DeepGCF learns the genomic conservation at the functional level between human and pig. The model was trained using 386 and 374 epigenome and gene expression profiles from human and pig, respectively. A core set of genomic regions identified as functionally conserved plays key roles in gene regulation and complex traits in humans. The codes used to develop the model can be found in the folder 'src', and those used to conduct the data analyses are in the folder 'analyses'.