摘要
为鉴定猪全基因组范围内蛋白编码基因3’UTR(3’-untranslated region)中反向重复PRE1(inverted repeated PRE1,IRPRE1)元件,对猪全基因组的22342个蛋白编码基因的3’UTR序列进行重复序列元件的生物信息学分析。结果表明:猪蛋白编码基因的3’UTR序列中短散在重复序列与简单重复序列在重复序列的类别中所占比例较高,分别为27.58%与31.08%;在SINE/t RNA的重复元件中,Pre0_SS和PRE1x元件所占的比例较高,分别为41.83%和37.51%;共有1 094个候选蛋白编码基因的3’UTR中含有IRPRE1元件;GO分析发现这些候选基因主要参与m RNA经由剪接体的剪接、细胞分裂、RNA通过酯交换反应发生的剪接、T细胞激活、RNA剪接、T细胞受体信号通路、对糖苷反应、甘油三酯稳态、外源性凋亡信号通路的正调节及胆固醇合成等生物过程;KEGG pathway分析发现这些候选基因参与了缬草碱、亮氨酸和异亮氨酸降解途径、TNF信号通路、T细胞受体信号通路、RIG-I样受体信号通路、吞噬体、剪接体、胆汁分泌、甲状腺激素合成和凋亡;对3个蛋白编码基因的3’UTR中的IRPRE1元件进行鉴定发现,其在多个组织中广泛表达。
In order to identify the inverted repeating PRE1 element in the 3'-untranslated region(3'UTR)of protein-coding gene porcine at whole genome-wide,the bioinformatics analysis of the repeating sequence elements was performed on the 22342 protein-coding genes of the pig genome.The results showed that the short interspersed nuclear element(SINE)and the simple_repeat in the 3'UTR sequence of the pig protein-coding gene accounted for the highest proportion of the repeat sequence,which were 27.58%and 31.08%,respectively.Among the repetitive elements of SINE/tRNA,Pre0_SS and PRE1x components accounted for the highest proportion,which were 41.83%and 37.51%,respectively.After layer analysis,a total of 1094 candidate protein-coding genes contained an IRPRE1 element in the 3'UTR.Gene Ontology analysis indicated that these candidate genes were mainly involved in mRNA splicing,via spliceosome,cell division,RNA splicing,via transesterification reactions,T cell activation,RNA splicing,T cell receptor signaling pathway,response to glycoside,triglyceride homeostasis,positive regulation of extrinsic apoptotic signaling pathway and cholesterol biosynthetic process.KEGG pathways showed that these candidate genes were mainly involved in Valine,leucine and isoleucine degradation,TNF signaling pathway,T cell receptor signaling pathway,RIG-I-like receptor signaling pathway,Phagosome,Spliceosome,Bile secretion,Thyroid hormone synthesis and Apoptosis.In addition,the IRPRE1 element in the 3'UTR of the three protein-coding genes was identified and was found to be widely expressed in multiple tissues.
作者
赵为民
曹静
邢菲
王丽
任守文
付言峰
李碧侠
方晓敏
ZHAO Weimin;CAO Jing;XING Fei;WANG Li;REN Shouwen;FU Yanfeng;LI Bixia;FANG Xiaomin(Institute of Animal Science,Jiangsu Academy of Agricultural Sciences,Nanjing,Jiangsu 210014,China;Jiangsu Germplasm Resources Protection and Utilization Platform,Nanjing,Jiangsu 210014,China;Key Laboratory of Crop and Livestock Integration Ministry of Agriculture,Nanjing,Jiangsu 210014,China;Jiangsu Agricultural Media Co.Ltd,Nanjing,Jiangsu 210014,China;College of Animal Science and Technology,Nanjing Agricultural University,Nanjing,Jiangsu 210095,China)
出处
《湖南农业大学学报（自然科学版）》
CAS
CSCD
北大核心
2020年第3期336-342,共7页
Journal of Hunan Agricultural University(Natural Sciences)
基金
国家自然科学基金项目(31601928)
国家生猪现代产业技术体系南京综合试验站(CARS-35)
江苏省农业重大新品种创制项目(PZCZ201733)。
关键词
猪
蛋白编码基因
3’UTR
IRPRE1元件
特征分析
porcine
protein-coding gene
3'-untranslated region
Inverted repeated PRE1 element
feature analysis
