Most “Dark Matter” Transcripts Are Associated With Known Genes
Figure 5
Seqfrags with read counts above background are conserved at the sequence level.
Distribution of maximum PhastCons conservation score measured across seqfrags mapping to trimmed intergenic regions in the pooled (A) human and (B) mouse RNA-Seq samples as a function of read coverage (red). PhastCons scores were obtained from the UCSC genome browser and reflect the degree of conservation in multiple alignments of the human and mouse genomes with 18 and 20 other mammalian species, respectively. Conservation scores obtained from a random shuffling of seqfrag positions within trimmed intergenic regions are shown in gray for comparison. (C and D) Bar plots indicating the PhastCons score distribution for seqfrags mapping to different genomic regions. The bars are color-coded according to the class of seqfrags (legend), with the score distribution for randomly mapped seqfrags shown in gray.