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Background

For a number of years the Mattick group at the Institute for Molecular Bioscience (IMB) has been developing an interest in one of the great mysteries of biology: what, if anything, is the role of the vast amount of introns and genomic sequences in the genes of the higher organisms that do not appear to have any function? These sequences are often referred to as "junk DNA" but many of them are in fact expressed as noncoding RNAs (ncRNAs), and may account for around 98% of all genomic output in humans.

RNAdb

We have developed a comprehensive mammalian noncoding RNA database (RNAdb) which contains sequences and annotations for tens of thousands of noncoding RNAs. The database currently provides nucleotide sequences and annotations for tens of thousands of non-housekeeping ncRNAs. These include a wide range of microRNAs, small nucleolar RNAs and larger mRNA-like ncRNAs. Some of these have documented functions and/or expression patterns, but the majority remains of unclear significance, and include PIWI-interacting RNAs, ncRNAs identified from the latest rounds of large-scale cDNA sequencing projects, putative antisense transcripts, as well as ncRNAs predicted on the basis of structural features and alignments.

The database can be accessed or queried in various ways. Users can casually browse the collection. Specific searches can be performed using keywords (with or without Boolean operators) and/or by applying filters across nominated fields. BLAST searches permit users to locate regions of similarity between sequences of interest and those stored in the database. The entire database, or the result of a user-specified query, is available for download in either FASTA or XML format via the website. Alternatively, search results can be returned as a custom track for loading directly into the UCSC Genome Browser. This feature allows users to easily take any definable subset of the database and readily apply it to the UCSC Genome Browser's extensive set of comparative and analytical tools.

One of today's principal challenges in the field of RNomics is to explore the functional significance of the thousands of ncRNAs. If this challenge is to be successfully met in coming years, then experimental proof of function will be paramount. Such proof often comes slowly and incrementally, and we hope that having bioinformatic resources such as RNAdb will prove helpful to guide and facilitate future discovery.

Reference

If you find this website useful and would like to cite RNAdb, please use the following reference:
Pang, K.C., Stephen, S., Engstrom, P.G., Tajul-Arifin, K., Chen, W., Wahlestedt, C., Lenhard, B., Hayashizaki, Y., Mattick, J.S. (2005) RNAdb - a comprehensive mammalian noncoding RNA database. Nucl. Acids Res. 33 (Database Issue): D125-D130.

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