Figure 6

Escherichia coli Small RNA Browser. Three screen shots are shown as examples of the Escherichia coli Small RNA Browser (ECSBrowser; http://rna.iab.keio.ac.jp/). The upper panel shows an overview of all the non-coding RNA genes encoded in the E. coli genome: novel sRNAs detected by northern blot analysis (red circles); novel candidate sRNAs (pink circles); previously known sRNAs (black circles); tRNAs (green circles); and rRNAs (yellow circles). The position of the replication origin, OriC, is shown as a black rhombus. The middle panel displays the entire CPS-53 prophage. The lower panel focuses on the ECS009 sRNA. Information is given in a balloon when the reader clicks on any of the symbols. For example, if one of the candidate sRNAs is clicked, the name of the candidate sRNA and the average number of deep sequencing reads mapped to that candidate sRNA would appear. The arrows on the right-hand side represent: (a) experimentally determined TSSs (pink vertical lines) and RBRs (red vertical lines) obtained from the published literature [30–33]; (b) consensus sequences of the predicted promoters (pink arrowheads), predicted terminators (blue vertical lines) and predicted RBSs (green rhombi); (c) novel sRNAs detected by northern blot analysis (red boxed arrows), novel transcribed regions (white boxed arrows) and known transcribed regions (black lines); (d) CDSs (blue boxed arrows) and pseudogenes (grey boxed arrows); (e) deep sequencing data; and (f) sRNAs predicted by computational methods (white boxed arrows) and sRNAs predicted by experimental procedures (pink boxed arrows) in previous studies.