In silico study of the transcriptional factor binding site for rhodopsin in zebrafish (danio rerio)

In silico study is a computational biological experiment simulation by means creating an artificial system that exhibit biological behaviour of the living system. In silico study had been used as one of the series of biological experiments, before conducting in vivo experiment. However, in silico have not much been used in the field area of researches in aquaculture species genetics. An important molecular protein in aqua genetic is rhodopsin. Rhodopsin is a photopigment presence in both animal and human. In zebrafish (Danio rerio) the presence rhodopsin is essential for its ability in vision. However, in some cases such as stress due to climate change for example severe hot season will cause bleaching of light exposure entering the retina. High exposure to light will cause destruction of rhodopsin. It is essential for the rhodopsin to be regulated in order to maintain or prevent it from lose its ability in vision and disrupt other biological processes. Thus, transcription factor binding site are essential to be studied to understand the regulation of rhodopsin. Zebrafish was used as model organism due to its established complete genome. This study was conducted by obtaining full genome sequence of rhodopsin in zebrafish at National Center for Biotechnology Information (NCBI) and using MatInspector software tool to obtain the suggested transcription factor
binding site. From this study several transcription factor binding sites that was suggested from MatInspector was selected and discussed in further its regulation and its relation to the rhodopsin protein.