Figure 3.

Analysis of selected novel ncRNA candidates by northern-blotting. (A) Expression and sizes of a subset of selected candidates was analysed by northern-blotting. Sizes of ncRNAs, as deduced by northern blotting, appeared in several cases larger than the corresponding cDNAs sizes (see Supplementary Table S1), reflecting that some sequenced clones might correspond to fragments of larger new ncRNA transcripts. hs: human candidate; mm: mouse candidate; AS: antisense; S: sense; SR: sense to repeats; ASR: antisense to repeat. (B) Predicted secondary-structures of putatively novel ncRNA candidates. Structures were predicted using the program RNAfold from the Vienna package (69). When the reads were too short to be folded, 50-nt up- and down-stream of the read were added to the sequence and locally stable structures containing the read were looked for. The corresponding structures were then folded, the grey backbone representing the read itself. The 0–1 color scale represents the base-pair probabilities.