Identification of mirtrons in rice using MirtronPred: A tool for predicting plant mirtrons

Pankaj Kumar Joshi, Dinesh Gupta, Umesh Kumar Nandal, Yusuf Khan, Sunil Kumar Mukherjee, Neeti Sanan-Mishra

Research output: Contribution to journalArticlepeer-review

20 Scopus citations

Abstract

Studies from flies and insects have reported the existence of a special class of miRNA, called mirtrons that are produced from spliced-out introns in a DROSHA-independent manner. The spliced-out lariat is debranched and refolded into a stem-loop structure resembling the pre-miRNA, which can then be processed by DICER into mature ~. 21 nt species. The mirtrons have not been reported from plants. In this study, we present MirtronPred, a web based server to predict mirtrons from intronic sequences. We have used the server to predict 70 mirtrons in rice introns that were put through a stringent selection filter to shortlist 16 best sequences. The prediction accuracy was subsequently validated by northern analysis and RT-PCR of a predicted Os-mirtron-109. The target sequences for this mirtron were also found in the rice degradome database. The possible role of the mirtron in rice regulon is discussed. The MirtronPred web server is available at http://bioinfo.icgeb.res.in/mirtronPred.

Original languageEnglish
Pages (from-to)370-375
Number of pages6
JournalGenomics
Volume99
Issue number6
DOIs
StatePublished - Jun 2012
Externally publishedYes

Keywords

  • MiRNA
  • MirtronPred server
  • Mirtrons
  • Plants
  • Stress

Fingerprint Dive into the research topics of 'Identification of mirtrons in rice using MirtronPred: A tool for predicting plant mirtrons'. Together they form a unique fingerprint.

Cite this