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LETTER: CDS Annotation in Full-Length cDNA Sequence
- Masaaki Furuno,
- Takeya Kasukawa,
- Rintaro Saito,
- Jun Adachi,
- Harukazu Suzuki,
- Richard Baldarelli,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1478-1487; doi:10.1101/gr.1060303
...: When nonsense affects RNA abundance. Trends Biochem. Sci. 23 : 198 -199. ↵ Numata, K., Kanai, A., Saito, R., Kondo, S., Adachi, J., Wilming, L.G., Hume, D.A., RIKEN GER Group and GSL Members, Hayashizaki, Y., and Tomita, M. 2003 . Identification of putative noncoding RNAs among the RIKEN mouse full-length...
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Resource: Long noncoding RNAs in C. elegans
- Jin-Wu Nam and
- David P. Bartel
Genome Res. December 2012 22: 2529-2540; Published in Advance June 15, 2012, doi:10.1101/gr.140475.112
.... elegans, >1000 operons have been identified, each containing two to eight genes and accounting for 15% of all C. elegans genes (Spieth et al. 1993; Blumenthal and Gleason 2003). Among the 170 lincRNA genes, three tandem clusters were found (Supplemental Table S4), each containing lincRNA genes within 1 kb...
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ARTICLE: Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
- Jasmina Ponjavic,
- Chris P. Ponting,
- and Gerton Lunter
Genome Res. May 2007 17: 556-565; Published in Advance March 26, 2007, doi:10.1101/gr.6036807
.../README.txt ). These were identified using several filtering procedures (for details, see Okazaki et al. 2002 ; Carninci et al. 2005 ) and therefore represent the strongest candidates for noncoding sequences from among the full-length FANTOM cDNA collection. Nevertheless, to exclude the possibility that signatures...
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RESOURCE: Numerous Novel Annotations of the Human Genome Sequence Supported by a 5′-End–Enriched cDNA Collection
- Betina M. Porcel,
- Olivier Delfour,
- Vanina Castelli,
- Veronique De Berardinis,
- Lucie Friedlander,
- Corinne Cruaud,
- Abel Ureta-Vidal,
- Claude Scarpelli,
- Patrick Wincker,
- Vincent Schächter,
- William Saurin,
- Gabor Gyapay,
- Marcel Salanoubat,
- and Jean Weissenbach
Genome Res. March 2004 14: 463-471; Published in Advance February 12, 2004, doi:10.1101/gr.1481104
.../167) was further supported by an ecore shared with Tetraodon . As an example, a putative gene (accession nos. BX409763, BX435024, and BX460561) located on the forward strand of human chromosome 3 ( Fig. 2B ), matches its mouse counterpart on chromosome 6, overlapping the Riken cDNA C630007B19 gene (LocusID 320265...
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Method: Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals
- Hidenori Tani,
- Rena Mizutani,
- Kazi Abdus Salam,
- Keiko Tano,
- Kenichi Ijiri,
- Ai Wakamatsu,
- Takao Isogai,
- Yutaka Suzuki,
- and Nobuyoshi Akimitsu
Genome Res. May 2012 22: 947-956; Published in Advance February 27, 2012, doi:10.1101/gr.130559.111
...NR of RefSeq (Sayers et al. 2010), 1738 RNAs fromFLJ full-length human cDNAs (Ota et al. 2004;Wakamatsu et al. 2009), 36 RNAs from the Mammalian Gene Collection (MGC Project Team et al. 2009); Deutsches Krebsforschungszentrum (DKFZ); KazusaDNAResearch Institute (KIAA), and 261 RNAs from human large...
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RESOURCE: Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
- Takeya Kasukawa,
- Masaaki Furuno,
- Itoshi Nikaido,
- Hidemasa Bono,
- David A. Hume,
- Carol Bult,
- David P. Hill,
- Richard Baldarelli,
- Julian Gough,
- Alexander Kanapin,
- Hideo Matsuda,
- Lynn M. Schriml,
- Yoshihide Hayashizaki,
- Yasushi Okazaki,
- and John Quackenbush
Genome Res. June 2003 13: 1542-1551; doi:10.1101/gr.992803
...of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res . (this issue). ↵ Carninci, P., Waki, K., Shiraki, T., Konno, H., Shibata, K., Itoh, M., Aizawa, K., Arakawa, T., Ishii, Y., Sasaki, D., et al. 2003 . Targeting a complex transcriptome: The construction of the mouse full-length cDNA...
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LETTER: Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
- Besma Ben Amor,
- Sonia Wirth,
- Francisco Merchan,
- Philippe Laporte,
- Yves d’Aubenton-Carafa,
- Judith Hirsch,
- Alexis Maizel,
- Allison Mallory,
- Antoine Lucas,
- Jean Marc Deragon,
- Herve Vaucheret,
- Claude Thermes,
- and Martin Crespi
Genome Res. January 2009 19: 57-69; Published in Advance November 7, 2008, doi:10.1101/gr.080275.108
..., much work needs to be done to identify regulatory RNAs among these genes. Using -wide mapping of full-length cDNAs, we describe 33 new npcRNAs that, when added to the 43 previously identified ( Hirsch et al. 2006 ), make a set of 76 npcRNAs dispersed throughout the Arabidopsis . These npcRNAs belong...
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Chicken Special/Resources: Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
- Simon J. Hubbard,
- Darren V. Grafham,
- Kevin J. Beattie,
- Ian M. Overton,
- Stuart R. McLaren,
- Michael D.R. Croning,
- Paul E. Boardman,
- James K. Bonfield,
- Joan Burnside,
- Robert M. Davies,
- Elizabeth R. Farrell,
- Matthew D. Francis,
- Sam Griffiths-Jones,
- Sean J. Humphray,
- Christopher Hyland,
- Carol E. Scott,
- Haizhou Tang,
- Ruth G. Taylor,
- Cheryll Tickle,
- William R.A. Brown,
- Ewan Birney,
- Jane Rogers,
- and Stuart A. Wilson
Genome Res. January 2005 15: 174-183; Published in Advance December 8, 2004, doi:10.1101/gr.3011405
..., contained in the representative protein set from the Riken mouse cDNA project ( Okazaki et al. 2002 ) and the TIGR gene indices ( Quackenbush et al. 2001 ). The 23 cDNAs annotated as “no match” were further searched against satellite, repeats, and transposable element sequences using BLASTN, which did...
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Methods: Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries
- Michiel J.L. de Hoon,
- Ryan J. Taft,
- Takehiro Hashimoto,
- Mutsumi Kanamori-Katayama,
- Hideya Kawaji,
- Mitsuoki Kawano,
- Mami Kishima,
- Timo Lassmann,
- Geoffrey J. Faulkner,
- John S. Mattick,
- Carsten O. Daub,
- Piero Carninci,
- Jun Kawai,
- Harukazu Suzuki,
- and Yoshihide Hayashizaki
Genome Res. February 2010 20: 257-264; Published in Advance January 5, 2010, doi:10.1101/gr.095273.109
..., as it differentiated from a monoblast-like to a monocyte-like cell after stimulation with PMA (The FANTOM Consortium and the Riken Omics Science Center 2009). As part of this effort, short RNAs, 10 to 26 nt in size, were harvested at eight time points over 96 h and were reverse-transcribed to produce cDNAs, whichwere...
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ARTICLE: Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
- Timothy Ravasi,
- Harukazu Suzuki,
- Ken C. Pang,
- Shintaro Katayama,
- Masaaki Furuno,
- Rie Okunishi,
- Shiro Fukuda,
- Kelin Ru,
- Martin C. Frith,
- M. Milena Gongora,
- Sean M. Grimmond,
- David A. Hume,
- Yoshihide Hayashizaki,
- and John S. Mattick
Genome Res. January 2006 16: 11-19; Published in Advance December 12, 2005, doi:10.1101/gr.4200206
...have emerged from the RIKEN Mouse Gene Encyclopedia project ( Okazaki et al. 2002 ; Numata et al. 2003 ). This project was based on construction of comprehensive full-length cDNA libraries using oligo(dT) priming and advanced techniques for trapping 5′-caps of mature RNAs, with the aim of fully...

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