Fig. 3.

Most mouse lncRNAs are not conserved in sequence or in transcription. a Pan-vertebrate conservation is low in promoters and exon sequence, as indicated, for a generic lncRNA locus. Y-axis: conservation (phastCons) scores sampled across 877 mouse multi-exon lncRNAs (reproduced from [82]). b An exception that establishes a more general rule: expression conservation of a lncRNA (AK082072) across mouse and marsupial (Monodelphis domestica) brain development (reproduced from [82]). c Normalised divergence (X-axis; d/d _AR ) and diversity (Y-axis; π/d) of lncRNAs whose expression is restricted to mouse, eutheria, theria, mammalia, amniota and tetrapoda where the area of a circle indicates relative lncRNA numbers (7306 in the mouse-only set). Divergence is the mouse-rat median substitution rate normalised by the local neutral mutation rate; diversity is the mouse median nucleotide diversity divided by local mouse-rat divergence. Increasing conservation is indicated by darker background hues. For comparison, significantly reduced divergence and diversity values are evident for protein-coding exons (shown in red); in general, tissue-specific transcription of protein-coding orthologues is highly conserved [83]. The diversity (π/d) of only eutherian-specific lncRNAs differs significantly from proposed neutral sequence. For a description of the data, definitions of d, d _AR and π, and further details see [32]. Median d/d _AR divergence estimates of promoter-like (p) and enhancer-like (e) lncRNA exons [33] are indicated by vertical blue and green dotted lines, respectively