Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection

Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L. G., Hume, D. A., RIKEN GER Group,, GSL Members,, Hayashizaki, Y. and Tomita, M. (2003) Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Research, 13 6B: 1301-1306. doi:10.1101/gr.1011603

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Author Numata, K.
Kanai, A.
Saito, R.
Kondo, S.
Adachi, J.
Wilming, L. G.
Hume, D. A.
RIKEN GER Group,
GSL Members,
Hayashizaki, Y.
Tomita, M.
Title Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
1549-5469
Publication date 2003
Sub-type Article (original research)
DOI 10.1101/gr.1011603
Open Access Status File (Publisher version)
Volume 13
Issue 6B
Start page 1301
End page 1306
Total pages 6
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Collection year 2003
Language eng
Abstract With the sequencing and annotation of genomes and transcriptomes of several eukaryotes, the importance of noncoding RNA (ncRNA)-RNA molecules that are not translated to protein products-has become more evident. A subclass of ncRNA transcripts are encoded by highly regulated, multi-exon, transcriptional units, are processed like typical protein-coding mRNAs and are increasingly implicated in regulation of many cellular functions in eukaryotes. This study describes the identification of candidate functional ncRNAs from among the RIKEN mouse full-length cDNA collection, which contains 60,770 sequences, by using a systematic computational filtering approach. We initially searched for previously reported ncRNAs and found nine murine ncRNAs and homologs of several previously described nonmouse ncRNAs. Through our computational approach to filter artifact-free clones that lack protein coding potential, we extracted 4280 transcripts as the largest-candidate set. Many clones in the set had EST hits, potential CpG islands surrounding the transcription start sites, and homologies with the human genome. This implies that many candidates are indeed transcribed in a regulated manner. Our results demonstrate that ncRNAs are a major functional subclass of processed transcripts in mammals.
Keyword Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Genetics & Heredity
Oligopyrimidine Gene Family
Comparative Genomics
Escherichia-coli
Messenger-rna
Cpg-islands
Host Gene
Transcript
Protein
Sequence
Expression
Q-Index Code C1
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2004 Higher Education Research Data Collection
Institute for Molecular Bioscience - Publications
 
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Created: Wed, 15 Aug 2007, 02:51:20 EST