Figure 3

Classification of potential sRNA genes by their positions relative to annotated protein-coding sequences. Transcripts with a downstream CDS in less than 100 nt distance from their 3′-ends were designated as “mRNA leader”. The class also includes riboswitches and ORF containing transcripts already predicted and stored in the Rfam database [9]. The class “antisense transcripts” comprises three sub-types (i) cis-antisense RNAs (asRNA) that start within a CDS, (ii) transcripts antisense to a 5′-UTR, starting within 100 nt from the 5′-end of a CDS (as5′-UTR) and (iii) transcripts antisense to a 3′-UTR, starting within 60 nt from the 3′-end of a CDS (as3′-UTR). All remaining intergenic transcripts were categorized as trans-encoded sRNAs.