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Comparative and Functional Genomics
Volume 2007 (2007), Article ID 21676, 7 pages
Research Article

Significant Comparative Characteristics between Orphan and Nonorphan Genes in the Rice (Oryza sativa L.) Genome

1Department of Biology, An-Kang University, An-kang, Shaan-Xi 725000, China
2Rice Research Institute, Si-Chuan Agricultural University, Wen-Jiang, Cheng-Du, Si-Chuan 611130, China

Received 25 September 2006; Accepted 16 April 2007

Academic Editor: Stephen Oliver

Copyright © 2007 Wen-Jiu Guo et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare) proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure than nonorphan genes. Orphan genes generally have shorter protein lengths and intron size, and are faster evolving. Additionally, orphan genes have fewer PROSITE patterns with larger pattern sizes than those in nonorphan genes. The average microsatellite content and the percentage of trinucleotide repeats in orphan genes are also significantly higher than in nonorphan genes. Microsatellites are found less often in PROSITE patterns in orphan genes. Taken together, these orphan gene characteristics suggest that microsatellites play an important role in orphan gene evolution and expression.