PURPOSE:To shed light on the pathogenicity of the mutations in the retinitis pigmentosa gene CERKL, the authors aimed to characterize its transcriptional repertoire and focused on the use of distinct promoters and alternative splicing in human and mouse tissues. METHODS:In silico genomic and transcriptomic computational customized analysis, combined with experimental RT-PCRs on different human and murine tissues and cell lines and immunohistochemistry, have been used to characterize the transcriptional spectrum of CERKL. In the mouse retina, Cerkl is detected primarily in ganglion cells and cones but can also be observed in rods. Cerkl is mainly cytosolic. It localizes in the outer segments of photoreceptors and in the perinuclear regions of some cells. RESULTS:An unexpected multiplicity of CERKL transcriptional start sites (four in each species) plus a high variety of alternative splicing events primarily affecting the 5' half of the gene generate >20 fully validated mRNA isoforms in human and 23 in mouse. Moreover, several translational start sites, compatible with a wide display of functional domains, contribute to the final protein complexity. CONCLUSIONS:This combined approach of in silico and experimental characterization of the CERKL gene provides a comprehensive picture of the species-specific transcriptional products in the retina, underscores highly tuned gene regulation in different tissues, and establishes a framework for the study of CERKL genotype-phenotype correlations.