Skip to main content

Table 3 Genes with class 2 (non-TATA box-containing) promoters in S. cerevisiae having orthologs which have TATA box in one or more other species of sensu stricto group.

From: Rate of promoter class turn-over in yeast evolution

     Presence of TATA box   
ORF Gene name Description Minimal distance from consensusa paradoxus mikatae kudriavtsevii bayanus Switch eventsb Ancestral statec
YDL139C SCM3 Suppressor of chromosome missegregation 1 + - - -   
YDR159W SAC3 Component of nuclear pore 2 + - - - 1 non-TATA
YGL091C NBP35   1 + - - - 1 non-TATA
YIR002C MPH1 Helicase 1 + - - - 1 non-TATA
YOL149W DCP1 Decapping enzyme 1 + - - - 1 non-TATA
YOR125C CAT5   1 + - - - 1 non-TATA
YLR011W LOT6   1 + GA - - 1 non-TATA
YOR154W   Hypothetical ORF 2 + GA - - 1 non-TATA
YKL207W   Hypothetical ORF 1 + GA GA GA 1 non-TATA
YDL005C MED2 RNA Polymerase II transcriptional regulation mediator 4 - + - - 1 non-TATA
YDL207W GLE1 Polyadenylated-RNA-export factor 1 - + - - 1 non-TATA
YDR459C    2 - + - - 1 non-TATA
YER099C PRS2 5-phospho-ribosyl-1(alpha)-pyrophosphate synthetase 2 - + - - 1 non-TATA
YIL002C INP51 Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, synaptojanin-like protein 3 - + - - 1 non-TATA
YNL125C ESBP6   1 - + - - 1 non-TATA
YOR201C PET56 Ribose methyltransferase 1 - + - - 1 non-TATA
YOR238W   Hypothetical ORF 5 - + - - 1 non-TATA
YOR280C FSH3 Serine hydrolase 1 - + - - 1 non-TATA
YPL034W   Hypothetical ORF 2 - + - - 1 non-TATA
YPL047W SGF11   1 - + - - 1 non-TATA
YPL096W PNG1 De-N-glycosylation enzyme 2 - + - - 1 non-TATA
YKL038W RGT1 Transcriptional activator 4 - + GA - 1 non-TATA
YDR422C SIP1 Protein kinase complex component 1 - + - GA 2 ?
YOR211C MGM1   3 - + - GA 1 non-TATA
YPL112C PEX25   2 - + GA GA 1 non-TATA
YKL012W PRP40 U1 snRNP protein involved in splicing 1 + + - - 2 non-TATA
YGR134W CAF130 CCR4 Associated Factor 1 + + - GA 2 non-TATA
YBL074C AAR2 Component of the U5 snRNP 1 - - + - 1 non-TATA
YFR042W    2 - - + - 1 non-TATA
YML065W ORC1 Largest subunit of the origin recognition complex 4 - - + - 1 non-TATA
YOR160W MTR10   1 - - + - 1 non-TATA
YOR228C   Hypothetical ORF 6 - - + - 1 non-TATA
YPL091W GLR1   1 - - + - 1 non-TATA
YLR165C PUS5   2 - GA + - 1 non-TATA
YDR160W SSY1 Component of the SPS plasma membrane amino acid sensor system (Ssy1p-Ptr3p-Ssy5p) 3 GA - + GA 1 non-TATA
YBR108W   Hypothetical ORF 1 - - - + 2 ?
YHR105W YPT35 Hypothetical ORF 2 - - - + 1 ?
YNL119W NCS2   4 - - - + 1 ?
YKR053C YSR3 Dihydrosphingosine 1-phosphate phosphatase 1 - GA GA + 1 ?
YOL020W TAT2 Tryptophan permease 1 + + - + 2 TATA
YMR169C ALD3   1 - + GA + 2 ?
YMR170C ALD2   1 - - + + 1 TATA
YPR073C LTP1   2 + + + + 1 TATA
YDL054C MCH1   5 + + + + 1 TATA
Total     14 22 11 9   
  1. a The minimal distance from TATA consensus is the minimal number of nucleotides different from the consensus sequence (TATA(A/T)A(A/T)(A/G)) in the octanucleotide of S. cerevisiae which is orthologous to the TATA box in the non-cerevisiae species. "Gap" indicates an alignment gap at the site of the TATA box; "GA" means that ORF was not conserved in the given species.
  2. b Parsimonious number of switch events in sensu stricto group; i.e., the minimum number of mutations within sensu stricto group necessary to produce this pattern.
  3. c Inferred state in last common ancestor. In cases when more than one equally parsimonious ancestral state was possible, it could not be inferred reliably (marked as '?').