1. Insight into Codon Utilization Pattern of Tumor Suppressor Gene EPB41L3 from Different Mammalian Species Indicates Dominant Role of Selection Force
- Author
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Kuldeep Dhama, Rekha Khandia, Meghna Tripathi, Utsang Kumar, Raju Khan, Ashok Munjal, A. K. Pateriya, Nidhi Puranik, Talha Bin Emran, Shailja Singhal, Ali Alqahtani, and Taha Alqahtani
- Subjects
0301 basic medicine ,Codon Adaptation Index ,Cancer Research ,Translational efficiency ,RSCU ,codon usage bias ,Biology ,medicine.disease_cause ,Genome ,Article ,03 medical and health sciences ,0302 clinical medicine ,mutational pressure ,medicine ,Gene ,Selection (genetic algorithm) ,RC254-282 ,Genetics ,Mutation ,Natural selection ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,natural selection ,EPB41L3 ,GC contents ,030104 developmental biology ,translational efficiency ,Oncology ,030220 oncology & carcinogenesis ,Codon usage bias - Abstract
Uneven codon usage within genes as well as among genomes is a usual phenomenon across organisms. It plays a significant role in the translational efficiency and evolution of a particular gene. EPB41L3 is a tumor suppressor protein-coding gene, and in the present study, the pattern of codon usage was envisaged. The full-length sequences of the EPB41L3 gene for the human, brown rat, domesticated cattle, and Sumatran orangutan available at the NCBI were retrieved and utilized to analyze CUB patterns across the selected mammalian species. Compositional properties, dinucleotide abundance, and parity analysis showed the dominance of A and G whilst RSCU analysis indicated the dominance of G/C-ending codons. The neutrality plot plotted between GC12 and GC3 to determine the variation between the mutation pressure and natural selection indicated the dominance of selection pressure (R = 0.926, p <, 0.00001) over the three codon positions across the gene. The result is in concordance with the codon adaptation index analysis and the ENc-GC3 plot analysis, as well as the translational selection index (P2). Overall selection pressure is the dominant pressure acting during the evolution of the EPB41L3 gene.
- Published
- 2021