Fig. 4
Conserved sequence motifs in tapRNAs. a Comparison of conservation between tapRNAs, lncRNAs and protein coding genes. The curves are kernel density estimation (KDE) of conservation scores calculated from the phastCons multiple alignments of 100 vertebrate species. b Clustered heatmap of conserved domains in transcribed tapRNAs. Aligned sequences (shown in red) in 279 non-redundant tapRNA isoforms are clustered (Euclidean distance). Sixteen minor clusters were identified and grouped into four major clusters. Each minor cluster’s centroids are shown with the number of tapRNAs belonging to each minor cluster. Thirty-nine tapRNAs (top group, blue) have a more than ~ 73 % conserved domain in their transcribed sequences. Functional category annotation search reveals that tapRNAs of the top group are highly related to developmental proteins or Homeobox proteins. In contrast, 76 tapRNAs of the bottom cluster (grey) do not have any sequence conservation and do not show significant common functionality. There are also some minor groups in which position-specific conservation is clearly present (e.g. 5′ end-specific or 3′ end-specific). c Example of conserved domains in a tapRNA. RNA sequence alignments of regions conserved between human and mouse HNF6-US-S tapRNA are represented in red. d Enriched RNA-binding motif in conserved domains of tapRNAs. Thirty-two significantly enriched 8-mer motifs (Additional file 2: Figure S13b; p value 1 × 10−4) in conserved domains in tapRNAs are identified and clustered into ten consensus motifs. De novo motif analysis discovers known RNA-binding proteins (RBPs) with matching binding consensus motifs. Seven out of ten consensus motifs are part of binding motifs of zinc finger proteins