Figure 2.

Characterisation of HK-lincRNA and TS-lincRNAs (A) Mean PhyloP²⁴ conservation scores across exonic nucleotides only, for each lincRNA transcript. (B) SNP density (total number of mutations/total length of the exonic region) in HK-lincRNAs and TS-lincRNAs. Mutation data were obtained from dbSNP (v137)²⁵. (C) Variability of HK-lincRNA and TS-lincRNA homologues. Homologues to human HK- and TS-lincRNAs were identified using nucleotide-BLAST²⁶, and expression levels calculated across nine different tissues in five vertebrate species⁶⁰. Heatmap represents an unsupervised clustering of CV values for each lincRNA (columns: orange: HK-lincRNAs; grey: TS-lincRNAs) in each species (rows). (D) Annotations of 11 major repeat elements were obtained from Repbase⁷⁴ database to calculate coverage of repeat elements in exonic regions of lincRNA transcripts. (E) Minimum free energy (MFE) for each lincRNA was calculated using Randfold²⁹ as an indicator of secondary structure stability. Histogram represents distribution of likelihood that each HK-linRNA or TS-lincRNA is more stable than expected by chance. p-values were estimated by comparing to a null distribution generated by permuting the sequences (n = 1000), whilst preserving dinucleotide compositions.