鸡6个功能基因microRNA靶标区域SNP的生物信息学预测

doi:10.3724/SP.J.1005.2008.01026

遗传 ›› 2008, Vol. 30 ›› Issue (8): 1026-1032.doi: 10.3724/SP.J.1005.2008.01026

鸡6个功能基因microRNA靶标区域SNP的生物信息学预测

耿立英¹; 张传生^{2, 3}; 杜立新³

1. 河北科技师范学院生命科学系, 昌黎 066600;
2. 河北科技师范学院动物科学系, 昌黎 066600;
3. 中国农业科学院北京畜牧兽医研究所国家畜禽分子遗传育种中心, 北京 100193

收稿日期:2007-12-15 修回日期:2008-05-29 出版日期:2008-08-10 发布日期:2008-08-10
通讯作者: 张传生

Identification of SNPs located in putative microRNA tar-get region of six functional genes in chickens through bioinformatic analysis

GENG Li-Ying ¹; ZHANG Chuan-Sheng ^{2, 3}; DU Li-Xin³

1. Department of Life Science, Hebei Normal University of Science & Technology, Changli 066600, China;
2. Department of Animal Science, Hebei Normal University of Science & Technology, Changli 066600, China;
3. National Center for Molecular and Breeding of Animal, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China

Received:2007-12-15 Revised:2008-05-29 Online:2008-08-10 Published:2008-08-10
Contact: ZHANG Chuan-Sheng

摘要/Abstract

摘要： GDF-8、IGF-I、IGF-III、IGF2R、IGFBP2和GHR是鸡的重要经济性状候选基因。利用miRanda和Targetscan软件预测6个基因3′UTR潜在的microRNA靶标, 并发掘靶标区域SNP位点。结果表明: 在6个基因的26个microRNA靶标区域, 共检测到125个SNP位点, 在靶标及其5′和3′邻接等长侧翼区分别检测到47个、44个和35个SNPs位点, 其中12个SNP定位于靶标种子序列互补区。种子序列互补区及其3′侧翼区的SNP位点可能会影响microRNA的调控, 导致家禽的表型变异

关键词: 小RNA, 生物信息学, 单核苷酸多态性, 鸡, 非翻译区

Abstract: GDF-8, IGF-I, IGF-III, IGF2R, IGFBP2, and GHR are candidate genes affecting important economic trait in chicken. The putative microRNA target sites of 3′ untranslated region of these genes were identified by means of specialized algorithms (miRanda and TargetScan), and the candidate SNPs located in the microRNA target region were also identified. Approximately 125 candidate SNPs were found throughout the 26 putative microRNA target regions in six gene 3′-UTR. Among the 125 SNPs, 47 were located in the microRNA targets, 44 and 35 were located in 5′and 3′flanking regions which equalled to the size of the given target. Twelve of the 47 candidates were located in the match of the microRNA seed. These SNPs, which were located in the match of the microRNA seed and 3 ′ flanking regions may affect microRNA regulation and contribute to poultry phenotypic variation.

耿立英，张传生，杜立新. 鸡6个功能基因microRNA靶标区域SNP的生物信息学预测[J]. 遗传, 2008, 30(8): 1026-1032.

GENG Li-Ying, ZHANG Chuan-Sheng , DU Li-Xin. Identification of SNPs located in putative microRNA tar-get region of six functional genes in chickens through bioinformatic analysis[J]. HEREDITAS, 2008, 30(8): 1026-1032.

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鸡6个功能基因microRNA靶标区域SNP的生物信息学预测

Identification of SNPs located in putative microRNA tar-get region of six functional genes in chickens through bioinformatic analysis

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