RT Journal
A1 Numata, Koji
A1 Kanai, Akio
A1 Saito, Rintaro
A1 Kondo, Shinji
A1 Adachi, Jun
A1 Wilming, Laurens G.
A1 Hume, David A.
A1 RIKEN GER Group
A1 GSL Members
A1 Hayashizaki, Yoshihide
A1 Tomita, Masaru
T1 Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection
JF Genome Research 
JO Genome Research 
YR 2003 
FD June 01 
VO 13 
IS 6b 
SP 1301 
OP 1306 
DO 10.1101/gr.1011603 
UL http://genome.cshlp.org/content/13/6b/1301.abstract 
AB 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.