title: Nucleotide composition and codon usage bias of SRY gene.
abstract: The SRY gene is present within the sex-determining region of the Y chromosome which is responsible for maleness in mammals. The nonuniform usage of synonymous codons in the mRNA transcript for encoding a particular amino acid is the codon usage bias (CUB). Analysis of codon usage pattern is important to understand the genetic and molecular organisation of a gene. It also helps in heterologous gene expression, design of primer and synthetic gene. However, the analysis of codon usage bias of SRY gene was not yet studied. We have used bioinformatic tools to analyse codon usage bias of SRY gene across mammals. Codon bias index (CBI) indicated that the overall extent of codon usage bias was weak. The relative synonymous codon usage (RSCU) analysis suggested that most frequently used codons had an A or C at the third codon position. Compositional constraint played an important role in codon usage pattern as evident from correspondence analysis (CA). Significant correlation among nucleotides constraints indicated that both mutation pressure and natural selection affect the codon usage pattern. Neutrality plot suggested that natural selection might play a major role, while mutation pressure might play a minor role in codon usage pattern in SRY gene in different species of mammals.
authors.affiliation: Department of Biotechnology, Assam University, Silchar, Assam, India.
authors.forename: M N
authors.initials: MN
authors.lastname: Choudhury
authors.affiliation: Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, India.
authors.forename: A
authors.initials: A
authors.lastname: Uddin
authors.affiliation: Department of Biotechnology, Assam University, Silchar, Assam, India.
authors.forename: S
authors.initials: S
authors.lastname: Chakraborty
mesh_terms: D000818:Animals; D003062:Codon / Q000235:genetics*; D030541:Databases, Genetic; D015870:Gene Expression; D024282:Genes, sry; D006801:Humans; D009711:Nucleotides / Q000235:genetics*; D051876:Sex-Determining Region Y Protein / Q000235:genetics*
chemical_list: D003062:Codon; D009711:Nucleotides; C497745:SRY protein, human; D051876:Sex-Determining Region Y Protein
keywords: SRY gene; codon usage bias; mammals; nucleotide composition