Using full-length cDNA cloning and sequencing strategies, the Functional Annotation of Mouse (FANTOM) project has identified thousands of novel transcripts from the mouse genome  (Carninci et al., 2005). In the most recent round of annotation, 34,030 cDNAs were manually annotated as putative ncRNAs (Maeda et al., 2006). Since both cloning and manual human annotation is subject to variation and error, the true number of ncRNAs remains unclear. To this end, we provide the results of various computational prediction strategies for use as additional filters in identifying ncRNAs (see Appendix A for more details). In addition to sequence data, details such as the Riken clone identifier, Genbank accession, genomic location, transcript length, likely imprinting status, and library of origin are provided. RNAdb also incorporates expression information from publicly available microarray datasets such as GNF Symatlas (Su et al., 2004). Although limited to only a small proportion of FANTOM3 ncRNAs, this information allows the identification of transcripts that are dynamically expressed across various tissues and cell types, and is expected to provide a useful starting point for their further characterization.