Graphical illustration of the experimental design. Experimental sow groups compared natural mating (NM) with cervical artificial insemination (AI) of semen of the sperm-peak fraction (control 1), of sperm-free SP from the sperm-peak fraction (control 2), of sperm-free SP from the whole ejaculate (control 3) or of saline BTS semen extender (control 4, sham–AI). Mucosal samples from the endocervix (Cvx), endometrium (distal: D-Endom or proximal: P-Endom) and the utero-tubal junction (UTJ) were surgically retrieved 24 h later and analyzed. NM was first compared to all experimental controls to isolate those DEGs not affected by semen, SP or AI-vagino-cervical stimulation, e.g., those being exclusively affected by copulation.