#/mnt/gattaca/jhughes/alignace/all_motifs_3/rrna_processing.ace #0 YBR141C_YBR142W 278 bp YBR141C 1-1014 YBR142W mak5 1-2322 Probable pre-mRNA splicing RNA-helicase of the DEAD box family #1 YBR167C_YBR168W 480 bp YBR167C RPP2 1-423 YBR168W 1-1242 #2 YBR256C_YBR257W 782 bp YBR256C rib5 1-717 Riboflavin synthase alpha-chain YBR257W POP4 1-840 #3 YCL031C 365 bp YCL031C RRP7 1-894 #4 YCR018C 500 bp YCR018C srd1 1-678 involved in the processing of pre-rRNA to mature rRNA #5 YDL015C_YDL014W 429 bp YDL015C 1-933 YDL014W NOP1 1-984 nucleolar protein, homologous to mammalian fibrillarin #6 YDL111C 401 bp YDL111C RRP42 1-798 Component of the exosome 3->5 exoribonuclease complex with Rrp4p, Rrp41p, Rrp43p and Dis3p (Rrp44p). #7 YDR020C_YDR021W 359 bp YDR020C 1-699 YDR021W FAL1 1-1200 DEAD-box protein, putative RNA helicase #8 YDR087C 190 bp YDR087C RRP1 1-837 #9 YFL002C_YFL001W 196 bp YFL002C SPB4 1-1821 ATP-dependent RNA helicase YFL001W deg1 1-1329 Similar to rRNA methyltransferase (Caenorhabditis elegans) and hypothetical 28K protein (alkaline endoglucanase gene 5' region) from Bacillus sp. #10 YGL078C 365 bp YGL078C DBP3 1-1572 ATP-dependent RNA helicase CA3 of the DEAD\/DEAH box family #11 YGL097W 500 bp YGL097W SRM1 1-1449 pheromone response pathway suppressor #12 YGL171W 271 bp YGL171W ROK1 1-1695 Contains domains found in the DEAD protein family of ATP-dependent RNA helicases\; high-copy suppressor of kem1 null mutant #13 YGL173C_YGL172W 586 bp YGL173C KEM1 1-4587 DNA strand-transfer protein exoribonuclease I\; catalyzes the formation of hybrid DNA in vitro\; has 5'-to-3' exonuclease activity on DNA and RNA\; binds to G4 tetraplex DNA and cuts in a single-stranded region 5' to the G4 structure\; protein increases several-fold in meiotic cells YGL172W NUP49 1-1419 nuclear pore complex protein with GLFG repetitive sequence motif #14 YGR158C 390 bp YGR158C MTR3 1-753 #15 YGR159C 500 bp YGR159C NSR1 1-1245 nuclear localization sequence binding protein #16 YGR195W 500 bp YGR195W SKI6 1-741 homolog of RNAse PH #17 YHL034C 500 bp YHL034C sbp1 1-885 #18 YHR062C 271 bp YHR062C RPP1 1-882 Protein subunit of nuclear ribonuclease P (RNase P) #19 YHR065C_YHR066W 171 bp YHR065C RRP3 1-1632 RRP3 is a DEAD box gene homologous to eIF-4a which encodes an RNA-dependent ATPase possessing helicase activity which is not specific for RNA YHR066W SSF1 1-1362 homologous to Ssf2p #20 YHR069C_YHR070W 222 bp YHR069C RRP4 1-1080 3->5 exoribonuclease\; Component of the exosome 3->5 exonuclease complex with Rrp41p, Rrp42p, Rrp43p and Dis3p (Rrp44p). YHR070W 1-1500 #21 YHR089C 478 bp YHR089C GAR1 1-618 small nucleolar RNP proteins #22 YJL033W 461 bp YJL033W HCA4 1-2313 putative RNA helicase #23 YJR002W 253 bp YJR002W MPP10 1-1782 Protein component of the U3 small nucleolar ribonucleoprotein (snoRNP) #24 YKR024C_YKR025W 397 bp YKR024C DBP7 1-2229 putative RNA helicase YKR025W 1-849 #25 YLL009C_YLL008W 314 bp YLL009C COX17 1-210 cysteine-rich cytoplasmic protein YLL008W DRS1 1-2259 putative ATP dependent RNA helicase #26 YLL011W 267 bp YLL011W SOF1 1-1470 56 kDa nucleolar snRNP protein that shows homology to beta subunits of G-proteins and the splicing factor Prp4 #27 YLR059C_YLR060W 431 bp YLR059C YNT20 1-810 YLR060W FRS1 1-1788 Phenylalanyl-tRNA synthetase, alpha subunit, cytoplasmic #28 YLR175W 304 bp YLR175W CBF5 1-1452 major low affinity 55 kDa Centromere\/microtubule binding protein #29 YLR197W 398 bp YLR197W SIK1 1-1515 homology to microtubule binding proteins and to X90565_5.cds #30 YLR223C_YLR224W 973 bp YLR223C IFH1 1-3258 has a weak RNA-dependent ATPase activity which is not specific for rRNA YLR224W 1-1110 #31 YMR229C 500 bp YMR229C FMI1 1-5190 #32 YMR235C_YMR236W 235 bp YMR235C rna1 1-1224 YMR236W TAF17 1-474 TFIID subunit #33 YMR239C 252 bp YMR239C RNT1 1-1416 Ribonuclease III #34 YNL062C_YNL061W 327 bp YNL062C GCD10 1-1437 RNA-binding (zeta) subunit of translation initiation factor 3 (eIF-3) YNL061W NOP2 1-1857 90-kDa protein, located in nucleolus, that is homologous to a human proliferation-associated nucleolar protein, p120 #35 YNL112W 439 bp YNL112W DBP2 1-1273, 2276-2643 ATP-dependent RNA helicase of DEAD box family #36 YNL221C_YNL220W 717 bp YNL221C POP1 1-2628 Component of nuclear RNase P and RNase MRP YNL220W ade12 1-1302 adenylosuccinate synthetase #37 YNL283C_YNL282W 991 bp YNL283C WSC2 1-1512 Putative integral membrane protein containing novel cysteine motif. Similarity to SLG1 (WSC1), WSC3 and WSC4 YNL282W POP3 1-588 #38 YNR037C_YNR038W 267 bp YNR037C 1-276 YNR038W DBP6 1-1890 putative RNA helicase #39 YOL021C_YOL020W 745 bp YOL021C DIS3 1-3006 YOL020W TAT2 1-1779 Tryptophan permease, high affinity #40 YOR048C 500 bp YOR048C rat1 1-3021 RNA trafficking protein\; transcription activator #41 YOR201C_YOR202W 237 bp YOR201C pet56 1-1239 Ribose methyltransferase for mitochondrial 21S rRNA YOR202W his3 1-663 imidazoleglycerol-phosphate dehydratase #42 YPL029W 259 bp YPL029W suv3 1-2214 putative ATP-dependent helicase #43 YPL043W 282 bp YPL043W NOP4 1-2058 RNA recognition motif-containing protein #44 YPL212C_YPL211W 345 bp YPL212C PUS1 1-1635 intranuclear protein which exhibits a nucleotide-specific intron-dependent tRNA pseudouridine synthase activity YPL211W NIP7 1-546 #45 YPL266W 322 bp YPL266W DIM1 1-957 dimethyladenosine transferase #Motif 2 TGAAAAATTT 3 232 0 TGAAAAATTT 9 92 1 TGAAAAATTT 15 293 1 TGAAAAATTT 29 285 1 TGAAAAATTT 31 331 1 TGAAAAATTT 33 106 0 TGAAAAATTT 16 295 1 TGAAAAATTT 34 135 0 TGAAAAATTT 35 222 1 TGAAAAATTT 37 912 0 TGAAAAATTT 19 23 0 TGAAAAATTT 43 141 1 TGAAAAATTT 44 107 1 TGAAAAATTT 5 201 1 TGAAAAATTT 21 338 1 TGAAAAATTT 10 207 1 TGAAAAATTT 22 337 0 TGAAAAATTT 24 141 0 TGAAAAATTT 12 151 1 TGAAAAATTT 26 158 1 TGAAAAATTT 27 332 1 TGAAAAATTT 28 157 1 TGAAAATTTT 29 224 1 TGAAAATTTT 15 328 0 TGAAAATTTT 7 186 1 TGAAAATTTT 34 185 0 TGAAAATTTT 44 204 1 TGAAAATTTT 23 161 0 TGAAAATTTT 25 177 0 TGAAAATTTT 28 101 1 AGAAAAATTT 45 160 1 AGAAAAATTT 17 329 0 AGAAAAATTT 39 103 0 AGAAAAATTT 39 503 0 TGAAAAAATT 42 88 0 TGAAATATTT 10 183 1 TGAAAAAATT 18 188 1 TGAAATATTT 22 398 1 TGAAATATTT 6 73 0 TGAAAAAATT 28 147 1 AGAAAATTTT 35 292 1 TGAAATTTTT 14 247 0 TGAAAATATT 45 195 1 TGAAATTTTT 29 255 1 AGAAATATTT 39 276 0 AGAAAAAATT 22 296 0 AGAAAAAATT 5 185 0 AGAAAAAATT 14 27 0 AGAAAAAATT 21 366 1 AGAAAATATT 39 546 1 AGAAAATATT 44 141 1 **********