Figure 3

Figure 3. Atxn1a gene in zebrafish. (A) Schematic presentation of the structure of atxn1a gene on chromosome 19 plus strand. The gene consists of eight exons (E1, E1′, E2, E2′, E3, E3′, E4, and E5) containing the coding sequence (black boxes) in the last two exons E4 and E5. (B) Four different transcripts (X1–X4) are predicted in the NCBI database. The atxn1a X1 variant is transcribed from five exons (E1, E2, E3, E4 and E5; grey boxes) such as the X2 variant with the alternative first exon E1′ (green box). The X3 variant contains the alternative exon E3′ (blue box) first, followed by E4 and E5. The X4 transcript variant is encoded by the alternative exon E2′ (orange), followed by sequences from exons E3, E4, and E5. (C) Experimental verification of predicted atxn1a X1–X4 variants. Four different upper primers (UX1a, UX2a, Ux3a, and Ux4a), specific for the alternative exons (shown in A and B), in combination with a lower primer (LX1-4a), specific for exon E4 sequence, were designed for RT-PCR of zebrafish cDNA as template to amplify the 5′ end of each variant (left panel). The lengths of the amplicons (right panel) and the following sequencing confirmed the predicted atxn1a X1–X4 transcript variants.