In Comparative Genomics we compare an unknown gene with some other known genes, for better inference of biological properties of that unknown gene. Identification of Gene Orthology Relation is the most important task of Comparative Genomics, as they tend to preserve similar molecular and biological functions. Thus if we can establish orthology relationships between two genes, we can obtain valuable evolutionary history of the two genes. However, with advanced sequencing depth and expansion in transcriptome data, genes are no longer the proper units for interrogation in functional conservation, evolutionary events, and expressional patterns, especially in the field of alternative splicing. As the accumulation of transcriptomic data, alternative splicing is taken into account in the assignments of gene orthologs and the orthology is suggested to be further considered at transcript level. Whether gene or transcript orthology, exons are the basic units that represent the whole gene structure; however, there is not much reported study on how to build exon level orthology in a whole genome scale. Therefore, it is essential to establish a transcription oriented gene orthology algorithm.