.36426	RPH1	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
YJL166W	5.34024	RPH1	YJL166W|QCR8|S000003702|Subunit 8 of ubiquinol cytochrome-c reductase complex, which is a component of the mitochondrial inner membrane electron transport chain; oriented facing the intermembrane space; expression is regulated by Abf1p and Cpf1p
YMR195W	5.32618	RPH1	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
YBR050C	5.32496	RPH1	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
YJR146W	5.30591	RPH1	YJR146W||S000003907|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene HMS2
YNL242W	5.29248	RPH1	YNL242W|ATG2|S000005186|Peripheral membrane protein required for vesicle formation during autophagy, pexophagy, and the cytoplasm-to-vaucole targeting (Cvt) pathway; involved in Atg9p cycling between the pre-autophagosomal structure and mitochondria
YGL104C	5.2747	RPH1	YGL104C|VPS73|S000003072|Mitochondrial protein; mutation affects vacuolar protein sorting; putative transporter; member of the sugar porter family
YDR443C	5.26102	RPH1	YDR443C|SSN2|S000002851|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; required for stable association of Srb10p-Srb11p kinase; essential for transcriptional regulation
YDR022C	5.23925	RPH1	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
YLR395C	5.23833	RPH1	YLR395C|COX8|S000004387|Subunit VIII of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain
YFL020C	5.21429	RPH1	YFL020C|PAU5|S000001874|Part of 23-member seripauperin multigene family encoded mainly in subtelomeric regions, active during alcoholic fermentation, regulated by anaerobiosis, negatively regulated by oxygen, repressed by heme
YHR211W	5.18365	RPH1	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
YEL030W	5.12927	RPH1	YEL030W|ECM10|S000000756|Heat shock protein of the Hsp70 family, localized in mitochondrial nucleoids, plays a role in protein translocation, interacts with Mge1p in an ATP-dependent manner; overexpression induces extensive mitochondrial DNA aggregations
YGR110W	5.12833	RPH1	YGR110W||S000003342|Putative protein of unknown function; transcription is increased in response to genotoxic stress; plays a role in restricting Ty1 transposition
YHR082C	5.08956	RPH1	YHR082C|KSP1|S000001124|Nonessential putative serine/threonine protein kinase of unknown cellular role; overproduction causes allele-specific suppression of the prp20-10 mutation
YOR020W-A	5.02006	RPH1	YOR020W-A||S000028526|Putative protein of unknown function, conserved in A. gossypii; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR178W	5.01971	RPH1	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
YCL039W	4.96533	RPH1	YCL039W|GID7|S000000544|Protein of unknown function, involved in proteasome-dependent catabolite inactivation of fructose-1,6-bisphosphatase; contains six WD40 repeats; computational analysis suggests that Gid7p and Moh1p have similar functions
YLR030W	4.95774	RPH1	YLR030W||S000004020|Putative protein of unknown function
YNL055C	4.94137	RPH1	YNL055C|POR1|S000005000|Mitochondrial porin (voltage-dependent anion channel), outer membrane protein required for the maintenance of mitochondrial osmotic stability and mitochondrial membrane permeability; phosphorylated
YCR083W	4.91889	RPH1	YCR083W|TRX3|S000000679|Mitochondrial thioredoxin, highly conserved oxidoreductase required to maintain the redox homeostasis of the cell, forms the mitochondrial thioredoxin system with Trr2p, redox state is maintained by both Trr2p and Glr1p
YKR058W	4.90827	RPH1	YKR058W|GLG1|S000001766|Self-glucosylating initiator of glycogen synthesis, also glucosylates n-dodecyl-beta-D-maltoside; similar to mammalian glycogenin
YCR021C	4.90392	RPH1	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
YLL055W	4.89247	RPH1	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
YDR479C	4.85025	RPH1	YDR479C|PEX29|S000002887|Peroxisomal integral membrane peroxin, involved in the regulation of peroxisomal size, number and distribution; genetic interactions suggest that Pex28p and Pex29p act at steps upstream of those mediated by Pex30p, Pex31p, and Pex32p
YLL042C	4.84826	RPH1	YLL042C|ATG10|S000003965|E2-like conjugating enzyme that mediates formation of the Atg12p-Atg5p conjugate, which is a critical step in autophagy
YDL021W	4.82062	RPH1	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
YGR053C	4.78704	RPH1	YGR053C||S000003285|Putative protein of unknown function
YNL009W	4.77614	RPH1	YNL009W|IDP3|S000004954|Peroxisomal NADP-dependent isocitrate dehydrogenase, catalyzes oxidation of isocitrate to alpha-ketoglutarate with the formation of NADP(H+), required for growth on unsaturated fatty acids
YMR017W	4.76482	RPH1	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
YHR171W	4.73005	RPH1	YHR171W|ATG7|S000001214|Autophagy-related protein and dual specificity member of the E1 family of ubiquitin-activating enzymes; mediates the conjugation of Atg12p with Atg5p and Atg8p with phosphatidylethanolamine, required steps in autophagosome formation
YIR027C	4.67273	RPH1	YIR027C|DAL1|S000001466|Allantoinase, converts allantoin to allantoate in the first step of allantoin degradation; expression sensitive to nitrogen catabolite repression
YPL087W	4.61798	RPH1	YPL087W|YDC1|S000006008|Alkaline dihydroceramidase, involved in sphingolipid metabolism; preferentially hydrolyzes dihydroceramide to a free fatty acid and dihydrosphingosine; has a minor reverse activity
YOR347C	4.58389	RPH1	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
YOL100W	4.54841	RPH1	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
YDR077W	4.49676	RPH1	YDR077W|SED1|S000002484|Major stress-induced structural GPI-cell wall glycoprotein in stationary-phase cells, associates with translating ribosomes, possible role in mitochondrial genome maintenance; ORF contains two distinct variable minisatellites
YBR147W	4.49534	RPH1	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
YKL044W	4.49098	RPH1	YKL044W||S000001527|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YHL032C	4.46748	RPH1	YHL032C|GUT1|S000001024|Glycerol kinase, converts glycerol to glycerol-3-phosphate; glucose repression of expression is mediated by Adr1p and Ino2p-Ino4p; derepression of expression on non-fermentable carbon sources is mediated by Opi1p and Rsf1p
YJR091C	4.45722	RPH1	YJR091C|JSN1|S000003851|Member of the Puf family of RNA-binding proteins, interacts with mRNAs encoding membrane-associated proteins; overexpression suppresses a tub2-150 mutation and causes increased sensitivity to benomyl in wild-type cells
YLR258W	4.43619	RPH1	YLR258W|GSY2|S000004248|Glycogen synthase, similar to Gsy1p; expression induced by glucose limitation, nitrogen starvation, heat shock, and stationary phase; activity regulated by cAMP-dependent, Snf1p and Pho85p kinases as well as by the Gac1p-Glc7p phosphatase
YIL146C	4.39852	RPH1	YIL146C|ECM37|S000001408|Non-essential protein of unknown function
YHR078W	4.39835	RPH1	YHR078W||S000001120|High osmolarity-regulated gene of unknown function
YJL102W	4.36142	RPH1	YJL102W|MEF2|S000003638|Mitochondrial elongation factor involved in translational elongation
YLR366W	4.34365	RPH1	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
YIR014W	4.30073	RPH1	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
YFL030W	4.29679	RPH1	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
YGR194C	4.29076	RPH1	YGR194C|XKS1|S000003426|Xylulokinase, converts D-xylulose and ATP to xylulose 5-phosphate and ADP; rate limiting step in fermentation of xylulose; required for xylose fermentation by recombinant S. cerevisiae strains
YJL213W	4.27062	RPH1	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
YOR227W	4.26504	RPH1	YOR227W||S000005753|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YLR431C	4.25211	RPH1	YLR431C|ATG23|S000004423|Peripheral membrane protein required for the cytoplasm-to-vacuole targeting (Cvt) pathway; cycles between the pre-autophagosome (PAS) and non-PAS locations; forms a complex with Atg9p and Atg27p
YNL015W	4.25068	RPH1	YNL015W|PBI2|S000004960|Cytosolic inhibitor of vacuolar proteinase B, required for efficient vacuole inheritance; with thioredoxin forms protein complex LMA1, which assists in priming SNARE molecules and promotes vacuole fusion
YBR183W	4.24396	RPH1	YBR183W|YPC1|S000000387|Alkaline ceramidase that also has reverse (CoA-independent) ceramide synthase activity, catalyzes both breakdown and synthesis of phytoceramide; overexpression confers fumonisin B1 resistance
YDR542W	4.2309	RPH1	YDR542W|PAU10|S000002950|Hypothetical protein
YJL067W	4.22243	RPH1	YJL067W||S000003603|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YCR018C-A	4.21768	RPH1	YCR018C-A||S000007230|Putative protein of unknown function; encoded opposite a Ty1 LTR
YIL006W	4.21249	RPH1	YIL006W|YIA6|S000001268|Mitochondrial NAD+ transporter, involved in the transport of NAD+ into the mitochondria (see also YEA6); member of the mitochondrial carrier subfamily; disputed role as a pyruvate transporter; has putative mouse and human orthologs
YIR037W	4.20219	RPH1	YIR037W|HYR1|S000001476|Thiol peroxidase that functions as a hydroperoxide receptor to sense intracellular hydroperoxide levels and transduce a redox signal to the Yap1p transcription factor
YKR016W	4.17618	RPH1	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
YJR038C	4.14346	RPH1	YJR038C||S000003799|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YLR346C	4.14177	RPH1	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
YHR071W	4.13069	RPH1	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
YLL026W	4.09937	RPH1	YLL026W|HSP104|S000003949|Heat shock protein that cooperates with Ydj1p (Hsp40) and Ssa1p (Hsp70) to refold and reactivate previously denatured, aggregated proteins; responsive to stresses including: heat, ethanol, and sodium arsenite; involved in [PSI+] propagation
YER121W	4.08811	RPH1	YER121W||S000000923|Putative protein of unknown function; may be involved in phosphatase regulation and/or generation of precursor metabolites and energy
YPL203W	4.07916	RPH1	YPL203W|TPK2|S000006124|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 Tpk1p and Tpk3p
YIL059C	4.06041	RPH1	YIL059C||S000001321|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YIL060W
YJL019W	4.04401	RPH1	YJL019W|MPS3|S000003556|Essential integral membrane protein required for spindle pole body duplication and for nuclear fusion, localizes to the spindle pole body half bridge, interacts with DnaJ-like chaperone Jem1p and with centrin homolog Cdc31p
YHR075C	4.03176	RPH1	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
YJL066C	3.94449	RPH1	YJL066C|MPM1|S000003602|Mitochondrial membrane protein of unknown function, contains no hydrophobic stretches
YHR104W	3.94364	RPH1	YHR104W|GRE3|S000001146|Aldose reductase involved in methylglyoxal, d-xylose and arabinose metabolism; stress induced (osmotic, ionic, oxidative, heat shock, starvation and heavy metals); regulated by the HOG pathway
YDR001C	3.89781	RPH1	YDR001C|NTH1|S000002408|Neutral trehalase, degrades trehalose; required for thermotolerance and may mediate resistance to other cellular stresses; may be phosphorylated by Cdc28p
YOR054C	3.89397	RPH1	YOR054C|VHS3|S000005580|Functionally redundant (see also SIS2) inhibitory subunit of Ppz1p, a PP1c-related ser/thr protein phosphatase Z isoform; synthetically lethal with sis2; putative phosphopantothenoylcysteine decarboxylase involved in coenzyme A biosynthesis
YGL227W	3.85279	RPH1	YGL227W|VID30|S000003196|Protein involved in proteasome-dependent catabolite degradation of fructose-1,6-bisphosphatase (FBPase); shifts the balance of nitrogen metabolism toward the production of glutamate; localized to the nucleus and the cytoplasm
YFL053W	3.84873	RPH1	YFL053W|DAK2|S000001841|Dihydroxyacetone kinase, required for detoxification of dihydroxyacetone (DHA); involved in stress adaptation
YOL117W	3.84495	RPH1	YOL117W|RRI2|S000005477|Subunit of the COP9 signalosome (CSN) complex that cleaves the ubiquitin-like protein Nedd8 from SCF ubiquitin ligases; plays a role in the mating pheromone response
YDL243C	3.82823	RPH1	YDL243C|AAD4|S000002402|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase, involved in the oxidative stress response
YBR298C	3.82236	RPH1	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
YCR030C	3.80586	RPH1	YCR030C|SYP1|S000000626|Protein with a potential role in actin cytoskeletal organization; overexpression suppresses a pfy1 (profilin) null mutation
YOL163W	3.7906	RPH1	YOL163W||S000005523|Putative protein of unknown function; member of the Dal5p subfamily of the major facilitator family
YDL169C	3.78886	RPH1	YDL169C|UGX2|S000002328|Protein of unknown function, transcript accumulates in response to any combination of stress conditions
YNR002C	3.77336	RPH1	YNR002C|ATO2|S000005285|Putative transmembrane protein involved in export of ammonia, a starvation signal that promotes cell death in aging colonies; phosphorylated in mitochondria; member of the TC 9.B.33 YaaH family; homolog of Ady2p and Y. lipolytica Gpr1p
YGL205W	3.77284	RPH1	YGL205W|POX1|S000003173|Fatty-acyl coenzyme A oxidase, involved in the fatty acid beta-oxidation pathway; localized to the peroxisomal matrix
YBR128C	3.77068	RPH1	YBR128C|ATG14|S000000332|Autophagy-specific subunit of phosphatidylinositol 3-kinase complex I (with Vps34p, Vps15p, and Vps30p); Atg14p targets complex I to the pre-autophagosomal structure (PAS); required for localizing additional ATG proteins to the PAS
YDL124W	3.77002	RPH1	YDL124W||S000002282|NADPH-dependent alpha-keto amide reductase; reduces aromatic alpha-keto amides, aliphatic alpha-keto esters, and aromatic alpha-keto esters; member of the aldo-keto reductase (AKR) family
YHL024W	3.75364	RPH1	YHL024W|RIM4|S000001016|Putative RNA-binding protein required for the expression of early and middle sporulation genes
YPL261C	3.75167	RPH1	YPL261C||S000006182|Dubious open reading frame unlikely to encode a protein; partially overlaps the uncharacterized ORF YPL260W
YNL125C	3.74322	RPH1	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
YLR296W	3.74135	RPH1	YLR296W||S000004287|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YOR386W	3.66695	RPH1	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
YAL066W	3.65516	RPH1	YAL066W||S000000061|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YBL064C	3.6411	RPH1	YBL064C|PRX1|S000000160|Mitochondrial peroxiredoxin (1-Cys Prx) with thioredoxin peroxidase activity, has a role in reduction of hydroperoxides; induced during respiratory growth and under conditions of oxidative stress; phosphorylated
YBR169C	3.61776	RPH1	YBR169C|SSE2|S000000373|Member of the heat shock protein 70 (HSP70) family; may be involved in protein folding; localized to the cytoplasm; highly homologous to the heat shock protein Sse1p
YDL110C	3.61215	RPH1	YDL110C|TMA17|S000002268|Protein of unknown function that associates with ribosomes
YCR007C	3.58303	RPH1	YCR007C||S000000600|Putative integral membrane protein, member of DUP240 gene family; YCR007C is not an essential gene
YLR205C	3.56845	RPH1	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
YLL025W	3.56386	RPH1	YLL025W|PAU17|S000003948|Putative protein of unknown function; YLL025W is not an essential gene
YBL101C	3.55008	RPH1	YBL101C|ECM21|S000000197|Non-essential protein of unknown function; promoter contains several Gcn4p binding elements
YMR271C	3.53366	RPH1	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
YPL021W	3.52913	RPH1	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
YGL177W	3.51018	RPH1	YGL177W||S000003145|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPL061W	3.50934	RPH1	YPL061W|ALD6|S000005982|Cytosolic aldehyde dehydrogenase, activated by Mg2+ and utilizes NADP+ as the preferred coenzyme; required for conversion of acetaldehyde to acetate; constitutively expressed; locates to the mitochondrial outer surface upon oxidative stress
YDR402C	3.48001	RPH1	YDR402C|DIT2|S000002810|N-formyltyrosine oxidase, sporulation-specific microsomal enzyme involved in the production of N,N-bisformyl dityrosine required for spore wall maturation, homologous to cytochrome P-450s
YLR174W	3.4756	RPH1	YLR174W|IDP2|S000004164|Cytosolic NADP-specific isocitrate dehydrogenase, catalyzes oxidation of isocitrate to alpha-ketoglutarate; levels are elevated during growth on non-fermentable carbon sources and reduced during growth on glucose
YOR055W	3.44804	RPH1	YOR055W||S000005581|Dubious open reading frame unlikely to encode a functional protein; based on available experimental and comparative sequence data
YHR176W	3.44436	RPH1	YHR176W|FMO1|S000001219|Flavin-containing monooxygenase, localized to the cytoplasmic face of the ER membrane; catalyzes oxidation of biological thiols to maintain the ER redox buffer ratio for correct folding of disulfide-bonded proteins
YGL045W	3.43943	RPH1	YGL045W|RIM8|S000003013|Protein of unknown function, involved in the proteolytic activation of Rim101p in response to alkaline pH; has similarity to A. nidulans PalF
YHR095W	3.42564	RPH1	YHR095W||S000001137|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGL258W-A	3.42195	RPH1	YGL258W-A||S000007607|Putative protein of unknown function
YPR098C	3.42098	RPH1	YPR098C||S000006302|Protein of unknown function, localized to the mitochondrial outer membrane
YPL123C	3.39926	RPH1	YPL123C|RNY1|S000006044|RNAse; member of the T(2) family of endoribonucleases
YAL055W	3.39553	RPH1	YAL055W|PEX22|S000000051|Putative peroxisomal membrane protein required for import of peroxisomal proteins, functionally complements a Pichia pastoris pex22 mutation
YOL110W	3.38484	RPH1	YOL110W|SHR5|S000005470|Subunit of a palmitoyltransferase, composed of Shr5p and Erf2p, that adds a palmitoyl lipid moiety to heterolipidated substrates such as Ras1p and Ras2p through a thioester linkage; palmitoylation is required for Ras2p membrane localization
YFL036W	3.3827	RPH1	YFL036W|RPO41|S000001858|Mitochondrial RNA polymerase; single subunit enzyme similar to those of T3 and T7 bacteriophages; requires a specificity subunit encoded by MTF1 for promoter recognition
YKL105C	3.37986	RPH1	YKL105C||S000001588|Putative protein of unknown function
YCR086W	3.33099	RPH1	YCR086W|CSM1|S000000682|Nucleolar protein that forms a complex with Lrs4p which binds Mam1p at kinetochores during meiosis I to mediate accurate chromosome segregation, may be involved in premeiotic DNA replication; possible role in telomere maintenance
YHR008C	3.31734	RPH1	YHR008C|SOD2|S000001050|Mitochondrial superoxide dismutase, protects cells against oxygen toxicity; phosphorylated
YBL045C	3.3147	RPH1	YBL045C|COR1|S000000141|Core subunit of the ubiquinol-cytochrome c reductase complex (bc1 complex), which is a component of the mitochondrial inner membrane electron transport chain
YOR152C	3.27867	RPH1	YOR152C||S000005678|Putative protein of unknown function; has no similarity to any known protein; YOR152C is not an essential gene
YIR036C	3.276	RPH1	YIR036C|IRC24|S000001475|Putative benzil reductase;(GFP)-fusion protein localizes to the cytoplasm and is induced by the DNA-damaging agent MMS; sequence similarity with short-chain dehydrogenase/reductases; null mutant has increased spontaneous Rad52p foci
YER039C-A	3.27152	RPH1	YER039C-A||S000007226|Putative protein of unknown function; YER039C-A is not an essential gene
YNL190W	3.24581	RPH1	YNL190W||S000005134|Cell wall protein of unknown function; proposed role as a hydrophilin induced by osmotic stress; contains a putative GPI-attachment site
YAL060W	3.22639	RPH1	YAL060W|BDH1|S000000056|NAD-dependent (R,R)-butanediol dehydrogenase, catalyzes oxidation of (R,R)-2,3-butanediol to (3R)-acetoin, oxidation of meso-butanediol to (3S)-acetoin, and reduction of acetoin; enhances use of 2,3-butanediol as an aerobic carbon source
YOL048C	3.20448	RPH1	YOL048C||S000005408|Putative protein of unknown function
YAL030W	3.19923	RPH1	YAL030W|SNC1|S000000028|Vesicle membrane receptor protein (v-SNARE) involved in the fusion between Golgi-derived secretory vesicles with the plasma membrane; proposed to be involved in endocytosis; member of the synaptobrevin/VAMP family of R-type v-SNARE proteins
YJR155W	3.19501	RPH1	YJR155W|AAD10|S000003916|Putative aryl-alcohol dehydrogenase with similarity to P. chrysosporium aryl-alcohol dehydrogenase; mutational analysis has not yet revealed a physiological role
YLR037C	3.19115	RPH1	YLR037C|DAN2|S000004027|Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, completely repressed during aerobic growth
YLR365W	3.15729	RPH1	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
YPR172W	3.15651	RPH1	YPR172W||S000006376|Protein of unknown function, transcriptionally activated by Yrm1p along with genes involved in multidrug resistance
YHR106W	3.13152	RPH1	YHR106W|TRR2|S000001148|Mitochondrial thioredoxin reductase involved in protection against oxidative stress, required with Glr1p to maintain the redox state of Trx3p; contains active-site motif (CAVC) present in prokaryotic orthologs; binds NADPH and FAD
YOR049C	3.12136	RPH1	YOR049C|RSB1|S000005575|Suppressor of sphingoid long chain base (LCB) sensitivity of an LCB-lyase mutation; putative integral membrane transporter or flippase that may transport LCBs from the cytoplasmic side toward the extracytoplasmic side of the membrane
YEL007W	3.11866	RPH1	YEL007W||S000000733|Putative protein with sequence similarity to S. pombe gti1+ (gluconate transport inducer 1)
YDR445C	3.11764	RPH1	YDR445C||S000002853|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGR238C	3.11552	RPH1	YGR238C|KEL2|S000003470|Protein that functions in a complex with Kel1p to negatively regulate mitotic exit, interacts with Tem1p and Lte1p; localizes to regions of polarized growth; potential Cdc28p substrate
YDR148C	3.07739	RPH1	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
YPR154W	3.052	RPH1	YPR154W|PIN3|S000006358|Protein that induces appearance of [PIN+] prion when overproduced
YPR150W	3.05083	RPH1	YPR150W||S000006354|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene SUE1/YPR151C
YDR335W	3.0354	RPH1	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
YJL037W	3.03004	RPH1	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
YCR096C	3.02029	RPH1	YCR096C|HMRA2|S000000692|Silenced copy of a2 at HMR; similarity to Alpha2p; required along with a1p for inhibiting expression of the HO endonuclease in a/alpha HO/HO diploid cells with an active mating-type interconversion system
YBR018C	3.01135	RPH1	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
YLR399C	2.99233	RPH1	YLR399C|BDF1|S000004391|Protein involved in transcription initiation at TATA-containing promoters; associates with the basal transcription factor TFIID; contains two bromodomains; corresponds to the C-terminal region of mammalian TAF1; redundant with Bdf2p
YOR329W-A	2.98412	RPH1	YOR329W-A||S000028585|Dubious open reading frame, unlikely to encode a functional protein; identified by fungal homology and RT-PCR
YLR295C	2.98128	RPH1	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
YLR251W	2.97886	RPH1	YLR251W|SYM1|S000004241|Protein required for ethanol metabolism; induced by heat shock and localized to the inner mitochondrial membrane; homologous to mammalian peroxisomal membrane protein Mpv17
YLR345W	2.97709	RPH1	YLR345W||S000004337|Similar to 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase enzymes responsible for the metabolism of fructoso-2,6-bisphosphate; mRNA expression is repressed by the Rfx1p-Tup1p-Ssn6p repressor complex; YLR345W is not an essential gene
YCL048W	2.97365	RPH1	YCL048W|SPS22|S000000553|Protein of unknown function, redundant with Sps2p for the organization of the beta-glucan layer of the spore wall
YOL084W	2.96651	RPH1	YOL084W|PHM7|S000005444|Protein of unknown function, expression is regulated by phosphate levels; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery and vacuole
YNL093W	2.96252	RPH1	YNL093W|YPT53|S000005037|GTPase, similar to Ypt51p and Ypt52p and to mammalian rab5; required for vacuolar protein sorting and endocytosis
YOR344C	2.95745	RPH1	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
YOR035C	2.93763	RPH1	YOR035C|SHE4|S000005561|Protein containing a UCS (UNC-45/CRO1/SHE4) domain, binds to myosin motor domains to regulate myosin function; involved in endocytosis, polarization of the actin cytoskeleton, and asymmetric mRNA localization
YER053C	2.92097	RPH1	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
YDL182W	2.91347	RPH1	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
YGR059W	2.90871	RPH1	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
YGL249W	2.90494	RPH1	YGL249W|ZIP2|S000003218|Meiosis-specific protein involved in normal synaptonemal complex formation and pairing between homologous chromosomes during meiosis
YDR173C	2.89571	RPH1	YDR173C|ARG82|S000002580|Inositol polyphosphate multikinase (IPMK), sequentially phosphorylates Ins(1,4,5)P3 to form Ins(1,3,4,5,6)P5; also has diphosphoinositol polyphosphate synthase activity; regulates arginine-, phosphate-, and nitrogen-responsive genes
YMR018W	2.88079	RPH1	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
YCR097W	2.87875	RPH1	YCR097W|HMRA1|S000000694|Silenced copy of a1 at HMR; homeobox corepressor that interacts with Alpha2p to repress haploid-specific gene transcription in diploid cells
YCL048W-A	2.85739	RPH1	YCL048W-A||S000087203|Putative protein of unknown function
YHR054W-A	2.85478	RPH1	YHR054W-A||S000028648|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps CUP1-2
YDR397C	2.84443	RPH1	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
YOR036W	2.83668	RPH1	YOR036W|PEP12|S000005562|Target membrane receptor (t-SNARE) for vesicular intermediates traveling between the Golgi apparatus and the vacuole; controls entry of biosynthetic, endocytic, and retrograde traffic into the prevacuolar compartment; syntaxin
YHR053C	2.83326	RPH1	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
YOR020C	2.82815	RPH1	YOR020C|HSP10|S000005546|Mitochondrial matrix co-chaperonin that inhibits the ATPase activity of Hsp60p, a mitochondrial chaperonin; involved in protein folding and sorting in the mitochondria; 10 kD heat shock protein with similarity to E. coli groES
YKL043W	2.80465	RPH1	YKL043W|PHD1|S000001526|Transcriptional activator that enhances pseudohyphal growth; regulates expression of FLO11, an adhesin required for pseudohyphal filament formation; similar to StuA, an A. nidulans developmental regulator; potential Cdc28p substrate
YER101C	2.79502	RPH1	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
YNL195C	2.79414	RPH1	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
YJL135W	2.79064	RPH1	YJL135W||S000003671|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified genes YJL134W/LCB3
YHR055C	2.78221	RPH1	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
YJL059W	2.77821	RPH1	YJL059W|YHC3|S000003595|Vacuolar membrane protein involved in the ATP-dependent transport of arginine into the vacuole and possibly in balancing ion homeostasis; homolog of human CLN3 involved in Batten disease (juvenile onset neuronal ceroid lipofuscinosis)
YLR347C	2.7753	RPH1	YLR347C|KAP95|S000004339|Karyopherin beta, forms a dimeric complex with Srp1p (Kap60p) that mediates nuclear import of cargo proteins via a nuclear localization signal (NLS), interacts with nucleoporins to guide transport across the nuclear pore complex
YOR032C	2.77383	RPH1	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
YDR490C	2.76762	RPH1	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
YNL305C	2.75476	RPH1	YNL305C||S000005249|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; YNL305C is not an essential gene
YBR053C	2.73132	RPH1	YBR053C||S000000257|Putative protein of unknown function; induced by cell wall perturbation
YHR080C	2.72119	RPH1	YHR080C||S000001122|Protein of unknown function that may interact with ribosomes, based on co-purification experiments; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YKL129C	2.7107	RPH1	YKL129C|MYO3|S000001612|One of two type I myosins; localizes to actin cortical patches; deletion of MYO3 has little effect on growth, but myo3 myo5 double deletion causes severe defects in growth and actin cytoskeleton organization
YOR211C	2.70181	RPH1	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
YOR377W	2.69275	RPH1	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
YNL091W	2.69059	RPH1	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
YEL060C	2.6836	RPH1	YEL060C|PRB1|S000000786|Vacuolar proteinase B (yscB), a serine protease of the subtilisin family; involved in protein degradation in the vacuole and required for full protein degradation during sporulation
YER054C	2.68224	RPH1	YER054C|GIP2|S000000856|Putative regulatory subunit of the protein phosphatase Glc7p, involved in glycogen metabolism; contains a conserved motif (GVNK motif) that is also found in Gac1p, Pig1p, and Pig2p
YDL070W	2.66261	RPH1	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
YER169W	2.6553	RPH1	YER169W|RPH1|S000000971|JmjC domain-containing histone demethylase which can specifically demethylate H3K36 tri- and dimethyl modification states; transcriptional repressor of PHR1; Rph1p phosphorylation during DNA damage is under control of the MEC1-RAD53 pathway
YOR376W	2.65322	RPH1	YOR376W||S000005903|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; YOR376W is not an essential gene.
YOL126C	2.64471	RPH1	YOL126C|MDH2|S000005486|Cytoplasmic malate dehydrogenase, one of three isozymes that catalyze interconversion of malate and oxaloacetate; involved in the glyoxylate cycle and gluconeogenesis during growth on two-carbon compounds; interacts with Pck1p and Fbp1
YLR001C	2.63781	RPH1	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
YNL144C	2.63003	RPH1	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
YHR199C	2.62584	RPH1	YHR199C|AIM46|S000001242|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YPL260W	2.57804	RPH1	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
YGR141W	2.55916	RPH1	YGR141W|VPS62|S000003373|Vacuolar protein sorting (VPS) protein required for cytoplasm to vacuole targeting of proteins
YIL054W	2.55433	RPH1	YIL054W||S000001316|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YFR019W	2.54853	RPH1	YFR019W|FAB1|S000001915|1-phosphatidylinositol-3-phosphate 5-kinase; vacuolar membrane kinase that generates phosphatidylinositol (3,5)P2, which is involved in vacuolar sorting and homeostasis
YHR210C	2.54664	RPH1	YHR210C||S000001253|Putative protein of unknown function; non-essential gene; highly expressed under anaeorbic conditions; sequence similarity to aldose 1-epimerases such as GAL10
YMR160W	2.54472	RPH1	YMR160W||S000004770|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the membrane of the vacuole; mutant has enhanced sensitivity to overexpression of mutant huntingtin; YMR160W is not an essential gene
YBR085C-A	2.5318	RPH1	YBR085C-A||S000007522|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and to the nucleus
YDL009C	2.52336	RPH1	YDL009C||S000002167|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the uncharacterized ORF YDL010W; YDL009C is not an essential gene
YNL011C	2.51291	RPH1	YNL011C||S000004956|Putative protein of unknown function; YNL011C is not an essential gene
YIL122W	2.50512	RPH1	YIL122W|POG1|S000001384|Putative transcriptional activator that promotes recovery from pheromone induced arrest; inhibits both alpha-factor induced G1 arrest and repression of CLN1 and CLN2 via SCB/MCB promoter elements; potential Cdc28p substrate; SBF regulated
YNL025C	2.50444	RPH1	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
YPL224C	2.47934	RPH1	YPL224C|MMT2|S000006145|Putative metal transporter involved in mitochondrial iron accumulation; closely related to Mmt1p
YMR297W	2.47264	RPH1	YMR297W|PRC1|S000004912|Vacuolar carboxypeptidase Y (proteinase C), broad-specificity C-terminal exopeptidase involved in non-specific protein degradation in the vacuole; member of the serine carboxypeptidase family
YIL007C	2.46987	RPH1	YIL007C|NAS2|S000001269|Protein with similarity to the p27 subunit of mammalian proteasome modulator; not essential; interacts with Rpn4p
YPL272C	2.45819	RPH1	YPL272C||S000006193|Putative protein of unknown function; gene expression induced in response to ketoconazole; YPL272C is not an essential gene
YJR039W	2.45593	RPH1	YJR039W||S000003800|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDL199C	2.44867	RPH1	YDL199C||S000002358|Putative transporter, member of the sugar porter family
YOR290C	2.44074	RPH1	YOR290C|SNF2|S000005816|Catalytic subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; contains DNA-stimulated ATPase activity; functions interdependently in transcriptional activation with Snf5p and Snf6p
YER084W	2.42916	RPH1	YER084W||S000000886|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDL072C	2.42889	RPH1	YDL072C|YET3|S000002230|Protein of unknown function; YET3 null mutant decreases the level of secreted invertase; homolog of human BAP31 protein
YPR028W	2.42558	RPH1	YPR028W|YOP1|S000006232|Membrane protein that interacts with Yip1p to mediate membrane traffic; overexpression results in cell death and accumulation of internal cell membranes; regulates vesicular traffic in stressed cells
YDR476C	2.40771	RPH1	YDR476C||S000002884|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YDR476C is not an essential gene
YHL036W	2.39245	RPH1	YHL036W|MUP3|S000001028|Low affinity methionine permease, similar to Mup1p
YDL149W	2.39242	RPH1	YDL149W|ATG9|S000002308|Transmembrane protein involved in formation of Cvt and autophagic vesicles; cycles between the pre-autophagosomal structure and other cytosolic punctate structures, not found in autophagosomes; forms a complex with Atg23p and Atg27p
YDL113C	2.38895	RPH1	YDL113C|ATG20|S000002271|Sorting nexin family member required for the cytoplasm-to-vacuole targeting (Cvt) pathway and for endosomal sorting; has a Phox homology domain that binds phosphatidylinositol-3-phosphate; interacts with Snx4p; potential Cdc28p substrate
YFL052W	2.37974	RPH1	YFL052W||S000001842|Putative zinc cluster protein that contains a DNA binding domain; null mutant sensitive to calcofluor white, low osmolarity and heat, suggesting a role for YFL052Wp in cell wall integrity
YDR541C	2.37809	RPH1	YDR541C||S000002949|Putative dihydrokaempferol 4-reductase
YBL039W-B	2.3751	RPH1	YBL039W-B||S000028517|Putative protein of unknown function
YDL244W	2.37214	RPH1	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
YAL031C	2.36462	RPH1	YAL031C|GIP4|S000000029|Cytoplasmic Glc7-interacting protein whose overexpression relocalizes Glc7p from the nucleus and prevents chromosome segregation; potential Cdc28p substrate
YOL160W	2.35745	RPH1	YOL160W||S000005520|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YKR067W	2.35271	RPH1	YKR067W|GPT2|S000001775|Glycerol-3-phosphate/dihydroxyacetone phosphate dual substrate-specific sn-1 acyltransferase located in lipid particles and the ER; involved in the stepwise acylation of glycerol-3-phosphate and dihydroxyacetone in lipid biosynthesis
YEL028W	2.35234	RPH1	YEL028W||S000000754|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YJR096W	2.34327	RPH1	YJR096W||S000003857|Putative xylose and arabinose reductase; member of the aldo-keto reductase (AKR) family; GFP-fusion protein is induced in response to the DNA-damaging agent MMS
YDR358W	2.34295	RPH1	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	2.33924	RPH1	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
YOL159C-A	2.33763	RPH1	YOL159C-A||S000007627|Putative protein of unknown function; identified by sequence comparison with hemiascomycetous yeast species
YMR052W	2.3233	RPH1	YMR052W|FAR3|S000004656|Protein involved in G1 cell cycle arrest in response to pheromone, in a pathway different from the Far1p-dependent pathway; interacts with Far7p, Far8p, Far9p, Far10p, and Far11p
YBL047C	2.31107	RPH1	YBL047C|EDE1|S000000143|Key endocytic protein involved in a network of interactions with other endocytic proteins, binds membranes in a ubiquitin-dependent manner, may also bind ubiquitinated membrane-associated proteins
YKR049C	2.30212	RPH1	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
YDR436W	2.29801	RPH1	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
YMR013C	2.28964	RPH1	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
YKL032C	2.27895	RPH1	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
YJL052W	2.25334	RPH1	YJL052W|TDH1|S000003588|Glyceraldehyde-3-phosphate dehydrogenase, isozyme 1, involved in glycolysis and gluconeogenesis; tetramer that catalyzes the reaction of glyceraldehyde-3-phosphate to 1,3 bis-phosphoglycerate; detected in the cytoplasm and cell-wall
YFR016C	2.24866	RPH1	YFR016C||S000001912|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and bud; interacts with Spa2p; YFL016C is not an essential gene
YGR072W	2.24847	RPH1	YGR072W|UPF3|S000003304|Component of the nonsense-mediated mRNA decay (NMD) pathway, along with Nam7p and Nmd2p; involved in decay of mRNA containing nonsense codons; involved in telomere maintenance
YBR284W	2.24702	RPH1	YBR284W||S000000488|Putative protein of unknown function; YBR284W is not an essential gene; null mutant exhibits decreased resistance to rapamycin and wortmannin
YDR444W	2.24576	RPH1	YDR444W||S000002852|Putative protein of unknown function
YNR050C	2.24523	RPH1	YNR050C|LYS9|S000005333|Saccharopine dehydrogenase (NADP+, L-glutamate-forming); catalyzes the formation of saccharopine from alpha-aminoadipate 6-semialdehyde, which is the seventh step in lysine biosynthesis pathway
YGR019W	2.24172	RPH1	YGR019W|UGA1|S000003251|Gamma-aminobutyrate (GABA) transaminase (4-aminobutyrate aminotransferase) involved in the 4-aminobutyrate and glutamate degradation pathways; required for normal oxidative stress tolerance and nitrogen utilization
YGR286C	2.23171	RPH1	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
YDR379C-A	2.21012	RPH1	YDR379C-A||S000007605|Hypothetical protein identified by homology. See FEBS Letters [2000] 487:31-36.
YDL221W	2.20849	RPH1	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
YDR536W	2.20546	RPH1	YDR536W|STL1|S000002944|Glycerol proton symporter of the plasma membrane, subject to glucose-induced inactivation, strongly but transiently induced when cells are subjected to osmotic shock
YCL012C	2.20372	RPH1	YCL012C||S000029705|Putative protein of unknown function; orthologs are present in S. bayanus, S. paradoxus and Ashbya gossypii; YCL012C is not an essential gene
YPR065W	2.19229	RPH1	YPR065W|ROX1|S000006269|Heme-dependent repressor of hypoxic genes; contains an HMG domain that is responsible for DNA bending activity
YNR069C	2.18926	RPH1	YNR069C|BSC5|S000005352|Protein of unknown function, ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression
YMR104C	2.1778	RPH1	YMR104C|YPK2|S000004710|Protein kinase with similarityto serine/threonine protein kinase Ypk1p; functionally redundant with YPK1 at the genetic level; participates in a signaling pathway required for optimal cell wall integrity; homolog of mammalian kinase SGK
YDL114W	2.1699	RPH1	YDL114W||S000002272|Putative protein of unknown function with similarity to acyl-carrier-protein reductases; YDL114W is not an essential gene
YHR016C	2.16252	RPH1	YHR016C|YSC84|S000001058|Protein involved in the organization of the actin cytoskeleton; contains SH3 domain similar to Rvs167p
YFL021W	2.15539	RPH1	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
YHR061C	2.14358	RPH1	YHR061C|GIC1|S000001103|Protein of unknown function involved in initiation of budding and cellular polarization, interacts with Cdc42p via the Cdc42/Rac-interactive binding (CRIB) domain
YBL015W	2.1385	RPH1	YBL015W|ACH1|S000000111|Acetyl-coA hydrolase, primarily localized to mitochondria; phosphorylated; required for acetate utilization and for diploid pseudohyphal growth
YER125W	2.11167	RPH1	YER125W|RSP5|S000000927|Ubiquitin-protein ligase involved in ubiquitin-mediated protein degradation; functions in multivesicular body sorting, heat shock response and ubiquitylation of arrested RNAPII; contains a hect (homologous to E6-AP carboxyl terminus) domain
YKL151C	2.1028	RPH1	YKL151C||S000001634|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YHR160C	2.06779	RPH1	YHR160C|PEX18|S000001203|Peroxin required for targeting of peroxisomal matrix proteins containing PTS2; interacts with Pex7p; partially redundant with Pex21p
YML100W	2.05713	RPH1	YML100W|TSL1|S000004566|Large subunit of trehalose 6-phosphate synthase (Tps1p)/phosphatase (Tps2p) complex, which converts uridine-5'-diphosphoglucose and glucose 6-phosphate to trehalose, homologous to Tps3p and may share function
YHR077C	2.04152	RPH1	YHR077C|NMD2|S000001119|Protein involved in the nonsense-mediated mRNA decay (NMD) pathway; interacts with Nam7p and Upf3p; involved in telomere maintenance
YIL162W	2.03979	RPH1	YIL162W|SUC2|S000001424|Invertase, sucrose hydrolyzing enzyme; a secreted, glycosylated form is regulated by glucose repression, and an intracellular, nonglycosylated enzyme is produced constitutively
YGR269W	2.03763	RPH1	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
YPL229W	2.02829	RPH1	YPL229W||S000006150|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YPL229W is not an essential gene
YLR454W	2.02373	RPH1	YLR454W|FMP27|S000004446|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YDR171W	2.01698	RPH1	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
YOR329C	2.01224	RPH1	YOR329C|SCD5|S000005856|Protein required for normal cortical actin organization and endocytosis; multicopy suppressor of clathrin deficiency; acts as a targeting subunit for protein phosphatase type 1
YBR109W-A	2.00881	RPH1	YBR109W-A||S000028737|Putative protein of unknown function; questionable ORF from MIPS
YHR180W	2.00602	RPH1	YHR180W||S000001223|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDL183C	1.99191	RPH1	YDL183C||S000002342|Putative protein of unknown function; YDL183C is not an essential gene
YOR292C	1.99167	RPH1	YOR292C||S000005818|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; YOR292C is not an essential gene
YML004C	1.98889	RPH1	YML004C|GLO1|S000004463|Monomeric glyoxalase I, catalyzes the detoxification of methylglyoxal (a by-product of glycolysis) via condensation with glutathione to produce S-D-lactoylglutathione; expression regulated by methylglyoxal levels and osmotic stress
YAR035W	1.98752	RPH1	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
YJL005W	1.97821	RPH1	YJL005W|CYR1|S000003542|Adenylate cyclase, required for cAMP production and cAMP-dependent protein kinase signaling; the cAMP pathway controls a variety of cellular processes, including metabolism, cell cycle, stress response, stationary phase, and sporulation
YDL079C	1.96478	RPH1	YDL079C|MRK1|S000002237|Glycogen synthase kinase 3 (GSK-3) homolog; one of four GSK-3 homologs in S. cerevisiae that function to activate Msn2p-dependent transcription of stress responsive genes and that function in protein degradation
YNL142W	1.96402	RPH1	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
YJL199C	1.96367	RPH1	YJL199C|MBB1|S000003735|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; protein detected in large-scale protein-protein interaction studies
YLR247C	1.95804	RPH1	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
YDR204W	1.94668	RPH1	YDR204W|COQ4|S000002612|Protein with a role in ubiquinone (Coenzyme Q) biosynthesis, possibly functioning in stabilization of Coq7p; located on the matrix face of the mitochondrial inner membrane; component of a mitochondrial ubiquinone-synthesizing complex
YBL029C-A	1.94348	RPH1	YBL029C-A||S000007591|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery; has potential orthologs in Saccharomyces species and in Yarrowia lipolytica
YJR036C	1.92213	RPH1	YJR036C|HUL4|S000003797|Protein with similarity to hect domain E3 ubiquitin-protein ligases, not essential for viability
YIL060W	1.92159	RPH1	YIL060W||S000001322|Putative protein of unknown function; mutant accumulates less glycogen than does wild type; YIL060W is not an essential gene
YML003W	1.9124	RPH1	YML003W||S000004462|Putative protein of unknown function
YFR015C	1.89674	RPH1	YFR015C|GSY1|S000001911|Glycogen synthase with similarity to Gsy2p, the more highly expressed yeast homolog; expression induced by glucose limitation, nitrogen starvation, environmental stress, and entry into stationary phase
YLL039C	1.89589	RPH1	YLL039C|UBI4|S000003962|Ubiquitin, becomes conjugated to proteins, marking them for selective degradation via the ubiquitin-26S proteasome system; essential for the cellular stress response; encoded as a polyubiquitin precursor comprised of 5 head-to-tail repeats
YER132C	1.88462	RPH1	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
YOR071C	1.87226	RPH1	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
YBR208C	1.87184	RPH1	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
YER088C	1.85445	RPH1	YER088C|DOT6|S000000890|Protein of unknown function, involved in telomeric gene silencing and filamentation
YJL038C	1.85156	RPH1	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
YAL018C	1.83061	RPH1	YAL018C||S000000016|Putative protein of unknown function
YER147C	1.8219	RPH1	YER147C|SCC4|S000000949|Subunit of cohesin loading factor (Scc2p-Scc4p), a complex required for the loading of cohesin complexes onto chromosomes; involved in establishing sister chromatid cohesion during double-strand break repair via phosphorylated histone H2AX
YOL045W	1.80847	RPH1	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)
YEL012W	1.80748	RPH1	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
YOR072W-A	1.79781	RPH1	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
YCL065W	1.79466	RPH1	YCL065W||S000000570|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps HMLALPHA1
YJL130C	1.79281	RPH1	YJL130C|URA2|S000003666|Bifunctional carbamoylphosphate synthetase (CPSase)-aspartate transcarbamylase (ATCase), catalyzes the first two enzymatic steps in the de novo biosynthesis of pyrimidines; both activities are subject to feedback inhibition by UTP
YKR076W	1.79266	RPH1	YKR076W|ECM4|S000001784|Omega class glutathione transferase; not essential; similar to Ygr154cp; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YML128C	1.78347	RPH1	YML128C|MSC1|S000004597|Protein of unknown function; mutant is defective in directing meiotic recombination events to homologous chromatids; the authentic, non-tagged protein is detected in highly purified mitochondria and is phosphorylated
YPR035W	1.78064	RPH1	YPR035W|GLN1|S000006239|Glutamine synthetase (GS), synthesizes glutamine from glutamate and ammonia; with Glt1p, forms the secondary pathway for glutamate biosynthesis from ammonia; expression regulated by nitrogen source and by amino acid limitation
YHR206W	1.76381	RPH1	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
YGR023W	1.76246	RPH1	YGR023W|MTL1|S000003255|Protein with both structural and functional similarity to Mid2p, which is a plasma membrane sensor required for cell integrity signaling during pheromone-induced morphogenesis; suppresses rgd1 null mutations
YPL116W	1.76025	RPH1	YPL116W|HOS3|S000006037|Trichostatin A-insensitive homodimeric histone deacetylase (HDAC) with specificity in vitro for histones H3, H4, H2A, and H2B; similar to Hda1p, Rpd3p, Hos1p, and Hos2p; deletion results in increased histone acetylation at rDNA repeats
YLR233C	1.73485	RPH1	YLR233C|EST1|S000004223|TLC1 RNA-associated factor involved in telomere length regulation as the recruitment subunit of the telomerase holoenzyme, has a possible role in activating Est2p-TLC1-RNA bound to the telomere
YPR026W	1.7315	RPH1	YPR026W|ATH1|S000006230|Acid trehalase required for utilization of extracellular trehalose
YLL019C	1.71938	RPH1	YLL019C|KNS1|S000003942|Nonessential putative protein kinase of unknown cellular role; member of the LAMMER family of protein kinases, which are serine/threonine kinases also capable of phosphorylating tyrosine residues
YCL017C	1.71677	RPH1	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
YJR152W	1.71595	RPH1	YJR152W|DAL5|S000003913|Allantoin permease; ureidosuccinate permease; expression is constitutive but sensitive to nitrogen catabolite repression
YKL101W	1.71247	RPH1	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
YHL010C	1.70112	RPH1	YHL010C|BRP2|S000001002|Putative protein of unknown function, contains a zinc finger region and has homology to human BRAP2, which is a cytoplasmic protein that binds nuclear localization sequences
YKR102W	1.69433	RPH1	YKR102W|FLO10|S000001810|Lectin-like protein with similarity to Flo1p, thought to be involved in flocculation
YJL082W	1.6937	RPH1	YJL082W|IML2|S000003618|Protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YKR039W	1.69095	RPH1	YKR039W|GAP1|S000001747|General amino acid permease; localization to the plasma membrane is regulated by nitrogen source
YIL166C	1.6833	RPH1	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
YOR064C	1.67682	RPH1	YOR064C|YNG1|S000005590|Subunit of the NuA3 histone acetyltransferase complex that acetylates histone H3; contains PHD finger domain that interacts with methylated histone H3, has similarity to the human tumor suppressor ING1
YDR223W	1.67058	RPH1	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
YGR022C	1.6605	RPH1	YGR022C||S000003254|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; overlaps almost completely with the verified ORF MTL1/YGR023W
YER066W	1.65674	RPH1	YER066W||S000000868|Putative protein of unknown function; YER066W is not an essential gene
YOR032W-A	1.65608	RPH1	YOR032W-A||S000028710|Identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YNL200C	1.64512	RPH1	YNL200C||S000005144|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YER061C	1.63887	RPH1	YER061C|CEM1|S000000863|Mitochondrial beta-keto-acyl synthase with possible role in fatty acid synthesis; required for mitochondrial respiration
YAL008W	1.63874	RPH1	YAL008W|FUN14|S000000006|Mitochondrial protein of unknown function
YER091C-A	1.63282	RPH1	YER091C-A||S000007238|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YER033C	1.62779	RPH1	YER033C|ZRG8|S000000835|Protein of unknown function; authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; GFP-fusion protein is localized to the cytoplasm; transcription induced under conditions of zinc deficiency
YLR297W	1.61674	RPH1	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
YLR234W	1.60805	RPH1	YLR234W|TOP3|S000004224|DNA Topoisomerase III, conserved protein that functions in a complex with Sgs1p and Rmi1p to relax single-stranded negatively-supercoiled DNA preferentially, involved in telomere stability and regulation of mitotic recombination
YOR291W	1.60636	RPH1	YOR291W||S000005817|Putative protein of unknown function; shares sequence similarity with the type V P-type ATPase Spf1p; YOR291W is not an essential protein
YIR028W	1.60202	RPH1	YIR028W|DAL4|S000001467|Allantoin permease; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation
YCR085W	1.59841	RPH1	YCR085W||S000000681|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR247W	1.59275	RPH1	YDR247W|VHS1|S000002655|Cytoplasmic serine/threonine protein kinase; identified as a high-copy suppressor of the synthetic lethality of a sis2 sit4 double mutant, suggesting a role in G1/S phase progression; homolog of Sks1p
YDR096W	1.58027	RPH1	YDR096W|GIS1|S000002503|JmjC domain-containing histone demethylase; transcription factor involved in the expression of genes during nutrient limitation; also involved in the negative regulation of DPP1 and PHR1
YJR147W	1.57849	RPH1	YJR147W|HMS2|S000003908|Protein with similarity to heat shock transcription factors; overexpression suppresses the pseudohyphal filamentation defect of a diploid mep1 mep2 homozygous null mutant
YJR037W	1.57332	RPH1	YJR037W||S000003798|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene HUL4/YJR036C; YJR037W is not an essential gene.
YDR250C	1.5727	RPH1	YDR250C||S000002658|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data
YLR064W	1.57147	RPH1	YLR064W||S000004054|Putative protein of unknown function; highly conserved across species and orthologous to human TMEM33; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YLR064W is not an essential gene
YGR161C	1.56825	RPH1	YGR161C|RTS3|S000003393|Putative component of the protein phosphatase type 2A complex
YCR061W	1.56587	RPH1	YCR061W||S000000657|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; induced by treatment with 8-methoxypsoralen and UVA irradiation
YDR375C	1.55981	RPH1	YDR375C|BCS1|S000002783|Protein of the mitochondrial inner membrane that functions as an ATP-dependent chaperone, required for the incorporation of the Rip1p and Qcr10p subunits into the cytochrome bc(1) complex; member of the CDC48/PAS1/SEC18 ATPase family
YLR176C	1.54833	RPH1	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
YLL010C	1.54599	RPH1	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
YNL274C	1.54595	RPH1	YNL274C|GOR1|S000005218|Glyoxylate reductase; null mutation results in increased biomass after diauxic shift; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YHL041W	1.54456	RPH1	YHL041W||S000001033|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data
YLR228C	1.54376	RPH1	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
YNL005C	1.53261	RPH1	YNL005C|MRP7|S000004950|Mitochondrial ribosomal protein of the large subunit
YHR007C-A	1.52702	RPH1	YHR007C-A||S000028830|Putative protein of unknown function; identified by expression profiling and mass spectrometry
YMR216C	1.52549	RPH1	YMR216C|SKY1|S000004829|SR protein kinase (SRPK) involved in regulating proteins involved in mRNA metabolism and cation homeostasis; similar to human SRPK1
YBR270C	1.51167	RPH1	YBR270C|BIT2|S000000474|Hypothetical protein
YGR112W	1.50682	RPH1	YGR112W|SHY1|S000003344|Mitochondrial inner membrane protein required for assembly of cytochrome c oxidase (complex IV); associates with complex IV assembly intermediates and complex III/complex IV supercomplexes; similar to human SURF1 involved in Leigh Syndrome
YDL004W	1.49172	RPH1	YDL004W|ATP16|S000002162|Delta subunit of the central stalk of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; phosphorylated
YHR054C	1.47991	RPH1	YHR054C||S000001096|Putative protein of unknown function
YOR208W	1.47354	RPH1	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
YDR251W	1.46558	RPH1	YDR251W|PAM1|S000002659|Essential protein of unknown function; exhibits variable expression during colony morphogenesis; overexpression permits survival without protein phosphatase 2A, inhibits growth, and induces a filamentous phenotype
YMR092C	1.46019	RPH1	YMR092C|AIP1|S000004698|Actin cortical patch component, interacts with the actin depolymerizing factor cofilin; required to restrict cofilin localization to cortical patches; contains WD repeats
YDR085C	1.44988	RPH1	YDR085C|AFR1|S000002492|Alpha-factor pheromone receptor regulator, negatively regulates pheromone receptor signaling; required for normal mating projection (shmoo) formation; required for Spa2p to recruit Mpk1p to shmoo tip during mating; interacts with Cdc12p
YJL205C	1.44726	RPH1	YJL205C|NCE101|S000003742|Protein of unknown function, involved in secretion of proteins that lack classical secretory signal sequences
YMR278W	1.44332	RPH1	YMR278W|PGM3|S000004891|Phosphoglucomutase, catalyzes interconversion of glucose-1-phosphate and glucose-6-phospate; transcription induced in response to stress; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; non-essential
YMR090W	1.44068	RPH1	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
YPL166W	1.4252	RPH1	YPL166W|ATG29|S000006087|Protein specifically required for autophagy; may function in autophagosome formation at the pre-autophagosomal structure in collaboration with other autophagy proteins
YMR210W	1.41607	RPH1	YMR210W||S000004823|Putative acyltransferase with similarity to Eeb1p and Eht1p, has a minor role in medium-chain fatty acid ethyl ester biosynthesis; may be involved in lipid metabolism and detoxification
YOR381W	1.41527	RPH1	YOR381W|FRE3|S000005908|Ferric reductase, reduces siderophore-bound iron prior to uptake by transporters; expression induced by low iron levels
YDL146W	1.40789	RPH1	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
YIL113W	1.39532	RPH1	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
YOR351C	1.38989	RPH1	YOR351C|MEK1|S000005878|Meiosis-specific serine/threonine protein kinase, functions in meiotic checkpoint, promotes recombination between homologous chromosomes by suppressing double strand break repair between sister chromatids
YKL085W	1.38695	RPH1	YKL085W|MDH1|S000001568|Mitochondrial malate dehydrogenase, catalyzes interconversion of malate and oxaloacetate; involved in the tricarboxylic acid (TCA) cycle; phosphorylated
YJR061W	1.3845	RPH1	YJR061W||S000003822|Putative protein of unknown function; non-essential gene with similarity to Mnn4, a putative membrane protein involved in glycosylation; transcription repressed by Rm101p
YPR155C	1.3827	RPH1	YPR155C|NCA2|S000006359|Protein involved in regulation of mitochondrial expression of subunits 6 (Atp6p) and 8 (Atp8p) of the Fo-F1 ATP synthase; functions with Nca3p
YOL085W-A	1.38236	RPH1	YOL085W-A||S000028708|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YOL085C
YPL148C	1.3763	RPH1	YPL148C|PPT2|S000006069|Phosphopantetheine:protein transferase (PPTase), activates mitochondrial acyl carrier protein (Acp1p) by phosphopantetheinylation
YKR066C	1.37491	RPH1	YKR066C|CCP1|S000001774|Mitochondrial cytochrome-c peroxidase; degrades reactive oxygen species in mitochondria, involved in the response to oxidative stress
YPR007C	1.37461	RPH1	YPR007C|REC8|S000006211|Meiosis-specific component of sister chromatid cohesion complex; maintains cohesion between sister chromatids during meiosis I; maintains cohesion between centromeres of sister chromatids until meiosis II; homolog of S. pombe Rec8p
YOR062C	1.37413	RPH1	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
YGL146C	1.36811	RPH1	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
YDR376W	1.35688	RPH1	YDR376W|ARH1|S000002784|Oxidoreductase of the mitochondrial inner membrane, involved in cytoplasmic and mitochondrial iron homeostasis and required for activity of Fe-S cluster-containing enzymes; one of the few mitochondrial proteins essential for viability
YJR046W	1.35619	RPH1	YJR046W|TAH11|S000003807|DNA replication licensing factor, required for pre-replication complex assembly
YNL143C	1.35304	RPH1	YNL143C||S000005087|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YPL274W	1.33565	RPH1	YPL274W|SAM3|S000006195|High-affinity S-adenosylmethionine permease, required for utilization of S-adenosylmethionine as a sulfur source; has similarity to S-methylmethionine permease Mmp1p
YBL017C	1.33481	RPH1	YBL017C|PEP1|S000000113|Type I transmembrane sorting receptor for multiple vacuolar hydrolases; cycles between the late-Golgi and prevacuolar endosome-like compartments
YCR005C	1.33462	RPH1	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
YBR139W	1.32098	RPH1	YBR139W||S000000343|Putative serine type carboxypeptidase with a role in phytochelatin synthesis; green fluorescent protein (GFP)-fusion protein localizes to the vacuole; expression induced by nitrogen limitation in a GLN3, GAT1-independent manner
YBL066C	1.31805	RPH1	YBL066C|SEF1|S000000162|Putative transcription factor, has homolog in Kluyveromyces lactis
YKR089C	1.31392	RPH1	YKR089C|TGL4|S000001797|Triacylglycerol lipase involved in triacylglycerol mobilization and degradation; found in lipid particles; potential Cdc28p substrate
YOR215C	1.31323	RPH1	YOR215C|AIM41|S000005741|Putative protein of unknown function; the authentic protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays altered rate of mitochondrial loss and reduced growth rate in minimal glycerol media
YLR425W	1.31286	RPH1	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
YLL049W	1.31189	RPH1	YLL049W|LDB18|S000003972|Protein of unknown function; null mutant shows a reduced affinity for the alcian blue dye suggesting a decreased net negative charge of the cell surface
YLR202C	1.31077	RPH1	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
YJL155C	1.30129	RPH1	YJL155C|FBP26|S000003691|Fructose-2,6-bisphosphatase, required for glucose metabolism
YHR198C	1.30081	RPH1	YHR198C|AIM18|S000001241|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies; null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YPL189C-A	1.29899	RPH1	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
YLR201C	1.2909	RPH1	YLR201C|COQ9|S000004191|Protein required for ubiquinone (coenzyme Q) biosynthesis and respiratory growth; localizes to the matrix face of the mitochondrial inner membrane in a large complex with ubiquinone biosynthetic enzymes
YMR124W	1.28915	RPH1	YMR124W||S000004731|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery, cytoplasm, bud, and bud neck; interacts with Crm1p in two-hybrid assay; YMR124W is not an essential gene
YER066C-A	1.28363	RPH1	YER066C-A||S000002959|Dubious open reading frame unlikely to encode a protein, partially overlaps uncharacterized ORF YER067W
YDR249C	1.27183	RPH1	YDR249C||S000002657|Putative protein of unknown function
YIR036W-A	1.26963	RPH1	YIR036W-A||S000028803|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YKL023W	1.26823	RPH1	YKL023W||S000001506|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YGL208W	1.26753	RPH1	YGL208W|SIP2|S000003176|One of three beta subunits of the Snf1 serine/threonine protein kinase complex involved in the response to glucose starvation; null mutants exhibit accelerated aging; N-myristoylprotein localized to the cytoplasm and the plasma membrane
YMR159C	1.26131	RPH1	YMR159C|ATG16|S000004769|Protein that interacts with the Atg12p-Atg5p conjugate during formation of the pre-autophagosomal structure; essential for autophagy
YKL010C	1.25244	RPH1	YKL010C|UFD4|S000001493|Ubiquitin-protein ligase (E3) that interacts with Rpt4p and Rpt6p, two subunits of the 19S particle of the 26S proteasome; cytoplasmic E3 involved in the degradation of ubiquitin fusion proteins
YGL163C	1.25175	RPH1	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
YDR271C	1.24773	RPH1	YDR271C||S000002679|Hypothetical protein
YGR154C	1.2388	RPH1	YGR154C|GTO1|S000003386|Omega-class glutathione transferase; induced under oxidative stress; putative peroxisomal localization
YBR295W	1.23298	RPH1	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
YJL197W	1.23034	RPH1	YJL197W|UBP12|S000003733|Ubiquitin carboxyl-terminal hydrolase, ubiquitin-specific protease present in the nucleus and cytoplasm that cleaves ubiquitin from ubiquitinated proteins
YGL160W	1.22671	RPH1	YGL160W|AIM14|S000003128|Putative protein of unknown function; similar to iron/copper reductases (FRE1-8), possibly involved in iron homeostasis; may interact with ribosomes, null mutant displays increased frequency of mitochondrial genome loss (petite formation)
YLR035C	1.22535	RPH1	YLR035C|MLH2|S000004025|Protein involved in the mismatch repair of certain frameshift intermediates and involved in meiotic recombination; forms a complex with Mlh1p
YJR045C	1.2205	RPH1	YJR045C|SSC1|S000003806|Mitochondrial matrix ATPase, subunit of the presequence translocase-associated protein import motor (PAM) and of SceI endonuclease; involved in protein folding and translocation into the matrix; phosphorylated; member of HSP70 family
YBR076W	1.21987	RPH1	YBR076W|ECM8|S000000280|Non-essential protein of unknown function
YJL141C	1.21921	RPH1	YJL141C|YAK1|S000003677|Serine-threonine protein kinase that is part of a glucose-sensing system involved in growth control in response to glucose availability; translocates from the cytoplasm to the nucleus and phosphorylates Pop2p in response to a glucose signal
YAL067W-A	1.21246	RPH1	YAL067W-A||S000028593|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YBR056W	1.2043	RPH1	YBR056W||S000000260|Putative cytoplasmic protein of unknown function
YNL006W	1.19264	RPH1	YNL006W|LST8|S000004951|Protein required for the transport of amino acid permease Gap1p from the Golgi to the cell surface; component of the TOR signaling pathway; associates with both Tor1p and Tor2p; contains a WD-repeat
YOR328W	1.18932	RPH1	YOR328W|PDR10|S000005855|ATP-binding cassette (ABC) transporter, multidrug transporter involved in the pleiotropic drug resistance network; regulated by Pdr1p and Pdr3p
YJL057C	1.18695	RPH1	YJL057C|IKS1|S000003593|Putative serine/threonine kinase; expression is induced during mild heat stress; deletion mutants are hypersensitive to copper sulphate and resistant to sorbate; interacts with an N-terminal fragment of Sst2p
YPL058C	1.18523	RPH1	YPL058C|PDR12|S000005979|Plasma membrane ATP-binding cassette (ABC) transporter, weak-acid-inducible multidrug transporter required for weak organic acid resistance; induced by sorbate and benzoate and regulated by War1p; mutants exhibit sorbate hypersensitivity
YML007W	1.18317	RPH1	YML007W|YAP1|S000004466|Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium
YMR135C	1.18093	RPH1	YMR135C|GID8|S000004742|Protein of unknown function, involved in proteasome-dependent catabolite inactivation of fructose-1,6-bisphosphatase; contains LisH and CTLH domains, like Vid30p; dosage-dependent regulator of START
YGL191W	1.17966	RPH1	YGL191W|COX13|S000003159|Subunit VIa of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; not essential for cytochrome c oxidase activity but may modulate activity in response to ATP
YCL052C	1.17084	RPH1	YCL052C|PBN1|S000000557|Essential component of glycosylphosphatidylinositol-mannosyltransferase I, required for the autocatalytic post-translational processing of the protease B precursor Prb1p, localizes to ER in lumenal orientation; homolog of mammalian PIG-X
YLL029W	1.16975	RPH1	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
YGL183C	1.15889	RPH1	YGL183C|MND1|S000003151|Protein required for recombination and meiotic nuclear division; forms a complex with Hop2p, which is involved in chromosome pairing and repair of meiotic double-strand breaks
YJL220W	1.15711	RPH1	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
YGR070W	1.15421	RPH1	YGR070W|ROM1|S000003302|GDP/GTP exchange protein (GEP) for Rho1p; mutations are synthetically lethal with mutations in rom2, which also encodes a GEP
YOR098C	1.14983	RPH1	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
YMR014W	1.14964	RPH1	YMR014W|BUD22|S000004616|Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern
YPL015C	1.14947	RPH1	YPL015C|HST2|S000005936|Cytoplasmic member of the silencing information regulator 2 (Sir2) family of NAD(+)-dependent protein deacetylases; modulates nucleolar (rDNA) and telomeric silencing; possesses NAD(+)-dependent histone deacetylase activity in vitro
YJR085C	1.14498	RPH1	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
YJL068C	1.14191	RPH1	YJL068C||S000003604|Non-essential intracellular esterase that can function as an S-formylglutathione hydrolase; may be involved in the detoxification of formaldehyde, which can be metabolized to S-formylglutathione; similar to human esterase D
YGL229C	1.13723	RPH1	YGL229C|SAP4|S000003198|Protein required for function of the Sit4p protein phosphatase, member of a family of similar proteins that form complexes with Sit4p, including Sap155p, Sap185p, and Sap190p
YBL065W	1.13712	RPH1	YBL065W||S000000161|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified ORF SEF1/YBL066C; YBL065W is a non-essential gene
YEL049W	1.13625	RPH1	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
YGL248W	1.13283	RPH1	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
YDL245C	1.12892	RPH1	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
YHR161C	1.12301	RPH1	YHR161C|YAP1801|S000001204|Protein involved in clathrin cage assembly; binds Pan1p and clathrin; homologous to Yap1802p, member of the AP180 protein family
YNL156C	1.12162	RPH1	YNL156C|NSG2|S000005100|Protein involved in regulation of sterol biosynthesis; specifically stabilizes Hmg2p, one of two HMG-CoA isoenzymes that catalyze the rate-limiting step in sterol biosynthesis; homolog of mammalian INSIG proteins
YDR516C	1.12104	RPH1	YDR516C|EMI2|S000002924|Non-essential protein of unknown function required for transcriptional induction of the early meiotic-specific transcription factor IME1; required for sporulation; expression is regulated by glucose-repression transcription factors Mig1/2p
YOR053W	1.11969	RPH1	YOR053W||S000005579|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene VHS3/YOR054C
YBR065C	1.1147	RPH1	YBR065C|ECM2|S000000269|Pre-mRNA splicing factor, facilitates the cooperative formation of U2/U6 helix II in association with stem II in the spliceosome, function may be regulated by Slu7p
YLR450W	1.09695	RPH1	YLR450W|HMG2|S000004442|One of two isozymes of HMG-CoA reductase that convert HMG-CoA to mevalonate, a rate-limiting step in sterol biosynthesis; overproduction induces assembly of peripheral ER membrane arrays and short nuclear-associated membrane stacks
YEL024W	1.0937	RPH1	YEL024W|RIP1|S000000750|Ubiquinol-cytochrome-c reductase, a Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex; transfers electrons from ubiquinol to cytochrome c1 during respiration
YPL109C	1.09052	RPH1	YPL109C||S000006030|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YPR169W-A	1.08397	RPH1	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
YJR128W	1.08231	RPH1	YJR128W||S000003889|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF RSF2
YLR332W	1.08202	RPH1	YLR332W|MID2|S000004324|O-glycosylated plasma membrane protein that acts as a sensor for cell wall integrity signaling and activates the pathway; interacts with Rom2p, a guanine nucleotide exchange factor for Rho1p, and with cell integrity pathway protein Zeo1p
YMR064W	1.07872	RPH1	YMR064W|AEP1|S000004668|Protein required for expression of the mitochondrial OLI1 gene encoding subunit 9 of F1-F0 ATP synthase
YKL150W	1.07627	RPH1	YKL150W|MCR1|S000001633|Mitochondrial NADH-cytochrome b5 reductase, involved in ergosterol biosynthesis
YDR029W	1.07585	RPH1	YDR029W||S000002436|Dubious ORF unlikely to encode a protein, based on available experimental and comparative sequence data
YJL149W	1.07255	RPH1	YJL149W|DAS1|S000003685|Putative SCF ubiquitin ligase F-box protein; interacts physically with both Cdc53p and Skp1 and genetically with CDC34; similar to putative F-box protein YDR131C; null mutant suppresses dst1delta sensitivity for 6-azauracil
YDR406W	1.07103	RPH1	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
YBR204C	1.06946	RPH1	YBR204C||S000000408|Serine hydrolase; YBR204C is not an essential gene
YKL187C	1.06806	RPH1	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
YER116C	1.06742	RPH1	YER116C|SLX8|S000000918|Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate
YBR099C	1.0573	RPH1	YBR099C||S000000303|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; completely overlaps the verified gene MMS4
YMR134W	1.05662	RPH1	YMR134W|ERG29|S000004741|Protein that binds to and regulates Erg25p; localized to the ER; null mutant is viable in a respiratory defective background; synthetic lethal with mmt1 and mmt2 mutations; highly conserved in ascomycetes
YDR319C	1.05629	RPH1	YDR319C|YFT2|S000002727|Putative protein of unknown function, identified as an ortholog of the highly conserved FIT family of proteins involved in triglyceride droplet biosynthesis; interacts with Sst2p and Hsp82p in high-throughput two-hybrid screens
YLL047W	1.05628	RPH1	YLL047W||S000003970|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps verified gene RNP1
YNL042W	1.04773	RPH1	YNL042W|BOP3|S000004987|Protein of unknown function, potential Cdc28p substrate; overproduction suppresses a pam1 slv3 double null mutation and confers resistance to methylmercury
YLR331C	1.04767	RPH1	YLR331C|JIP3|S000004323|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; 98% of ORF overlaps the verified gene MID2
YOL164W-A	1.04619	RPH1	YOL164W-A||S000028580|Putative protein of unknown function; identified by fungal homology and RT-PCR
YJL219W	1.04121	RPH1	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
YGL006W	1.03733	RPH1	YGL006W|PMC1|S000002974|Vacuolar Ca2+ ATPase involved in depleting cytosol of Ca2+ ions; prevents growth inhibition by activation of calcineurin in the presence of elevated concentrations of calcium; similar to mammalian PMCA1a
YPR013C	1.03716	RPH1	YPR013C||S000006217|Putative zinc finger protein; YPR013C is not an essential gene
YPR138C	1.03473	RPH1	YPR138C|MEP3|S000006342|Ammonium permease of high capacity and low affinity; belongs to a ubiquitous family of cytoplasmic membrane proteins that transport only ammonium (NH4+); expression is under the nitrogen catabolite repression regulation ammonia permease
YER010C	1.03371	RPH1	YER010C||S000000812|Protein of unknown function, forms a ring-shaped homotrimer; has similarity to members of the prokaryotic rraA family; possibly involved in a phosphotransfer reaction
YLL057C	1.02967	RPH1	YLL057C|JLP1|S000003980|Fe(II)-dependent sulfonate/alpha-ketoglutarate dioxygenase, involved in sulfonate catabolism for use as a sulfur source, contains sequence that closely resembles a J domain (typified by the E. coli DnaJ protein)
YER181C	1.02307	RPH1	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
YJL221C	1.00814	RPH1	YJL221C|FSP2|S000003757|Protein of unknown function, expression is induced during nitrogen limitation
YOR192C	1.00755	RPH1	YOR192C|THI72|S000005718|Transporter of thiamine or related compound; shares sequence similarity with Thi7p
YOR192C-C	1.00742	RPH1	YOR192C-C||S000028857|Putative protein of unknown function; identified by expression profiling and mass spectrometry
YPL258C	1.00602	RPH1	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
YLR304C	1.00347	RPH1	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
YJR160C	0.994273	RPH1	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
YDR380W	0.986777	RPH1	YDR380W|ARO10|S000002788|Phenylpyruvate decarboxylase, catalyzes decarboxylation of phenylpyruvate to phenylacetaldehyde, which is the first specific step in the Ehrlich pathway
YKR002W	0.984046	RPH1	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
YER014C-A	0.981049	RPH1	YER014C-A|BUD25|S000007590|Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern
YDR466W	0.980292	RPH1	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
YFL033C	0.977528	RPH1	YFL033C|RIM15|S000001861|Glucose-repressible protein kinase involved in signal transduction during cell proliferation in response to nutrients, specifically the establishment of stationary phase; identified as a regulator of IME2; substrate of Pho80p-Pho85p kinase
YMR101C	0.974159	RPH1	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
YPL040C	0.970788	RPH1	YPL040C|ISM1|S000005961|Mitochondrial isoleucyl-tRNA synthetase, null mutant is deficient in respiratory growth
YIR041W	0.969727	RPH1	YIR041W|PAU15|S000001480|Hypothetical protein
YJR121W	0.963587	RPH1	YJR121W|ATP2|S000003882|Beta subunit of the F1 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; phosphorylated
YDL024C	0.961086	RPH1	YDL024C|DIA3|S000002182|Protein of unknown function, involved in invasive and pseudohyphal growth
YAR023C	0.958409	RPH1	YAR023C||S000000074|Putative integral membrane protein, member of DUP240 gene family
YGR127W	0.956657	RPH1	YGR127W||S000003359|Putative protein of unknown function; expression is regulated by Msn2p/Msn4p, indicating a possible role in stress response
YDL224C	0.946835	RPH1	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
YER119C	0.944776	RPH1	YER119C|AVT6|S000000921|Vacuolar amino acid transporter, exports aspartate and glutamate from the vacuole; member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters
YMR264W	0.943646	RPH1	YMR264W|CUE1|S000004877|Endoplasmic reticulum membrane protein that recruits the ubiquitin-conjugating enzyme Ubc7p to the ER where it functions in protein degradation; contains a CUE domain that binds ubiquitin to facilitate intramolecular monoubiquitination
YDR540C	0.936804	RPH1	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
YNL063W	0.92061	RPH1	YNL063W|MTQ1|S000005007|S-adenosylmethionine-dependent methyltransferase; methylates translational release factor Mrf1p; similar to E.coli PrmC; is not an essential gene
YPR085C	0.919622	RPH1	YPR085C||S000006289|Putative protein of unknown function; YPR085C is an essential gene
YDR475C	0.917945	RPH1	YDR475C|JIP4|S000002883|Protein of unknown function; previously annotated as two separate ORFs, YDR474C and YDR475C, which were merged as a result of corrections to the systematic reference sequence
YLR016C	0.916721	RPH1	YLR016C|PML1|S000004006|Subunit of the RES complex, which is required for nuclear retention of unspliced pre-mRNAs; acts in the same pathway as Pml39p and Mlp1p
YLR122C	0.915354	RPH1	YLR122C||S000004112|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YLR123C
YIR040C	0.909233	RPH1	YIR040C||S000001479|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data
YPR064W	0.900126	RPH1	YPR064W||S000006268|Dubious open reading frame, unlikely to encode a functional protein; based on available experimental and comparative sequence data
YPL183W-A	0.898932	RPH1	YPL183W-A|RTC6|S000007224|Homolog of the prokaryotic ribosomal protein L36, likely to be a mitochondrial ribosomal protein coded in the nuclear genome; null mutation suppresses cdc13-1 temperature sensitivity
YBR110W	0.894976	RPH1	YBR110W|ALG1|S000000314|Mannosyltransferase, involved in asparagine-linked glycosylation in the endoplasmic reticulum (ER); essential for viability, mutation is functionally complemented by human ortholog
YFR040W	0.894243	RPH1	YFR040W|SAP155|S000001936|Protein that forms a complex with the Sit4p protein phosphatase and is required for its function; member of a family of similar proteins including Sap4p, Sap185p, and Sap190p
YJR035W	0.893007	RPH1	YJR035W|RAD26|S000003796|Protein involved in transcription-coupled repair nucleotide excision repair of UV-induced DNA lesions; homolog of human CSB protein
YGR230W	0.88501	RPH1	YGR230W|BNS1|S000003462|Protein with some similarity to Spo12p; overexpression bypasses need for Spo12p, but not required for meiosis
YIL047C	0.884647	RPH1	YIL047C|SYG1|S000001309|Plasma membrane protein of unknown function; truncation and overexpression suppresses lethality of G-alpha protein deficiency
YEL057C	0.883099	RPH1	YEL057C||S000000783|Protein of unknown function involved in telomere maintenance; target of UME6 regulation
YKL067W	0.880905	RPH1	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
YOL128C	0.87703	RPH1	YOL128C|YGK3|S000005488|Protein kinase related to mammalian glycogen synthase kinases of the GSK-3 family; GSK-3 homologs (Mck1p, Rim11p, Mrk1p, Ygk3p) are involved in control of Msn2p-dependent transcription of stress responsive genes and in protein degradation
YLR111W	0.870741	RPH1	YLR111W||S000004101|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YBR250W	0.869333	RPH1	YBR250W|SPO23|S000000454|Protein of unknown function; associates with meiosis-specific protein Spo1p
YDR441C	0.868759	RPH1	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
YGR008C	0.863392	RPH1	YGR008C|STF2|S000003240|Protein involved in regulation of the mitochondrial F1F0-ATP synthase; Stf1p and Stf2p may act as stabilizing factors that enhance inhibitory action of the Inh1p protein
YOR070C	0.859407	RPH1	YOR070C|GYP1|S000005596|Cis-golgi GTPase-activating protein (GAP) for the Rab family members Ypt1p (in vivo) and for Ypt1p, Sec4p, Ypt7p, and Ypt51p (in vitro); involved in vesicle docking and fusion
YBR262C	0.856401	RPH1	YBR262C|AIM5|S000000466|Protein of unknown function; non-tagged protein is detected in purified mitochondria in high-throughput studies; null mutant displays decreased frequency of mitochondrial genome loss and reduced growth rate in minimal glycerol media
YDR350C	0.85278	RPH1	YDR350C|ATP22|S000002758|Mitochondrial inner membrane protein required for assembly of the F0 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis
YML035C	0.852125	RPH1	YML035C|AMD1|S000004498|AMP deaminase, tetrameric enzyme that catalyzes the deamination of AMP to form IMP and ammonia; may be involved in regulation of intracellular adenine nucleotide pools
YMR291W	0.838765	RPH1	YMR291W||S000004905|Putative kinase of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YMR291W is not an essential gene
YGL203C	0.838498	RPH1	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
YAL017W	0.838035	RPH1	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
YLR422W	0.835146	RPH1	YLR422W||S000004414|Protein of unknown function with similarity to human DOCK proteins (guanine nucleotide exchange factors); interacts with Ino4p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm, YLR422W is not an essential protein
YDL025C	0.831214	RPH1	YDL025C||S000002183|Putative protein kinase, potentially phosphorylated by Cdc28p; YDL025C is not an essential gene
YOL164W	0.828903	RPH1	YOL164W|BDS1|S000005524|Bacterially-derived sulfatase required for use of alkyl- and aryl-sulfates as sulfur sources
YKL071W	0.820063	RPH1	YKL071W||S000001554|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YGR254W	0.81445	RPH1	YGR254W|ENO1|S000003486|Enolase I, a phosphopyruvate hydratase that catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate during glycolysis and the reverse reaction during gluconeogenesis; expression is repressed in response to glucose
YPL219W	0.812762	RPH1	YPL219W|PCL8|S000006140|Cyclin, interacts with Pho85p cyclin-dependent kinase (Cdk) to phosphorylate and regulate glycogen synthase, also activates Pho85p for Glc8p phosphorylation
YPL167C	0.804486	RPH1	YPL167C|REV3|S000006088|Catalytic subunit of DNA polymerase zeta, which is involved in DNA repair and translesion synthesis; required for mutagenesis induced by DNA damage
YBL001C	0.796201	RPH1	YBL001C|ECM15|S000000097|Non-essential protein of unknown function, likely exists as tetramer, may be regulated by the binding of small-molecule ligands (possibly sulfate ions), may have a role in yeast cell-wall biogenesis
YEL044W	0.794088	RPH1	YEL044W|IES6|S000000770|Protein that associates with the INO80 chromatin remodeling complex under low-salt conditions
YGR221C	0.789327	RPH1	YGR221C|TOS2|S000003453|Protein involved in localization of Cdc24p to the site of bud growth; may act as a membrane anchor; localizes to the bud neck and bud tip; potentially phosphorylated by Cdc28p
YJL036W	0.786338	RPH1	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
YLR423C	0.785533	RPH1	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
YNL146W	0.78405	RPH1	YNL146W||S000005090|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YNL146W is not an essential gene
YER020W	0.78281	RPH1	YER020W|GPA2|S000000822|Nucleotide binding alpha subunit of the heterotrimeric G protein that interacts with the receptor Gpr1p, has signaling role in response to nutrients; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery
YMR140W	0.77802	RPH1	YMR140W|SIP5|S000004748|Protein of unknown function; interacts with both the Reg1p/Glc7p phosphatase and the Snf1p kinase
YFL029C	0.777886	RPH1	YFL029C|CAK1|S000001865|Cyclin-dependent kinase-activating kinase required for passage through the cell cycle, phosphorylates and activates Cdc28p; nucleotide-binding pocket differs significantly from those of most other protein kinases
YDL115C	0.777043	RPH1	YDL115C|IWR1|S000002273|Protein of unknown function, deletion causes hypersensitivity to the K1 killer toxin
YDR186C	0.77624	RPH1	YDR186C||S000002594|Putative protein of unknown function; may interact with ribosomes, based on co-purification experiments; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YDR515W	0.767676	RPH1	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
YLR123C	0.766153	RPH1	YLR123C||S000004113|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YLR122C; contains characteristic aminoacyl-tRNA motif
YER040W	0.760733	RPH1	YER040W|GLN3|S000000842|Transcriptional activator of genes regulated by nitrogen catabolite repression (NCR), localization and activity regulated by quality of nitrogen source
YML133C	0.754464	RPH1	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
YDR334W	0.750184	RPH1	YDR334W|SWR1|S000002742|Swi2/Snf2-related ATPase that is the structural component of the SWR1 complex, which exchanges histone variant H2AZ (Htz1p) for chromatin-bound histone H2A
YNL220W	0.746114	RPH1	YNL220W|ADE12|S000005164|Adenylosuccinate synthase, catalyzes the first step in synthesis of adenosine monophosphate from inosine 5'monophosphate during purine nucleotide biosynthesis; exhibits binding to single-stranded autonomously replicating (ARS) core sequence
YOL111C	0.741899	RPH1	YOL111C|MDY2|S000005471|Protein required for efficient mating; involved in shmoo formation and nuclear migration in the pre-zygote; associates with ribosomes and interacts with YOR164C; contains a ubiquitin-like (UBL) domain
YPL046C	0.736883	RPH1	YPL046C|ELC1|S000005967|Elongin C, forms heterodimer with Ela1p that participates in transcription elongation; required for ubiquitin-dependent degradation of the RNA Polymerase II subunit RPO21; expression dramatically upregulated during sporulation
YJR109C	0.733747	RPH1	YJR109C|CPA2|S000003870|Large subunit of carbamoyl phosphate synthetase, which catalyzes a step in the synthesis of citrulline, an arginine precursor
YKR103W	0.72879	RPH1	YKR103W|NFT1|S000001811|Putative transporter of the multidrug resistance-associated protein (MRP) subfamily; adjacent ORFs YKR103W and YKR104W are merged in different strain backgrounds.
YJL131C	0.719462	RPH1	YJL131C|AIM23|S000003667|Putative protein of unknown function; the authentic non-tagged protein is detected in highly purified mitochondria; null mutant is viable, displays increased frequency of mitochondrial genome loss (petite formation)
YHR131W-A	0.718965	RPH1	YHR131W-A||S000028782|Dubious open reading frame unlikely to encode a protein; partially overlaps the uncharacterized ORF YHR131C
YEL072W	0.717398	RPH1	YEL072W|RMD6|S000000798|Protein required for sporulation
YBR215W	0.715443	RPH1	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
YKL142W	0.714116	RPH1	YKL142W|MRP8|S000001625|Putative mitochondrial ribosomal protein, has similarity to E. coli ribosomal protein S2
YML055W	0.714086	RPH1	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
YMR292W	0.710401	RPH1	YMR292W|GOT1|S000004906|Evolutionarily conserved non-essential protein present in early Golgi cisternae that may be involved in ER-Golgi transport at a step after vesicle tethering to Golgi membranes, exhibits membrane topology similar to that of Sft2p
YLR436C	0.707874	RPH1	YLR436C|ECM30|S000004428|Non-essential protein of unknown function
YPR081C	0.703232	RPH1	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
YGR258C	0.70284	RPH1	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
YDL168W	0.701525	RPH1	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
YCL004W	0.699104	RPH1	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
YIL088C	0.695992	RPH1	YIL088C|AVT7|S000001350|Putative transporter, member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters
YGL237C	0.692325	RPH1	YGL237C|HAP2|S000003206|Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression; contains sequences sufficient for both complex assembly and DNA binding
YDL128W	0.683568	RPH1	YDL128W|VCX1|S000002286|Vacuolar H+/Ca2+ exchanger involved in control of cytosolic Ca2+ concentration; has similarity to sodium/calcium exchangers, including the bovine Na+/Ca2+,K+ antiporter
YML116W-A	0.68147	RPH1	YML116W-A||S000004586|Putative protein of unknown function
YGR069W	0.678432	RPH1	YGR069W||S000003301|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YGL215W	0.674887	RPH1	YGL215W|CLG1|S000003183|Cyclin-like protein that interacts with Pho85p; has sequence similarity to G1 cyclins PCL1 and PCL2
YDR310C	0.673176	RPH1	YDR310C|SUM1|S000002718|Transcriptional repressor required for mitotic repression of middle sporulation-specific genes; involved in telomere maintenance, regulated by the pachytene checkpoint
YBR033W	0.672776	RPH1	YBR033W|EDS1|S000000237|Putative zinc cluster protein; YBR033W is not an essential gene
YDL156W	0.671671	RPH1	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
YIL046W	0.671638	RPH1	YIL046W|MET30|S000001308|F-box protein containing five copies of the WD40 motif, controls cell cycle function, sulfur metabolism, and methionine biosynthesis as part of the ubiquitin ligase complex; interacts with and regulates Met4p, localizes within the nucleus
YLR248W	0.669097	RPH1	YLR248W|RCK2|S000004238|Protein kinase involved in the response to oxidative and osmotic stress; identified as suppressor of S. pombe cell cycle checkpoint mutations
YJL093C	0.668281	RPH1	YJL093C|TOK1|S000003629|Outward-rectifier potassium channel of the plasma membrane with two pore domains in tandem, each of which forms a functional channel permeable to potassium; carboxy tail functions to prevent inner gate closures; target of K1 toxin
YNL034W	0.664746	RPH1	YNL034W||S000004979|Putative protein of unknown function; YNL034W is not an essential gene
YDL109C	0.664221	RPH1	YDL109C||S000002267|Putative lipase; involved in lipid metabolism; YDL109C is not an essential gene
YBL033C	0.660038	RPH1	YBL033C|RIB1|S000000129|GTP cyclohydrolase II; catalyzes the first step of the riboflavin biosynthesis pathway
YOR114W	0.659116	RPH1	YOR114W||S000005640|Putative protein of unknown function; null mutant is viable
YKL002W	0.650304	RPH1	YKL002W|DID4|S000001485|Class E Vps protein of the ESCRT-III complex, required for sorting of integral membrane proteins into lumenal vesicles of multivesicular bodies, and for delivery of newly synthesized vacuolar enzymes to the vacuole, involved in endocytosis
YPR022C	0.649742	RPH1	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
YHR092C	0.646625	RPH1	YHR092C|HXT4|S000001134|High-affinity glucose transporter of the major facilitator superfamily, expression is induced by low levels of glucose and repressed by high levels of glucose
YKL168C	0.642733	RPH1	YKL168C|KKQ8|S000001651|Putative serine/threonine protein kinase with unknown cellular role
YCR088W	0.642335	RPH1	YCR088W|ABP1|S000000684|Actin-binding protein of the cortical actin cytoskeleton, important for activation of the Arp2/3 complex that plays a key role actin in cytoskeleton organization
YLR216C	0.642244	RPH1	YLR216C|CPR6|S000004206|Peptidyl-prolyl cis-trans isomerase (cyclophilin), catalyzes the cis-trans isomerization of peptide bonds N-terminal to proline residues; binds to Hsp82p and contributes to chaperone activity
YIL065C	0.639964	RPH1	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
YER115C	0.637557	RPH1	YER115C|SPR6|S000000917|Protein of unknown function, expressed during sporulation; not required for sporulation, but gene exhibits genetic interactions with other genes required for sporulation
YER087C-A	0.636389	RPH1	YER087C-A||S000028753|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data; overlaps the uncharacterized gene YER087W, a putative tRNA synthetase
YHL037C	0.631471	RPH1	YHL037C||S000001029|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YMR139W	0.624498	RPH1	YMR139W|RIM11|S000004747|Protein kinase required for signal transduction during entry into meiosis; promotes the formation of the Ime1p-Ume6p complex by phosphorylating Ime1p and Ume6p; shares similarity with mammalian glycogen synthase kinase 3-beta
YBR179C	0.621669	RPH1	YBR179C|FZO1|S000000383|Mitochondrial integral membrane protein involved in mitochondrial fusion and maintenance of the mitochondrial genome; contains N-terminal GTPase domain
YGR126W	0.617326	RPH1	YGR126W||S000003358|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
YDR272W	0.606173	RPH1	YDR272W|GLO2|S000002680|Cytoplasmic glyoxalase II, catalyzes the hydrolysis of S-D-lactoylglutathione into glutathione and D-lactate
YIL071C	0.603933	RPH1	YIL071C|PCI8|S000001333|Possible shared subunit of Cop9 signalosome (CSN) and eIF3, binds eIF3b subunit Prt1p, has possible dual functions in transcriptional and translational control, contains a PCI (Proteasome-COP9 signalosome (CSN)-eIF3) domain
YLR007W	0.601546	RPH1	YLR007W|NSE1|S000003997|Essential subunit of the Mms21-Smc5-Smc6 complex; nuclear protein required for DNA repair and growth; has a nonstructural role in the maintenance of chromosomes
YLR217W	0.601151	RPH1	YLR217W||S000004207|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene CPR6
YLR241W	0.600567	RPH1	YLR241W||S000004231|Putative protein of unknown function, may be involved in detoxification
YDR242W	0.595392	RPH1	YDR242W|AMD2|S000002650|Putative amidase
YNL019C	0.593661	RPH1	YNL019C||S000004964|Putative protein of unknown function
YDR442W	0.591123	RPH1	YDR442W||S000002850|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YDL190C	0.585301	RPH1	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
YCR033W	0.583469	RPH1	YCR033W|SNT1|S000000629|Subunit of the Set3C deacetylase complex that interacts directly with the Set3C subunit, Sif2p; putative DNA-binding protein
YHL044W	0.581072	RPH1	YHL044W||S000001036|Putative integral membrane protein, member of DUP240 gene family; green fluorescent protein (GFP)-fusion protein localizes to the plasma membrane in a punctate pattern
YLR124W	0.579858	RPH1	YLR124W||S000004114|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YGL139W	0.573997	RPH1	YGL139W|FLC3|S000003107|Putative FAD transporter, similar to Flc1p and Flc2p; localized to the ER
YOR388C	0.568192	RPH1	YOR388C|FDH1|S000005915|NAD(+)-dependent formate dehydrogenase, may protect cells from exogenous formate
YOL013C	0.563064	RPH1	YOL013C|HRD1|S000005373|Ubiquitin-protein ligase required for endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins; genetically linked to the unfolded protein response (UPR); regulated through association with Hrd3p; contains an H2 ring finger
YJL027C	0.559949	RPH1	YJL027C||S000003564|Putative protein of unknown function
YGL083W	0.558759	RPH1	YGL083W|SCY1|S000003051|Putative kinase, suppressor of GTPase mutant, similar to bovine rhodopsin kinase
YIR038C	0.558517	RPH1	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
YGL255W	0.558415	RPH1	YGL255W|ZRT1|S000003224|High-affinity zinc transporter of the plasma membrane, responsible for the majority of zinc uptake; transcription is induced under low-zinc conditions by the Zap1p transcription factor
YBR218C	0.554337	RPH1	YBR218C|PYC2|S000000422|Pyruvate carboxylase isoform, cytoplasmic enzyme that converts pyruvate to oxaloacetate; highly similar to isoform Pyc1p but differentially regulated; mutations in the human homolog are associated with lactic acidosis
YBR180W	0.552491	RPH1	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
YBR037C	0.54578	RPH1	YBR037C|SCO1|S000000241|Copper-binding protein of the mitochondrial inner membrane, required for cytochrome c oxidase activity and respiration; may function to deliver copper to cytochrome c oxidase; has similarity to thioredoxins
YKL020C	0.545527	RPH1	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
YPR196W	0.54382	RPH1	YPR196W||S000006400|Putative maltose activator
YDL091C	0.543469	RPH1	YDL091C|UBX3|S000002249|UBX (ubiquitin regulatory X) domain-containing protein that interacts with Cdc48p, green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern
YOL044W	0.540797	RPH1	YOL044W|PEX15|S000005404|Phosphorylated tail-anchored type II integral peroxisomal membrane protein required for peroxisome biogenesis, cells lacking Pex15p mislocalize peroxisomal matrix proteins to cytosol, overexpression results in impaired peroxisome assembly
YMR156C	0.536297	RPH1	YMR156C|TPP1|S000004765|DNA 3'-phosphatase that functions in repair of endogenous damage of double-stranded DNA, activity is specific for removal of 3' phosphates at strand breaks; has similarity to the l-2-haloacid dehalogenase superfamily
YMR258C	0.535682	RPH1	YMR258C||S000004871|Protein of unknown function with similarity to F-box proteins; physically interacts with Skp1p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus; YMR258C is not an essential gene
YPL082C	0.535549	RPH1	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
YML066C	0.533012	RPH1	YML066C|SMA2|S000004531|Protein of unknown function involved in the assembly of the prospore membrane during sporulation
YDL216C	0.528575	RPH1	YDL216C|RRI1|S000002375|Catalytic subunit of the COP9 signalosome (CSN) complex that acts as an isopeptidase in cleaving the ubiquitin-like protein Nedd8 from SCF ubiquitin ligases; metalloendopeptidase involved in the adaptation to pheromone signaling
YDR136C	0.527861	RPH1	YDR136C|VPS61|S000002543|Dubious open reading frame, unlikely to encode a protein; not conserved in closely related Saccharomyces species; 4% of ORF overlaps the verified gene RGP1; deletion causes a vacuolar protein sorting defect
YPL039W	0.527842	RPH1	YPL039W||S000005960|Putative protein of unknown function; YPL039W is not an essential gene
YER144C	0.527461	RPH1	YER144C|UBP5|S000000946|Putative ubiquitin-specific protease, closest paralog of Doa4p but has no functional overlap; concentrates at the bud neck
YGL140C	0.526784	RPH1	YGL140C||S000003108|Putative protein of unknown function; non-essential gene; contains multiple predicted transmembrane domains
YNR063W	0.522654	RPH1	YNR063W||S000005346|Putative zinc-cluster protein of unknown function
YPR149W	0.5221	RPH1	YPR149W|NCE102|S000006353|Protein of unknown function; contains transmembrane domains; involved in secretion of proteins that lack classical secretory signal sequences; component of the detergent-insoluble glycolipid-enriched complexes (DIGs)
YKL121W	0.52012	RPH1	YKL121W||S000001604|Putative protein of unknown function
YER167W	0.517174	RPH1	YER167W|BCK2|S000000969|Protein rich in serine and threonine residues involved in protein kinase C signaling pathway, which controls cell integrity; overproduction suppresses pkc1 mutations
YOR231W	0.513731	RPH1	YOR231W|MKK1|S000005757|Mitogen-activated kinase kinase involved in protein kinase C signaling pathway that controls cell integrity; upon activation by Bck1p phosphorylates downstream target, Slt2p; functionally redundant with Mkk2p
YNL243W	0.509698	RPH1	YNL243W|SLA2|S000005187|Transmembrane actin-binding protein involved in membrane cytoskeleton assembly and cell polarization; adaptor protein that links actin to clathrin and endocytosis; present in the actin cortical patch of the emerging bud tip; dimer in vivo
YML114C	0.505854	RPH1	YML114C|TAF8|S000004582|TFIID subunit (65 kDa), involved in RNA polymerase II transcription initiation
YLR015W	0.505473	RPH1	YLR015W|BRE2|S000004005|Subunit of the COMPASS (Set1C) complex, which methylates histone H3 on lysine 4 and is required in transcriptional silencing near telomeres; involved in telomere maintenance; similar to trithorax-group protein ASH2L
YHR009C	0.50509	RPH1	YHR009C||S000001051|Putative protein of unknown function; not an essential gene
YLR324W	0.504851	RPH1	YLR324W|PEX30|S000004316|Peroxisomal integral membrane protein, involved in negative regulation of peroxisome number; partially functionally redundant with Pex31p; genetic interactions suggest action at a step downstream of steps mediated by Pex28p and Pex29p
YLR352W	0.498231	RPH1	YLR352W||S000004344|Putative protein of unknown function with similarity to F-box proteins; interacts with Skp1p and Cdc53p; YLR352W is not an essential gene
YPL117C	0.492393	RPH1	YPL117C|IDI1|S000006038|Isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IPP isomerase), catalyzes an essential activation step in the isoprenoid biosynthetic pathway; required for viability
YJR062C	0.490408	RPH1	YJR062C|NTA1|S000003823|Amidase, removes the amide group from N-terminal asparagine and glutamine residues to generate proteins with N-terminal aspartate and glutamate residues that are targets of ubiquitin-mediated degradation
YGL098W	0.486864	RPH1	YGL098W|USE1|S000003066|Essential SNARE protein localized to the ER, involved in retrograde traffic from the Golgi to the ER; forms a complex with the SNAREs Sec22p, Sec20p and Ufe1p
YEL071W	0.484643	RPH1	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
YLR125W	0.4758	RPH1	YLR125W||S000004115|Putative protein of unknown function; mutant has decreased Ty3 transposition; YLR125W is not an essential gene
YBR059C	0.475049	RPH1	YBR059C|AKL1|S000000263|Ser-Thr protein kinase, member (with Ark1p and Prk1p) of the Ark kinase family; involved in endocytosis and actin cytoskeleton organization
YCR084C	0.473856	RPH1	YCR084C|TUP1|S000000680|General repressor of transcription, forms complex with Cyc8p, involved in the establishment of repressive chromatin structure through interactions with histones H3 and H4, appears to enhance expression of some genes
YLR223C	0.473787	RPH1	YLR223C|IFH1|S000004213|Essential protein with a highly acidic N-terminal domain; IFH1 exhibits genetic interactions with FHL1, overexpression interferes with silencing at telomeres and HM loci; potential Cdc28p substrate
YDR282C	0.473532	RPH1	YDR282C||S000002690|Putative protein of unknown function
YOL157C	0.470388	RPH1	YOL157C||S000005517|Putative protein of unknown function
YJL112W	0.469493	RPH1	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
YLR255C	0.467942	RPH1	YLR255C||S000004245|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YPL189W	0.467517	RPH1	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
YKL003C	0.466559	RPH1	YKL003C|MRP17|S000001486|Mitochondrial ribosomal protein of the small subunit; MRP17 exhibits genetic interactions with PET122, encoding a COX3-specific translational activator
YBL099W	0.465737	RPH1	YBL099W|ATP1|S000000195|Alpha subunit of the F1 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis; phosphorylated
YDR333C	0.463713	RPH1	YDR333C||S000002741|Putative protein of unknown function
YNL173C	0.463499	RPH1	YNL173C|MDG1|S000005117|Plasma membrane protein involved in G-protein mediated pheromone signaling pathway; overproduction suppresses bem1 mutations
YHL046C	0.455961	RPH1	YHL046C|PAU13|S000001038|Putative protein of unknown function; not an essential gene
YCR076C	0.45596	RPH1	YCR076C||S000000672|Putative protein of unknown function; YCR076C is not an essential gene
YML132W	0.453513	RPH1	YML132W|COS3|S000004601|Protein involved in salt resistance; interacts with sodium:hydrogen antiporter Nha1p; member of the DUP380 subfamily of conserved, often subtelomerically-encoded proteins
YDR229W	0.453279	RPH1	YDR229W|IVY1|S000002637|Phospholipid-binding protein that interacts with both Ypt7p and Vps33p, may partially counteract the action of Vps33p and vice versa, localizes to the rim of the vacuole as cells approach stationary phase
YOL004W	0.4496	RPH1	YOL004W|SIN3|S000005364|Component of the Sin3p-Rpd3p histone deacetylase complex, involved in transcriptional repression and activation of diverse processes, including mating-type switching and meiosis; involved in the maintenance of chromosomal integrity
YPL191C	0.444722	RPH1	YPL191C||S000006112|Putative protein of unknown function; diploid deletion strain exhibits high budding index; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YOL156W	0.437855	RPH1	YOL156W|HXT11|S000005516|Putative hexose transporter that is nearly identical to Hxt9p, has similarity to major facilitator superfamily (MFS) transporters and is involved in pleiotropic drug resistance
YBR044C	0.436083	RPH1	YBR044C|TCM62|S000000248|Protein involved in the assembly of the mitochondrial succinate dehydrogenase complex; putative chaperone
YDR351W	0.430794	RPH1	YDR351W|SBE2|S000002759|Protein involved in the transport of cell wall components from the Golgi to the cell surface; required for bud growth
YPL154C	0.425077	RPH1	YPL154C|PEP4|S000006075|Vacuolar aspartyl protease (proteinase A), required for the posttranslational precursor maturation of vacuolar proteinases; important for protein turnover after oxidative damage; synthesized as a zymogen, self-activates
YBR150C	0.423745	RPH1	YBR150C|TBS1|S000000354|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YER098W	0.417529	RPH1	YER098W|UBP9|S000000900|Ubiquitin carboxyl-terminal hydrolase, ubiquitin-specific protease that cleaves ubiquitin-protein fusions
YLL015W	0.414813	RPH1	YLL015W|BPT1|S000003938|ABC type transmembrane transporter of MRP/CFTR family, found in vacuolar membrane, involved in the transport of unconjugated bilirubin and in heavy metal detoxification via glutathione conjugates, along with Ycf1p
YIL117C	0.414784	RPH1	YIL117C|PRM5|S000001379|Pheromone-regulated protein, predicted to have 1 transmembrane segment; induced during cell integrity signaling
YHR022C	0.411369	RPH1	YHR022C||S000001064|Putative protein of unknown function; YHR022C is not an essential gene.
YKL220C	0.410128	RPH1	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
YBR255W	0.407722	RPH1	YBR255W|MTC4|S000000459|Protein of unknown function, required for normal growth rate at 15 degrees C; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm in a punctate pattern; YBR255W is synthetically sick with cdc13-1
YGR281W	0.40319	RPH1	YGR281W|YOR1|S000003513|Plasma membrane ATP-binding cassette (ABC) transporter, multidrug transporter mediates export of many different organic anions including oligomycin
YOR141C	0.402395	RPH1	YOR141C|ARP8|S000005667|Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes
YPL214C	0.393478	RPH1	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
YDR409W	0.393046	RPH1	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
YOR389W	0.389764	RPH1	YOR389W||S000005916|Putative protein of unknown function; expression regulated by copper levels
YNL339C	0.384402	RPH1	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
YBR209W	0.382443	RPH1	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
YPL032C	0.381542	RPH1	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
YLL030C	0.379692	RPH1	YLL030C||S000003953|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YPL133C	0.376512	RPH1	YPL133C|RDS2|S000006054|Zinc cluster transcriptional activator involved in conferring resistance to ketoconazole
YCR023C	0.37497	RPH1	YCR023C||S000000617|Vacuolar membrane protein of unknown function; member of the multidrug resistance family; YCR023C is not an essential gene
YML116W	0.372914	RPH1	YML116W|ATR1|S000004584|Multidrug efflux pump of the major facilitator superfamily, required for resistance to aminotriazole and 4-nitroquinoline-N-oxide
YNL267W	0.371768	RPH1	YNL267W|PIK1|S000005211|Phosphatidylinositol 4-kinase; catalyzes first step in the biosynthesis of phosphatidylinositol-4,5-biphosphate; may control cytokineses through the actin cytoskeleton
YPL016W	0.368466	RPH1	YPL016W|SWI1|S000005937|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; can become prion [SWI+]
YGL084C	0.36299	RPH1	YGL084C|GUP1|S000003052|Plasma membrane protein involved in remodeling GPI anchors; member of the MBOAT family of putative membrane-bound O-acyltransferases; proposed to be involved in glycerol transport
YDR079W	0.362276	RPH1	YDR079W|PET100|S000002486|Chaperone that specifically facilitates the assembly of cytochrome c oxidase, integral to the mitochondrial inner membrane; interacts with a subcomplex of subunits VII, VIIa, and VIII (Cox7p, Cox9p, and Cox8p) but not with the holoenzyme
YJL165C	0.355017	RPH1	YJL165C|HAL5|S000003701|Putative protein kinase; overexpression increases sodium and lithium tolerance, whereas gene disruption increases cation and low pH sensitivity and impairs potassium uptake, suggesting a role in regulation of Trk1p and/or Trk2p transporters
YDR293C	0.351192	RPH1	YDR293C|SSD1|S000002701|Protein with a role in maintenance of cellular integrity, interacts with components of the TOR pathway; ssd1 mutant of a clinical S. cerevisiae strain displays elevated virulence
YNR032C-A	0.349862	RPH1	YNR032C-A|HUB1|S000007251|Ubiquitin-like protein modifier, may function in modification of Sph1p and Hbt1p, functionally complemented by the human or S. pombe ortholog; mechanism of Hub1p adduct formation not yet clear
YKL193C	0.347837	RPH1	YKL193C|SDS22|S000001676|Conserved nuclear regulatory subunit of Glc7p type 1 protein serine-threonine phosphatase (PP1), functions positively with Glc7p to promote dephosphorylation of nuclear substrates required for chromosome transmission during mitosis
YNL157W	0.347827	RPH1	YNL157W|IGO1|S000005101|Hypothetical protein
YKL139W	0.346276	RPH1	YKL139W|CTK1|S000001622|Catalytic (alpha) 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
YER137W-A	0.343473	RPH1	YER137W-A||S000028757|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YER084W-A	0.342676	RPH1	YER084W-A||S000028752|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YCL051W	0.340304	RPH1	YCL051W|LRE1|S000000556|Protein involved in control of cell wall structure and stress response; inhibits Cbk1p protein kinase activity; overproduction confers resistance to cell-wall degrading enzymes
YKL210W	0.340002	RPH1	YKL210W|UBA1|S000001693|Ubiquitin activating enzyme (E1), involved in ubiquitin-mediated protein degradation and essential for viability
YPR115W	0.335497	RPH1	YPR115W|GCA1|S000006319|Pleckstrin homology domain containing protein proposed to function as a glycerol channel activator; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YMR284W	0.334305	RPH1	YMR284W|YKU70|S000004897|Subunit of the telomeric Ku complex (Yku70p-Yku80p), involved in telomere length maintenance, structure and telomere position effect; relocates to sites of double-strand cleavage to promote nonhomologous end joining during DSB repair
YGL002W	0.333734	RPH1	YGL002W|ERP6|S000002970|Protein with similarity to Emp24p and Erv25p, member of the p24 family involved in ER to Golgi transport; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YEL050C	0.329939	RPH1	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
YOL158C	0.327912	RPH1	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
YKR080W	0.323162	RPH1	YKR080W|MTD1|S000001788|NAD-dependent 5,10-methylenetetrahydrafolate dehydrogenase, plays a catalytic role in oxidation of cytoplasmic one-carbon units; expression is regulated by Bas1p and Bas2p, repressed by adenine, and may be induced by inositol and choline
YGL003C	0.322941	RPH1	YGL003C|CDH1|S000002971|Cell-cycle regulated activator of the anaphase-promoting complex/cyclosome (APC/C), which directs ubiquitination of cyclins resulting in mitotic exit; targets the APC/C to specific substrates including CDC20, ASE1, CIN8 and FIN1
YNL007C	0.320312	RPH1	YNL007C|SIS1|S000004952|Type II HSP40 co-chaperone that interacts with the HSP70 protein Ssa1p; not functionally redundant with Ydj1p due to due to substrate specificity; shares similarity with bacterial DnaJ proteins
YEL069C	0.319172	RPH1	YEL069C|HXT13|S000000795|Hexose transporter, induced in the presence of non-fermentable carbon sources, induced by low levels of glucose, repressed by high levels of glucose
YNR033W	0.318897	RPH1	YNR033W|ABZ1|S000005316|Para-aminobenzoate (PABA) synthase, has similarity to Escherichia coli PABA synthase components PabA and PabB
YGL089C	0.31884	RPH1	YGL089C|MF(ALPHA)2|S000003057|Mating pheromone alpha-factor, made by alpha cells; interacts with mating type a cells to induce cell cycle arrest and other responses leading to mating; also encoded by MF(ALPHA)1, which is more highly expressed than MF(ALPHA)2
YBL100C	0.317951	RPH1	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
YMR041C	0.317626	RPH1	YMR041C|ARA2|S000004644|NAD-dependent arabinose dehydrogenase, involved in biosynthesis of erythroascorbic acid; similar to plant L-galactose dehydrogenase
YGL228W	0.317393	RPH1	YGL228W|SHE10|S000003197|Putative glycosylphosphatidylinositol (GPI)-anchored protein of unknown function; overexpression causes growth arrest
YMR163C	0.315153	RPH1	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
YDR311W	0.31259	RPH1	YDR311W|TFB1|S000002719|Subunit of TFIIH and nucleotide excision repair factor 3 complexes, required for nucleotide excision repair, target for transcriptional activators
YDR275W	0.311433	RPH1	YDR275W|BSC2|S000002683|Protein of unknown function, ORF exhibits genomic organization compatible with a translational readthrough-dependent mode of expression
YLR456W	0.308158	RPH1	YLR456W||S000004448|Putative protein of unknown function; null mutant displays increased resistance to antifungal agents gliotoxin, cycloheximide and H2O2
YIR016W	0.307886	RPH1	YIR016W||S000001455|Putative protein of unknown function; expression directly regulated by the metabolic and meiotic transcriptional regulator Ume6p; YIR016W is a non-essential gene
YOL058W	0.301996	RPH1	YOL058W|ARG1|S000005419|Arginosuccinate synthetase, catalyzes the formation of L-argininosuccinate from citrulline and L-aspartate in the arginine biosynthesis pathway; potential Cdc28p substrate
YIL075C	0.301346	RPH1	YIL075C|RPN2|S000001337|Subunit of the 26S proteasome, substrate of the N-acetyltransferase Nat1p
YHL045W	0.299828	RPH1	YHL045W||S000001037|Putative protein of unknown function; not an essential gene
YAL024C	0.296717	RPH1	YAL024C|LTE1|S000000022|Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP
YIL001W	0.293774	RPH1	YIL001W||S000001263|Hypothetical protein
YNL124W	0.288591	RPH1	YNL124W|NAF1|S000005068|Protein required for the assembly of box H/ACA snoRNPs and for pre-rRNA processing, forms a complex with Shq1p and interacts with H/ACA snoRNP components Nhp2p and Cbf5p; has similarity to Gar1p and other RNA-binding proteins
YNL337W	0.284654	RPH1	YNL337W||S000005281|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YDR078C	0.282678	RPH1	YDR078C|SHU2|S000002485|Protein of unassigned function involved in mutation suppression, important for error-free repair of spontaneous and induced DNA lesions to protect the genome from mutation; associates with Shu1p, Psy3p, and Csm2p
YLR044C	0.281573	RPH1	YLR044C|PDC1|S000004034|Major of three pyruvate decarboxylase isozymes, key enzyme in alcoholic fermentation, decarboxylates pyruvate to acetaldehyde; subject to glucose-, ethanol-, and autoregulation; involved in amino acid catabolism
YKR042W	0.281327	RPH1	YKR042W|UTH1|S000001750|Mitochondrial outer membrane and cell wall localized SUN family member required for mitochondrial autophagy; involved in the oxidative stress response, life span during starvation, mitochondrial biogenesis, and cell death
YGL064C	0.280417	RPH1	YGL064C|MRH4|S000003032|Mitochondrial ATP-dependent RNA helicase of the DEAD-box family, plays an essential role in mitochondrial function
YOR370C	0.278565	RPH1	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)
YER153C	0.276602	RPH1	YER153C|PET122|S000000955|Mitochondrial translational activator specific for the COX3 mRNA, acts together with Pet54p and Pet494p; located in the mitochondrial inner membrane
YDL061C	0.273142	RPH1	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
YNR070W	0.272181	RPH1	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
YIL058W	0.270983	RPH1	YIL058W||S000001320|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YGL013C	0.2709	RPH1	YGL013C|PDR1|S000002981|Zinc cluster protein that is a master regulator involved in recruiting other zinc cluster proteins to pleiotropic drug response elements (PDREs) to fine tune the regulation of multidrug resistance genes
YNL336W	0.26993	RPH1	YNL336W|COS1|S000005280|Protein of unknown function, member of the DUP380 subfamily of conserved, often subtelomerically-encoded proteins
YJR127C	0.269608	RPH1	YJR127C|RSF2|S000003888|Zinc-finger protein involved in transcriptional control of both nuclear and mitochondrial genes, many of which specify products required for glycerol-based growth, respiration, and other functions
YMR089C	0.266476	RPH1	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
YNL201C	0.263536	RPH1	YNL201C|PSY2|S000005145|Putative subunit of an evolutionarily conserved protein phosphatase complex containing the catalytic subunit Pph3p and the regulatory subunit Psy4p; required for cisplatin and oxaliplatin resistance; localizes to nucleus
YER097W	0.257623	RPH1	YER097W||S000000899|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YCR063W	0.255804	RPH1	YCR063W|BUD31|S000000659|Protein involved in bud-site selection; analysis of integrated high-throughput datasets predicts an involvement in RNA splicing; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern
YGL053W	0.254874	RPH1	YGL053W|PRM8|S000003021|Pheromone-regulated protein with 2 predicted transmembrane segments and an FF sequence, a motif involved in COPII binding; forms a complex with Prp9p in the ER; member of DUP240 gene family
YOR306C	0.252222	RPH1	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
YKL039W	0.245592	RPH1	YKL039W|PTM1|S000001522|Protein of unknown function, copurifies with late Golgi vesicles containing the v-SNARE Tlg2p
YJL151C	0.238322	RPH1	YJL151C|SNA3|S000003687|Integral membrane protein localized to vacuolar intralumenal vesicles, computational analysis of large-scale protein-protein interaction data suggests a possible role in either cell wall synthesis or protein-vacuolar targeting
YOR267C	0.232503	RPH1	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
YFR036W	0.231822	RPH1	YFR036W|CDC26|S000001932|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
YOR052C	0.231385	RPH1	YOR052C||S000005578|Nuclear protein of unknown function; expression induced by nitrogen limitation in a GLN3, GAT1-independent manner and by weak acid
YCL069W	0.230413	RPH1	YCL069W|VBA3|S000000574|Permease of basic amino acids in the vacuolar membrane
YHR131C	0.228527	RPH1	YHR131C||S000001173|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YBR220C	0.223945	RPH1	YBR220C||S000000424|Putative protein of unknown function; YBR220C is not an essential gene
YOR010C	0.2218	RPH1	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
YGL056C	0.216407	RPH1	YGL056C|SDS23|S000003024|One of two S. cerevisiae homologs (Sds23p and Sds24p) of the Schizosaccharomyces pombe Sds23 protein, which genetic studies have implicated in APC/cyclosome regulation
YCR032W	0.214165	RPH1	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
YPL071C	0.213166	RPH1	YPL071C||S000005992|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to both the cytoplasm and the nucleus
YBR155W	0.211482	RPH1	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
YNL020C	0.211333	RPH1	YNL020C|ARK1|S000004965|Serine/threonine protein kinase involved in regulation of the cortical actin cytoskeleton; involved in control of endocytosis
YDR135C	0.210328	RPH1	YDR135C|YCF1|S000002542|Vacuolar glutathione S-conjugate transporter of the ATP-binding cassette family, has a role in detoxifying metals such as cadmium, mercury, and arsenite; also transports unconjugated bilirubin; similar to human cystic fibrosis protein CFTR
YNL083W	0.209919	RPH1	YNL083W|SAL1|S000005027|Probable transporter, member of the Ca2+-binding subfamily of the mitochondrial carrier family, with two EF-hand motifs; Pet9p and Sal1p have an overlapping function critical for viability; polymorphic in different S. cerevisiae strains
YER008C	0.209733	RPH1	YER008C|SEC3|S000000810|Non-essential subunit of the exocyst complex (Sec3p, Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, Exo70p, Exo84p) which mediates targeting of post-Golgi vesicles to sites of active exocytosis; Sec3p specifically is a spatial landmark for secretion
YJR055W	0.207452	RPH1	YJR055W|HIT1|S000003816|Protein of unknown function, required for growth at high temperature
YER129W	0.206643	RPH1	YER129W|SAK1|S000000931|Upstream serine/threonine kinase for the SNF1 complex; partially redundant with Elm1p and Tos3p; members of this family have functional orthology with LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome
YMR145C	0.205166	RPH1	YMR145C|NDE1|S000004753|Mitochondrial external NADH dehydrogenase, a type II NAD(P)H:quinone oxidoreductase that catalyzes the oxidation of cytosolic NADH; Nde1p and Nde2p provide cytosolic NADH to the mitochondrial respiratory chain
YLR014C	0.203382	RPH1	YLR014C|PPR1|S000004004|Zinc finger transcription factor containing a Zn(2)-Cys(6) binuclear cluster domain, positively regulates transcription of genes involved in uracil biosynthesis; activity may be modulated by interaction with Tup1p
YBL086C	0.201404	RPH1	YBL086C||S000000182|Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cell periphery
YGL150C	0.200905	RPH1	YGL150C|INO80|S000003118|ATPase that forms a large complex, containing actin and several actin-related proteins, that has chromatin remodeling activity and 3' to 5' DNA helicase activity in vitro; shows similarity to the Snf2p family of ATPases
YPL070W	0.193783	RPH1	YPL070W|MUK1|S000005991|Cytoplasmic protein of unknown function; computational analysis of large-scale protein-protein interaction data suggests a possible role in transcriptional regulation
YPR100W	0.192062	RPH1	YPR100W|MRPL51|S000006304|Mitochondrial ribosomal protein of the large subunit
YGR222W	0.191579	RPH1	YGR222W|PET54|S000003454|Mitochondrial inner membrane protein that binds to the 5' UTR of the COX3 mRNA to activate its translation together with Pet122p and Pet494p; also binds to the COX1 Group I intron AI5 beta to facilitate exon ligation during splicing
YLR371W	0.191097	RPH1	YLR371W|ROM2|S000004363|GDP/GTP exchange protein (GEP) for Rho1p and Rho2p; mutations are synthetically lethal with mutations in rom1, which also encodes a GEP
YNL004W	0.189907	RPH1	YNL004W|HRB1|S000004949|Poly(A+) RNA-binding protein, involved in the export of mRNAs from the nucleus to the cytoplasm; similar to Gbp2p and Npl3p
YMR042W	0.18841	RPH1	YMR042W|ARG80|S000004645|Transcription factor involved in regulation of arginine-responsive genes; acts with Arg81p and Arg82p
YLR024C	0.183972	RPH1	YLR024C|UBR2|S000004014|Cytoplasmic ubiquitin-protein ligase (E3)
YER154W	0.183012	RPH1	YER154W|OXA1|S000000956|Mitochondrial inner membrane insertase, mediates the insertion of both mitochondrial- and nuclear-encoded proteins from the matrix into the inner membrane, interacts with mitochondrial ribosomes; conserved from bacteria to animals
YAR027W	0.182383	RPH1	YAR027W|UIP3|S000000075|Putative integral membrane protein of unknown function; interacts with Ulp1p at the nuclear periphery; member of DUP240 gene family
YJL110C	0.178344	RPH1	YJL110C|GZF3|S000003646|GATA zinc finger protein and Dal80p homolog that negatively regulates nitrogen catabolic gene expression by competing with Gat1p for GATA site binding; function requires a repressive carbon source; dimerizes with Dal80p and binds to Tor1p
YGR270W	0.177347	RPH1	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
YPL184C	0.176877	RPH1	YPL184C|MRN1|S000006105|Putative RNA binding protein
YPL130W	0.176498	RPH1	YPL130W|SPO19|S000006051|Meiosis-specific protein of unknown function, involved in completion of nuclear divisions; identified as a weak high-copy suppressor of the spo1-1 ts mutation; putative GPI-dependent cell-wall protein
YER179W	0.172425	RPH1	YER179W|DMC1|S000000981|Meiosis-specific protein required for repair of double-strand breaks and pairing between homologous chromosomes; homolog of Rad51p and the bacterial RecA protein
YHR110W	0.172375	RPH1	YHR110W|ERP5|S000001152|Protein with similarity to Emp24p and Erv25p, member of the p24 family involved in ER to Golgi transport
YJL159W	0.171098	RPH1	YJL159W|HSP150|S000003695|O-mannosylated heat shock protein that is secreted and covalently attached to the cell wall via beta-1,3-glucan and disulfide bridges; required for cell wall stability; induced by heat shock, oxidative stress, and nitrogen limitation
YFR045W	0.170763	RPH1	YFR045W||S000001941|Putative mitochondrial transport protein; null mutant is viable, exhibits decreased levels of chitin and normal resistance to calcofluor white
YCR093W	0.163442	RPH1	YCR093W|CDC39|S000000689|Component of the CCR4-NOT complex, which has multiple roles in regulating mRNA levels including regulation of transcription and destabilizing mRNAs by deadenylation; basal transcription factor
YKR098C	0.162807	RPH1	YKR098C|UBP11|S000001806|Ubiquitin-specific protease that cleaves ubiquitin from ubiquitinated proteins
YBL034C	0.161282	RPH1	YBL034C|STU1|S000000130|Component of the mitotic spindle that binds to interpolar microtubules via its association with beta-tubulin (Tub2p); required for interpolar microtubules to provide an outward force on the spindle poles
YJL092W	0.158472	RPH1	YJL092W|SRS2|S000003628|DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination
YDR248C	0.155288	RPH1	YDR248C||S000002656|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YJL210W	0.151857	RPH1	YJL210W|PEX2|S000003746|RING-finger peroxin, peroxisomal membrane protein with a C-terminal zinc-binding RING domain, forms translocation subcomplex with Pex10p and Pex12p which functions in peroxisomal matrix protein import
YDR032C	0.151532	RPH1	YDR032C|PST2|S000002439|Protein with similarity to members of a family of flavodoxin-like proteins; induced by oxidative stress in a Yap1p dependent manner; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YKR017C	0.149185	RPH1	YKR017C||S000001725|Putative protein of unknown function; contains a RING finger motif
YJR079W	0.148862	RPH1	YJR079W||S000003840|Putative protein of unknown function; mutation results in impaired mitochondrial respiration
YDL060W	0.146763	RPH1	YDL060W|TSR1|S000002218|Protein required for processing of 20S pre-rRNA in the cytoplasm, associates with pre-40S ribosomal particles
YLR010C	0.146371	RPH1	YLR010C|TEN1|S000004000|Protein that regulates telomeric length; protects telomeric ends in a complex with Cdc13p and Stn1p
YDL005C	0.144435	RPH1	YDL005C|MED2|S000002163|Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation
YGR250C	0.142776	RPH1	YGR250C||S000003482|Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm
YPL213W	0.14259	RPH1	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
YDR116C	0.141063	RPH1	YDR116C|MRPL1|S000002523|Mitochondrial ribosomal protein of the large subunit
YPL153C	0.140834	RPH1	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
YGL162W	0.140704	RPH1	YGL162W|SUT1|S000003130|Transcription factor of the Zn[II]2Cys6 family involved in sterol uptake; involved in induction of hypoxic gene expression
YNL244C	0.140238	RPH1	YNL244C|SUI1|S000005188|Translation initiation factor eIF1; component of a complex involved in recognition of the initiator codon; modulates translation accuracy at the initiation phase
YNR062C	0.138765	RPH1	YNR062C||S000005345|Putative membrane protein of unknown function
YBR219C	0.137483	RPH1	YBR219C||S000000423|Putative protein of unknown function; YBR219C is not an essential gene
YLR121C	0.137262	RPH1	YLR121C|YPS3|S000004111|Aspartic protease, attached to the plasma membrane via a glycosylphosphatidylinositol (GPI) anchor
YNL042W-B	0.136215	RPH1	YNL042W-B||S000028850|Putative protein of unknown function
YMR313C	0.133277	RPH1	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
YJR059W	0.13138	RPH1	YJR059W|PTK2|S000003820|Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake
YLR390W	0.129461	RPH1	YLR390W|ECM19|S000004382|Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies
YHR177W	0.128412	RPH1	YHR177W||S000001220|Putative protein of unknown function
YLR034C	0.127615	RPH1	YLR034C|SMF3|S000004024|Putative divalent metal ion transporter involved in iron homeostasis; transcriptionally regulated by metal ions; member of the Nramp family of metal transport proteins
YLR415C	0.123477	RPH1	YLR415C||S000004407|Putative protein of unknown function; YLR415C is not an essential gene
YDR294C	0.123449	RPH1	YDR294C|DPL1|S000002702|Dihydrosphingosine phosphate lyase, regulates intracellular levels of sphingolipid long-chain base phosphates (LCBPs), degrades phosphorylated long chain bases, prefers C16 dihydrosphingosine-l-phosphate as a substrate
YEL017W	0.121764	RPH1	YEL017W|GTT3|S000000743|Protein of unknown function with a possible role in glutathione metabolism, as suggested by computational analysis of large-scale protein-protein interaction data; GFP-fusion protein localizes to the nuclear periphery
YGR246C	0.120002	RPH1	YGR246C|BRF1|S000003478|TFIIIB B-related factor, one of three subunits of RNA polymerase III transcription initiation factor TFIIIB, binds TFIIIC and TBP and recruits RNA pol III to promoters, amino-terminal half is homologous to TFIIB
YFR032C-B	0.116929	RPH1	YFR032C-B||S000028630|Putative protein of unknown function; identified by gene-trapping, microarray-based expression analysis, and genome-wide homology searching
YML122C	0.115657	RPH1	YML122C||S000004591|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data
YHR093W	0.115643	RPH1	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
YOR142W	0.114037	RPH1	YOR142W|LSC1|S000005668|Alpha subunit of succinyl-CoA ligase, which is a mitochondrial enzyme of the TCA cycle that catalyzes the nucleotide-dependent conversion of succinyl-CoA to succinate; phosphorylated
YBR120C	0.112055	RPH1	YBR120C|CBP6|S000000324|Mitochondrial translational activator of the COB mRNA; phosphorylated
YDL044C	0.108472	RPH1	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
YCL073C	0.108468	RPH1	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
YOR261C	0.107184	RPH1	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
YMR141W-A	0.105927	RPH1	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
YEL073C	0.104079	RPH1	YEL073C||S000000799|Putative protein of unknown function; located adjacent to ARS503 and the telomere on the left arm of chromosome V; regulated by inositol/choline
YJL098W	0.102586	RPH1	YJL098W|SAP185|S000003634|Protein that forms a complex with the Sit4p protein phosphatase and is required for its function; member of a family of similar proteins including Sap4p, Sap155p, and Sap190p
YML117W	0.0976775	RPH1	YML117W|NAB6|S000004585|Putative RNA-binding protein, based on computational analysis of large-scale protein-protein interaction data
YGR260W	0.0946002	RPH1	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)
YJL146W	0.0928112	RPH1	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
YNL167C	0.0834506	RPH1	YNL167C|SKO1|S000005111|Basic leucine zipper (bZIP) transcription factor of the ATF/CREB family, forms a complex with Tup1p and Ssn6p to both activate and repress transcription; cytosolic and nuclear protein involved in osmotic and oxidative stress responses
YNL221C	0.0826198	RPH1	YNL221C|POP1|S000005165|Subunit of both RNase MRP, which cleaves pre-rRNA, and nuclear RNase P, which cleaves tRNA precursors to generate mature 5' ends; binds to the RPR1 RNA subunit in RNase P
YMR268C	0.0801027	RPH1	YMR268C|PRP24|S000004881|Splicing factor that reanneals U4 and U6 snRNPs during spliceosome recycling
YOR072W-B	0.0793295	RPH1	YOR072W-B||S000028516|Putative protein of unknown function; identified by expression profiling and mass spectrometry
YLR113W	0.079088	RPH1	YLR113W|HOG1|S000004103|Mitogen-activated protein kinase involved in osmoregulation via three independent osmosensors; mediates the recruitment and activation of RNA Pol II at Hot1p-dependent promoters; localization regulated by Ptp2p and Ptp3p
YER030W	0.0789535	RPH1	YER030W|CHZ1|S000000832|Histone chaperone for Htz1p/H2A-H2B dimer; required for the stabilization of the Chz1p-Htz1-H2B complex; has overlapping function with Nap1p; null mutant displays weak sensitivity to MMS and benomyl; contains a highly conserved CHZ motif
YBR277C	0.0763101	RPH1	YBR277C||S000000481|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified gene YBR278W
YBR157C	0.07617	RPH1	YBR157C|ICS2|S000000361|Protein of unknown function; null mutation does not confer any obvious defects in growth, spore germination, viability, or carbohydrate utilization
YGR224W	0.0757949	RPH1	YGR224W|AZR1|S000003456|Plasma membrane transporter of the major facilitator superfamily, involved in resistance to azole drugs such as ketoconazole and fluconazole
YJR044C	0.0741949	RPH1	YJR044C|VPS55|S000003805|Late endosomal protein involved in late endosome to vacuole trafficking; functional homolog of human obesity receptor gene-related protein (OB-RGRP)
YEL045C	0.0741592	RPH1	YEL045C||S000000771|Dubious open reading frame unlikely to encode a protein based on available experimental and comparative sequence data; deletion gives MMS sensitivity, growth defect under alkaline conditions, less than optimal growth upon citric acid stress
YMR016C	0.0736039	RPH1	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
YPL232W	0.0734881	RPH1	YPL232W|SSO1|S000006153|Plasma membrane t-SNARE involved in fusion of secretory vesicles at the plasma membrane and in vesicle fusion during sporulation; forms a complex with Sec9p that binds v-SNARE Snc2p; syntaxin homolog; functionally redundant with Sso2p
YLR323C	0.0723404	RPH1	YLR323C|CWC24|S000004315|Essential protein, component of a complex containing Cef1p; has similarity to S. pombe Cwf24p
YFR020W	0.0652573	RPH1	YFR020W||S000001916|Dubious open reading frame unlikely to encode a functional protein, based on available experimental and comparative sequence data
YBR278W	0.0629812	RPH1	YBR278W|DPB3|S000000482|Third-largest subunit of DNA polymerase II (DNA polymerase epsilon), required to maintain fidelity of chromosomal replication and also for inheritance of telomeric silencing; mRNA abundance peaks at the G1/S boundary of the cell cycle
YHR178W	0.0626758	RPH1	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
YCR050C	0.0602464	RPH1	YCR050C||S000000646|Non-essential protein of unknown function; deletion mutant is synthetically sick or lethal with alpha-synuclein
YIL029W-A	0.059426	RPH1	YIL029W-A||S000028788|Dubious ORF unlikely to encode a functional protein, based on available experimental and comparative sequence data
YEL041W	0.0585604	RPH1	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
YER062C	0.0558822	RPH1	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
YDL045C	0.0551438	RPH1	YDL045C|FAD1|S000002203|Flavin adenine dinucleotide (FAD) synthetase, performs the second step in synthesis of FAD from riboflavin
YOR093C	0.0546764	RPH1	YOR093C||S000005619|Putative protein of unknown function; deletion causes sensitivity to unfolded protein response-inducing agents
YBR097W	0.0535995	RPH1	YBR097W|VPS15|S000000301|Myristoylated serine/threonine protein kinase involved in vacuolar protein sorting; functions as a membrane-associated complex with Vps34p; active form recruits Vps34p to the Golgi membrane; interacts with the GDP-bound form of Gpa1p
YDR283C	0.0482166	RPH1	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
YOR262W	0.04692	RPH1	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
YNL051W	0.0439232	RPH1	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
YDR356W	0.0435972	RPH1	YDR356W|SPC110|S000002764|Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner
YCR017C	0.0408607	RPH1	YCR017C|CWH43|S000000610|Putative sensor/transporter protein involved in cell wall biogenesis; contains 14-16 transmembrane segments and several putative glycosylation and phosphorylation sites; null mutation is synthetically lethal with pkc1 deletion
YPL205C	0.0402921	RPH1	YPL205C||S000006126|Hypothetical protein; deletion of locus affects telomere length
YML113W	0.03976	RPH1	YML113W|DAT1|S000004581|DNA binding protein that recognizes oligo(dA).oligo(dT) tracts; Arg side chain in its N-terminal pentad Gly-Arg-Lys-Pro-Gly repeat is required for DNA-binding; not essential for viability
YAL035W	0.0393357	RPH1	YAL035W|FUN12|S000000033|GTPase, required for general translation initiation by promoting Met-tRNAiMet binding to ribosomes and ribosomal subunit joining; homolog of bacterial IF2
YPL249C	0.0382278	RPH1	YPL249C|GYP5|S000006170|GTPase-activating protein (GAP) for yeast Rab family members, involved in ER to Golgi trafficking; exhibits GAP activity toward Ypt1p that is stimulated by Gyl1p, also acts on Sec4p; interacts with Gyl1p, Rvs161p and Rvs167p
YBR024W	0.0284814	RPH1	YBR024W|SCO2|S000000228|Protein anchored to the mitochondrial inner membrane, similar to Sco1p and may have a redundant function with Sco1p in delivery of copper to cytochrome c oxidase; interacts with Cox2p
YCR064C	0.0262747	RPH1	YCR064C||S000000660|Dubious open reading frame unlikely to encode a protein, based on experimental and comparative sequence data; partially overlaps the verified gene BUD31
YNL254C	0.0236319	RPH1	YNL254C|RTC4|S000005198|Hypothetical protein; null mutation suppresses cdc13-1 temperature sensitivity
YER095W	0.0193157	RPH1	YER095W|RAD51|S000000897|Strand exchange protein, forms a helical filament with DNA that searches for homology; involved in the recombinational repair of double-strand breaks in DNA during vegetative growth and meiosis; homolog of Dmc1p and bacterial RecA protein
YIL050W	0.0189182	RPH1	YIL050W|PCL7|S000001312|Pho85p cyclin of the Pho80p subfamily, forms a functional kinase complex with Pho85p which phosphorylates Mmr1p and is regulated by Pho81p; involved in glycogen metabolism, expression is cell-cycle regulated
YNL219C	0.0189175	RPH1	YNL219C|ALG9|S000005163|Mannosyltransferase, involved in N-linked glycosylation; catalyzes the transfer of mannose from Dol-P-Man to lipid-linked oligosaccharides; mutation of the human ortholog causes type 1 congenital disorders of glycosylation
YOR089C	0.0176233	RPH1	YOR089C|VPS21|S000005615|GTPase required for transport during endocytosis and for correct sorting of vacuolar hydrolases; localized in endocytic intermediates; detected in mitochondria; geranylgeranylation required for membrane association; mammalian Rab5 homolog
YNL171C	0.0134239	RPH1	YNL171C||S000005115|Dubious open reading frame unlikely to encode a functional protein; based on available experimental and comparative sequence data
YBR067C	0.0123593	RPH1	YBR067C|TIP1|S000000271|Major cell wall mannoprotein with possible lipase activity; transcription is induced by heat- and cold-shock; member of the Srp1p/Tip1p family of serine-alanine-rich proteins
YOR390W	0.0123225	RPH1	YOR390W||S000005917|Putative protein of unknown function
YBR271W	0.0119347	RPH1	YBR271W||S000000475|Putative S-adenosylmethionine-dependent methyltransferase of the seven beta-strand family; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YBR271W is not as essential gene
YGR068C	0.00866493	RPH1	YGR068C||S000003300|Putative protein of unknown function; YGR068C is not an essential gene.
YIR006C	0.00789656	RPH1	YIR006C|PAN1|S000001445|Part of actin cytoskeleton-regulatory complex Pan1p-Sla1p-End3p, associates with actin patches on the cell cortex; promotes protein-protein interactions essential for endocytosis; previously thought to be a subunit of poly(A) ribonuclease
YGL149W	0.00429937	RPH1	YGL149W||S000003117|Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the verified ORF INO80/YGL150C.
