水牛SND1基因克隆及生物信息学分析

doi:10.16431/j.cnki.1671-7236.2018.07.004

Abstract

Abstract:

This study was aimed to clone and sequence the buffalo staphylococcal nuclease and tudor domain containing 1 (SND1) gene using the electronic cloning method,and analyze its genetic struction with bioinformatics,which laid a foundation for investigating the effect of SND1 gene on the milk performance in buffaloes.In this experiment,three pairs of specific primers were designed by Primer Premier 5.0 according the sequence of Bos taurus SND1 gene in GenBank (accession No.NM_205784.1),the buffalo DNA was used as the template,the sequence of buffalo SND1 gene mRNA was ampified by PCR,the target fragment linked into the cloning vector pMD18-T was sequenced and systemically analyzed by bioinformatics.The results showed that the length of SND1 gene mRNA was 3 503 bp,containing a CDS of 2 733 bp,which encoded 910 amino acids.The protein molecular formula was C₄₅₂₃H₇₁₈₃N₁₂₈₁O₁₃₅₄S₂₆, the molecular weight was 102.01 ku,the theory isoelectric point was 6.74,the instability coefficient was 42.07,grand average of hydropathy was -0.419,SND1 was the soluble acid protein.The secondary structures prediction of buffalo SND1 protein showed that alpha helices and random coils accounted for 37.80% and 34.18%,which were the main structure of the protein.Gene function prediction showed that the possibility of the gene function in the purine and pyrimidine,central intermediary metabolism,energy metabolism,biosynthesis of amino acids were 0.449,0.401,0.303 and 0.262,respectively.Sequence homology analysis indicated that the buffalo SND1 showed 98.7%,97.8%,97.8%,93.8%,93.1% and 91.7% identity with those of Bos taurus,Ovis aries,Capra hircus,Sus scrofa,Equus caballus and Homo sapiens,respectively.Sequence analysis revealed that buffalo SND1 gene was conserved,and showed high sequence similarity with other species.Online predicting tool SMART was used to predict protein structure domain,it showed that buffalo SND1 protein contains four SN area.This results suggested that the SND1 gene CDS was more conservative in the evolution process.

Key words: buffalo; SND1 gene; bioinformatics analysis

CLC Number:

HUANG Yunqi, DENG Tingxian, TANG Hui, MA Xiaoya, LIANG Shasha, LU Xingrong, DUAN Anqin, WANG Wenwen, PANG Chunying, LIANG Xianwei. Cloning and Bioinformatics Analysis of SND1 Gene in Buffalo[J]. , 2018, 45(7): 1759-1767.

References

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Cloning and Bioinformatics Analysis of SND1 Gene in Buffalo

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