In the third step of the α-oxidation of 3-methyl-branched fatty acids such as phytanic acid, a 2-hydroxy-3-methylacyl-CoA is cleaved into formyl-CoA and a 2-methyl-branched fatty aldehyde, which is regulated by 2-hydroxypanthyl-CoA lyase HPCL2. Using shot-gun sequencing technique, the genome sequence of the gene (HPCL2) code for the lyase was obtained. The gene is 40 829 bp in genome size including 17 exons and 16 introns, with an average 116 bp in exon size and 2 429 bp in intron size. The different transcriptional isoforms were also investigated by using method of alternative splicing in silica. In order to investigate the level of alternative splicing and to search for novel splice variants, total 213 ESTs derived from 29 different tissues were collected and aligned against the genome sequence of the gene. 17 ESTs were found having different splicing type that could be classified into three types of alternative splicing. 14 of the ESTs were detected to have exon skipping, 2 intron not spliced and 1 splice site shift. The data suggested that exon skipping was possibly one of the major mechanisms of transcription regulation of HPCL2 gene.