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Conditional knockout mouse models are indispensable for studying gene function in complex organ systems. The Short Conditional intrON (SCON) system accelerates the generation of such models by inserting the artificial SCON into a coding exon. SCON is designed to be spliced out after transcription, without affecting gene expression. Upon Cre activity, SCON is converted into the \u0394SCON allele which cannot be spliced out, introducing premature termination codons (PTCs) to inactivate the gene. Previous validation of the SCON system in mice has focused primarily on phenotypic outcomes. Here, we provide a molecular characterization of the SCON system in Cdh12\u2014a candidate gene implicated in kidney damage in CAKUT. We found that both Cdh12\n                    <jats:sup>SCON<\/jats:sup>\n                    and Cdh12\n                    <jats:sup>\u0394SCON<\/jats:sup>\n                    alleles caused unintended skipping of the exon downstream of the insertion site, culminating in a frameshift and PTC. Consequently, the Cdh12\n                    <jats:sup>SCON<\/jats:sup>\n                    allele led to a\u2009~\u200925% reduction in mRNA expression, indicating that it was not transcriptionally inert as designed. Despite unintended exon skipping, the Cdh12\n                    <jats:sup>\u0394SCON<\/jats:sup>\n                    allele still effectively suppressed mRNA expression. These findings highlight the importance of transcript-level characterization of engineered alleles prior to functional studies, as artefactual splicing events may occur across multiple gene-targeting strategies, including artificial intron-based conditional alleles as shown here.\n                  <\/jats:p>","DOI":"10.1007\/s11248-026-00496-7","type":"journal-article","created":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T20:57:33Z","timestamp":1777755453000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Molecular characterization of Cdh12-SCON conditional knockout mice reveals unexpected splicing changes"],"prefix":"10.1007","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4868-6844","authenticated-orcid":false,"given":"Mayke A. 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