Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors
Figure 2
Assigning AltAnalyze mRNA and protein annotations.
Theoretical transcripts with distinct exon compositions are shown. (A) Distinct alternative (Alt.) exon annotations for five mRNA transcripts, where the filled boxes are sequences retained in the processed mRNA transcript. Black filled boxes are exons common to all isoforms (constitutive). AltAnalyze considers all alternative exon annotations as AS except for alternative-N-terminal exons (expressed through alternative promoter selection). (B) All pairs of mRNA transcripts that do or do not align to an exon array probe set are compared to identify a single pair of competitive isoforms that minimally differ in exon composition. Curved arrows indicate all possible competitive transcript comparisons. The top selected competitive isoforms (dashed box) have the fewest exon differences and have the most exons in common. AltAnalyze selects this transcript pair for analysis of downstream protein domain/motif composition, after corresponding protein sequences are selected. (C) Protein domains and motifs differing between competitive isoforms. Exons for the two transcripts are labeled in order, 5′ to 3′, with protein sequence and Uniprot features (UPF) or InterPro regions (IPR) corresponding to each exon displayed above or below them. Yellow filled boxes indicate domains and motifs differencing between the competitive isoforms. (D) Domains and motifs directly aligning to a probe set's genomic position. A theoretical probe set aligning to the intron of a gene is shown. InterPro domains/motifs whose genomic position (genomic exon start and exon end position) overlaps with a given probe set (genomic start and end position) are shown with a yellow filled box. Rather than comparison of two protein sequences with the competitive isoform analysis, only a single protein sequence is required for the direct genomic alignment method.