Cloning sequencing and bioinformatics analysis of DRA gene of yak

doi:10.3969/j.issn.1004-1524.20212021

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (7): 1564-1570.DOI: 10.3969/j.issn.1004-1524.20212021

• Animal Science • Previous Articles Next Articles

Cloning sequencing and bioinformatics analysis of DRA gene of yak

ZHANG Li(), WANG Yuanyuan, WANG Rui, LIU Lixia()

College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China

Received:2021-12-14 Online:2023-07-25 Published:2023-08-17
Contact: LIU Lixia

Abstract

Abstract:

In order to comprehensively analyze the structure and function of yak MHCⅡ gene, molecular cloning and sequencing technology was used to estimate the coding region of DRA gene of Datong yak and conduct bioinformatics analysis. The results showed a DRA gene open reading frame in the coding region containing 762 bp, a total of 253 amino acids encoding; a total of 3 SNPs (g.2376C>T, g.2851C>G, g.3016C>A). In exons 2 and 3, there was one synonymous mutation in C→T and a missense mutation (L→M) in C→A, respectively, both mutations reduced the stability of mRNA secondary structure of DRA gene. There were differences in the molecular mass, total number of atoms, fat coefficient, instability coefficient, and total average hydrophilicity of the protein encoded by the g.3016C>A mutation. Methodological analysis by bioinformatics revealed that the BoLA-DRA gene were highly conserved genes in the MHC gene family. The results laid the foundation for the structure and function of DRA in Datong yak.

Key words: DRA gene, coding region cloning, mutation site, bioinformatics

CLC Number:

S823.85

ZHANG Li, WANG Yuanyuan, WANG Rui, LIU Lixia. Cloning sequencing and bioinformatics analysis of DRA gene of yak[J]. Acta Agriculturae Zhejiangensis, 2023, 35(7): 1564-1570.

Figures/Tables 9

References 18

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位置 Location	引物序列 Primer sequence(5'→3')	退火温度 Annealing temperature/℃	片段长度 Fragment length/bp
外显子1 Exon1(1~93 bp) 外显子2 Exon2(263~508 bp)	F:CACCAAAGAAGTGGCC R:CCACAGTTCATTTCTCCGAAGC F:CCTGACCCCCTTTCTTGTCT R:AGGAGGACTGGAGCAGAGGT	57.3 58.5	93 246
外显子3 Exon3(938~1 219 bp)	F:GTCAGCCTCGATGGGACGAA R:CTCACCCCAGTGCTTGAGAA	63.0	282
外显子4 Exon4(1 510~1 664 bp)	F:GTGCTAAGCTGCTCCCTA R:TCCTCTGACCACAGCAGACTC	61.2	155

位置 Location	引物序列 Primer sequence(5'→3')	退火温度 Annealing temperature/℃	片段长度 Fragment length/bp
外显子1 Exon1(1~93 bp) 外显子2 Exon2(263~508 bp)	F:CACCAAAGAAGTGGCC R:CCACAGTTCATTTCTCCGAAGC F:CCTGACCCCCTTTCTTGTCT R:AGGAGGACTGGAGCAGAGGT	57.3 58.5	93 246
外显子3 Exon3(938~1 219 bp)	F:GTCAGCCTCGATGGGACGAA R:CTCACCCCAGTGCTTGAGAA	63.0	282
外显子4 Exon4(1 510~1 664 bp)	F:GTGCTAAGCTGCTCCCTA R:TCCTCTGACCACAGCAGACTC	61.2	155

蛋白质理化特性 Physicochemical properties of proteins	突变类型Mutation type
蛋白质理化特性 Physicochemical properties of proteins	突变前Before mutation	突变后After mutation
分子量Molecular weight/u	28 407.01	28 425.04
原子总数Total number of atoms	4 035	4 033
消光系数Extinction coefficients	28 085/27 960	28 085/27 960
等电点Theoretical pI	5.41	5.41
分子式Formula	C₁₃₀₅H₂₀₃₀N₃₃₀O₃₆₁S₉	C₁₃₀₄H₂₀₂₈N₃₃₀O₃₆₁S₁₀
不稳定系数The instability index (Ⅱ)	38.81	39.78
脂肪系数Aliphatic index	100.16	98.62
总平均亲水性Grand average of hydropathicity (GRAVY)	0.056	0.049
半衰期Estimated half-life/h	30	30
正电荷残基数Total number of negatively charged residues (Asp+Glu)	31	31
负电荷残基数Total number of positively charged residues (Arg+Lys)	23	23

蛋白质理化特性 Physicochemical properties of proteins	突变类型Mutation type
蛋白质理化特性 Physicochemical properties of proteins	突变前Before mutation	突变后After mutation
分子量Molecular weight/u	28 407.01	28 425.04
原子总数Total number of atoms	4 035	4 033
消光系数Extinction coefficients	28 085/27 960	28 085/27 960
等电点Theoretical pI	5.41	5.41
分子式Formula	C₁₃₀₅H₂₀₃₀N₃₃₀O₃₆₁S₉	C₁₃₀₄H₂₀₂₈N₃₃₀O₃₆₁S₁₀
不稳定系数The instability index (Ⅱ)	38.81	39.78
脂肪系数Aliphatic index	100.16	98.62
总平均亲水性Grand average of hydropathicity (GRAVY)	0.056	0.049
半衰期Estimated half-life/h	30	30
正电荷残基数Total number of negatively charged residues (Asp+Glu)	31	31
负电荷残基数Total number of positively charged residues (Arg+Lys)	23	23

突变位点 Mutant site	突变位置 Mutant location	突变类型 Mutation type	氨基酸变化 Amino acid variation	等位基因频率Allele frequency
突变位点 Mutant site	突变位置 Mutant location	突变类型 Mutation type	氨基酸变化 Amino acid variation	突变前Before mutation	突变后After mutation
g.2376C>T	Exon2	同义突变	—	0.156 2	0.843 8
		Synonymous mutation
g.2851C>G	Intron2	—	—	0.343 7	0.656 3
g.3016C>A	Exon3	错义突变	L→M	0.333 3	0.666 7
		Missense mutation

Cloning sequencing and bioinformatics analysis of DRA gene of yak

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突变类型 Mutation type	α螺旋 α-Helix	β转角 β-Turn	β折叠 β-Sheet	无规则卷曲 Random coil
突变前Before mutation	18.58(47)	6.72(17)	38.58(49)	44.66(113)
突变后After mutation	18.58(47)	6.72(17)	30.04(76)	47.43(120)

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