Degree Type

Creative Component

Semester of Graduation

Fall 2018


Computer Science

First Major Professor

Eve Wurtele

Second Major Professor

David Fernández-Baca


Master of Science (MS)


Computer Science


Orphan genes are the genes that lack detectable homologs in other species. Orphan genes also known as TRS (Taxonomically Restricted Genes) are an elliptical component of the genome because their ancestry and functions are mostly unknown. Understanding the functional significance and the origin of such orphan genes may give us insights into novel traits that can be evolutionary and physiologically important. Using bioinformatics computation and statistical analysis of Oryza sativa japonica, the total of 1,507 orphan genes was found. Around 5,173,767 unannotated open reading frames (ORFs) in Oryza sativa japonica genome which could be potential coding for a novel protein specific to Oryza sativa japonica is obtained. The publicly available RNAseq data from SRAdb were then used in order to explore the expression patterns of these orphan genes under various conditions. Most of the research disregards orphan genes as its importance and functions are not well known. Orphan genes are related to stress responses and specific traits which might be the key to improve crop yields and disease resistance in domestic plants.

Copyright Owner

Rakesh Shah

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