Title: Identification of single exon genes and their encoded proteins in rice (Oryza sativa L.) genome: an in silico approach

Authors: Ashutosh Kumar; Amita Barik; Megha Kumari; Ambarish S. Vidyarthi; Dev Mani Pandey

Addresses: Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835 215, India. ' Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835 215, India. ' Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835 215, India. ' Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835 215, India. ' Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835 215, India

Abstract: In this study, we predicted Single Exon Genes (SEGs) distributed in whole rice genome and their expressed proteins. Complete genome of rice was retrieved from TIGR. CDS annotation in the FEATURE (GenBank format) was used to predict SEGs sequences. Organelle gene sequences, pseudogenes, tRNA genes, rRNA genes and duplicated genes were eliminated through different bioinformatics tools. A sizeable number (8.1%) of SEGs in whole rice genome were detected. Predicted SEGs were further searched for their differential response under anoxia. Out of total detected SEGs, only 39.33% were anoxia responsive. Among the total detected anoxia-responsive SEG, only 23.48% encode the known proteins.

Keywords: anoxia; differentially expressed genes; in-silico; microarrays; non-protein-coding functional RNAs; Oryza sativa; pseudogenes; single exon genes; rice genome; bioinformatics; proteins; gene sequences.

DOI: 10.1504/IJBRA.2011.043769

International Journal of Bioinformatics Research and Applications, 2011 Vol.7 No.4, pp.376 - 389

Received: 15 Mar 2010
Accepted: 08 Nov 2010

Published online: 24 Jan 2015 *

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