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DNA Research Advance Access originally published online on October 17, 2006
DNA Research 2006 13(4):135-140; doi:10.1093/dnares/dsl007
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© The Author 2006. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Short Communication

Negative Correlation of G+C Content at Silent Substitution Sites Between Orthologous Human and Mouse Protein-Coding Sequences

Naoki Takahashi and Hiroshi Nakashima*

Department of Clinical Laboratory Science, Graduate Course of Medical Science and Technology Division of Health Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa 920-0942, Japan

We conducted a genome-wide analysis of variations in guanine plus cytosine (G+C) content at the third codon position at silent substitution sites of orthologous human and mouse protein-coding nucleotide sequences. Alignments of 3776 human protein-coding DNA sequences with mouse orthologs having >50 synonymous codons were analyzed, and nucleotide substitutions were counted by comparing sequences in the alignments extracted from gap-free regions. The G+C content at silent sites in these pairs of genes showed a strong negative correlation (r = –0.93). Some gene pairs showed significant differences in G+C content at the third codon position at silent substitution sites. For example, human thymine-DNA glycosylase was A+T-rich at the silent substitution sites, while the orthologous mouse sequence was G+C-rich at the corresponding sites. In contrast, human matrix metalloproteinase 23B was G+C-rich at silent substitution sites, while the mouse ortholog was A+T-rich. We discuss possible implications of this significant negative correlation of G+C content at silent sites.

Key words: G+C content variation; human–mouse orthologs; nucleotide substitutions in synonymous codons

*To whom correspondence should be addressed. Tel. +81-76-265-2582, Fax. +81-76-234-4360, E-mail: naka{at}kenroku.kanazawa-u.ac.jp

Communicated by Hiroyuki Toh


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S. K. Bag, S. Paul, S. Ghosh, and C. Dutta
Reverse Polarization in Amino acid and Nucleotide Substitution Patterns Between Human Mouse Orthologs of Two Compositional Extrema
DNA Res, September 25, 2007; (2007) dsm015v1.
[Abstract] [Full Text] [PDF]


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