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Table 2 Common upstream motifs in the genes involved in cytoplasmic protein synthesis

From: Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level

Presence of regulatory motif    COG general functional category COG pathway/system Subcellular localization GOC number ORF name Gene description
Genes identified experimentally to be regulated by Rap1
rap1 - - EH E7 - COG0028 YLR044C PDC1 pyruvate decarboxylase, isozyme 1
rap1 - - G G1 - COG0469 YAL038W CDC19 pyruvate kinase
RAP1 - - G G2 - COG0126 YCR012W PGK1 phosphoglycerate kinase
RAP1 - - G G2 - COG0057 YGR192C TDH3 glyceraldehyde-3-phosphate dehydrogenase 3
RAP1 - - G G2 - COG0588 YKL152C GPM1 phosphoglycerate mutase
rap1 - - G G2 - COG0148 YHR174W ENO2 enolase II (2-phosphoglycerate dehydratase)
rap1 - - G G2 - COG0057 YJR009C TDH2 glyceraldehyde-3-phosphate dehydrogenase 2
RAP1 RRPE - J - - COG2238 YOL121C RPS19A 40S small subunit ribosomal protein S19.E
RAP1 - - J - - COG2238 YNL302C RPS19B 40S small subunit ribosomal protein S19.E
rap1 - PAC J - - COG2451 YPL143W RPL33A ribosomal protein L35A.E.C16
rap1 - - J - - COG2451 YOR234C RPL33B ribosomal protein L35A.E.C15
RAP1 - - J J2 - COG1190 YDR037W KRS1 lysyl-tRNA synthetase, cytosolic
rap1 RRPE - J J2 - COG0008 YOR168W GLN4 glutaminyl-tRNA synthetase
RAP1 RRPE PAC J J3 - COG0199 YDL061C RPS29B ribosomal protein S29.E.B
RAP1 RRPE PAC J J3 - COG0092 YNL178W RPS3 ribosomal protein S3.E
RAP1 RRPE PAC J J3 - COG0522 YPL081W RPS9A ribosomal protein S9.E.A
RAP1 RRPE - J J3 - COG0103 YDL083C RPS16B ribosomal protein S16.E
RAP1 RRPE - J J3 - COG2004 YIL069C RPS24B 40S small subunit ribosomal protein S24.E
RAP1 RRPE - J J3 - COG0052 YLR048W RPS0B 40S ribosomal protein P40 HOMOLOG B
RAP1 RRPE - J J3 - COG0185 YOL040C RPS15 40S small subunit ribosomal protein
RAP1 - PAC J J3 - COG0052 YGR214W RPS0A 40S ribosomal protein P40 HOMOLOG A
RAP1 - - J J3 - COG0186 YBR048W RPS11B ribosomal protein S11.E.B
RAP1 - - J J3 - COG2125 YBR181C RPS6B ribosomal protein S6.E
RAP1 - - J J3 - COG0522 YBR189W RPS9B ribosomal protein S9.E.B
RAP1 - - J J3 - COG0100 YCR031C RPS14A 40S ribosomal protein S14.E
RAP1 - - J J3 - COG0184 YDR064W RPS13 ribosomal protein
RAP1 - - J J3 - COG1383 YDR447C RPS17B ribosomal protein S17.E.B
RAP1 - - J J3 - COG0099 YDR450W RPS18A ribosomal protein S18.E.C4
RAP1 - - J J3 - COG2004 YER074W RPS24A 40S small subunit ribosomal protein S24.E
RAP1 - - J J3 - COG0098 YGL123W RPS2 40S small subunit ribosomal protein
RAP1 - - J J3 - COG0048 YGR118W RPS23A 40S small subunit ribosomal protein S23.E
RAP1 - - J J3 - COG0051 YHL015W RPS20 ribosomal protein
RAP1 - - J J3 - COG1471 YHR203C RPS4B ribosomal protein S4.E.C8
RAP1 - - J J3 - COG0096 YJL190C RPS22A ribosomal protein S15A.E.C10
RAP1 - - J J3 - COG0049 YJR123W RPS5 ribosomal protein S5.E
RAP1 - - J J3 - COG1471 YJR145C RPS4A ribosomal protein S4.E.C10
RAP1 - - J J3 - COG2051 YKL156W RPS27A ribosomal protein S27.E
RAP1 - - J J3 - COG1890 YLR441C RPS1A ribosomal protein S3A.E
RAP1 - - J J3 - COG1890 YML063W RPS1B ribosomal protein S3A.E
RAP1 - - J J3 - COG2125 YPL090C RPS6A ribosomal protein S6.E
rap1 RRPE - J J3 - COG0100 YJL191W RPS14B 40S small subunit ribosomal protein S14.E.B
rap1 RRPE - J J3 - COG2053 YOR167C RPS28A 40S small subunit ribosomal protein S28.E.C15
rap1 - - J J3 - COG2007 YBL072C RPS8A ribosomal protein S8.E
rap1 - - J J3 - COG0186 YDR025W RPS11A ribosomal protein S11.E
rap1 - - J J3 - COG2007 YER102W RPS8B ribosomal protein S8.E
rap1 - - J J3 - COG0048 YPR132W RPS23B 40S small subunit ribosomal protein S23.E
RAP1 RRPE - J J4 - COG2058 YDL130W RPP1B 60S large subunit acidic ribosomal protein L44PRIME
RAP1 RRPE - J J4 - COG0093 YER117W RPL23B ribosomal protein L23.E
RAP1 RRPE - J J4 - COG0081 YGL135W RPL1B 60S large subunit ribosomal protein
RAP1 RRPE - J J4 - COG0097 YGL147C RPL9A ribosomal protein L9.E
RAP1 RRPE - J J4 - COG0198 YGR034W RPL26B 60S large subunit ribosomal protein
RAP1 RRPE - J J4 - COG1631 YHR141C RPL42B ribosomal protein L36A.E
RAP1 RRPE - J J4 - COG1552 YIL148W RPL40A ubiquitin
RAP1 RRPE - J J4 - COG0091 YJL177W RPL17B 60S large subunit ribosomal protein L17.E
RAP1 RRPE - J J4 - COG1358 YLL045C RPL8B 60S large subunit ribosomal protein L7A.E.B
RAP1 RRPE - J J4 - COG1632 YLR029C RPL15A 60S large subunit ribosomal protein L15.E.C12
RAP1 RRPE - J J4 - COG2058 YOL039W RPP2A acidic ribosomal protein P2.BETA
RAP1 RRPE - J J4 - COG1727 YOL120C RPL18A 60S large subunit ribosomal protein S18.E
RAP1 RRPE - J J4 - COG1841 YPL198W RPL7B 60S large subunit ribosomal protein
RAP1 - PAC J J4 - COG2147 YBL027W RPL19B 60S large subunit ribosomal protein L19.E
RAP1 - PAC J J4 - COG0197 YLR075W RPL10 60S large subunit ribosomal protein
RAP1 - - J J4 - COG0093 YBL087C RPL23A 60S large subunit ribosomal protein L23.E
RAP1 - - J J4 - COG2147 YBR084C-A RPL19A 60S large subunit ribosomal protein L19.E
RAP1 - - J J4 - COG2139 YBR191W RPL21A ribosomal protein L21.E
RAP1 - - J J4 - COG0255 YDL191W RPL35A 60S large subunit ribosomal protein
RAP1 - - J J4 - COG0080 YDR418W RPL12B 60S large subunit ribosomal protein L12.E
RAP1 - - J J4 - COG2126 YDR500C RPL37B ribosomal protein L.37.E
RAP1 - - J J4 - COG1911 YGL030W RPL30 60S large subunit ribosomal protein L30.E
RAP1 - - J J4 - COG1841 YGL076C RPL7A 60S large subunit ribosomal protein L7.E.A
RAP1 - - J J4 - COG0200 YGL103W RPL28 60S large subunit ribosomal protein L27A.E
RAP1 - - J J4 - COG0094 YGR085C RPL11B ribosomal protein
RAP1 - - J J4 - COG1358 YHL033C RPL8A 60S large subunit ribosomal protein L7A.E.A
RAP1 - - J J4 - COG0090 YIL018W RPL2B 60S large subunit ribosomal protein L8.E
RAP1 - - J J4 - COG2174 YIL052C RPL34B ribosomal protein L34.E
RAP1 - - J J4 - COG2167 YJL189W RPL39 60S large subunit ribosomal protein L39.E
RAP1 - - J J4 - COG2163 YKL006W RPL14A ribosomal protein
RAP1 - - J J4 - COG0244 YLR340W RPP0 acidic ribosomal protein L10.E
RAP1 - - J J4 - COG0198 YLR344W RPL26A 60S large subunit ribosomal protein
RAP1 - - J J4 - COG0102 YNL069C RPL16B 60S large subunit ribosomal protein
RAP1 - - J J4 - COG1631 YNL162W RPL42A ribosomal protein L36A.E
RAP1 - - J J4 - COG0089 YOL127W RPL25 ribosomal protein L23A.E
RAP1 - - J J4 - COG2157 YOR312C RPL20B 60S large subunit ribosomal protein
RAP1 - - J J4 - COG1358 YOR369C RPS12 40S small subunit acidic ribosomal protein S12
RAP1 - - J J4 - COG2139 YPL079W RPL21B ribosomal protein L21
RAP1 - - J J4 - COG0256 YPL131W RPL5 60S large subunit ribosomal protein L5.E
RAP1 - - J J4 - COG1997 YPR043W RPL43A ribosomal protein L37A.E
RAP1 - - J J4 - COG0094 YPR102C RPL11A ribosomal protein L11.E
rap1 RRPE - J J4 - COG2058 YDR382W RPP2B 60S large subunit acidic ribosomal protein
rap1 RRPE - J J4 - COG1727 YNL301C RPL18B 60S large subunit ribosomal protein L18.E
rap1 RRPE - J J4 - COG0087 YOR063W RPL3 60S large subunit ribosomal protein L3.E
rap1 - - J J4 - COG1717 YBL092W RPL32 60S large subunit ribosomal protein L32.E
rap1 - - J J4 - COG2097 YDL075W RPL31A 60S large subunit ribosomal protein L31.E
rap1 - - J J4 - COG0080 YEL054C RPL12A 60S large subunit ribosomal protein L12.E
rap1 - - J J4 - COG2075 YGL031C RPL24A 60S large subunit ribosomal protein L24.E.A
rap1 - - J J4 - COG2075 YGR148C RPL24B 60S large subunit ribosomal protein L24.E.B
rap1 - - J J4 - COG2163 YHL001W RPL14B ribosomal protein
rap1 - - J J4 - COG0102 YIL133C RPL16A 60S large subunit ribosomal protein
rap1 - - J J4 - COG1552 YKR094C RPL40B ubiquitin
rap1 - - J J4 - COG2126 YLR185W RPL37A ribosomal protein L37.E
RAP1 RRPE PAC K - - COG0724 YGR159C NSR1 nuclear localization sequence binding protein
RAP1 RRPE PAC K K1 - COG0202 YPR110C RPC40 DNA-directed RNA polymerase I, III 40 kD
       subunit   
Genes not identified experimentally to be regulated by rap1
RAP1 RRPE - E - - COG0421 YLR146C SPE4 spermine synthase
- RRPE - E - - COG0031 YGR155W CYS4 cystathionine beta-synthase
- - PAC E - - COG0833 YGR191W HIP1 histidine permease
- - - E - - COG0531 YGL077C HNM1 choline permease
- - - E - - COG0367 YGR124W ASN2 asparagine synthetase
- - - E - - COG0367 YPR145W ASN1 asparagine synthetase
- RRPE - E E7 MIT COG0059 YLR355C ILV5 ketol-acid reducto-isomerase
- - - E E7 MIT COG0473 YIL094C LYS12 homoisocitrate dehydrogenase
- - - E H7 - COG0722 YBR249C ARO4 2-dehydro-3-deoxyphosphoheptonate aldolase, tyrosine-inhibited
- - - E H7 - COG0082 YGL148W ARO2 chorismate synthase
- - - EH E7 - COG0028 YGR087C PDC6 pyruvate decarboxylase 3
- - - EH E7 - COG0028 YLR134W PDC5 pyruvate decarboxylase, isozyme 2
- RRPE - F F2 - COG0503 YML022W APT1 adenine phosphoribosyltransferase
- - PAC F F2 - COG0005 YLR017W MEU1 multiple enhancer of UAS2
- RRPE PAC F F3 - COG0504 YBL039C URA7 CTP synthase 1
- RRPE - F F3 - COG0167 YKL216W URA1 dihydroorotate dehydrogenase
- RRPE - F F3 - COG0461 YML106W URA5 orotate phosphoribosyltransferase
- - - F F3 - COG0563 YDR226W ADK1 adenylate kinase, cytosolic
- - - F F3 - COG0284 YEL021W URA3 orotidine-5'-phosphate decarboxylase
- - - F F3 - COG0563 YKL024C URA6 uridine-monophosphate kinase
- - - F F3 - COG0418 YLR420W URA4 dihydroorotase
- RRPE - FE F1 - COG0462 YHL011C PRS3 ribose-phosphate pyrophosphokinase
- RRPE - FE F1 - COG0462 YKL181W PRS1 ribose-phosphate pyrophosphokinase
- RRPE - G G1 - COG0205 YGR240C PFK1 6-phosphofructokinase, alpha subunit
- - - G G1 - COG0205 YMR205C PFK2 6-phosphofructokinase, beta subunit
- - - G G2 - COG0166 YBR196C PGI1 glucose-6-phosphate isomerase
- - - G G2 - COG0149 YDR050C TPI1 triose-phosphate isomerase
- - - G G2 - COG0057 YJL052W TDH1 glyceraldehyde-3-phosphate dehydrogenase 1
- - - G G2 - COG0191 YKL060C FBA1 fructose-bisphosphate aldolase
- - - G G2 - COG0158 YLR377C FBP1 fructose-1,6-bisphosphatase
- RRPE PAC G G3 - COG0120 YOR095C RKI1 D-ribose-5-phosphate ketol-isomerase
- RRPE PAC G G3 - COG0021 YPR074C TKL1 transketolase 1
- RRPE - H - - COG0499 YER043C SAH1 S-adenosyl-l-homocysteine hydrolase
- - - H - - COG0192 YDR502C SAM2 S-adenosylmethionine synthetase 2
- - - H - - COG0192 YLR180W SAM1 S-adenosylmethionine synthetase 1
- RRPE PAC J - - COG1889 YDL014W NOP1 fibrillarin
- RRPE PAC J - - COG1499 YHR170W NMD3 nonsense-mediated mRNA decay protein
- RRPE PAC J - - COG1498 YLR197W SIK1 involved in pre-rRNA processing
- RRPE PAC J - - COG0144 YNL061W NOP2 nucleolar protein
- RRPE PAC J - - COG1498 YOR310C NOP58 required for pre-18S rRNA processing
- RRPE PAC J - - COG1374 YPL211W NIP7 required for efficient 60S ribosome subunit biogenesis
- RRPE PAC J - - COG0030 YPL266W DIM1 rRNA (adenine-N6, N6-)-dimethyltransferase
- RRPE - J - - COG0293 YCL054W SPB1 required for ribosome synthesis, putative methylase
- RRPE - J - - COG0689 YGR095C RRP46 involved in rRNA processing
- RRPE pac J - - COG3277 YHR089C GAR1 nucleolar rrna processing protein
- RRPE - J - - COG2519 YJL125C GCD14 translational repressor of GCN4
- RRPE - J - - COG0349 YOR001W RRP6 similarity to human nucleolar 100K polymyositis-scleroderma protein
- - PAC J - - COG0009 YGL169W SUA5 translation initiation protein
- rrpe PAC J - - COG1097 YHR069C RRP4 3' → 5' exoribonuclease required for 3' end formation of 5.8S rRNA
- - PAC J - - COG1736 YKL191W DPH2 diphtheria toxin resistance protein
- - PAC J - - COG1798 YLR172C DPH5 diphthamide methyltransferase
- - - J - - COG2123 YDR280W RRP45 rRNA processing protein
RAP1 RRPE - J J1 - COG2092 YAL003W EFB1 translation elongation factor eEF1beta
- RRPE - J J1 - COG1503 YBR143C SUP45 translational release factor
- RRPE - J J1 - COG0480 YOR133W EFT1 translation elongation factor EEF2
- RRPE - J J1 - COG1601 YPL237W SUI3 translation initiation factor EIF2 beta subunit
- - - J J1 - COG0480 YDR385W EFT2 translation elongation factor EEF2
- - - J J1 - COG0361 YMR260C TIF11 translation initiation factor EIF1A
- RRPE PAC J J2 - COG0215 YNL247W Cysteinyl-tRNA synthetase
- RRPE - J J2 - COG0423 YBR121C GRS1 glycine-tRNA ligase
- RRPE - J J2 - COG0008 YGL245W Strong similarity to glutamine-tRNA ligase
- RRPE - J J2 - COG0017 YHR019C DED81 asparaginyl-tRNA-Synthetase
- RRPE - J J2 - COG0008 YOR168W GLN4 glutaminyl-tRNA synthetase
- - - J J2 - COG0172 YDR023W SES1 seryl-tRNA synthetase, cytosolic
RAP1 - - J J3 - COG2051 YHR021C RPS27B ribosomal protein S27.E
- RRPE - J J3 - COG0199 YLR388W RPS29A ribosomal protein S29.E.A
- RRPE - J J3 - COG2053 YOR167C RPS28A 40S small subunit ribosomal protein S28.E.C15
- - - J J3 - COG1998 YLR167W RPS31 ubiquitin/40S small subunit ribosomal protein
- - - J J3 - COG2053 YLR264W RPS28B 40S small subunit ribosomal protein S28.E.C12
- - - J J3 - COG0096 YLR367W RPS22B ribosomal protein S15A.E.C12
- RRPE PAC J J4 - COG0244 YKL009W MRT4 mRNA turnover 4
- RRPE PAC J J4 - COG2075 YLR009W Similarity to ribosomal protein L24.E.B
- RRPE - J J4 - COG0088 YBR031W RPL4A ribosomal protein
- RRPE - J J4 - COG0088 YDR012W RPL4B ribosomal protein L4.E.B
- - - J J4 - COG2058 YDL081C RPP1A 60S large subunit acidic ribosomal protein A1
- - - J J4 - COG1632 YMR121C RPL15B 60S large subunit ribosomal protein L15.E.C13
- - - J J4 - COG2157 YMR242C RPL20A 60S large subunit ribosomal protein
- - - J J4 - COG0097 YNL067W RPL9B ribosomal protein L9.E.C14
- - - J J4 - COG0081 YPL220W RPL1A ribosomal protein
- RRPE - JE J1 - COG0050 YDR172W SUP35 eukaryotic peptide chain release factor GTP-binding subunit
- RRPE - JE J1 - COG0050 YER025W GCD11 translation initiation factor EIF2 gamma chain
- RRPE PAC K - - COG0571 YMR239C RNT1 double-stranded ribonuclease
- RRPE PAC K - - COG0724 YPL043W NOP4 nucleolar protein
- RRPE - K - - COG0724 YER165W PAB1 mRNA polyadenylate-binding protein
- - - K - - COG0724 YDR429C TIF35 translation initiation factor EIF3 (P33 subunit)
- - - K - - COG0724 YOR361C PRT1 translation initiation factor EIF3 subunit
- RRPE PAC K K1 - COG2012 YBR154C RPB5 DNA-directed RNA polymerase I, II, III 25 kD subunit
- - PAC K K1 - COG1761 YNL113W RPC19 DNA-directed RNA polymerase I, III 16 kD subunit
- - - K K1 - COG0202 YIL021W RPB3 DNA-directed RNA-polymerase II, 45 kDA
- - - K K1 - COG1644 YOR210W RPB10 DNA-directed polymerase I, II, III 8.3 subunit
- - - K K1 - COG1758 YPR187W RPO26 DNA-directed RNA polymerase I, II, III 18 kD subunit
- RRPE PAC L - - COG1643 YGL120C PRP43 involved in spliceosome disassembly
- RRPE PAC L - - COG1643 YMR128W ECM16 similarity to helicases
- RRPE PAC LKJ - - COG0513 YGL078C DBP3 putative RNA helicase required for pre-rRNA processing
- RRPE PAC LKJ - - COG0513 YGL171W ROK1 ATP-dependent RNA helicase
- RRPE PAC LKJ - - COG0513 YJL033W HCA4 can suppress the U14 snoRNA rRNA processing function
- RRPE PAC LKJ - - COG0513 YKR024C DBP7 RNA helicase required for 60S ribosomal subunit assembly
- RRPE PAC LKJ - - COG0513 YLL008W DRS1 RNA helicase of the DEAD box family
- RRPE - LKJ - - COG0513 YKR059W TIF1 translation initiation factor 4A
- - PAC LKJ - - COG0513 YJL138C TIF2 translation initiation factor EIF4A
- RRPE - O - - COG0545 YLR449W FPR4 strong similarity to peptidylprolyl isomerase FPR3P
- RRPE - O - - COG0443 YNL209W SSB2 heat shock protein of HSP70 family, cytosolic
- - - O - - COG0443 YHR064C PDR13 regulator protein involved in pleiotropic drug resistance
  1. The first list comprises those genes known to be targeted by Rap1 [18] and the second one those that are not. In the presence of motif columns, '-' means that no motif was identified. Regulatory motifs in uppercase correspond to those found by our computational analysis, those in lowercase correspond to motifs found by others [10,18]. The genes are ordered by their functional category.