TITLE

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

AUTHOR(S)
Okazaki, Y.; Furuno, M.; Kasukawa, T.; Adachi, J.; Bono, H.; Kondo, S.; Nikaido, I.; Osato, N.; Saito, R.; Suzuki, H.; Yamanaka, I.; Kiyosawa, H.; Yagi, K.; Tomaru, Y.; Hasegawa, Y.; Nogami, A.; Schönbach, C.; Gojobori, T.; Baldarelli, R.
PUB. DATE
December 2002
SOURCE
Nature;12/5/2002, Vol. 420 Issue 6915, p563
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
ACCESSION #
8639069

 

Related Articles

  • Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. Khrameeva, Ekaterina E.; Gelfand, Mikhail S. // BMC Bioinformatics;2012 Supplement 6, Vol. 13 Issue Suppl 6, p1 

    High-throughput sequencing of whole genomes and transcriptomes allows one to generate large amounts of sequence data very rapidly and at a low cost. The goal of most mRNA sequencing studies is to perform the comparison of the expression level between different samples. However, given a broad...

  • Long-Short-Long Games in mRNA Identification: The Length Matters. San Ming Wang // Current Pharmaceutical Biotechnology;Oct2008, Vol. 9 Issue 5, p362 

    The multiple levels of post-transcriptional processing and million-fold differences in expression levels make fully decoding the transcriptome in any given species extremely challenging. This review addresses the influence of sequenced length on transcriptome decoding under current DNA...

  • Understanding alternative splicing: towards a cellular code. Matlin, Arianne J.; Clark, Francis; Smith, Christopher W. J. // Nature Reviews Molecular Cell Biology;May2005, Vol. 6 Issue 5, p386 

    In violation of the 'one gene, one polypeptide' rule, alternative splicing allows individual genes to produce multiple protein isoforms — thereby playing a central part in generating complex proteomes. Alternative splicing also has a largely hidden function in quantitative gene control,...

  • Structural biology: RNA exerts self-control. Chetnani, Bhaskar; Mondragón, Alfonso // Nature;8/15/2013, Vol. 500 Issue 7462, p279 

    In this article, the authors discuss the role of RNA in cellular processes. They discuss how the structures of the regula­tory RNA sequences called riboswitches affect the transcription or translation of their downstream messenger RNA sequences. Also discussed is an article in the current...

  • Genome Network and FANTOM3: Assessing the Complexity of the Transcriptome. Hayashizaki, Yoshihide; Carninci, Piero // PLoS Genetics;Apr2006, Vol. 2 Issue 4, pe63 

    The article presents an overview of the FANTOM3/Genome Network Project. The analysis of transcriptome is significant to understanding genome function. Technologies including the hybridization of nucleic acids and the sequencing of products from messenger RNA libraries are efficient in analyzing...

  • In Situ Transcription and Detection of CD1a mRNA in Epidermal Cells: an Alternative to Standard In Situ Hybridization Techniques. Longley, Jack; Merchant, Margaret Anne; Kacinski, Barry M. // Journal of Investigative Dermatology;Sep89, Vol. 93 Issue 3, p432 

    To develop methods for the investigation of mRNA transcription in rare epidermal cells, we used in situ transcription to study CD1a mRNA in isolated CD1a positive cells. We chose to study this Langerhans cell marker because it is not known which epidermal cells actually produce the CD1a...

  • A first glimpse at the transcriptome of Physarum polycephalum. Glöckner, Gernot; Golderer, Georg; Werner-Felmayer, Gabriele; Meyer, Sonja; Marwan, Wolfgang // BMC Genomics;2008, Vol. 9, Special section p1 

    Background: Physarum polycephalum, an acellular plasmodial species belongs to the amoebozoa, a major branch in eukaryote evolution. Its complex life cycle and rich cell biology is reflected in more than 2500 publications on various aspects of its biochemistry, developmental biology,...

  • RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity. Kazuhiko Ohshima // International Journal of Evolutionary Biology;2013, p1 

    A substantial number of "retrogenes" that are derived from the mRNA of various intron-containing genes have been reported. A class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been shown to be involved in the reverse transcription of retrogenes (or processed...

  • New alternative promoter in regulation of the oct-1 human gene transcription. Portseva, T.; Krylova, I.; Georgieva, S.; Stepchenko, A.; Pankratova, E. // Doklady Biochemistry & Biophysics;Mar2013, Vol. 449 Issue 1, p72 

    For the first time, the presence of a new alternative promoter in the gene of the oct-1 transcription factor from which a previously unknown mRNA isoform Oct-1X, with 5′-terminus different from the previously described isoforms, was demonstrated. The nucleotide sequence of the Oct-1X cDNA...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics