Compositional features and codon usage pattern of TP63 gene |
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| Affiliation: | 1. Department of Biotechnology, Assam University, Silchar, 788011, Assam, India;2. Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, 788150, Assam, India;1. Kazan State Architect and Civil Engineering University, Zelenaya, 1, 420043 Kazan, Russia;2. A.E. Arbuzov Institute of Organic and Physical Chemistry, Russian Academy of Science, Arbuzov Str., 8, 420088 Kazan, Russia;3. Laboratorie de Chimie de Coordination, CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France;1. Department of Virology, Iran University of Medical Sciences, Tehran, IR Iran;2. Department of Biology, Faculty of Genetics, Tarbiat Modares University, Tehran, IR Iran;3. HIV Laboratory of National Center, Deputy of Health, Iran University of Medical Sciences, Tehran, IR Iran;4. Gastrointestinal & Liver Disease Research Center (GILDRC), Iran University of Medical Sciences, Tehran, IR Iran;1. School of Life Sciences, Fudan University, Shanghai 200433, China;2. Fudan International School, High School Affiliated to Fudan University, Shanghai 200433, China;3. Wolfson College, Oxford University, Oxford, OX2 6UD, UK;4. Institute of Biomedical and Environmental Science and Technology, University of Bedfordshire, Luton, LU1 3JU, UK;5. Institute of Biodiversity Science and Geobiology, Tibet University, Lhasa 850000, China;1. Molecular and Cellular Engineering Group, BioQuant, University of Heidelberg, Heidelberg, Germany;2. The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany |
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| Abstract: | The tumor protein p63encoded by the gene TP63 acts as a homologue of p53 protein. TP63 gene is the transformation factor with two initiation sites for transcriptional process and is related with stress, signal transduction and cell cycle control. The biasness in the preference of a few codons more frequently over other synonymous codons is the codon usage bias (CUB). Natural selection and mutational pressure are the two prime evolutionary forces acting on CUB. Here, the bioinformatic based analysis was performed to investigate the base distribution and CUB of TP63transcript variants (isoforms) as no work was performed earlier. Analysis of compositional features revealed variation in base content across TP63 gene isoforms and the GC content was more than 50%, indicating GC richness of its isoforms. The mean effective number of codons (ENC), a measure of CUB, was 51.83, i.e. overall CUB of TP63 gene was low. Among 13 isoforms of TP63 gene, nature selected against the CTA codon in 8 isoforms and favored five over-represented (RSCU > 1.6) codons namely CTG, CAG, ATC, AAC and GCC during evolution. Correlation between overall nucleotide composition and its 3rd codon position revealed that both mutational pressure and natural selection moulded its CUB. Further, the correlation between ENC and aromaticity depicted that variation of CUB was related to the degree of aromaticity of p63 protein. |
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| Keywords: | Codon usage bias Compositional features Mutation pressure |
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