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Table 1 Comparison of stop codon context compositional biases in ORFs and uORFS

From: Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast

  3' context ORF observed Frequency All uORFs Observed Frequency Log Odd Ratio (uORF/ORF)
Over-represented 6-mers downstream of stop codons ATCNNC 0.007478 0.003891 -0.942
  ATCNNT 0.009572 0.003891 -1.299
  AGGNNA 0.009423 0.004669 -1.013
  TCANNT 0.008376 0.007004 -0.258
  GCCNNC 0.003290 0.001556 -1.080
  ATANNA 0.014508 0.011673 -0.314
  GCTNNC 0.002393 0.000778 -1.621
  TAGNNT 0.006132 0.006226 0.022
  ATCNAN 0.016303 0.000778 -4.389
  ACANAN 0.011666 0.010117 -0.206
  AGGNAN 0.008376 0.006226 -0.428
  GCCNAN 0.003889 0.001556 -1.321
  TGANAN 0.010171 0.007004 -0.538
  ATANAN 0.018546 0.010895 -0.767
Under-represented 6-mers downstream of stop codons CAANNA 0.003440 0.010117 1.556
  TTTNNT 0.014059 0.017899 0.348
  AAGNNG 0.002842 0.004669 0.716
  CAANNC 0.001645 0.000778 -1.080
  CAANNT 0.003590 0.004669 0.379
  CTCNNT 0.001346 0.003891 1.531
  CATNNT 0.003440 0.000778 -2.144
  CAANAN 0.003590 0.010895 1.601
  TTTNTN 0.013760 0.020233 0.556
  CCGNTN 0.000150 0.000778 2.379
  CTCNAN 0.001346 0.001556 0.209
  GATNAN 0.002991 0.007782 1.379
  CAANTN 0.003290 0.003113 -0.080
  CAANGN 0.002393 0.003891 0.701
  1. The under-represented 6-mers favoured by uORFs are highlighted in bold text.