Circular RNA Interactome

Site updated: 2020-01-30, 16:52 EST

Welcome to Circular RNA Interactome

Hundreds of RNA-binding proteins and miRNAs has been shown to regulate gene expression in mammals. Recently, circular RNAs (circRNAs) have been reported to regulate gene expression by sponging miRNA. Here we have used 109 datasets of RNA-binding proteins (RBPs) and queried circRNAs (Gla┼żar et al. 2014) for RNA-binding sites. CircInteractome predicts the miRNAs which can potentially target the circRNAs using the Targetscan prediction tool (Grimson et al., 2007). This computational tool enables the prediction and mapping of binding sites for RBPs and miRNAs on reported circRNAs.

Highlights of CircInteractome:

  • Searches circRNAs name
  • Searches the genomic position and best-matching transcripts of the circRNA
  • Retrieves genomic and mature circRNA sequences
  • Searches RBPs binding to a circRNA and to sequences upstream/downstream of the circRNA
  • Identifies RBPs binding to the circRNA junctions
  • Identifies miRNAs targeting a circRNA
  • Designs divergent primers for circRNAs
  • Designs siRNAs Specific to circRNA
Citing CircInteractome

Dudekula DB, Panda AC, Grammatikakis I, De S, Abdelmohsen K, and Gorospe M. CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs. RNA Biology, 2016, Jan 2;13(1):34-42  [PDF Download]


CircInteractome computationally identifies potential binding sites for RNA binding proteins within circRNAs. Authors emphasize that the binding sites identified here are only potential or predicted based on CLIP data sets and are subject to experimental validation.

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