Journal Article

Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing

Ai Wakamatsu, Kouichi Kimura, Jun-ichi Yamamoto, Tetsuo Nishikawa, Nobuo Nomura, Sumio Sugano and Takao Isogai

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 16, issue 6, pages 371-383
Published in print December 2009 | ISSN: 1340-2838
Published online October 2009 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsp022

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We analyzed diversity of mRNA produced as a result of alternative splicing in order to evaluate gene function. First, we predicted the number of human genes transcribed into protein-coding mRNAs by using the sequence information of full-length cDNAs and 5′-ESTs and obtained 23 241 of such human genes. Next, using these genes, we analyzed the mRNA diversity and consequently sequenced and identified 11 769 human full-length cDNAs whose predicted open reading frames were different from other known full-length cDNAs. Especially, 30% of the cDNAs we identified contained variation in the transcription start site (TSS). Our analysis, which particularly focused on multiple variable first exons (FEVs) formed due to the alternative utilization of TSSs, led to the identification of 261 FEVs expressed in the tissue-specific manner. Quantification of the expression profiles of 13 genes by real-time PCR analysis further confirmed the tissue-specific expression of FEVs, e.g. OXR1 had specific TSS in brain and tumor tissues, and so on. Finally, based on the results of our mRNA diversity analysis, we have created the FLJ Human cDNA Database. From our result, it has been understood mechanisms that one gene produces suitable protein-coding transcripts responding to the situation and the environment.

Keywords: full-length cDNA; alternative splicing; alternative transcription start site; mRNA diversity; tissue-specific expression

Journal Article.  7634 words.  Illustrated.

Subjects: Genetics and Genomics

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