Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.)
AbstractSingle nucleotide polymorphisms (SNPs) are widely used in functional genomics and genetics research work. The high-quality sequence of rice genome has provided a genome-wide SNP and proteome resource. However, the impact of SNPs on protein phosphorylation status in rice is not fully understood. In this paper, we firstly updated rice SNP resource based on the new rice genome Ver. 7.0, then systematically analyzed the potential impact of Non-synonymous SNPs (nsSNPs) on the protein phosphorylation status. There were 3,897,312 SNPs in Ver. 7.0 rice genome, among which 9.9% was nsSNPs. Whilst, a total 2,508,261 phosphorylated sites were predicted in rice proteome. Interestingly, we observed that 150,197 (39.1%) nsSNPs could influence protein phosphorylation status, among which 52.2% might induce changes of protein kinase (PK) types for adjacent phosphorylation sites. We constructed a database, SNP_rice, to deposit the updated rice SNP resource and phosSNPs information. It was freely available to academic researchers at
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Lin, S.; Chen, L.; Tao, H.; Huang, J.; Xu, C.; Li, L.; Ma, S.; Tian, T.; Liu, W.; Xue, L.; Ai, Y.; He, H. Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.). Int. J. Mol. Sci. 2016, 17, 1738.
Lin S, Chen L, Tao H, Huang J, Xu C, Li L, Ma S, Tian T, Liu W, Xue L, Ai Y, He H. Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.). International Journal of Molecular Sciences. 2016; 17(11):1738.Chicago/Turabian Style
Lin, Shoukai; Chen, Lijuan; Tao, Huan; Huang, Jian; Xu, Chaoqun; Li, Lin; Ma, Shiwei; Tian, Tian; Liu, Wei; Xue, Lichun; Ai, Yufang; He, Huaqin. 2016. "Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.)." Int. J. Mol. Sci. 17, no. 11: 1738.
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