Bioinformatics analysis of the promoter sequence of the 9f-2.8 gene encoding germin

Abstract

Bioinformatics is a field of study having an enormous potential, allowing to solve a number of problems arising as a result of dynamic development of natural sciences with the use of computer science methodologies. It is widely used and constitutes a basis for most scientific research conducted in the field of molecular biology. The aim of this study was in silico analysis of the promoter sequence of the 9f-2.8 gene encoding isoform of the germin protein considered as a germination marker in common wheat’s (Triticum aestivum L.). The gene mentioned above has already been characterized, however, with the use of experimental methods instead of bioinformatics. Analysis with the use of TSSP and TSSPlant software identified the promoter region and classified it as the TATA-box containing promoter. For 9f-2.8 gene including 2.8 kbp, the TSSP software indicated that the TATA-box sequence was located in the position 1665 nt, while the TSSPlant tool showed that TSS [+1] was located in the position 1699 nt. At the second stage, transcription factors were analyzed. Four main families of transcription factors were detected within the analyzed region: MADS, AP2, bZIP and NAC. The most common were MADS-box and bZIP motifs. In the final step of analysis the presence of CpG islands have been checked using the PlantPAN software. The region which could be potentially considered as CpG island have been detected and localized. Software used in analysis above is free online tool.

Keywords

• Triticum aestivum L.
• bioinformatic tools
• germin protein
• in silico analyse