Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection

Dec. 11, 2003
Cheng-Kai, Shiau

Abstract

The importance of non-coding RNAs (ncRNAs) has become more evident. In this paper, the authors use a computational approach to extract the candidates of ncRNAs. They use the 15815 clones of non-coding-protein  RNAs data set which annotated in FANTOM2 project as source. After homology searching, aligning to mouse genomic sequence and GENSCAN prediction, they extract 4280 transcripts as the candidates of ncRNA. Finally they do the homology searching against EST data set, CpG island signal analysis, polyadenylation signal analysis to characterize these candidates.

from Genome Research, Vol. 13, 1301-6, 2003.

References:

1. Okazaki, Y., Furuno M., Kasukawa T., Adachi J., Bono H., Kondo S., Nikaido I., Osato N., Saito R., Suzuki, H., et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420, 563-573.
2. Sean R. Eddy. (2001) Non-coding RNA genes and the modern RNA world. Nature Reviews Genetics, 2, 919-929.
3. Erdmann, V.A., Barciszewska, M.Z., Hochberg, A., de Groot, N., and Barciszewski, J. (2001) Regulatory RNAs. Cell. Mol. Life Sci., 58, 960-977.
4. Erdmann, V.A., V.A., Szymanski, M., Hochberg, A., Groot, N., and Barciszewski, J. (2000) Non-coding, mRNA-like RNAs database Y2K. Nucleic Acids Res., 28, 197-200.