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Nucleic Acids Research 2005 33(Database Issue):D125-D130; doi:10.1093/nar/gki089
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Nucleic Acids Research, 2005, Vol. 33, Database issue D125-D130
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

RNAdb—a comprehensive mammalian noncoding RNA database

Ken C. Pang1,2, Stuart Stephen1, Pär G. Engström3, Khairina Tajul-Arifin1, Weisan Chen2, Claes Wahlestedt3, Boris Lenhard3, Yoshihide Hayashizaki4 and John S. Mattick1,*

1 ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, 2 T cell Laboratory, Ludwig Institute for Cancer Research, Austin and Repatriation Medical Centre, Heidelberg, Victoria 3084, Australia, 3 Center for Genomics and Bioinformatics, Karolinska Institutet, 171 77 Stockholm, Sweden and 4 Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Centre, Yokohama, Kanagawa 230-0045, Japan

* To whom correspondence should be addressed. Tel: +61 7 3346 2110; Fax: +61 7 3346 2111; Email: j.mattick{at}imb.uq.edu.au

Received August 14, 2004; Revised and Accepted October 12, 2004

In recent years, there have been increasing numbers of transcripts identified that do not encode proteins, many of which are developmentally regulated and appear to have regulatory functions. Here, we describe the construction of a comprehensive mammalian noncoding RNA database (RNAdb) which contains over 800 unique experimentally studied non-coding RNAs (ncRNAs), including many associated with diseases and/or developmental processes. The database is available at http://research.imb.uq.edu.au/RNAdb and is searchable by many criteria. It includes microRNAs and snoRNAs, but not infrastructural RNAs, such as rRNAs and tRNAs, which are catalogued elsewhere. The database also includes over 1100 putative antisense ncRNAs and almost 20 000 putative ncRNAs identified in high-quality murine and human cDNA libraries, with more to be added in the near future. Many of these RNAs are large, and many are spliced, some alternatively. The database will be useful as a foundation for the emerging field of RNomics and the characterization of the roles of ncRNAs in mammalian gene expression and regulation.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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