The Commd1 gene is imprinted in the adult mouse brain and is predominantly expressed from the maternal allele. A paternally expressing imprinted gene, U2af1-rs1, resides in the first intron of Commd1 in an antisense orientation. We found that RNA polymerase II phosphorylated at serine 2 of the carboxyl-terminal domain repeats, a marker of transcription elongation, is enriched on the paternal allele than on the maternal allele in the Commd1 promoter. The Commd1 promoter harbours no allelic differences in DNA methylation and histone modifications. These results strongly suggested that imprinting of Commd1 is generated by interference with paternal Commd1 transcription by the oppositely directed U2af1-rs1 transcription.