不同物种GATA-3基因编码区生物信息学分析

Bioinformatics analysis of the coding regions of GATA- 3 genes from different species

为了研究不同物种GATA-3基因的遗传多样性,试验采用生物信息学的方法分析了人、黑猩猩、倭黑猩猩、大猩猩、毛猩猩、猿、猕猴、东非狒狒、亚马逊松鼠猴、小耳大婴猴、白犀牛、美洲海牛、星鼻鼹、八齿鼠、宽吻海豚、小马岛猬、虎鲸、海象、小家鼠、灰仓鼠、野猪、牛、九带犰狳、非洲跳鼠、欧洲兔、北美鼠兔、绵羊、袋獾、狼、非洲象、灰短尾负鼠、荷兰猪、褐家鼠、普通鼠句鼠青34个物种GATA-3基因编码区(CDS),并对该基因的遗传多样性导肽、信号肽、跨膜结构域、疏水性/亲水性、蛋白质二级结构、氨基酸序列进行了分析和预测。结果表明:在34个物种67条基因序列中共检测到479个多态位点,生成45种单倍型,GATA-3基因序列编码区的种内、种间存在丰富的遗传多样性;GATA-3蛋白不具有导肽,N端无信号肽,没有跨膜结构域,表现为亲水性,蛋白质二级结构主要结构元件是无规卷曲、α-螺旋和延伸链,理论等电点为9.47,GATA-3蛋白呈碱性。

To study the genetic diversity of the GATA -3 genes from different species. The coding sequences （CDS） of GATA -3 gene se- quences from the following 34 species were analyzed using the method of bioinformatics ： Homo sapiens, Pan troglodytes, Pan paniscus, Gorilla, Pongo abelii, Nomascus leucogenys, Macaca mulatta, Papio anubis, Saimiri boliviensis, Otolemur garnetti, Ceratotherium simum, Trichechus manatus , Condylura cristata , octodon degus , Tursiops truncates, Echinops telfairi , Orcinus orca , Odobenus rosmarus , Mus musculus , Cricetulus griseus , Sus scrofa , Bos taurus, Dasypus novemcinctus , Jaculus jaculus , Oryctolagus cuniculus , Ochotona princeps, Ovis aries, Sarcophilus har- risii, Canis lupus, Loxodonta Africana, Monodelphis domestica, Cavia porcellus, Rattus norvegicus and Sorex araneus. The genetic diversity, a- mino acid sequences, leader peptides, signal peptides, transmembrane domain, hydrophobicity or hydrophilicity, protein secondary structure and the composition of nucleic acid sequences of the GATA - 3 genes were also analyzed and predicted. The results showed that a total of 479 polymorphic sites were detected from 67 sequences of the 34 species, from which 45 haplotypes were generated, and rich genetic diversity was detected in the CDS of the GATA - 3 genes within and among the species. The protein of the GATA - 3 gene had no transmembrane domain without leader peptides and signal peptide in N - terminal, showing hydrophilic properties; the main structural elements of predicted secondary structure of GATA - 3 included random coil, ct - helix and extended strand, its theoretical isoelectric point was 9.47, and the GATA - 3 pro- tein was alkaline.