Identification of a new non-coding exon and haplotype variability in the cattle DEFB103 gene

•A new non-coding exon 1a and an intron were identified in the cattle DEFB103 gene.•At least two complete copies of DEFB103 with an ATG start codon were identified.•Two small deletions were present in both cloning and assembly sequences.

The DEFB103 gene is a member of the β-defensin gene family. In this study, we applied multiple sets of primers to characterize the DEFB103 transcript. RT-PCR was used to determine the cDNA boundaries and it indicated that the cDNA start point is at least 514 bp before the start codon and not further than 678 bp. In addition, the length of the 3′UTR was determined to be at least 53 bp after the stop codon. Seven SNPs were located in the 5′UTR, and comprised 4 different haplotypes in genomic DNA. Using these haplotype data, it could be proven that at least two complete copies of DEFB103 with an ATG start codon are present in cDNA in most cattle. Additionally haplotype data indicated that there are also multiple incomplete copies in most cattle. A non-coding exon 1a, and a 261 bp intron 1a were identified in cattle, and subsequently predicted in sheep and goats. DEFB103 sequence assemblies and partial cloning sequences revealed two types of deletion (4 bp and 8 bp) in the 5′UTR. These observations could prove that these copies are not assembly artifact.