The cerebral cortex is one of the brain structures with the highest cell type diversity. Yet the mechanisms underlying this diversity remain elusive. While various parameters such as gene expression and chromatin accessibility can be assessed within these cells, a dimension of variability that has been largely overlooked is isoform diversity. Pax6 is a fundamental transcription factor during development of the nervous system, especially eye and cortical development. It is also a largely studied homeobox gene, but there is limited knowledge about its isoforms and their specific roles. We studie