#/home/jhughes/alignace/all_motifs_2/general_transcription_activities_ye.ace #1 YBR154C 600 bp YBR154C rpb5 1-648 25-kDa RNA polymerase subunit (common to polymerases I, II and III) #2 YBR198C 385 bp YBR198C TAF90 1-2397 Component of the TAF(II) complex (TBP-associated protein complex) required for activated transcription by RNA polymerase II #3 YBR253W 300 bp YBR253W SRB6 1-366 transcription factor, part of Srb\/Mediator complex #4 YCR081W 300 bp YCR081W SRB8 1-3681 activation mediator subcomplex of RNA polymerase I holoenzyme #5 YDL140C 600 bp YDL140C rpo21 1-5202 RNA polymerase II large subunit #6 YDL108W 496 bp YDL108W kin28 1-28, 110-1002 serine-threonine kinase #7 YDR045C 451 bp YDR045C 1-333 #8 YDR145W 600 bp YDR145W TAF61 1-1620 TFIID subunit #9 YDR167W 300 bp YDR167W TAF25 1-621 TFIID subunit #10 YDR190C 341 bp YDR190C 1-1392 #11 YDR308C 598 bp YDR308C SRB7 1-423 RNA polymerase II holoenzyme component #12 YDR311W 600 bp YDR311W TFB1 1-1929 Component of transcription initiation factor IIb, 75 kDa subunit #13 YDR404C 476 bp YDR404C rpb7 1-516 dissociable subunit of RNA polymerase II #14 YDR443C 351 bp YDR443C ssn2 1-4263 RNA polymerase II holoenzyme component #15 YDR460W 367 bp YDR460W TFB3 1-966 TFIIH subunit Tfb3 , contains ring finger motif\; similar to mammalian CAK subunit #16 YER022W 300 bp YER022W SRB4 1-2064 subunit of RNA polymerase II holoenzyme\/mediator complex #17 YER148W 460 bp YER148W spt15 1-723 TATA-binding protein (tfIId) #18 YER171W 430 bp YER171W rad3 1-2337 #19 YFL036W 600 bp YFL036W RPO41 1-4056 mitochondrial RNA polymerase II #20 YGL244W 348 bp YGL244W RTF1 1-1677 Nuclear protein #21 YGL112C 300 bp YGL112C TAF60 1-1551 #22 YGL070C 300 bp YGL070C rpb9 1-369 RNA polymerase II subunit #23 YGL043W 446 bp YGL043W dst1 1-930 RNA polymerase II elongation factor #24 YGR005C 300 bp YGR005C TFG2 1-1203 transcription initiation factor TFIIF middle subunit #25 YGR063C 300 bp YGR063C spt4 1-309 Zn-finger protein, transcriptional regulator #26 YGR104C 300 bp YGR104C SRB5 1-924 subunit of RNA polymerase II holoenzyme\/mediator complex #27 YGR116W 507 bp YGR116W SPT6 1-4356 transcription factor #28 YGR186W 300 bp YGR186W TFG1 1-2208 Transcription factor TFIIF large subunit #29 YGR274C 300 bp YGR274C TAF145 1-3201 Component of the TAFII complex required for activated transcription #30 YHR041C 600 bp YHR041C srb2 1-14, 116-734 RNA polymerase II #31 YHR143W-A 600 bp YHR143W-A RPB12 1-213 subunit of RNA polymerase II #32 YIL143C 300 bp YIL143C SSL2 1-2532 DNA helicase homolog\; homolog of human XPBC #33 YIL128W 568 bp YIL128W MET18 1-3099 Involved in nucleotide excision repair and regulation of TFIIH #34 YIL021W 444 bp YIL021W RPB3 1-957 45 kDa subunit of RNA polymerase II #35 YJL140W 570 bp YJL140W RPB4 1-666 fourth-largest subunit of RNA polymerase II #36 YKL058W 600 bp YKL058W TOA2 1-369 Transcription factor IIA, small chain #37 YKL028W 600 bp YKL028W TFA1 1-1449 Large subunit of transcription factor tfIIE #38 YKR062W 300 bp YKR062W TFA2 1-987 Small subunit of TFIIE transcription factor #39 YLR005W 543 bp YLR005W SSL1 1-1386 #40 YLR071C 300 bp YLR071C rgr1 1-3249 component of RNA polymerase II holoenzyme\/mediator complex, interacts with Sin4p, Gal11p, and a 50 kd polypeptide #41 YML098W 300 bp YML098W TAF19 1-504 TFIID subunit #42 YML015C 300 bp YML015C TAF40 1-1041 TFIID subunit #43 YML010W 300 bp YML010W spt5 1-3192 transcription factor #44 YMR227C_YMR228W 360 bp YMR227C TAF67 1-1773 TFIID subunit YMR228W mtf1 1-1026 Mitochondrial RNA polymerase specificity factor #45 YMR236W 300 bp YMR236W TAF17 1-474 TFIID subunit #46 YNL025C 600 bp YNL025C ssn8 1-972 C-type cyclin associated with the Ssn3p cyclin-dependent kinase #47 YOL051W 600 bp YOL051W gal11 1-3246 Component of the RNA polymerase II holoenzyme complex, positive and negative transcriptional regulator of genes involved in mating-type specialization #48 YOL005C 600 bp YOL005C RPB11 1-363 RNA polymerase II subunit, homologous to S. pombe Rpb11p subunit #49 YOR151C 600 bp YOR151C RPB2 1-3675 RNA polymerase II subunit #50 YOR194C 322 bp YOR194C TOA1 1-861 Transcription factor IIA, large chain #51 YOR210W 593 bp YOR210W RPB10 1-213 RNA polymerase II subunit #52 YOR224C 300 bp YOR224C rpb8 1-441 16-kDa RNA polymerase subunit (common to polymerases I, II and III) #53 YPL129W 300 bp YPL129W 1-9, 115-840 #54 YPL122C 300 bp YPL122C TFB2 1-1542 TFIIH subunit Tfb2\; has homology to CAK and human IIH subunits #55 YPL046C 316 bp YPL046C ELC1 1-300 Elongin C transcription elongation factor #56 YPL011C 314 bp YPL011C TAF47 1-1062 Component of the TAF(II) complex (TBP-associated protein complex) #57 YPR025C 600 bp YPR025C CCL1 1-1182 cyclin #58 YPR056W 300 bp YPR056W TFB4 1-1017 #59 YPR086W 300 bp YPR086W SUA7 1-1038 transcription factor TFIIB homolog #60 YPR187W 300 bp YPR187W RPO26 1-20, 97-544 subunit common to RNA polymerases I, II, and III #Motif number 13 AGCTGTAAATATCATCTTTTACGGGTTCAGATGA 2 214 1 ATCATTACGG 0.865493 -172 GAATCATACTATCATTTTTAAAGATTGGTTTCCA 12 415 0 ATCATTAAGA 0.566086 -186 GAGCAGCCTTATCATGTCCCACGGGTTGTGGCTT 12 464 0 ATCATCACGG 0.781345 -137 TTAATACGTAATCGCGTTATACGAATTTTCTCGA 13 166 0 ATCGCTACGA 0.771561 -311 TCCTATATTAATCATGGCCGACGGCATTTAAGCG 18 190 1 ATCATCACGG 0.781345 -241 GCAACCCCAGATCACTGAATACGAAATGTATATC 19 206 0 ATCACAACGA 0.907756 -395 TTATTCGAGCATCACTAAGAACGGAACTCGAACA 28 171 0 ATCACAACGG 0.901858 -130 TACTACCACGATCACAGTTCACGACACATCACGT 30 170 0 ATCACTACGA 0.95049 -431 ATTCAGAAAAATCATATTCTACGACCGCAGCGTT 31 430 0 ATCATTACGA 0.87327 -171 TTATGGTTGTATCACTAACCACGAAACGACAGCC 33 190 0 ATCACAACGA 0.907756 -379 ATATCTTTCAATCGCCTTGAACGGTTGACAAGAC 37 106 1 ATCGCTACGG 0.759264 -495 CAGTGCAAGGATCACTCTTAACGAAGGAAGAAAA 37 248 0 ATCACTACGA 0.95049 -353 ATAGCGATTCATCACAGTGCAAGGATCACTCTTA 37 262 0 ATCACTAAGG 0.77242 -339 CGCTTAGATAATCACTACACACGGTAACGCTTAG 37 461 0 ATCACCACGG 0.908724 -140 AAGGCATAATATCACGGTAAAAGGTGAATATAGG 45 115 0 ATCACTAAGG 0.77242 -186 TACTACTCTTATCATGCAAGAAGATGTGAAAAAG 47 192 0 ATCATAAAGA 0.400741 -409 ACTGTCTCACATCATACTTGACGAAGCTTTTTTT 50 166 0 ATCATTACGA 0.87327 -157 GAACACAAAGATCACGTTGAACGAAAAGTAATTT 51 426 1 ATCACTACGA 0.95049 -168 GAGAAAACCTATCACGTCTGACGAACATGAAAAA 52 135 0 ATCACCACGA 0.914248 -166 ACTTTTTAAAATCACTCAAGACGAGAAAGCTCTT 53 135 1 ATCACAACGA 0.907756 -166 GAGAATAATCATCACTTATAAAGACAACTTAATA 59 224 1 ATCACAAAGA 0.65073 -77 TCAATTAAATATCATACTATACGAATAATCAATA 60 159 0 ATCATTACGA 0.87327 -142 ***** * ****