Examples of human-specific protein-coding exons with novel splice sites. In each part, the top panel shows the exonic structures of the human DYNC2LI1 (A), LMAN1L (B), CLK1 (C), and PAX3 (D) gene transcripts. The transcript isoform with a novel protein-coding exon is marked by an arrow at the right. A multiple sequence alignment of the orthologous segments from the human, chimpanzee, and orangutan genomes is shown below each panel (see Additional file 2: Tables S2A and S2B for the alignment of all species examined). The coding regions of the human-specific exon is in uppercase. The novel splice sites (gt and ag), start codon (ATG), and stop codon (TAA) in humans are highlighted in black. The conserved ancestral splice sites, stop codon (taa in D), and human cryptic splice sites are highlighted in grey. The underlined sequence in the human PAX3 (D) gene indicates the intronized region. Dots indicate that the sequences are the same as the human sequence.