JetGene—Online Database and Toolkit for an Analysis of Regulatory Regions or Nucleotide Contexts at Differently Translated Plants Transcripts

Abstract

mRNAs have some regulatory codes which can define the fate of an individual mRNA in translation. We have developed a flexible online database JetGene (https://jetgene.bioset.org/; accessed on 23 October 2020) that contains cDNA, CDS, 5′-UTR, 3′-UTR sequences from Bacteria, Fungi, Metazoa, Plants, Protists and Vertebrates with the aim of searching regulatory codes in mRNA and studying their correlation with the translational efficiency. It has a friendly interface and puts together a set of tools which are necessary for designing experiments. JetGene allows doing a benchmark analysis of sequences, namely: (1) to estimate the variation of length, nucleotide composition, frequency of codon usage, to analyze GC-content, CpG-islands, to study nucleotides surrounding the start codon and much more; (2) to identify and define the statistically significant representation of potential regulatory contexts at mRNA with different translation efficiency. A user can make a bioinformatics analysis for full-length transcripts or for a fragment of transcripts, or for coding/non-coding regions. Every step of the work is accompanied by a graphical interpretation of the results. Moreover, the beta-version of JetGene (https://beta.bioset.org, under construction; accessed on 23 October 2020) allows users to compare two datasets of mRNA and to apply omics data for searching and predicting the regulatory determinants of translation.