高级检索+

大白猪GABRR2基因SNP筛选及结构、功能的预测和分析

SNP Screening, Structure and Function Prediction and Analysis of GABRR2 Gene in Yorkshire Pigs

  • 摘要: 为了筛选大白猪GABRR2基因的SNP和对GABRR2基因进行结构、功能的预测和分析,本研究利用30头大白猪混池为模板,通过PCR扩增GABRR2基因外显子,测序后进行SNP筛选,并对测序结果进行拼接,利用多种生物信息学软件对大白猪GABRR2基因启动子区、编码区、3'UTR区进行了一系列的分析。结果显示,大白猪GABRR2基因在c615、c660、c798和c1134共有4个同义突变;RNGTT、SRSF12和ANKRD6 3个基因在GABRR2基因连锁区间内,且编码的蛋白具有相互作用;起始密码子上游2 000 bp区域在385~435号碱基和759~806号碱基区域有2个核心启动子区域,在核心启动子386~395、769~778有Sp1转录因子结合位点,757~766有CREB-2转录因子结合位点,775~784有NF-1转录因子结合位点,在1 593~1 752号碱基区间内有一个Cp G岛;3'UTR区域有14个miRNA结合位点,其中miR-365-3p、miR-497-5p、miR-5195-3p和miR-145-5p评分高于80。研究结果表明,大白猪GABRR2基因CDS区全长1 380 bp,存在4个同义突变,保守性高;编码一个具有4个跨膜结构、1个信号肽的亲水性蛋白,与RNGTT基因功能可能有密切联系;2个核心启动子区域内含有Sp1、CREB-2和NF-1三种共4个转录因子结合位点,且启动子区有一个特征的CpG岛;3'UTR区域存在miR-365-3p、miR-497-5p、miR-5195-3p和miR-145-5p共4个miRNA结合区域。

     

    Abstract: In order to screen the SNP and analyze the structure and function of GABRR2 genes in Yorkshire pigs,30 Yorkshire pigs were used as templates to amplify the exons of GABRR2 gene by PCR. The SNPs were screened after sequence, and the sequences were spliced. And then a series of analyses were carried out on the promoter region, coding region and 3 ’UTR region of GABRR2 gene in Yorkshire pigs by using a variety of bioinformatics software. The results showed that there were four synonymous mutations in c615, c660, c798 and c1134 of GABRR2 gene in Yorkshire pigs. The genes, RNGTT, SRSF12 and ANKRD6, were in the linkage region of GABRR2 gene, and the proteins encoded by the gene interacted with each other. There were two core promoters in the 2 000 bp region upstream of the initiation codon which Sp1 in 386~395 and 769~778, CREB-2 in 757~766,NF-1 in 775~784, and a CpG island in the 1593~1752 base region. There were 14 miRNA binding sites in 3’UTR region, of which the scores of miR-365-3 p, miR-497-5 p, miR-5195-3 p and miR-145-5 p were higher than 80.Conclusion: GABRR2 gene had four synonymous mutations in the CDS region, which were highly conserved. It encoded a hydrophilic protein with four transmembrane structures and one signal peptide GABRR2 gene, which may be closely related to the function of RNGTT gene. The two core promoter regions contained four transcription factor binding sites of Sp1, CREB-2 and NF-1, and a characteristic CpG island in promoter regions. There were four miRNA binding regions in the 3’UTR region: miR-365-3 p, miR-497-5 p, miR-5195-3 p and miR-145-5 p.

     

/

返回文章
返回