Fig. 4

Five Examples of YCAY Cluster Conservation and RT-PCR Analysis of Associated Exons Multiple nucleotide alignment of five YCAY clusters. Introns are in lowercase, exons in uppercase, YCAY silencer motifs in bold blue, and YCAY enhancer motifs in bold red. The abbreviations for the following species are used: H. sapiens (hs), M. musculus (mm), M. domestica (md), G. gallus (gg), and D. rerio (dr). Next to the alignment are RT-PCR data from wild-type and Nova2 knockout brain, and below are RT-PCR data from chicken and zebrafish brain and liver and diagrams of the splicing pattern. Blue represents silencing, red enhancement by Nova, rectangles represent exons, and circles represent the position of Nova binding.
(A) Nova-dependent splicing silencer in neogenin (Neo1) pre-mRNA and brain-specific splicing of exon 27 conserved.
(B) Nova-dependent splicing silencer in syntaxin binding protein 2 (Stxbp2/Munc18–2) pre-mRNA and brain-specific splicing of exon 3 are not conserved.
(C) Nova-dependent splicing enhancer in protein tyrosine phosphatase, receptor type, F (Ptprf) pre-mRNA and brain-specific splicing of exon 6a are conserved.
(D) Nova-dependent splicing enhancer is not conserved in zebrafish amyloid beta precursor-like protein 2 (Aplp2) pre-mRNA, in contrast with conserved brain-specific splicing of exon 12a.
(E) Nova-dependent splicing enhancer in suppression of tumorigenicity 7 (St7) pre-mRNA and brain-specific splicing of exon 12a are not conserved.
(F) The diagram obtained from the human genome browser shows the human St7 mRNAs that either contain or exclude the alternative exon 12a. Underneath, alignment of vertebrate genomes demonstrates lack of conservation in the region containing exon 12a in the genomes of oppossum, chicken, and zebrafish.