| 合作猪IFN-ε基因克隆及生物信息学分析 |
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| 引用本文：杨姣姣，谢开会，王 伟，闫尊强 ，杨巧丽，马艳萍，滚双宝.合作猪IFN-ε基因克隆及生物信息学分析[J].西北农业学报,2020,30(1):11~20 |
| DOI:10.7606/j.issn.1004-1389.2020.01.002 |
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| 基金项目:国家自然科学基金（31660646）;甘肃农业大学人才专项经费(2017RCZX-15)。 |
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| 中文摘要:旨在克隆合作猪干扰素ε（Interferon epsilon,IFN-ε）基因，并对其结构和编码蛋白进行生物信息学分析，为进一步研究合作猪IFN-ε生物学功能提供参考。根据GenBank上公布的猪IFN-ε基因序列（登录号：NM_001105310.1）设计引物，PCR扩增及测序获得合作猪IFN-ε基因完整编码区序列（Coding sequence,CDS），并对其进行生物信息学分析。结果显示，合作猪IFN-ε基因编码区长582 bp，编码193个氨基酸。该基因编码区序列与杜洛克猪、人、小鼠、黑猩猩、狗、瘤牛、蒙古野马、山羊和绵羊的同源性分别为 98.4%、 77.7%、56.8%、78.2%、76.5%、87.0%、85.5%、85.0%和86.0%；系统进化树结果表明，合作猪与瘤牛、蒙古野马、绵羊、山羊亲缘关系较近。此外，在合作猪IFN-ε基因CDS上共发现3个碱基突变，均为错义突变。氨基酸序列分析表明，合作猪IFN-ε蛋白分子式为C1027H1630N278O290S10，理论分子质量为22.83 ku，等电点（pI）为8.43，属于碱性蛋白；平均亲水系数为-0.240，属于亲水蛋白质；IFN-ε蛋白无跨膜结构，存在信号肽序列，属于分泌型蛋白；IFN-ε蛋白只包含1个超家族保守结构域，即IFab结构域。二级结构分析表明，该蛋白中α-螺旋、无规则卷曲、β-转角和延伸链所占比例分别为61.66%、30.05%、3.11%和5.18%。 |
| 中文关键词:合作猪 IFN-ε基因 CDS 克隆 生物信息学分析 |
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| Cloning and Bioinformatics Analysis of IFN-ε Gene in Hezuo Pigs |
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| Abstract:This study aimes at the structure and encoded protein of the interferon epsilon (IFN-ε) gene in Hezuo pig by clone and bioinformatic methods,which will provide a reference for further studyon the biological function of IFN-ε in Hezuo pig. The primers were designed based on the porcine IFN-ε gene reference sequence in GenBank (accession number:NM_001105310.1). Additionally,the complete coding sequence (CDS) of the porcine IFN-ε gene was obtained by PCR amplification and sequencing,and then was analyzed byusing bioinformatics. The results showed that the coding region of IFN-ε gene in Hezuo pig was 582 bp in length and encoded 193 amino acids. The homology analysis found that coding region sequence of IFN-ε in Hezuo pighad similarity of 98.4%,77.7%, 56.8%,78.2%,76.5%,87.0%,85.5%,85.0% and 86.0%compared with Duroc,human,mouse,chimpanzee,dog,zebu,Equus przewalskii,goats and sheep,respectively; the result of phylogenetic tree showed that IFN-ε gene in Hezuo pigs was closely related to zebu,Equus przewalskii,sheep and goats. In addition,a total ofthree bases of IFN-ε gene CDS shappened missense mutations. Amino acid sequence analysis showed that the molecular formula,theoretical molecular mass,and isoelectric point of IFN-ε protein were C1027H1630N278O290S10,22.83 ku and 8.43,respectively. The IFN-ε protein was the hydrophilic and basic protein with total average hydrophilic index -0.240; IFN-ε protein was a secretory protein and had a signal peptide sequence without membrane structure; IFN-ε protein contained one superfamily conserved domain,the IFab domain. The secondary structure analysis of IFN-ε protein showed that the percent of amino acids of α-helix,random coil,β-turn and extended chain were 61.66%,30.05%,3.11% and 5.18%,respectively. This study will provide the basis for further research on the function of IFN-ε in Hezuo pigs. |
| keywords:Hezuo pig IFN-ε CDS Clone Bioinformatics analysis |
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