Cloning,Bioinformatics and Tissue Expression Analysis of PID1 Gene in Yak

doi:10.7668/hbnxb.20194907

Abstract

Abstract:

To study the structure and function of phosphotyrosine interaction domain 1 (PID1) gene in yak,and to explore its expression in various tissues.The CDS region of Sangsang yak PID1 gene was cloned using Sangsang yak adipose tissue cDNA as template,and the sequence was analyzed bioinformatically.Meanwhile,the relative expression level of PID1 gene was detected in seven tissues of yak namely heart,liver,spleen,lung,kidney,longissimus dorsi muscle and adipose tissue by Real-time Fluorescence Quantitative PCR(RT-qPCR).The results showed that the PID1 gene in yaks had a coding region length of 654 bp,which encoded 217 amino acids.Homology comparison showed that yak and wild yak were closely related,and the similarity reached 100%.The molecular weight of yak PID1 protein was about 24.84 ku and the theoretical isoelectric point was 6.30.According to the calculation results of instability coefficient,the instability of the protein was high (47.96),and it belonged to an unstable protein.The protein had one N-glycosylation site and 23 phosphorylation sites,with no signal peptide or transmembrane structure.The results of RT-qPCR showed that the expression of PID1 gene could be detected in all tissues,with the highest expression in the lung.The yak PID1 gene was cloned and its protein structure was analyzed.The expression of PID1 gene in yak tissue was also studied.Further study on the role of PID1 gene in yak fat deposition provided preliminary data.

Key words: Yak, PID1 gene, Gene cloning, Bioinformatics

YU Daoning, WANG Tong, LOBSANG Dondrub, PINGCUO Zhandui, ZHANG Qiang, ZHUOMA Ciren, NIMA Jiacuo, ZHANG Derong, LIANG Chunnian. Cloning,Bioinformatics and Tissue Expression Analysis of PID1 Gene in Yak[J]. Acta Agriculturae Boreali-Sinica, 2024, 39(6): 216-223. doi: 10.7668/hbnxb.20194907.

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References 29

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基因 Gene	引物序列(5'—3') Primer sequences(5'—3')	产物长度/bp Product size	退火温度/℃ Annealing temperature	用途 Application
PID1	F:CCCATCGACAGAGTCTTGCC	750	60.0	PCR
	R:TTCCTTGACCAATGCTGCCT
PID1	F:TCTTTCCGGCTAATGCCCTC	153	59.0	RT-qPCR
	R:AGATGTTGGGGCTCACGTTG
GAPDH	F:GGCATCGTGGAGGGACTTATG	186	59.0	RT-qPCR
	R:GCCAGTGAGCTTCCCGTTGAG

基因 Gene	引物序列(5'—3') Primer sequences(5'—3')	产物长度/bp Product size	退火温度/℃ Annealing temperature	用途 Application
PID1	F:CCCATCGACAGAGTCTTGCC	750	60.0	PCR
	R:TTCCTTGACCAATGCTGCCT
PID1	F:TCTTTCCGGCTAATGCCCTC	153	59.0	RT-qPCR
	R:AGATGTTGGGGCTCACGTTG
GAPDH	F:GGCATCGTGGAGGGACTTATG	186	59.0	RT-qPCR
	R:GCCAGTGAGCTTCCCGTTGAG

工具 Online tools	功能 Analysis content
ORF Finder	开放阅读框分析
Blast	相似性比对分析
ProtParam	蛋白质理化性质分析
ProtScale	蛋白质亲疏水性分析
SignalP 4.1	蛋白质信号肽分析
TMHMM 2.0	蛋白质跨膜结构预测
NetPhos 3.1	蛋白磷酸化位点预测
NetNGlyc	蛋白糖基化位点预测
SOPMA	蛋白质二级结构预测
SWISS-MODEL	蛋白质三级结构预测
STRING	蛋白互作网络预测

工具 Online tools	功能 Analysis content
ORF Finder	开放阅读框分析
Blast	相似性比对分析
ProtParam	蛋白质理化性质分析
ProtScale	蛋白质亲疏水性分析
SignalP 4.1	蛋白质信号肽分析
TMHMM 2.0	蛋白质跨膜结构预测
NetPhos 3.1	蛋白磷酸化位点预测
NetNGlyc	蛋白糖基化位点预测
SOPMA	蛋白质二级结构预测
SWISS-MODEL	蛋白质三级结构预测
STRING	蛋白互作网络预测

氨基酸种类 Amino acid	占比/% Proportion	氨基酸种类 Amino acid	占比/% Proportion
丙氨酸Ala (A)	7.8	亮氨酸Leu (L)	9.2
精氨酸Arg (R)	3.7	赖氨酸Lys (K)	7.8
天冬酰胺Asn (N)	2.8	甲硫氨酸Met (M)	4.1
天冬氨酸Asp (D)	4.6	苯丙氨酸Phe (F)	4.1
半胱氨酸Cys (C)	2.8	脯氨酸Pro (P)	4.6
谷氨酰胺Gln (Q)	4.1	丝氨酸Ser (S)	6.0
谷氨酸Glu (E)	8.8	苏氨酸Thr (T)	7.8
甘氨酸Gly (G)	3.2	色氨酸Trp (W)	1.8
组氨酸His (H)	5.5	酪氨酸Tyr (Y)	1.8
异亮氨酸Ile (I)	3.7	缬氨酸Val (V)	5.5

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