Alternative splicing (AS) is one of the most significant components of the functional complexity of the eukaryote genome, increasing protein diversity, creating isoforms, and affecting mRNA stability. Recently, whole genome sequences and large microarray data sets have become available, making data integration feasible and allowing the study of the possible regulatory mechanism of AS in rice (Oryza sativa) by erecting and testing hypotheses before doing bench studies. We have developed a new strategy and have identified 215 rice genes with alternative expression isoforms related to insertion and deletion (indel) between subspecies indica and subspecies japonica. We did a case study for alternative expression isoforms of the rice peroxidase gene LOC_Os06g48030 to investigate possible mechanisms by which indels caused alternative splicing between the indica and the japonica varieties by mining of array data together with validation by RT-PCR and genome sequencing analysis. Multiple poly(A) signals were detected in the specific indel region for LOC_Os06g48030. We present a new methodology to promote more discoveries of potentially indel-caused AS genes in rice, which may serve as the foundation for research into the regulatory mechanism of alternative expression isoforms between subspecies.