Characteristics of TIC events. (A) Comparison of TIC gene pairs found in previous EST-based surveys and those found by RNA-Seq in this study. (B) Distribution of TIC events across tissues. Only TIC events with multiple supporting reads are included. HBR = human brain reference, UHR = universal human reference. (C) Coding potential of TIC events. The label "Full CDS" indicates that the coding region (CDS) extends from the original transcription start site (TSS) of the 5' gene and to the original stop codon of the 3' gene; "3' shift" signifies a frameshift in the 3' gene; "New TSS" indicates that the TIC breakpoint occurs before the original TSS of the 5' gene and a new TSS is predicted from the longest open reading frame; "TLE" indicates that termination occurs in the last exon of the transcript; and "PTC" indicates premature termination codon, subjecting the transcript to nonsense-mediated decay. (D) Distribution of TIC splice distances. (E) Distribution of splice distances in the artificial exon-exon junctions. (F) Predicted effect on domains. Separate results are presented for TICs having a PTC, or having a TLE despite a new TSS or 3' frameshift, or having a full CDS. Each pair of bars show the effect on the 5' (left) and 3' (right) domains. "ND" indicates that no domain was originally present in the 5' or 3' gene; "Null" indicates no intersection of the predicted TIC domains with the original domains; "Subset" indicates that at least one, but not all domains were preserved in the TIC; and "Cover" indicates all domains were preserved. (G) Distribution of expression levels in 5' genes with observed TICs downstream compared to those without. (H) Distribution of expression levels in 3' genes with observed TICs compared to those without. For panels F and G, distributions are taken over genes with at least one observed intragenic splice in a given sample and with a potential TIC exon within 200,000 bp in the downstream or upstream direction, respectively.