Fig. 4

Intron retention in clbn is specific to U12-type introns and highly variable. (A) Scatterplot of normalized intron expression derived by RNAseq for reference (Refseq) introns (gray dots) and U12-type introns (red dots). U12-type introns lie almost entirely above the midline representing equal expression, indicating enhanced intron retention in clbn. Intron expression is given in RPuKM. (B) To quantitate U12-type intron retention in individual transcripts, we defined an intron retention coefficient, which calculates intron retention relative to transcript level. (C) Comparison of the median log₂ of the IRCs for Refseq introns and U12-type introns between WT and clbn demonstrates that the clbn splicing defect is specific to U12-type introns. See also Fig. S4. Statistical significance was determined by Student t test. (D) University of California at Santa Cruz genome browser views of three genes with high, intermediate, and low IRCs. ccdc43 shows a high IRC of 0.97, dcp2 an intermediate IRC of 0.41, and hsbp1 shows a low IRC of 0.05.