Non3nExonFinder: transcript-aware identification of shared non-triplet coding exons

Selection of an appropriate coding exon is an important upstream step in exon deletion-based loss-of-function strategies, particularly for genes with multiple transcript isoforms. However, manual comparison of exon structures across multiple transcripts can be time-consuming and may overlook transcript-specific differences in exon boundaries and coding sequence (CDS) composition. Non3nExonFinder was developed as an interactive R/Shiny-based tool for identifying shared non-triplet coding exons across user-defined human or mouse NCBI RefSeq protein-coding transcripts. Non3nExonFinder evaluates exon/CDS annotations and coding contributions for each transcript, identifies common exons with identical genomic boundaries, and prioritizes candidates based on CDS-only status and coding-length divisibility by three. Non-triplet CDS-only exons that are internal in all selected transcripts are classified as high-confidence candidates. Independent reconstruction from the original RefSeq GTF files across 80 genes (40 human and 40 mouse), comprising 6,848 transcript-specific exon instances, showed complete concordance with Non3nExonFinder outputs, with exact recovery of all candidate sets. Non3nExonFinder provides a reproducible upstream framework for transcript-aware prioritization of exon-deletion targets.