Non3nExonFinder: transcript-aware identification of shared non-triplet coding exons
- 1GEM divison, Macrogen Inc.
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.
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BibTeX
@misc{lee2026non3nexonfinder,
title = {{Non3nExonFinder: transcript-aware identification of shared non-triplet coding exons}},
author = {S.-Y. Lee and J.-H. Lee},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.22.753378},
url = {https://www.biorxiv.org/content/10.64898/2026.09.22.753378v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Non3nExonFinder: transcript-aware identification of shared non-triplet coding exons
AU - S.-Y. Lee
AU - J.-H. Lee
PY - 2026
DA - 2026/09/22
PB - bioRxiv
DO - 10.64898/2026.09.22.753378
UR - https://www.biorxiv.org/content/10.64898/2026.09.22.753378v1
AB - 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.
ER -