Computer analysis of distribution of putative cis- and trans- regulatory elements in milk protein gene promoters

Multiple alignment of 28 milk protein gene promoters belonging to seven protein superfamilies is described. In these gene promoters three groups of common motifs were found: group I—specific for all milk protein gene promoters; group II—specific only for one gene superfamily; and group III—motifs shared by several gene superfamilies. Motifs of group I and III do not have any preferential location in the promoters, while group II motifs are located in the proximal part, from −36 to −224. Milk protein gene promoters were analysed for presence of putative binding sites for nine transcription factors important for the expression of this group of genes. The transcription factor binding sites for C/EBP, CTF/NF1, MAF and MGF were found in all promoters investigated. The set of putative transcription factor binding sites or response elements for GRE, IRE, PMF, STR and YY1 is unique for every gene superfamily.