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Open Access Highly Accessed Open Badges Research article

Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs

Hirokazu Chiba1, Riu Yamashita1, Kengo Kinoshita1 and Kenta Nakai12*

Author Affiliations

1 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

2 Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Agency (JST), Science Plaza, 5-3 Yonban-cho, Chiyoda-ku, Tokyo 102-8666, Japan

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BMC Genomics 2008, 9:152  doi:10.1186/1471-2164-9-152

Published: 2 April 2008



Interspecies sequence comparison is a powerful tool to extract functional or evolutionary information from the genomes of organisms. A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial.


We examined promoter conservation as well as protein conservation for 6,901 human and mouse orthologous genes, and observed a very weak correlation between them. We further investigated their relationship by decomposing it based on functional categories, and identified categories with significant tendencies. Remarkably, the 'ribosome' category showed significantly low promoter conservation, despite its high protein conservation, and the 'extracellular matrix' category showed significantly high promoter conservation, in spite of its low protein conservation.


Our results show the relation of gene function to protein conservation and promoter conservation, and revealed that there seem to be nonparallel components between protein and promoter sequence evolution.