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Open Access Research article

Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment

Mugdha Khaladkar12, Jianghui Liu12, Dongrong Wen2, Jason TL Wang2 and Bin Tian1*

Author Affiliations

1 Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA

2 Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA

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BMC Genomics 2008, 9:189  doi:10.1186/1471-2164-9-189

Published: 25 April 2008



UnTranslated Regions (UTRs) of mRNAs contain regulatory elements for various aspects of mRNA metabolism, such as mRNA localization, translation, and mRNA stability. Several RNA stem-loop structures in UTRs have been experimentally identified, including the histone 3' UTR stem-loop structure (HSL3) and iron response element (IRE). These stem-loop structures are conserved among mammalian orthologs, and exist in a group of genes encoding proteins involved in the same biological pathways. It is not known to what extent RNA structures like these exist in all mammalian UTRs.


In this paper we took a systematic approach, named GLEAN-UTR, to identify small stem-loop RNA structure elements in UTRs that are conserved between human and mouse orthologs and exist in multiple genes with common Gene Ontology terms. This approach resulted in 90 distinct RNA structure groups containing 748 structures, with HSL3 and IRE among the top hits based on conservation of structure.


Our result indicates that there may exist many conserved stem-loop structures in mammalian UTRs that are involved in coordinate post-transcriptional regulation of biological pathways.