Fig. 2

Three examples of novel ncRNAs detected using transcriptome and translatome analysis. A genomic area is visualized in Artemis 15.0.0 [43]. In the lower part of the panels, the genome (shown as grey lines) is visualized in a six-frame translation mode. Numbers given between the grey lines indicate the genome coordinates. On top of the forward strand are three reading frames and on the reverse DNA strand are three further reading frames. Each reading frame represented is visible by the indicated stop codons (vertical black bars). Annotated genes are shown in their respective reading frame (turquoise arrows) and also on the DNA strand itself (white arrows). The gene name is written below each arrow. Any protein-coding ORF must be at least located between two black bars, with the downstream stop codon being the translational stop. In the upper part of the panels, the DNA is indicated by a thin black line and the sequencing reads matching to the forward or reverse strand are shown above or below this line. The sequencing reads from the footprint (yellow line) and transcriptome (blue line) sequencing are shown as coverage plot, respectively. The pink shaded area in the coverage plot corresponds to the novel ncRNAs, which are drawn in by red arrows. Novel ncRNAs were identified by their very low RCV, thus, hardly any footprint reads (in yellow) but a number of transcriptome reads (in blue; see Table 2). Known ncRNAs are indicated on the DNA by a bright green arrow. Since ncRNAs supposedly do not contain a protein-coding ORF, these genes are only shown on the DNA. a ncR3665651. b ncR3690952. c ncR1085800