What should I choose to best specify background sequences when looking for motifs under peaks in Homer?

Question

[a.rex]

I have a file with a set of intervals (corresponding to ATAC peaks) that are within introns or close to a specific type of gene (i.e. stem cell genes). I have another file of intervals for peaks that are within introns or close to another type of gene (i.e. genes expressed in the liver). I wish to look at the motifs under these two different peak sets? But what should I specify as background for homer? Can I for example give exons? Or look at motifs specific to one gene type and give it the peaks of the other gene type as background?