| 应用生物信息学寻找大鼠中新的microRNA分子及其实验验证 |
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| 引用本文： | 王琳,张双,董素珍. 应用生物信息学寻找大鼠中新的microRNA分子及其实验验证[J]. 华东师范大学学报(自然科学版), 2012, 2012(3): 154-160,170 |
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| 作者姓名： | 王琳 张双 董素珍 |
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| 作者单位： | 华东师范大学脑功能基因组学教育部重点实验室,上海市脑功能基因组学重点实验室,上海200062 |
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| 基金项目： | 国家自然科学基金，中央高校基本科研业务费专项资金 |
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| 摘 要： | 大鼠已公布的microRNA(miRNA) 数量明显少于小鼠及人miRNA的数量.本文采用同源搜索的计算方法预测大鼠新的miRNA.从miRBase数据库中下载已知动物的pre- miRNAs， 在UCSC数据库中对大鼠的全基因组序列进行了Blat分析，并根据miRNAs的筛选标准，获得45条新的大鼠miRNAs；随后随机选取其中的9条新miRNAs进行RT- PCR实验验证，发现大部分miRNAs在脑、心、肺、肾、肌肉、脾、睾丸和肝8种组织中均有表达.在此基础上，对预测的新miRNAs进行了miRNA成簇分析和miRNA基因家族分析.
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| 关 键 词： | miRNA 大鼠 生物信息学 同源性搜索 |
| 收稿时间： | 2011-03-01 |
Computational and experimental identification of novel microRNAs in rats |
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| WANG Lin , ZHANG Shuang , DONG Su-zhen. Computational and experimental identification of novel microRNAs in rats[J]. Journal of East China Normal University(Natural Science), 2012, 2012(3): 154-160,170 |
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| Authors: | WANG Lin ZHANG Shuang DONG Su-zhen |
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| Affiliation: | (Key Laboratory of Brain Functional Genomics,Ministory of Education,Shanghai Key Laboratory of Brain Functional Genomics,East China Normal University,Shanghai 200062,China) |
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| Abstract: | The number of miRNAs in rat genome in miRBase is much less than that of mouse and human.One effective method to identify new miRNAs is to utilize the homolog-based bioinformatrical method.In this report,this method was applied to predict new miRNAs of rats.The known miRNAs sequences were downloaded from miRBase,and used as query sequences to search the rat genome at UCSC Genome Bioinformatics by BLAT analysis.New miRNAs were selected based on commonly-used miRNA standards.As a result,45 new miRNAs were obtained. Nine of them were chosen to be validated by RT-PCR,and most of them were found expressed in brain,heart,lung,kidney,muscle,spleen,testis and liver.Based on the results, miRNA cluster analysis and miRNA gene family analysis were performed in rat genome. |
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| Keywords: | miRNA rat bioinformatics homology search |
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