{
  "abstract": "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.",
  "abstract_shown": true,
  "affiliations": [
    "GEM divison, Macrogen Inc."
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "S.-Y. Lee"
    },
    {
      "affs": [
        0
      ],
      "name": "J.-H. Lee"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/cgk84ykk9sa84.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.22.753378",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.22.753378v1.full",
  "id": "cgk84ykk9sa84",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.22.753378v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1312|RNA Research and Splicing"
    ]
  ],
  "openalex": "W7214601170",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.22.753378v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-22",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/cgk84ykk9sa84.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:24:56Z",
      "native_id": "10.64898/2026.09.22.753378",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.22.753378v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Non3nExonFinder: transcript-aware identification of shared non-triplet coding exons",
  "title_text": "Non3nExonFinder: transcript-aware identification of shared non-triplet coding exons",
  "type": "preprint",
  "updated_at": "2026-10-30T12:24:56Z",
  "url": "https://research.draconitic.com/paper/cgk84ykk9sa84",
  "venue": "bioRxiv",
  "versions": []
}