tRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana

Plant Cell Physiol. 2018 Jan 1;59(1):e1. doi: 10.1093/pcp/pcx173.


tRNA-derived fragments (tRFs) constitute a new class of short regulatory RNAs that are a product of nascent or mature tRNA processing. tRF sequences have been identified in all domains of life; however, most published research pertains to human, yeast and some bacterial organisms. Despite growing interest in plant tRFs and accumulating evidence of their function in plant development and stress responses, no public, web-based repository dedicated to these molecules is currently available. Here, we introduce tRex ( first comprehensive data-driven online resource specifically dedicated to tRFs in the model plant Arabidopsis thaliana. The portal is based on verified Arabidopsis tRNA annotation and includes in-house-generated and publicly available small RNA sequencing experiments from various tissues, ecotypes, genotypes and stress conditions. The provided web-based tools are designed in a user-friendly manner and allow for seamless exploration of the data that are presented in the form of dynamic tables and cumulative coverage profiles. The tRex database is connected to external genomic and citation resources, which makes it a one-stop solution for Arabidopsis tRF-related research.

Keywords: Arabidopsis thaliana; Database; Web portal; sRNA-seq; tRF; tRNA-derived fragments.

MeSH terms

  • Arabidopsis / genetics*
  • Base Sequence
  • Computational Biology / methods*
  • Databases, Genetic*
  • Internet
  • Nucleic Acid Conformation
  • RNA, Plant / chemistry
  • RNA, Plant / genetics*
  • RNA, Transfer / chemistry
  • RNA, Transfer / genetics*
  • Sequence Analysis, RNA / methods
  • Sequence Homology, Nucleic Acid


  • RNA, Plant
  • RNA, Transfer