WHRN transcript isoforms identified by IsoQuant analysis compared to known isoforms from the literature. (A) The GENCODE reference transcript is depicted at the top in green, followed by human WHRN transcript isoforms from literature in blue (van Wijk et al. 2006) and the murine transcript isoforms in gray (Mburu et al. 2003; Belyantseva et al. 2005; Ebrahim et al. 2016). The WHRN IsoQuant transcripts are depicted in red. The light green, blue, gray, and red colors indicate the UTR and the dark green, blue, gray, and red colors indicate the ORF of each transcript. Differences between the IsoQuant transcripts and the GENCODE reference transcript are highlighted in gray boxes. (B) Relative expression of WHRN isoforms based on literature in either the retina or the cochlea. (C) The TPM (based on data set 1) for each IsoQuant transcript isoform are presented for the three individual samples. (D) The predicted 2D protein domain architecture of the encoded WHRN protein isoforms. Light blue and green boxes highlight the difference between the WHRN reference isoform and the protein isoform encoded by exon 7B-containing transcript13724.Chr9.nic. (E) AlphaFold2 3D protein predictions of two WHRN isoforms; reference isoform ENST00000362057.4 in green and transcript13724.Chr9.nic in red, with the alpha helix encoded by the novel exon 7B highlighted in blue. (F) RT-qPCR analysis of the expression of the WHRN transcripts containing exon 7B, and WHRN transcripts with intron 4 retention, relative to all WHRN transcripts containing exons 8–9.
