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Table 2 Conserved mRNA motifs that recognize modular sRNA sequences

From: Codon usage and modular interactions between messenger RNA coding regions and small RNAs in Escherichia coli

sRNA(a) p-value(b) Motif size(c) Targets(d) Motif(e) Number of sequences(f)
OmrA-A1 9.6 × 10−10 6 21 (gntP, ygjN, hokB, ssuC, csgD, ybeT, mipA, clpB, yzgL, ompT, narH, fecA, xylH, fepA, fecD, uup, csgB, csiE, folP, sufD, glmM) 21/39
OmrA-A2 7.9 × 10−3 6 20 (malK, gmhB, xylH, yrfC, deoR, btuB, yccS, cydD, glcD, hokD, yhbE, yaeP, cheZ, yeaZ, yadD, hisM, ydhT, ydbC, fdoI, fimF) 20/20
RyhB-A2 8.9 × 10−13 8 19 (sucD, proA, ygiQ, yagJ, yegK, yiaM, bfr, ydaN, sucB, sugE, yadS, metH, ygiT, mdh, metI, citG, yagT, fumA, shiA) 19/33
RyhB-A3 1.4 × 10−3 8 5 (ompC, galK, metI, sodB, iscS) 5/8
GcvB-A 7.3 × 10−6 10 17 (oppA, ybdH, ilvC, livK, thrL, ompA, iciA, ompF, dppA, ompC, sodB, ndK, livJ, ptsG, yaeC, gltI, sstT) 17/19
Spot42-A1 5.1 × 10−5 8 6 (gltA, atoD, nanC, paaK, galK, xylF) 6/6
Spot42-A3 1.7 × 10−11 8 10 (fucP, ompC, ompA, glpF, fucI, ompF, puuE, ascF, dppA, galK) 10/14
OxyS-A 1.4 × 10−2 7 6 (yccE, gfcB, yheN, yobF, yeaK, moaD) 6/6
  1. The table shows the motifs identified in the region of interaction mRNA-sRNA present in target mRNAs. The table indicates the sRNA zone of interaction(a), p-values of identified motifs(b), size of motifs(c), number and identity of target mRNAs containing the identified motifs(d), logo representation of motifs(e) and the fraction of target mRNAs containing the identified motifs(f)