Validated circadian exons show a variety of acrophases in alternative splicing and transcript-level expression. (a) UCSC genome browser [73,79] screen-shots. Top: the structure of the Refseq mRNA and the location of the identified cassette exon for Pcsk4 (genome assembly mm9). Bottom: the closer genomic context of the identified exon, including the location of core exon-array probesets and phastCons conservation . (b) Upper panel: plot of the log2 FIRMA score (black line, n = 3, standard error of the mean (SEM)) and alternative splicing (red line, n = 6, SEM) through time. Lower panel: plot of the alternative splicing (red line, n = 6, SEM) and transcript-level expression (blue line, n = 6, SEM) through time (GE, gene expression). (c) Scatter-plot relating the acrophase in transcript-level expression to the acrophase in alternative splicing for each of the validated exons. Acrophase is the circadian time of peak expression. Peak expression was defined as the circadian time of the largest positive fold change versus CT0. Decr1 is not included in this plot as its transcript-level expression was not rhythmic.
McGlincy et al. Genome Biology 2012 13:R54 doi:10.1186/gb-2012-13-6-r54