Supplemental Data

A Posttranscriptional Role for the Yeast

Paf1-RNA Polymerase II Complex Is Revealed

by Identification of Primary Targets Kristi L. Penheiter, Taylor M. Washburn, Stephanie E. Porter, Matthew G. Hoffman, and Judith A. Jaehning Genes down in paf1∆

Common Name Systematic Name Fold Change Description

HO YDL227C -2 Homothallic switching endonuclease SRB7 YDR308C -2 RNA polymerase II holoenzyme component TRP4 YDR354W -2 anthranilate phosphoribosyl transferase APT2 YDR441C -2 Adenine phosphoribosyltransferase HOR2 YER062C -2 DL-glycerol-3-phosphatase RNR1 YER070W -2 Ribonucleotide-diphosphate reductase YER066W -2 strong similarity to cell division control protein Cdc4p YER078C -2 similarity to E.coli X-Pro aminopeptidase II ACB1 YGR037C -2 Acyl-CoA-binding protein MTO1 YGL236C -2 strong similarity to gidA E.coli protein PCT1 YGR202C -2 phosphorylcholine transferase\; or cholinephosphate cytidylyltransferase EPT1 YHR123W -2 sn-1,2-diacylglycerol ethanolamine- and cholinephosphotranferase YIL064W -2 weak similarity to fowlpox virus major core protein POR2 YIL114C -2 voltage dependent anion channel (YVDAC2) YJL010C -2 weak similarity to C.elegans hypothetical protei ZK792.5 PAU1 YJL223C -2 strong similarity to members of the Srp1p/Tip1p family FKS1 YLR342W -2 Catalytic subunit of 1,3 beta-D-glucan synthase YLR073C -2 hypothetical protein YLR456W -2 strong similarity to YPR172w SEN15 YMR059W -2 15kDa subunit of the tetrameric tRNA splicing endonuclease YMR259C -2 hypothetical protein AAH1 YNL141W -2 Adenosine deaminase\/adenine aminohydrolase

YOR051C -2 weak similarity to myosin heavy chain proteins LEU9 YOR108W -2 putative isoform of Leu4p HEM4 YOR278W -2 uroporphyrinogen III synthase KAP120 YPL125W -2 weak similarity to YDR395w and cellular apoptosis susceptibility protein HAA1 YPR008W -2 similarity to transcription factor SOY1 YBR194W -2.1 hypothetical protein PYC2 YBR218C -2.1 pyruvate carboxylase TRM8 YDL201W -2.1 strong similarity to human D1075-like protein BUD16 YEL029C -2.1 similarity to hypothetical protein YNR027w POL5 YEL055C -2.1 DNA polymerase V that has motifs typical of DNA polymerase family HIS1 YER055C -2.1 ATP phosphoribosyltransferase YER158C -2.1 weak similarity to Afr1p YER186C -2.1 weak similarity to hypothetical protein YMR316w SAD1 YFR005C -2.1 similarity to hypothetical A. thaliana proteins CDC43 YGL155W -2.1 polypeptide subunit of a yeast type 1 protein geranylgeranyltransferase THI4 YGR144W -2.1 component of the biosynthetic pathway producing the thiazole precursor of thiamine TNA1 YGR260W -2.1 similarity to allantoate transport protein EST3 YIL009C-A -2.1 181aa protein - 20.5 kD YNL035C -2.1 hypothetical protein YNL129W -2.1 weak similarity to M.pneumoniae uridine kinase udk RRP12 YPL012W -2.1 hypothetical protein BBP1 YPL255W -2.1 Involved in mitotic cell cycle and meiosis DPM1 YPR183W -2.1 dolichol phosphate mannose synthase YBR187W -2.2 probable membrane protein PRM7 YDL039C -2.2 questionable ORF MAK21 YDR060W -2.2 similarity to mouse putative CCAAT binding factor CBF1 and CBF2 RRP8 YDR083W -2.2 similarity to hypothetical S.pombe protein YDR352W -2.2 weak similarity to hypothetical proteins YOL092w, YBR147w and YMR010w ISC1 YER019W -2.2 putative neutral sphingomyelinase CGR1 YGL029W -2.2 weak similarity to human chromatin assembly factor I p150 chain YGR011W -2.2 questionable ORF ELP2 YGR200C -2.2 weak similarity to rape guanine nucleotide regulatory protein ECM17 YJR137C -2.2 ExtraCellular Mutant YML018C -2.2 similarity to YDR438w

ATR1 YML116W -2.2 predicted protein is very hydrophobic, has many membrane-spanning regions, several potential glycosylation sites, potential ATP-binding site

YPL146C -2.2 weak similarity to myosin heavy chain proteins YBR220C -2.3 similarity to human acetyl-coenzyme A transporter

ERP3 YDL018C -2.3 p24 protein involved in membrane trafficking BNA6 YFR047C -2.3 strong similarity to human quinolinate phosphoribosyltransferase SUT1 YGL162W -2.3 Involved in sterol uptake RHR2 YIL053W -2.3 DL-glycerol-3-phosphatase MET28 YIR017C -2.3 Transcriptional activator of sulfur amino acid metabolism MGA2 YIR033W -2.3 may be involved in the remodeling chromatin structure ARG80 YMR042W -2.3 Regulator of arginine-responsive genes with ARG81 and ARG82 RPC34 YNR003C -2.3 34-kDa subunit of RNA polymerase III (C) YNR053C -2.3 strong similarity to human breast tumor associated autoantigen ECM3 YOR092W -2.3 ExtraCellular Mutant RAS1 YOR101W -2.3 ras proto-oncogene homolog DFR1 YOR236W -2.3 dihydrofolate reductase SUR1 YPL057C -2.3 Multicopy suppressor of cls2-2\; also suppresses rvs161 mutations YPR147C -2.3 hypothetical protein TPO3 YPR156C -2.3 similarity to multidrug resistance proteins YDL038C -2.4 similarity to mucin proteins YDR336W -2.4 weak similarity to B.subtilis hypothetical protein X YDR365C -2.4 weak similarity to Streptococcus M protein MNN1 YER001W -2.4 Alpha-1,3-mannosyltransferase KAP122 YGL016W -2.4 pleiotropic drug resistance regulatory protein YGL050W -2.4 hypothetical protein FZF1 YGL254W -2.4 putative transcription factor, has five zinc fingers PPT1 YGR123C -2.4 serine\/threonine phosphatase SDA1 YGR245C -2.4 similarity to hypothetical S.pombe protein CUP1-1 YHR053C -2.4 copper-binding metallothionein ILV3 YJR016C -2.4 dihydroxyacid dehydratase PDR16 YNL231C -2.4 weak similarity to Sec14p YNR066C -2.4 strong similarity to Pep1p TRF4 YOL115W -2.4 homologous to Trf5p and Top1p, associates with Smc1p and Smc2p THI2 YBR240C -2.5 Probable Zn-finger protein YCR024C -2.5 Asn-tRNA synthetase THI3 YDL080C -2.5 positive regulatory factor with thiamin pyrophosphate-binding motif for thiamin metabolism BTT1 YDR252W -2.5 Negative effect on expression of several genes transcribed by RNA polymerase II\; BTF3 homolog ERV1 YGR029W -2.5 Protein essential for mitochondrial biogenesis and cell viability CLB1/SCB1 YGR108W -2.5 G(sub)2-specific B-type cyclin MRS11/TIM10 YHR005C-A -2.5 May act cooperatively with Mrs5p in mitochondrial protein import or other related essential mitochondrial processes FSH1 YHR049W -2.5 similarity to S.pombe dihydrofolate reductase and YOR280c YKL027W -2.5 similarity to E.coli molybdopterin-converting factor chlN MDN1 YLR106C -2.5 similarity to Kaposi s sarcoma-associated herpes-like virus ORF73 homolog gene

CIN4 YMR138W -2.5 GTP-binding protein ICY1 YMR195W -2.5 similarity to YPL250c CLN1 YMR199W -2.5 G(sub)1 cyclin NRG2 YBR066C -2.6 Probable Zn-finger protein YGL232W -2.6 weak similarity to P.falciparum dihydropteroate synthase YGR203W -2.6 weak similarity to X.laevis protein-tyrosin-phosphatase cdc homolog 2 and to hypothetical protein YPR200c MUP3 YHL036W -2.6 very low affinity methionine permease YHR100C -2.6 hypothetical protein YNL086W -2.6 hypothetical protein

COS10 YNR075W -2.6 Protein with strong similarity to subtelomerically-encoded proteins such as Cos5p, Ybr302p, Cos3p, Cos1p, Cos4p, Cos8p, Cos6p, Cos9p

WSC3 YOL105C -2.6 Putative integral membrane protein containing novel cysteine motif. Similarity to SLG1 (WSC1), WSC2 and WSC4 YAH1 YPL252C -2.6 iron-sulfur protein homologous to human adrenodoxin YPR146C -2.6 questionable ORF SDC1/CPS25/SAF19 YDR469W -2.7 hypothetical protein YGR001C -2.7 similarity to C.elegans hypothetical M142.5 protein YML082W -2.7 similarity to N.crassa O-succinylhomoserine (thiol)-lyase YOR060C -2.7 hypothetical protein ODC2 YOR222W -2.7 similarity to ADP/ATP carrier proteins THI6 YPL214C -2.7 TMP pyrophosphorylase, hydroxyethylthiazole kinase YCR023C -2.8 Membrane transporter YDL037C -2.8 strong similarity to glucan 1,4-alpha-glucosidase YDR111C -2.8 strong similarity to alanine transaminase YER071C -2.8 hypothetical protein PTC2 YER089C -2.8 Protein phosphatase type 2C FUR1 YHR128W -2.8 UPRTase SER33 YIL074C -2.8 strong similarity to E.coli phosphoglycerate dehydrogenase ZRT2 YLR130C -2.8 Low-affinity zinc transport protein YLR364W -2.8 hypothetical protein SNO2 YNL334C -2.8 SNZ2 proximal ORF, stationary phase induced gene ARO4 YBR249C -2.9 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme YGR210C -2.9 similarity to M.jannaschii GTP-binding protein and to M.capricolum hypothetical protein SGC3 ANB1/HYP1/TIF51B YJR047C -2.9 anaerobically expressed form of translation initiation factor eIF-5A SAM1/ETH10 YLR180W -2.9 S-adenosylmethionine synthetase HAP1/CYP1 YLR256W -2.9 zinc-finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type YLR315W -2.9 weak similarity to rat apolipoprotein A-IV PPT2 YPL148C -2.9 Phosphopantetheine

YCL049C -3 hypothetical protein MAK32 YCR019W -3 MAK32 sugar kinase RHB1 YCR027C -3 GTPase (RAS-related) GLT1 YDL171C -3 Glutamate synthase (NADPH) YDR089W -3 weak similarity to Streptococcus transposase UTR2/CRH2 YEL040W -3 weak similarity to Bacillus 1,3-1,4-beta-glucanase THO1 YER063W -3 Suppressor of the Transcriptional (T) defect of Hpr1 (H) by Overexpression (O) FLX1 YIL134W -3 mitochondrial inner membrane carrier protein for FAD YJR116W -3 similarity to hypothetical protein YPR114w YLR036C -3 similarity to YIL089w MET22/HAL2 YNL277W -3 homoserine O-trans-acetylase SUT2 YPR009W -3 similarity to sterol uptake protein Sut1p YDL036C -3.1 strong similarity to RIB2 protein GTR2 YGR163W -3.1 GTP-binding protein MED11 YMR112C -3.1 hypothetical protein RKI1 YOR095C -3.1 Ribose-5-phosphate ketol-isomerase YOR179C -3.1 similarity to BRR5 protein YOR390W -3.1 nearly identical to YPL279c SCM4 YGR049W -3.2 Protein that suppresses ts allele of CDC4 when overexpressed YHR049C-A -3.2 questionable ORF ICT1 YLR099C -3.2 similarity to YDR125c POP5/FUN53 YAL033W -3.3 An integral subunit of RNase P and apparent subunit of RNase MRP YJR115W -3.3 similarity to hypothetical protein YBL043w YKL051W -3.3 hypothetical protein YLR040C -3.3 weak similartity to hypothetical protein YIL011w YLR297W -3.3 weak similarity to Vibrio vulnificus VvpC protein SEC59 YMR013C -3.3 membrane protein required for core glycosylation YPR013C -3.3 similarity to transcription factors YBR292C -3.4 hypothetical protein STP4 YDL048C -3.4 Involved in pre-tRNA splicing and in uptake of branched-chain amino acids TOS2 YDR213W -3.4 regulatory protein involved in control of sterol uptake YIL028W -3.4 putative pseudogene MET22/HAL2 YOL064C -3.4 3 (2 )5 -bisphosphate nucleotidase YDR414C -3.5 Protein required for retention of luminal ER proteins YGR138C -3.5 similarity to multidrug resistance proteins YLR413W -3.5 strong similarity to YKL187c YPL258C -3.5 similarity to B.subtilis transcriptional activator tenA, and strong similarity to hypothetical proteins YOL055c and YPR12 YGL184C -3.6 strong similarity to Emericella nidulans cystathionine beta-lyase MAE1 YKL029C -3.7 mitochondrial malic enzyme

YPL014W -3.7 hypothetical protein LEU2 YCL018W -3.9 beta-IPM (isopropylmalate) dehydrogenase YAR066W -4 identical to YHR214w hypothetical protein, similarity to Sta1p YHM1 YDL198C -4 high copy suppressor of abf2 lacking the HMG1-like mitochondrial HM protein\; putative mitochondrial carrier protein YBR238C -4.1 strong similarity to general chromatin factor Spt16p PDC5 YLR134W -4.2 pyruvate decarboxylase TRI1 YMR233W -4.2 strong similarity to YOR295w YOL002C -4.3 strong similarity to YDR492w and S.pombe hypothetical protein ORT1/ARG11 YOR130C -4.4 mitochondrial integral membrane protein YGR039W -4.5 questionable ORF YPL099C -4.5 weak similarity to Sulfolobus hypothetical protein GAT2 YMR136W -4.6 weak similarity to YIR013c and YLR013w MUC1/FLO11/STA4 YIR019C -4.7 cell surface flocculin with structure similar to serine\/threonine-rich GPI-anchored cell wall proteins AAC3/ANC3 YBR085W -4.9 mitochondrial ADP\/ATP translocator YGL159W -4.9 hypothetical protein YDL241W -5 hypothetical protein PLB2 YMR006C -5 strong similarity to Plb1p TIR1/SRP1 YER011W -5.1 Cold-shock induced protein of the Srp1p\/Tip1p family of serine-alanine-rich proteins YNR014W -5.1 weak similarity to hypothetical protein YMR206w CWP1 YKL096W -5.2 cell wall mannoprotein HEM13 YDR044W -5.4 Coproporphyrinogen III oxidase YGL039W -5.5 similarity to V. vinifera dihydroflavonol reductase FET4 YMR319C -5.5 Low-affinity Fe(II) transport protein MET3 YJR010W -5.7 ATP sulfurylase YHR048W -5.8 similarity to multidrug resistance proteins THI20 YOL055C -6 similarity to B. subtilis transcriptional activator tenA RPS9A YPL081W -6.3 Ribosomal protein S9A (S13) (rp21) (YS11) YPR157W -6.7 strong similarity to YGR141w BNA1/HAD1 YJR025C -6.9 3-hydroxyanthranilic acid dioxygenase

MET6 YER091C -7

vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase)

HXT1 YHR094C -7.6 High-affinity hexose (glucose) transporter YOL014W -8.4 hypothetical protein MGA1 YGR249W -8.9 Mga1p shows similarity to heat shock transcription factor ADH5 YBR145W -10.7 alcohol dehydrogenase isoenzyme V ATF2 YGR177C -11.6 Alcohol acetyltransferase

YOL101C -11.7 similarity to YOL002c and YDR492w HXT4/LGT1/RAG1 YHR092C -12 High-affinity glucose transporter PET18 YCR020C -13.7 Transcription regulator RGS2 YOR107W -29.8 weak similarity to human G-0/G-1 switch regulatory protein 8 Genes Up in paf1∆

Common Name Systematic Name Fold Change Description

PET112 YBL080C 2 62-kDa protein SRO77 YBL106C 2 yeast homolog of the Drosphila tumor suppressor, lethal giant larvae SMP1 YBR182C 2 Probable DNA-binding transcription factor, Homolog to SRF\/SL-2 SDS24 YBR214W 2 strong similarity to hypothetical protein YGL056c SLX1 YBR228W 2 similarity to hypothetical A.thaliana protein DCC1 YCL016C 2 hypothetical protein GLK1 YCL040W 2 Glucokinase YCR068W-A 2 similarity to starvation induced pSI-7 protein of C. fluvum YDL089W 2 hypothetical protein PCL2 YDL127W 2 G1 cyclin YDR003W 2 strong similarity to hypothetical protein YBR005w ENA2 YDR039C 2 plasma membrane protein\; putative Na+ pump\; P-type ATPase KGD2 YDR148C 2 dihydrolipoyl transsuccinylase component of alpha-ketoglutarate dehydrogenase complex in mitochondria ATP5 YDR298C 2 ATP synthase subunit 5\; oligomycin sensitivity-conferring protein FRQ1 YDR370C 2 hypothetical protein YDR373W 2 strong similarity to human BDR-1 protein and other calcium binding proteins PPN1 YDR452W 2 similarity to human sphingomyelin phosphodiesterase PHO8 YDR481C 2 repressible alkaline phosphatase TTR1 YDR513W 2 Glutaredoxin (thioltransferase) (glutathione reductase) QCR7 YDR529C 2 ubiquinol-cytochrome c oxidoreductase subunit 7 (14 kDa) ARG5 YER069W 2 N-acetyl-gamma-glutamyl-phosphate reductase and acetylglutamate kinase UBP6 YFR010W 2 encodes putative deubiquitinating enzyme MRM2 YGL136C 2 weak similarity to E.coli ftsJ protein YGL242C 2 weak similarity to Drosophila ANK protein YGR243W 2 strong similarity to hypothetical protein YHR162w MYO1 YHR023W 2 Class II Myosin YNG2 YHR090C 2 NuBbiN YHR184W 2 Involved in the control of meiotic nuclear divisions and spore formation

MAD2 YJL030W 2 spindle-assembly checkpoint protein SNX4 YJL036W 2 weak similarity to Mvp1p YJL132W 2 weak similarity to human phospholipase D TPK1 YJL164C 2 putative catalytic subunit of cAMP-dependent protein kinase QCR8 YJL166W 2 Ubiquinol cytochrome-c reductase subunit 8 (11 kDa protein) ENT3 YJR125C 2 similarity to human KIAA0171 protein PAN3 YKL025C 2 76-kDa subunit of Pab1p-dependent poly(A) ribonuclease (PAN) YET1 YKL065C 2 Yeast endoplasmic reticulum 25 kDa transmembrane protein YKL098W 2 hypothetical protein HAP4 YKL109W 2 transcriptional activator protein of CYC1 (component of HAP2\/HAP3 heteromer) YKR022C 2 hypothetical protein

FPS1 YLL043W 2 Suppressor of tps1\/fdp1 and member of the MIP family of transmembrane channels\; may be involved in glycerol efflux

YLL067C 2 strong similarity to subtelomeric encoded proteins IOC2 YLR095C 2 hypothetical protein YLR152C 2 similarity to YOR3165w and YNL095c VTA1 YLR181C 2 hypothetical protein YLR257W 2 hypothetical protein CDC3 YLR314C 2 Component of 10 nm filaments of mother-bud neck TAD3 YLR316C 2 weak similarity to H.influenzae hypothetical protein HI0906 YLR326W 2 hypothetical protein GLO1 YML004C 2 lactoylglutathione lyase (glyoxalase I) RAD52 YML032C 2 Interacts with Rad51p by two hybrid analysis. mRNA is induced in meiosis during recombination TAF4/MPT1 YMR005W 2 Protein required for protein synthesis

TOM37 YMR060C 2

mitochondrial import receptor, heterodimerizes with Tom70p, preferentially recognizes the mature regions of precursor proteins associated with ATP-dependent cytosolic chaperones

AVO2 YMR068W 2 weak similarity to mouse transcription factor NF-kappaB SIP18 YMR175W 2 protein of unknown function YMR194C-A 2 hypothetical protein identified by SAGE SCJ1 YMR214W 2 dnaJ homolog MET4 YNL103W 2 member of the leucine zipper family of transcriptional activators STB1 YNL309W 2 Binds Sin3p in two-hybrid assay and is present in a large protein complex with Sin3p and Stb2p DSE4 YNR067C 2 similarity to beta-glucan-elicitor receptor - Glycine max YOL070C 2 hypothetical protein HRP1 YOL123W 2 Putative polyadenylated-RNA-binding protein located in nucleus\; similar to vertebrate hnRNP A\/B protein family SPT20 YOL148C 2 transcription factor, member of the histone acetyltransferase SAGA complex LSC1 YOR142W 2 Succinate-CoA Ligase (ADP-Forming) ALD6 YPL061W 2 cytosolic aldehyde dehydrogenase

SSU1 YPL092W 2 sensitive to sulfite PIN4 YBL051C 2.1 similarity to S.pombe Z66568_C protein YBR126C 2.1 56 kD synthase subunit of trehalose-6-phosphate synthase\/phosphatase complex TPS1 YBR222C 2.1 Probable AMP-binding protein YDL072C 2.1 weak similarity to hypothetical protein YMR040w SHS1 YDL225W 2.1 similarity to Cdc11p, Cdc3p and human CDC10 protein ADY3 YDL239C 2.1 hypothetical protein PST2 YDR032C 2.1 strong similarity to S.pombe obr1 COX20 YDR231C 2.1 hypothetical protein STP1 YDR463W 2.1 Nuclear-localized protein containing zinc finger motifs FAA2 YER015W 2.1 Acyl-CoA synthetase (fatty acid activator 2) YGL051W 2.1 strong similarity to YAR033w protein YGL052W 2.1 questionable ORF ITC1 YGL133W 2.1 similarity to hypothetical protein YPL216w YIP5 YGL161C 2.1 hypothetical protein COX13 YGL191W 2.1 subunit VIa of cytochrome c oxidase, may specifically interact with ATP HAP2 YGL237C 2.1 transcriptional activator protein of CYC1 CUL3 YGR003W 2.1 similarity to D.melanogaster lin19 protein FYV8 YGR196C 2.1 weak similarity to Tetrahymena acidic repetitive protein arp1 PUT2 YHR037W 2.1 delta-1-pyrroline-5-carboxylate dehydrogenase YHR087W 2.1 hypothetical protein TRR2 YHR106W 2.1 Thioredoxin reductase PEX28 YHR150W 2.1 weak similarity to YDR479c STB5 YHR178W 2.1 Zinc finger (6-Cys) YHR199C 2.1 strong similarity to hypothetical protein YHR198c YHC3/BTN1 YJL059W 2.1 Homolog of human CLN3 NFU1 YKL040C 2.1 NifU-like protein B MUD2 YKL074C 2.1 involved in early pre-mRNA splicing YKL151C 2.1 similarity to C.elegans hypothetical protein R107.2 YPT2 YKR014C 2.1 probable purine nucleotide-binding protein YKR021W 2.1 strong similarity to hypothetical protein YJL084c PRP16 YKR086W 2.1 putative ATP-binding protein VPS13 YLL040C 2.1 involved in regulating membrane traffic YLR177W 2.1 similarity to suppressor protein Psp5p VPS63 YLR261C 2.1 questionable ORF YML025C 2.1 ribosomal protein, mitochondrial POB3 YML069W 2.1 Binds to catalytic subunit of DNA polymerase alpha (Pol1p) YMR003W 2.1 hypothetical protein YMR067C 2.1 hypothetical protein

YMR115W 2.1 similarity to YKL133c NUP53 YMR153W 2.1 similarity to Asm4p YMR169C 2.1 Aldehyde Dehydrogenase (NAD(P)+) ESC1 YMR219W 2.1 Establishes Silent omatin YMR262W 2.1 similarity to S.pombe scn1 protein NCE103 YNL036W 2.1 involved in secretion of proteins that lack classical secretory signal sequences YNL050C 2.1 hypothetical protein

SNF12 YNR023W 2.1 73 kDa subunit of the SWI\/SNF transcription activation complex, homolog of Rsc6p subunit of the RSC chromatin remodeling complex

RPT5 YOR117W 2.1 Probable 26S protease subunit and member of the CDC48\/PAS1\/SEC18 family of ATPases MPC54 YOR177C 2.1 weak similarity to rat SCP1 protein ALD4 YOR374W 2.1 YPL004C 2.1 strong similarity to YGR086c TAF3 YPL011C 2.1 Component of the TAF(II) complex (TBP-associated protein complex) ISU1 YPL135W 2.1 NifU-like protein A YPL141C 2.1 strong similarity to protein kinase Kin4p YPL206C 2.1 weak similarity to glycerophosphoryl diester phosphodiesterases NTO1 YPR031W 2.1 similarity to human zinc-finger protein BR140 PHO11 YAR071W 2.2 Acid phosphatase, secreted EDS1 YBR033W 2.2 Probable regulatory Zn-finger protein,\/ homolog to YKL251\/ AQR2 YBR043C 2.2 similarity to benomyl/methotrexate resistance protein KTR4 YBR199W 2.2 Putative alpha-1,2-mannosyltransferase INH1 YDL181W 2.2 ATPase inhibitor CWC2 YDL209C 2.2 similarity to hypothetical S. pombe protein

COS7 YDL248W 2.2 Protein with strong similarity to other subtelomerically-encoded proteins such as Cos5p, Ybr302p, Cos3p, Cos1p, Cos4p, Cos8p, Cos6p, Cos9p

KIN1 YDR122W 2.2 Serine\/threonine protein kinase BFR2 YDR299W 2.2 involved in protein transport step at the Brefeldin A blocks YEL020C 2.2 similarity to O.formigenes oxalyl-CoA decarboxylase FCY22 YER060w-A 2.2 purine-cytosine permease ICL1 YER065C 2.2 isocitrate lyase MAG1 YER142C 2.2 3-methyladenine DNA glycosylase YGL250W 2.2 hypothetical protein YGR182C 2.2 questionable ORF GRE3 YHR104W 2.2 Aldo-keto reductase POT1 YIL160C 2.2 peroxisomal 3-oxoacyl CoA thiolase

CTK2 YJL006C 2.2 cyclin-related subunit of the kinase complex that phosphorylates the RPO21 CTD (carboxy-terminal domain)\; also called CTDK-I beta subunit

YKL086W 2.2 hypothetical protein SBA1 YKL117W 2.2 Hsp90 (Ninety) Associated Co-chaperone YKL121W 2.2 strong similarity to YMR102c PXA2 YKL188C 2.2 peroxisomal ABC transporter 2 PCK1 YKR097W 2.2 phosphoenolpyruvate carboxylkinase ACO1/GLU1 YLR304C 2.2 Aconitase, mitochondrial VRP1/END5/MDP2 YLR337C 2.2 Proline-rich protein verprolin YLR345W 2.2 similarity to Pfk26p and other 6-phosphofructo-2-kinases YLR464W 2.2 strong similarity to subtelomeric encoded proteins YML041C 2.2 hypothetical protein MAC1 YMR021C 2.2 metal-binding transcriptional activator YMR031C 2.2 similarity to YKL050c and human restin AIP1 YMR092C 2.2 Protein localizes to actin cortical patches. Probable binding site on actin lies on front surface of subdomain 3 and 4. NDE1 YMR145C 2.2 mitochondrial cytosolically directed NADH dehydrogenase YNL011C 2.2 similarity to hypothetical A. thaliana protein T14G11.21 AVT4 YNL101W 2.2 similarity to YKL146w SLA2 YNL243W 2.2 transmembrane protein YNR064C 2.2 similarity to R.capsulatus 1-chloroalkane halidohydrolase ARG1 YOL058W 2.2 arginosuccinate synthetase YRR1 YOR162C 2.2 transcription factor GAC1 YOR178C 2.2 Regulatory subunit for Glc7p YPL039W 2.2 hypothetical protein ATP4 YPL078C 2.2 F(1)F(0)-ATPase complex delta subunit, mitochondrial YPL159C 2.2 weak similarity to YPR151c APG1 YPR185W 2.2 Autophagy YBR071W 2.3 hypothetical protein YBR109w-a 2.3 questionable ORF - upstream ORF of ALG1 TKL2 YBR117C 2.3 transketolase, homologous to tkl1 YBR139W 2.3 Probable serine-type carboxypeptidase (EC 3.4.16.1) SYP1 YCR030C 2.3 weak similarity to S.pombe hypothetical protein SPBC4C3.06 YDL025C 2.3 ser/thr protein kinase of the DEAD/DEAH box family YDL233W 2.3 hypothetical protein

LYS14 YDR034C 2.3 Transcriptional activator of lysine pathway genes with 2-aminoadipate semialdehyde as co-inducer\; saccharopine reductase synthesis

PIB1 YDR313C 2.3 Phosphatidylinositol(3)-phosphate binding YDR504C 2.3 similarity to hypothetical T.brucei protein DDI1 YER143W 2.3 DNA Damage Inducible

MDJ1 YFL016C 2.3 DnaJ homolog involved in mitochondrial biogenesis and protein folding YFL063W 2.3 strong similarity to subtelomeric encoded proteins DST1 YGL043W 2.3 RNA polymerase II elongation factor HSF1 YGL073W 2.3 heat shock transcription factor SPC105 YGL093W 2.3 component of spindle pole YHR080C 2.3 similarity to hypothetical protein YDR326c, YFL042c and YLR072w YIL006W 2.3 similarity to Flx1p RPL34B YIL042C 2.3 similarity to rat branched-chain alpha-ketoacid dehydrogenase kinase MPH1 YIR002C 2.3 weak similarity to ATP-dependent RNA helicases YJL048C 2.3 similarity to hypothetical protein YBR273c MPM1 YJL066C 2.3 hypothetical protein NNF1 YJR112W 2.3 involved in nuclear function CAP1 YKL007W 2.3 alpha subunit of capping protein UFD4 YKL010C 2.3 Ubiquitin Fusion Degradation ATP7 YKL016C 2.3 ATP synthase d subunit RGT1 YKL038W 2.3 transcriptional repressor and activator PRM1 YKL039W 2.3 Putative membrane protein YKL066W 2.3 hypothetical protein RSM22 YKL155C 2.3 hypothetical protein ZRT3 YKL175W 2.3 weak similarity to E.coli hypothetical protein PET10 YKR046C 2.3 hypothetical protein RHO4 YKR055W 2.3 ras homolog--GTP binding protein YKR064W 2.3 weak similarity to transcription factors YLL023C 2.3 similarity to hypothetical protein YLR064w CLF1/SYF3 YLR117C 2.3 SYnthetic lethal with cdc40 (Forty) MSC3 YLR219W 2.3 hypothetical protein YLR252W 2.3 questionable ORF DCS1 YLR270W 2.3 strong similarity to YOR173w ZDS2 YML109W 2.3 multicopy suppressor of a sin4 defect YMR114C 2.3 similarity to B. subtilis conserved hypothetical proteins yoqW and yoaM YIM1 YMR152W 2.3 mitochondrial inner membrane protease BUL1 YMR275C 2.3 Involved in the ubiquination pathway, possibly by functioning with Rsp5

FAP1 YNL023C 2.3 Transcription factor homolog\; similarity to Drosophila melanogaster shuttle craft protein\; similarity to human NFX1 protein\; similarity to human DNA-binding protein tenascin

YNL034W 2.3 nearly identical to YNL018c MDH2 YOL126C 2.3 cytosolic malate dehydrogenase YOR227W 2.3 similarity to microtubule-interacting protein Mhp1p YOR292C 2.3 similarity to human and mouse glomerulosclerosis protein Mpv17

YPL056C 2.3 hypothetical protein MLH3 YPL164C 2.3 similarity to mismatch repair protein Mlh1p YPR115W 2.3 similarity to probable transcription factor Ask10p, and to YNL047c and YIL105c YBL109W 2.4 similarity to subtelomeric encoded proteins YBR053C 2.4 similarity to rat regucalcin GPD1 YDL022W 2.4 glycerol-3-phosphate dehydrogenase CCC2 YDR270W 2.4 Copper-transporting P-type ATPase with similarity to human Menkes and Wilsons genes MTH1 YDR277C 2.4 Protein is 61\% identical to Msn3p PEX3 YDR329C 2.4 48-kDa peroxisomal integral membrane protein PPZ2 YDR436W 2.4 serine-threonine phosphatase Z HVG1 YER039C 2.4 Homologous to VRG4 YER039C-A 2.4 hypothetical protein RAD24 YER173W 2.4 checkpoint protein GSY1 YFR015C 2.4 Glycogen synthase (UDP-gluocse--starch glucosyltransferase) PTR3 YFR029W 2.4 Regulator of expression of the PTR2, GAP1, and BAP2 genes\; involved in the the control of peptide transport RTF1 YGL244W 2.4 Nuclear protein

HFM1 YGL251C 2.4 C4 zinc finger DNA-binding protein of low sequence specificity in vitro\; Probable 119 kD DNA\/RNA helicase family member

YGR266W 2.4 hypothetical protein SOD2 YHR008C 2.4 Manganese-containing superoxide dismutase TPM2 YIL138C 2.4 Tropomyosin isoform 2 AVT3 YKL146W 2.4 strong similarity to S.pombe hypothetical protein C3H1.09C YLR023C 2.4 similarity to S.pombe hypothetical protein SPAC30D11.11 YLR187W 2.4 similarity to hypothetical protein YNL278w YLR225C 2.4 strong similarity to YDR222w YLR352W 2.4 hypothetical protein YLR387C 2.4 similarity to YBR267w CTR3 YLR411W 2.4 Copper Transporter CTL1 YMR180C 2.4 similarity to YPL228w YMR253C 2.4 strong similarity to YPL264c JNM1 YMR294W 2.4 Coiled-coil domain protein required for proper nuclear migration during mitosis (but not during conjugation)

YGP1 YNL160W 2.4 YGP1 encodes gp37, a glycoprotein synthesized in response to nutrient limitation which is homologous to the sporulation-specific SPS100 gene

IES2 YNL215W 2.4 similarity to hypothetical S. pombe protein YNL311C 2.4 hypothetical protein IFM1 YOL023W 2.4 mitochondrial initiation factor 2 YOL036W 2.4 weak similarity to YMR317w ESA1 YOR244W 2.4 Acetyltransferase in the SAS gene family YOR287C 2.4 weak similarity to PITSLRE protein kinase isoforms

DIP5 YPL265W 2.4 dicarboxylic amino acid permease YPL277C 2.4 strong similarity to hypothetical protein YOR389w/putative pseudogene PIN3 YPR154W 2.4 similarity to chicken growth factor receptor-binding protein GRB2 homolog SSA1/YG100 YAL005C 2.5 Heat shock protein of HSP70 family, cytoplasmic YBL086C 2.5 involved in sugar metabolism AOR1 YBR231C 2.5 similarity to human p97 homologous protein SNF5/HAF4/SWI10/TYE4 YBR289W 2.5 transcriptional activator PEX19/PAS12 YDL065C 2.5 40 kDa farnesylated protein associated with peroxisomes YER079W 2.5 hypothetical protein SDS23 YGL056C 2.5 homologue of pombe SDS23\; localizes to spindle pole body PYC1 YGL062W 2.5 pyruvate carboxylase ARN1 YHL040C 2.5 similarity to C.carbonum toxin pump MEF2 YJL102W 2.5 mitochondrial elongation factor G-like protein NTA1/DEA1 YJR062C 2.5 52-kDa amidase specific for N-terminal asparagine and glutamine OP13 YJR073C 2.5 Methylene-fatty-acyl-phospholipid synthase (unsaturated phospholipid N-methyltransferase) YJR149W 2.5 similarity to 2-nitropropane dioxygenase YNK1 YKL067W 2.5 Nucleoside diphosphate kinase YKR016W 2.5 weak similarity to mysoin heavy chain proteins GPT2 YKR067W 2.5 strong similarity to Sct1p SFI1 YLL003W 2.5 protein of unknown function YLL020C 2.5 questionable ORF SNF7 YLR025W 2.5 involved in derepression of SUC2 in response to glucose limitation YLR046C 2.5 strong similarity to Rta1p and Rtm1p protein YLR050C 2.5 weak similarity to human MAC30 C-terminus SIC1 YLR079W 2.5 P40 inhibitor of Cdc28p-Clb5 protein kinase complex REX3 YLR107W 2.5 similarity to Pan troglodytes prot GOR SRC1/YML033W YML033W 2.5 similarity to YDR458c YMR034C 2.5 weak similarity to YPR201w YMR184W 2.5 hypothetical protein YMR210W 2.5 similarity to P.glauca late embryogenesis abundant protein and YBR177c and YPL095c YNL116W 2.5 weak similarity to RING zinc finger protein from Gallus gallus YNL134C 2.5 similarity to C.carbonum toxD gene AHC1 YOR023C 2.5 hypothetical protein UFE1 YOR075W 2.5 endoplasmic reticulum t-SNARE, coprecipitates with Sec20p, Tip1p. and Sec22p SKI7 YOR076C 2.5 similarity to Hbs1p, Sup2p and EF1-alpha

AZF1 YOR113W 2.5 probable transcription factor, asparagine-rich zinc-finger protein, suppressor of mutation in the nuclear gene for the core subunit of mitochondrial RNA polymerase

ARP8 YOR141C 2.5 Actin-related protein YOR205C 2.5 hypothetical protein YPL107W 2.5 hypothetical protein FUN19 YAL034C 2.6 Function unknown now SWH1 YAR042W 2.6 ankyrin repeat YBL096C 2.6 questionable ORF ATP3 YBR039W 2.6 gamma subunit of mitochondrial ATP synthase CVT17/AUT5 YCR068W 2.6 similarity to hypothetical S.pombe protein YDL110C 2.6 hypothetical protein TSA2 YDR453C 2.6 strong similarity to thiol-specific antioxidant proteins DIG2/RST2 YDR480W 2.6 MAP kinase-associated protein YDR533C 2.6 strong similarity to hypothetical proteins YPL280w, YOR391c and YMR322c YER137C 2.6 weak similarity to Mycoplasma hominis P120 protein GAT1 YFL021W 2.6 transcriptional activator with GATA-1-type Zn finger DNA-binding motif YGL045W 2.6 hypothetical protein ZRT1 YGL255W 2.6 high-affinity zinc transport protein YHL002c-a 2.6 questionable ORF PEX18 YHR160C 2.6 weak similarity to hypothetical protein YGR239c GTT1 YIR038C 2.6 Glutathione transferase BAT2 YJR148W 2.6 Branched-Chain Amino Acid Transaminase SPT23 YKL020C 2.6 suppressor protein YKL023W 2.6 weak similarity to human cylicin II YKR077W 2.6 hypothetical protein YKR089C 2.6 strong similarity to YOR081c TIS11/CTH2 YLR136C 2.6 zinc finger containing homolog of mammalian TIS11, glucose repressible gene YLR271W 2.6 hypothetical protein YMR185W 2.6 hypothetical protein GLC8 YMR311C 2.6 Regulates activity of protein phosphatase 1, Glc7p, which is involved in proper chromosome segregation YNL305C 2.6 similarity to C-term. of A.nidulans regulatory protein (qutR) YOR052C 2.6 hypothetical protein YOR192C 2.6 strong similarity to Thi10p YOR289W 2.6 similarity to C.elegans hypothetical protein MSD1/LPG5 YPL104W 2.6 Aspartyl-tRNA synthetase, mitochondrial DLD1 YDL174C 2.7 mitochondrial enzyme D-lactate ferricytochrome c oxidoreductase RAD28 YDR030C 2.7 Protein involved in the same pathway as Rad26p, has beta-transducin (WD-40) repeats ARO10 YDR380W 2.7 similarity to Pdc6p, Thi3p and to pyruvate decarboxylases PDR15 YDR406W 2.7 probable multidrug resistance transporter

SOM1 YEL059C-A 2.7 high copy suppressor of imp1 mutation, may be required for the function of the Imp1 peptidase and\/or the protein sorting machinery

YAT2 YER024W 2.7 similarity to carnitine O-acetyltransferase Yat1p SPI1 YER150W 2.7 strong similarity to putative cell surface glycoprotein Sed1p YER188c-a 2.7 strong similarity to subtelomeric encoded proteins YFR055W 2.7 strong similarity to beta-cystathionases LIF1 YGL090W 2.7 Ligase Interacting Factor 1\; physically interacts with DNA ligase 4 protein (Lig4p) APG1/AUT3 YGL180W 2.7 Protein kinase SOL4 YGR248W 2.7 similar to SOL3 YHR015W 2.7 PolyA-binding protein YIL055C 2.7 hypothetical protein YIR014W 2.7 hypothetical protein MEC3/PIP3 YLR288C 2.7 involved in checkpoint control and DNA repair VIP1 YLR410W 2.7 Homologous to S. pombe asp1+ YAP1/PAR1/SNQ13 YML007W 2.7 jun-like transcription factor YNL208W 2.7 weak similarity to Colletotrichum gloeosporioides nitrogen starvation-induced glutamine rich protein MCT1 YOR221C 2.7 malonyl-CoA:ACP transferase PYK2 YOR347C 2.7 Pyruvate kinase, glucose-repressed isoform PZF1/TFC2 YPR186C 2.7 Transcription factor IIIA (TFIIIA) with putative Zn-fingers NTG1/FUN33 YAL015C 2.8 DNA glycosylase OSH1 YAR044W 2.8 Shows homology to the human oxysterol binding protein (OSBP) YDL173W 2.8 hypothetical protein SPO71 YDR104C 2.8 hypothetical protein AHA1 YDR214W 2.8 similarity to hypothetical protein YNL281w YDR330W 2.8 similarity to hypothetical S. pombe protein RIP1 YEL024W 2.8 Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex AST2 YER101C 2.8 Protein involved in targeting of plasma membrane [H+]ATPase SCY1 YGL083W 2.8 suppressor of GTPase mutant YGR207C 2.8 electron-transferring flavoprotein, beta chain YJL049W 2.8 hypothetical protein YJL142C 2.8 questionable ORF YLL049W 2.8 hypothetical protein MMP1 YLL061W 2.8 strong similarity to amino acid transport protein Gap1p UGT51 YLR189C 2.8 similarity to P.aeruginosa rhamnosyltransferase 1 chain B CLB4 YLR210W 2.8 G(sub)2-specific B-type cyclin IMH1/SYS3 YLR309C 2.8 similarity to human centromere protein E PGM2/GAL5 YMR105C 2.8 Phosphoglucomutase

YMR252C 2.8 hypothetical protein YOL083W 2.8 similarity to YOL082w STI1 YOR027W 2.8 Heat shock protein also induced by canavanine and entry into stationary phase PTP2 YOR208W 2.8 protein tyrosine phosphatase YOR223W 2.8 protein of unknown function LEA1 YPL213W 2.8 similarity to A.thaliana U2 snRNP protein A GFD2 YCL036W 2.9 similarity to hypothetical protein YDR514c MSH5 YDL154W 2.9 MutS homolog involved in chromosome exchange YGR102C 2.9 hypothetical protein IKS1 YJL057C 2.9 probable serine\/threonine kinase YJL149W 2.9 similarity to hypothetical protein YDR131c LCB5 YLR260W 2.9 sphingoid long chain base (LCB) kinase YMR140W 2.9 hypothetical protein CIT/CSI/LYS6 YNR001C 2.9 citrate synthase. Nuclear encoded mitochondrial protein. YOR215C 2.9 similarity to M.xanthus hypothetical protein MLC2 YPR188C 2.9 similarity to calmodulin and calmodulin-related proteins ZTA1 YBR046C 3 Homolog to quinone oxidoreductase (E. coli) GDH2 YDL215C 3 NAD-dependent glutamate dehydrogenase YDR262W 3 hypothetical protein PRB1/CVT1 YEL060C 3 vacuolar protease B FYV11 YFL023W 3 similarity to repeat structures in a Plasmodium falciparum protein (MESA) that binds human erythrocyte protein 4.1. BTN2 YGR142W 3 similarity to hypothetical protein YPR158w ECM37 YIL146C 3 ExtraCellular Mutant ASG7 YJL170C 3 An a-specific gene that is induced to a higher expression level by alpha factor PRP40 YKL012W 3 Splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle MCR1 YKL150W 3 NADH-cytochrome b5 reductase SDH2 YLL041C 3 Succinate dehydrogenase (ubiquinone) iron-sulfur protein subunit APG10 YLL042C 3 hypothetical protein GTT2 YLL060C 3 Glutathione transferase YMR002W 3 similarity to hypothetical S.pombe and C.elegans proteins ESBP6/MCH3 YNL125C 3 Protein with similarity to mammalian monocarboxylate transporters MCT1 and MCT2 YOL048C 3 similarity to YAL018c and YOL047c CVT19 YOL082W 3 similarity to YOL083w SKM1 YOL113W 3 Serine\/threonine protein kinase with similarity to Ste20p and Cla4p HOS3 YPL116W 3 Protein with similarity to Hda1p, Rpd3p, Hos2p, and Hos1p RNY1 YPL123C 3 Similairty to ribonucleases YPR158W 3 similarity to YGR142w YBL094C 3.1 questionable ORF YCL033C 3.1 Transcription regulator

HLR1 YDR528W 3.1 similarity to Lre1p GND2 YGR256W 3.1 6-phosphogluconate dehydrogenase TDH1/GLD3 YJL052W 3.1 Glyceraldehyde-3-phosphate dehydrogenase 1 SED5 YLR026C 3.1 Sed5p is a t-SNARE (soluble NSF attachment protein receptor) required in ER to Golgi transport. YML119W 3.1 hypothetical protein RRD2 YPL152W 3.1 Resistant to Rapamycin Deletion 2 FUS1 YCL027W 3.2 serine\/threonine-rich membrane protein DON1 YDR273W 3.2 weak similarity to YOR042w YEL073C 3.2 similarity to YJR108w YHL021C 3.2 weak similarity to Pseudomonas gamma-butyrobetaine hydroxylase SRC1 YML034W 3.2 similarity to YDR458c YMR087W 3.2 hypothetical protein SIS1 YNL007C 3.2 sit4 suppressor, dnaJ homolog YNL156C 3.2 similarity to YHR133c AUT1/APG3 YNR007C 3.2 Protein involved in autophagocytosis during starvation YOR114W 3.2 hypothetical protein IDH2 YOR136W 3.2 NAD+-dependent isocitrate dehydrogenase MCM16 YPR046W 3.2 Required for chromosome segregation YDR248C 3.3 strong similarity to E.coli thermoresistant gluconokinase SIT1/ARN3 YEL065W 3.3 probably multidrug resistance protein YHL035C 3.3 ABC transporter YHR138C 3.3 hypothetical protein IKI1/HAP2/ELP5/TOT5 YHR187W 3.3 confers sensitivity to killer toxin MDV1/NET2/FIS2/GAG3 YJL112W 3.3 similarity to Met30p and N.crassa sulfur controller-2 YAK1 YJL141C 3.3 Serine-threonine protein kinase TOP3/EDR1 YLR234W 3.3 DNA Topoisomerase III PIG1 YLR273C 3.3 Protein similar to Gac1p, a putative type 1 protein phosphatase targeting subunit HUG1 YML058w-a 3.3 identified by SAGE YMR196W 3.3 hypothetical protein YMR278W 3.3 similarity to phosphomannomutases SLK19 YOR195W 3.3 possible leucine zipper YOR389W 3.3 strong similarity to putative pseudogenes YPL277c and YPL278c YBR047W 3.4 hypothetical protein YBR116C 3.4 questionable ORF NGR1 YBR212W 3.4 negative growth regulatory protein GRX1 YCL035C 3.4 Glutaredoxin (thiol-transferase) GYP7 YDL234C 3.4 protein of unknown function

UBC5 YDR059C 3.4 ubiquitin-conjugating enzyme YDR391C 3.4 strong similarity to hypothetical protein YOR013w YJR096W 3.4 similarity to Corynebacterium 2,5-diketo-D-gluconic acid reductase and aldehyde reductases CWC24 YLR323C 3.4 weak similarity to N.crassa uvs2 protein CYT1/CTC1 YOR065W 3.4 Cytochrome c1 PDR10 YOR328W 3.4 Putative ABC transporter highly similar to Pdr5p YBR056w-a 3.5 identified by SAGE SHC1 YER096W 3.5 sporulation-specific homolog of csd4 SCW11 YGL028C 3.5 glucanase gene family member KNS1 YLL019C 3.5 protein kinase homolog PRP12/RNA12/YME2 YMR302C 3.5 Integral membrane mitochondrial protein ADH2/ADR2 YMR303C 3.5 alcohol dehydrogenase II KAR3/OSR11 YPR141C 3.5 kinesin-like nuclear fusion protein DIA3 YDL024C 3.6 strong similarity to acid phosphatase YGR079W 3.6 hypothetical protein SGA1 YIL099W 3.6 intracellular glucoamylase ECM38/CIS2 YLR299W 3.6 gamma-glutamyltransferase homolog PAI3 YMR174C 3.6 Cytoplasmic inhibitor of proteinase Pep4p YOR152C 3.6 hypothetical protein OPY2 YPR075C 3.6 imparts Far- phenotype

AUT7 YBL078C 3.7

Form a protein complex with Aut2p, to mediate attachment of autophagosomes to microtubules. Aut7p shows homologies to LC3, a microtubule-associated protein from rat. AUT7 was identified as a suppressor of mutant phenotypes of aut2-1 cells. Uptake of prec

YBR085c-a 3.7 hypothetical protein HXK1 YFR053C 3.7 Hexokinase I (PI) (also called Hexokinase A) LYS1 YIR034C 3.7 saccharopine dehydrogenase GIS3 YLR094C 3.7 hypothetical protein YMR317W 3.7 similarity to mucins, glucan 1,4-alpha-glucosidase and exo-alpha-sialidase NTH2 YBR001C 3.8 Neutral trehalase, highly homologous to Nth1p YBR269C 3.8 hypothetical protein YDL124W 3.8 similarity to aldose reductases

GGA1 YDR358W 3.8 strong similarity to hypothetical protein YHR108w and weak similarity to signal transducing adaptor from mouse and man

YEL074W 3.8 similarity to subtelomeric encoded proteins YIL024C 3.8 hypothetical protein

CDC16 YKL022C 3.8 putative metal-binding nucleic acid-binding protein, interacts with Cdc23p and Cdc27p to catalyze the conjugation of ubiquitin to cyclin B

YPL044C 3.8 questionable ORF YPL113C 3.8 similarity to glycerate dehydrogenases YBL064C 3.9 Homolog to thiol-specific antioxidant YFR017C 3.9 hypothetical protein YHR033W 3.9 Pro1p (Gamma-glutamyl kinase) YLR251W 3.9 similarity to peroxisomal rat membrane protein PMP22 YLR324W 3.9 strong similarity to YGR004w ATH1 YPR026W 3.9 null mutant is viable\; increased tolerance to dehydration, freezing, and toxic levels of ethanol SER3 YER081W 4 strong similarity to phosphoglycerate dehydrogenases ROM1/SKC1 YGR070W 4 GDP-GTP Exchange Protein (GEP) for the Rho1p Small GTP-binding Protein HSP104 YLL026W 4 heat shock protein 104 AGA1 YNR044W 4 anchorage subunit of a-agglutinin CSR2/MRG19 YPR030W 4 similarity to YBL101c YBR230C 4.1 hypothetical protein RIM4 YHL024W 4.1 RNA binding domain (N-term) with asparagine rich region? YKL133C 4.1 probable purine nucleotide-binding protein CPR6 YLR216C 4.1 a cyclophilin related to the mammalian CyP-40\; physically interacts with RPD3 gene product RTN2 YDL204W 4.2 Similar to YDR233c VPS73 YGL104C 4.2 similarity to glucose transport proteins YJL103C 4.2 putative regulatory protein LEU3 YLR451W 4.2 zinc-finger transcription factor of the Zn(2)-Cys(6) binuclear cluster domain type GRE1 YPL223C 4.2 Induced by osmotic stress CYC7 YEL039C 4.3 iso-2-cytochrome c ARO9 YHR137W 4.3 aromatic amino acid aminotransferase II NTH1 YDR001C 4.4 neutral trehalase (alpha,alpha-trehalase) YHR159W 4.4 hypothetical protein NDI1 YML120C 4.4 mitochondrial NADH ubiquinone 6 oxidoreductase YMR323W 4.4 strong similarity to phosphopyruvate hydratases PUT4 YOR348C 4.4 putative proline-specific permease CTR1 YPR124W 4.4 High affinity copper transporter into the cell, probable integral membrane protein YCR062W 4.5 similarity to Ytp1p protein IDP2 YLR174W 4.5 Cytosolic form of NADP-dependent isocitrate dehydrogenase IDH1 YNL037C 4.5 alpha-4-beta-4 subunit of mitochondrial isocitrate dehydrogenase 1 YOR389W 4.5 strong similarity to putative pseudogenes YPL277c and YPL278c MGT1 YDL200C 4.6 6-O-methylguanine-DNA methylase GUT2 YIL155C 4.6 glycerol-3-phosphate dehydrogenase, mitochondrial MCH4 YOL119C 4.6 similarity to monocarboxylate transporter proteins YHR209W 4.8 similarity to hypothetical protein YER175c YCR061W 4.9 hypothetical protein

YFL054C 4.9 similarity to channel proteins TOS5 YKR011C 4.9 hypothetical protein PBI2 YNL015W 4.9 Proteinase inhibitor I2B (PBI2), that inhibits protease Prb1p (yscB) YNL033W 4.9 nearly identical to YNL019c YOL154W 4.9 similarity to S.fumigata Asp FII YER004W 5 similarity to hypothetical E.coli and C.elegans proteins MBR1 YKL093W 5 MBR1 protein precursor SSA4 YER103W 5.1 member of 70 kDa heat shock protein family YKR049C 5.2 hypothetical protein MSF1'/MSF1 YLR168C 5.2 probably involved in intramitochondrial protein sorting MEP2 YNL142W 5.2 Ammonia transport protein YBR116C 5.3 questionable ORF GLC3/GHA1 YEL011W 5.3 1,4-glucan-6-(1,4-glucano)-transferase YMR090W 5.3 strong similarity to B. subtilis conserved hypothetical protein yhfK FIG2 YCR089W 5.4 predicted GPI-anchored cell wall protein HSP42 YDR171W 5.4 Similar to HSP26\; expression is regulated by stress conditions GSY2 YLR258W 5.4 Glycogen synthase (UDP-gluocse--starch glucosyltransferase) MSC1 YML128C 5.4 C-terminal part starting with aa 262 cause growth inhibition when overexpressed YNL337W 5.4 strong similarity to subtelomeric encoded proteins ECM13 YBL043W 5.6 ExtraCellular Mutant YLR356W 5.7 similarity to SCM4 protein THI11 YJR156C 5.8 Thiamine biosynthetic enzyme TFS1/DKA1 YLR178C 5.8 suppressor of cdc25 FRE1 YLR214W 5.8 Ferric (and cupric) reductase YFL030W 5.9 similarity to several transaminases UGA1 YGR019W 5.9 gamma-aminobutyrate (GABA) transaminase (4-aminobutyrate aminotransferase) YML131W 5.9 similarity to human leukotriene b4 12-hydroxydehydrogenase STF1/AIS2 YDL130W-A 6 ATPase stabilizing factor UGX2 YDL169C 6 protein of unknown function YLR054C 6 hypothetical protein FIT2 YOR382W 6 hypothetical protein YPL277C 6 strong similarity to hypothetical protein YOR389w/putative pseudogene YJR097W 6.1 weak similarity to Caj1p RPM2 YML091C 6.1 subunit of mitochondrial RNase P SSE2 YBR169C 6.2 HSP70 family member, highly homologous to Sse1p YDR070C 6.2 hypothetical protein CTT1 YGR088W 6.2 cytoplasmic catalase T YBR284W 6.4 similarity to AMP deaminase YMR191W 6.4 hypothetical protein

FUN34 YNR002C 6.4 Putative transmembrane protein DUR3 YHL016C 6.6 Urea transporter HMX1 YLR205C 6.8 hypothetical protein

TSL1 YML100W 6.8 123 kD regulatory subunit of trehalose-6-phosphate synthase\/phosphatase complex\; homologous to TPS3 gene product

LAP4 YKL103C 7 vacuolar aminopeptidase ysc1 YNL115C 7.1 weak similarity to S.pombe hypothetical protein SPAC23C11 GDB1 YPR184W 7.1 similarity to human 4-alpha-glucanotransferase (EC 2.4.1.25)/amylo-1,6-glucosidase (EC 3.2.1.33) PHM7 YOL084W 7.5 similarity to A.thaliana hyp1 protein GYC1 YOR120W 7.5 Similar to mammalian aldo\/keto reductases AQY2 YLL052C 7.7 member of mip family transmembrane channels YTP1 YNL237W 7.7 Yeast putative Transmembrane Protein GSC2/FKS2 YGR032W 7.9 catalytic component of 1,3-beta-D-glucan synthase YPS5 YGL259W 8.2 GPI-anchored aspartic protease SPS100 YHR139C 8.2 sporulation-specific wall maturation protein ARG3 YJL088W 8.2 Ornithine carbamoyltransferase YNR034w-a 8.3 hypothetical protein OYE3/ZRG6 YPL171C 8.3 NAD(P)H dehydrogenase YBL049W 8.5 hypothetical protein ADR1 YDR216W 8.5 positive transcriptional regulator of ADH2 and peroxisomal protein genes AZR1 YGR224W 8.5 strong similarity to drug resistance protein SGE1 YPL205C 8.5 questionable ORF YLL053C 8.8 similarity to water channel proteins

COS12 YGL263W 9.4 Protein with strong similarity to subtelomerically-encoded proteins including Cos2p, Cos4p, Cos8p, YIR040c, Cos5p, Cos9p, and Cos6p

SNZ1 YMR096W 9.6 encodes highly conserved 35 kDa protein that shows increased expression after entry into stationary phase NCA3 YJL116C 10.3 With NCA2, regulates proper expression of subunits 6 (Atp6p) and 8 (Atp8p ) of the Fo-F1 ATP synthase PRM1 YNL279W 10.4 hypothetical protein YPL222W 10.4 similarity to C.perfringens hypothetical protein YOL155C 10.5 similarity to glucan 1,4-alpha-glucosidase Sta1p and YAR066w RNR3 YIL066C 10.8 Ribonucleotide reductase (ribonucleoside-diphosphate reductase) large subunit UBI4 YLL039C 10.8 ubiquitin GAD1 YMR250W 11.1 similarity to glutamate decarboxylases HSP82/HSP83/HSP90 YPL240C 12 heat shock protein AMS1 YGL156W 12.1 vacuolar alpha mannosidase HXT5 YHR096C 13.2 hexose transporter YER185W 13.8 strong similarity to Rtm1p YDR042C 13.9 hypothetical protein

HSP78 YDR258C 13.9 Mitochondrial heat shock protein 78 kDa CTS1 YLR286C 14.3 Endochitinase YDL223C 14.4 weak similarity to mucin SPS19/SPX19 YNL202W 14.5 peroxisomal 2,4-dienoyl-CoA reductase YBL048W 14.7 hypothetical protein PUT1 YLR142W 14.7 proline oxidase GAP1 YKR039W 15.1 general amino acid permease YNL274C 16.8 similarity to glycerate- and formate-dehydrogenases GPH1 YPR160W 16.9 Glycogen phosphorylase YGR110W 17.3 weak similarity to YLR099c and YDR125c AGP2 YBR132C 17.4 Amino acid permease GSP2/CNR2 YOR185C 17.9 GTP binding protein, almost identical to Gsp1p FIG1 YBR040W 19.6 integral membrane protein SAG1 YJR004C 20.5 alpha-agglutinin SNO1 YMR095C 22.6 SNZ1 proximal ORF, stationary phase induced gene HSP26 YBR072W 30.3 heat shock protein 26 YOL053C-A 38.8 DNA Damage Responsive HSP12 YFL014W 42 12 kDa heat shock protein