ZFIN ID: ZDB-FIG-140806-2
Markmiller et al., 2014 - Minor class splicing shapes the zebrafish transcriptome during development. Proceedings of the National Academy of Sciences of the United States of America   111(8):3062-3067 Full text @ Proc. Natl. Acad. Sci. USA
ADDITIONAL FIGURES
PHENOTYPE:
Fish:
Observed In:
Stage: Day 4

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.

Gene Expression Details No data available
Antibody Labeling Details No data available
Phenotype Details
Fish Conditions Stage Phenotype
rnpc3s846/s846 standard conditions Day 4 mRNA splicing, via spliceosome process quality, abnormal
Acknowledgments:
ZFIN wishes to thank the journal Proceedings of the National Academy of Sciences of the United States of America for permission to reproduce figures from this article. Please note that this material may be protected by copyright. Full text @ Proc. Natl. Acad. Sci. USA