Fig. 15

Clcc1 transcripts detected in the retina. a RNAseq profiles expressed in FPKM of the three Clcc1 transcripts detected in retinal and RGC-derived samples of Brn3a and Brn3b WT and KO mice at P3. b Predicted Clcc1 splicing variants. Exon and splicing connection annotations (labelled as in Fig. 14), for five distinct transcript variants are annotated: NM_145543, NM_001177771, NM_001177770, XM_006501416, XM_011240107. Red arrows show the positions of diagnostic primers (see also Table 2). Translation start sites are in exons e1d, e1e and e3 (ATGs indicated). c Confirmed Clcc1 splicing variants. Purple line indicates a novel transcript suggested by our RT-PCR analysis. d RT-PCR reactions from P3 retina RNA. Primer pairs as in b. Pairs marked with a star indicate negative or nonspecific (weak bands of incorrect size) reactions. Duplicates are shown for each primer combination. For expected product sizes, see Table 2. All bands generated by RT-PCR were gel-extracted, subcloned and sequenced for confirmation. e in situ hybridization in retinal sections from WT and Brn3a-KO retinas at five developmental stages. RNA probes were targeted against exons that are specific for different transcript variants. For pr2 + pr9, the probe was generated from the longer product (see panel d), and is predicted to detect both NM_145543 (green) and XM_006501416 (red) isoforms. Probe generated from pr7 + pr8 targets exon2 and therefore detects the newly identified transcript. Scale bar – 50 μm