SIREs: searching for iron-responsive elements

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W360-7. doi: 10.1093/nar/gkq371. Epub 2010 May 11.


The iron regulatory protein/iron-responsive element regulatory system plays a crucial role in the post-transcriptional regulation of gene expression and its disruption results in human disease. IREs are cis-acting regulatory motifs present in mRNAs that encode proteins involved in iron metabolism. They function as binding sites for two related trans-acting factors, namely the IRP-1 and -2. Among cis-acting RNA regulatory elements, the IRE is one of the best characterized. It is defined by a combination of RNA sequence and structure. However, currently available programs to predict IREs do not show a satisfactory level of sensitivity and fail to detect some of the functional IREs. Here, we report an improved software for the prediction of IREs implemented as a user-friendly web server tool. The SIREs web server uses a simple data input interface and provides structure analysis, predicted RNA folds, folding energy data and an overall quality flag based on properties of well characterized IREs. Results are reported in a tabular format and as a schematic visual representation that highlights important features of the IRE. The SIREs (Search for iron-responsive elements) web server is freely available on the web at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Binding Sites
  • Humans
  • Internet
  • Iron / metabolism
  • Iron-Regulatory Proteins / metabolism*
  • Nucleic Acid Conformation
  • RNA / chemistry
  • Regulatory Sequences, Ribonucleic Acid*
  • Software*
  • Untranslated Regions*


  • Iron-Regulatory Proteins
  • Regulatory Sequences, Ribonucleic Acid
  • Untranslated Regions
  • RNA
  • Iron