“…To identify potential TFs driving conserved alternative promoter use in the three species, FIMO ( Grant et al, 2011 ) was used to predict the locations of TF-binding motifs in the MLT1F1 sequences, revealing a core “GTCATAAAA” sequence shared by all three species, predicted to bind to 14 TFs (Supplementary Figure S8). Among these TFs, HOX proteins are crucial for testicular and epididymal physiological functions and can affect male fertility ( Ferguson & Agoulnik, 2013 ; Topaloğlu et al, 2021 ; Xian et al, 2015 ). Species-conserved TE-derived alternative promoters were not limited to the same subfamily of TEs, i.e., different TE subfamilies acted on the same gene across the three species.…”