In order to identify a novel transcript of BRPF1 (BRPF2), a clone separated from mouse cDNA library was sequenced and submitted to GenBank. The expressions of BRPF1 and BRPF2 in different mice tissues were detected using RT-PCR and Northern blotting assays. The preliminary protein functions and conservative domains were analyzed by bioinformatic methods. The results indicated that BRPF2 was a novel transcript of BRPF1. Both BRPF1 and BRPF2 transcripts could be detected in most mice tissues, including liver, embryo, epididymis, testis, ovary and muscle. However, only BRPF2 transcript could be detected in the spleen. BRPF1 mRNA encoded 1 246 aa and the predicted molecular mass was 140 kDa, while BRPF2 encoded 442 aa, partly owing to the absence of a new stop codon. The results of CDD analysis suggested that BRPF2 lost the bromodomain and the PWWP domain compared to BRPF1. Because the bromodomain and the PWWP domain are the critical structures of BRPF1 to interact with histones and recruit the other transcriptional factors, BRPF2 (without these two critical domains) may serve as a negative regulatory factor of BRPF1 and be involved in the chromosome remodeling and transcriptional regulating.