Fig. 3

The case studies for AnnoLnc. a-b The case study of lncRNA SRA. In the interactive secondary structure plot with vertebrate phyloP scores as the color overlay, two sub-structures are very easy to be identified because most bases are colored red. a is a hairpin region that corresponds to the most conserved H2 sub-structure highlighted by Novikova et al. [42]. b is a three-way junction hairpin region that is very similar to the conserved regions H15, H16 and H17 verified by Novikova et al. [42]. c-e The case study of lncRNA H19. c is a summary of the annotation results, which helps users quickly grasp the essentials. d is the expression profile of H19 in normal samples. It has the highest expression in “skeletal muscle”. e is the predicted GO terms based on positively correlated coding genes in normal samples. The terms are all muscle related. f The integrative view of lncRNA CCAT2 in the UCSC genome browser for annotations at the transcript level. It is easy to determine that rs6983267 is within the seed binding site of the miRNA family miR-148ab-3p/152