miRcode: a map of putative microRNA target sites in the long non-coding transcriptome

Bioinformatics. 2012 Aug 1;28(15):2062-3. doi: 10.1093/bioinformatics/bts344. Epub 2012 Jun 19.


Summary: Although small non-coding RNAs, such as microRNAs, have well-established functions in the cell, long non-coding RNAs (lncRNAs) have only recently started to emerge as abundant regulators of cell physiology, and their functions may be diverse. A small number of studies describe interactions between small and lncRNAs, with lncRNAs acting either as inhibitory decoys or as regulatory targets of microRNAs, but such interactions are still poorly explored. To facilitate the study of microRNA-lncRNA interactions, we implemented miRcode: a comprehensive searchable map of putative microRNA target sites across the complete GENCODE annotated transcriptome, including 10 419 lncRNA genes in the current version.

Availability: http://www.mircode.org

Contact: erik.larsson@gu.se

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • MicroRNAs / genetics*
  • RNA, Long Noncoding / genetics*
  • Software*
  • Transcriptome*


  • MicroRNAs
  • RNA, Long Noncoding