MOTIVATION: Incomplete gene models negatively impact single-cell gene expression quantification. This is particularly true in non-model species where often gene 3' ends are inaccurately annotated, while most scRNA-seq methods only capture the 3' transcript region. This results in many genes being incorrectly quantified or not detected. RESULTS: GeneExt leverages scRNA-seq data to refine gene annotations. We exemplify GeneExt usage and its impact on the gene expression quantification of eight non-model organism single-cell atlases. By extending and homogenizing gene annotations, our tool will help improve biological interpretation and cross-species comparisons of cell type expression atlases. AVAILABILITY: GeneExt is available at https://github.com/sebepedroslab/GeneExt (DOI: https://doi.org/10.5281/zenodo.18712940) under a GNU General Public license, together with test data and usage instructions.