452 Cerebellum (2009) 8:448–453 Fig. 3. Alternative splicing of the senataxin gene. a The genomic structure of the senataxin gene is shown. Exons are boxed and introns are shown by a dashed line. Predicted transcription start sites are indicated by arrows. Suspected alternative exons are indicated by dotted boxes and the alternative splicing pattern is shown by a black line. The region of exons 23–26 is expanded to highlight the details of this alternative splicing. Supporting data from ESTs is shown in the table. Data compiled from the Alternative Splicing and Transcript Diversity database and the National Center for Biotechnology Information EST database. The number of ESTs with at least one splice junction represented is shown with the number of ESTs covering both splice junctions shown in parentheses. For events involving multiple exons, the number of transcripts including both junctions is shown for each exon. Asterisk: the pattern excluding exon 25b is the established pattern of senataxin splicing in the literature. b Confirmation of senataxin alternative splicing in human fetal and adult brain. Total RNA from human fetal (upper panel) or adult (lower panel) brain was used for RT-PCR with primers (black arrows) designed to amplify the suspected alternative splice products shown in the diagram. HPRT (489 bp) was used as a positive control. Products not detected in the initial PCR reaction were re-evaluated using a nested PCR reaction (underlined lanes) to detect lower abundance messages. Due to the size of the senataxin message, product 1517 can require nested PCR (gray arrows) to detect with oligo-dT primed cDNA. All PCR products were confirmed by sequencing. Molecular weight markers are indicated in base pairs. Asterisk: these additional bands are PCR artifacts (data not shown) produced by mispriming of the primer used to detect the exon 23—exon 25 splice junction