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