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This article is part of the supplement: Selected articles from the Tenth Asia Pacific Bioinformatics Conference (APBC 2012)

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Identification of gene-oriented exon orthology between human and mouse

Gloria C-L Fu123 and Wen-chang Lin3*

Author Affiliations

1 Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan

2 Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan

3 Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan

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BMC Genomics 2012, 13(Suppl 1):S10  doi:10.1186/1471-2164-13-S1-S10

Published: 17 January 2012



Gene orthology has been well studied in the evolutionary area and is thought to be an important implication to functional genome annotations. 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 no any reported study on how to build exon level orthology in a whole genome scale. Therefore, it is essential to establish a gene-oriented exon orthology dataset.


Using a customized pipeline, we first build exon orthologous relationships from assigned gene orthologs pairs in two well-annotated genomes: human and mouse. More than 92% of non-overlapping exons have at least one ortholog between human and mouse and only a small portion of them own more than one ortholog. The exons located in the coding region are more conserved in terms of finding their ortholog counterparts. Within the untranslated region, the 5' UTR seems to have more diversity than the 3' UTR according to exon orthology designations. Interestingly, most exons located in the coding region are also conserved in length but this conservation phenomenon dramatically drops down in untranslated regions. In addition, we allowed multiple assignments in exon orthologs and a subset of exons with possible fusion/split events were defined here after a thorough analysis procedure.


Identification of orthologs at the exon level is essential to provide a detailed way to interrogate gene orthology and splicing analysis. It could be used to extend the genome annotation as well. Besides examining the one-to-one orthologous relationship, we manage the one-to-multi exon pairs to represent complicated exon generation behavior. Our results can be further applied in many research fields studying intron-exon structure and alternative/constitutive exons in functional genomic areas.