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Table 2 The nine most abundant cis-antisense candidate sRNAs with predicted sigma 70 promoters

From: Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

sRNA name Size (nt) Mean no. of
Putative target genes*b   Northern blot band size*c (nt)   Ref.*d
    Name Product Total LM  
ECS003 116 357.9 ymfL & ymfM e14 prophage; predicted protein ~70 ~70 -
ECS008 75 53.4 yfaS_1 pseudogene; predicted protein ND ND -
ECS0011 71 46.5 IS128 small RNA (unknown function) ~95 ~95 [9]
      ~100 ~100  
ECS0012 66 39.6 ybhJ predicted hydratase smear ~120 -
ECS0013 67 38.1 rumA 23S ribosomal RNA 5-methyluridine methyltransferase ND ND -
ECS0015 54 25.7 nudC NADH pyrophosphatase ND ND -
ECS0017 92 22.3 ykgM &ykgO predicted ribosomal protein ~275 ND [11]
ECS0018 90 21.6 gltBDF operon glutamate synthase & periplasmic protein ND ND [9, 13]
ECS0021 57 17.6 ytfP &ytfN conserved protein ND ND -
  1. Nine cis-antisense candidate sRNAs were extracted from classes A and B (Figure 1B) for northern blot analysis. *a The average number of deep sequencing reads mapped to each candidate sRNA: total number of reads divided by the length of the candidate sRNA. *b The names and products of the sense-strand genes (putative target genes) corresponding to each cis- antisense candidate sRNA. *c Major signal sizes detected by northern blotting (Figure 3). Total, total RNA; LM, low-molecular-weight RNA. Hyphens indicate that no signal was detected in the northern blot analysis. *d References to predicted sRNAs in previous studies located around each candidate sRNA. The details of the candidate sRNAs are given in Additional File 4.