德国牧羊犬RBFOX1基因SNP位点筛选及生物信息学分析

SNP locus screening and bioinformatics analysis of RBFOX1 gene in German Shepherd dogs

为了深入认识德国牧羊犬RNA结合蛋白FOX1同源体1(RNA binding protein fox-1 homolog 1,RBFOX1)基因的基本信息,揭示德国牧羊犬RBFOX1基因遗传特征,试验采用DNA混合池扩增后直接测序的方法,检测德国牧羊犬RBFOX1基因外显子区SNP位点,将测序获得的序列翻译成氨基酸,利用生物信息学分析软件对该基因编码氨基酸序列进行生物信息学分析。结果表明:德国牧羊犬RBFOX1基因外显子1上存在1个SNP位点,为G988031C,该位点位于5′非翻译区(UTR)。G988031C位点使RBFOX1基因mRNA二级结构自由能升高。RBFOX1基因编码序列(CDS)区长度为1383 bp,共编码460个氨基酸,其分子量为49853.88 u,理论等电点为5.82;该基因编码的蛋白质是不稳定的亲水性蛋白,没有信号肽和跨膜结构域,有磷酸化位点和N-糖基化位点,主要定位于细胞核;蛋白质二级结构上含有23.26%的α-螺旋,17.83%的延伸链,7.61%的β-转角和51.30%的无规则卷曲;蛋白三级结构与二级结构基本一致。德国牧羊犬RBFOX1基因编码氨基酸序列与猫的遗传距离最近,与鸡的遗传距离最远。说明RBFOX1基因外显子区的突变可能与德国牧羊犬攻击行为相关,其突变位点有可能成为德国牧羊犬攻击行为选育的分子标记。

In order to gain a deeper understanding of the basic information of the RNA binding protein fox-1 homolog 1(RBFOX1)gene of the German Shepherd dog,and to reveal the genetic characteristics of the RBFOX1 gene of the German Shepherd dog,in the test,the SNP site in the exon region of the RBFOX1 gene of the German Shepherd dog was detected by direct sequencing after DNA mixed pool amplification;the sequences obtained by sequencing were translated into amino acids,and then the coding amino acid sequences of the gene were analyzed by bioinformatics analysis software.The results showed that there was one SNP site in exon 1 of RBFOX1 gene of German Shepherd dog,G988031C,which was located in the 5′UTR region.The G988031C site elevated the free energy of the secondary structure of mRNA of RBFOX1 gene.The CDS region of the RBFOX1 gene was 1383 bp in length and encoded 460 amino acids,with a molecular weight of 49853.88 u and a theoretical isoelectric point of 5.82.The protein encoded by this gene was an unstable hydrophilic protein without signal peptide and transmembrane structural domains;it had phosphorylation sites and N-glycosylation sites,and was mainly localized in the nucleus.The protein secondary structure contained 23.26%α-helices,17.83%extended chains,7.61%β-turns and 51.30%irregular coils;the protein tertiary structure was basically consistent with the secondary structure.Amino acid sequence encoding the RBFOX1 gene of the German Shepherd dog was the closest to the cat and the furthest from the chicken.The results suggested that mutations in the exonic region of the RBFOX1 gene might be associated with German Shepherd dog aggression,and its mutation site had the potential to be a molecular marker for selection and breeding of German Shepherd dog aggression.