• Human RUNX1a orthologs are only found in primates.• Alternative splicing of Runx1 involving exon 6 affects the pool size of hematopoietic stem cells.RUNX1 is an important transcription factor for hematopoiesis. There are multiple alternatively spliced isoforms of RUNX1. The best known isoforms are RUNX1a from use of exon 7A and RUNX1b and c from use of exon 7B. RUNX1a has unique functions due to its lack of C-terminal regions common to RUNX1b and c. Here, we report that the ortholog of human RUNX1a was only found in primates. Furthermore, we characterized 3 Runx1 isoforms generated by exon 6 alternative splicing. Runx1bEx6 2 (Runx1b without exon 6) and a unique mouse Runx1bEx6e showed higher colony-forming activity than the fulllength Runx1b (Runx1bEx6