Cargando…
Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing
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 gene...
Autores principales: | , , , , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2009
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780955/ https://www.ncbi.nlm.nih.gov/pubmed/19880432 http://dx.doi.org/10.1093/dnares/dsp022 |
_version_ | 1782174541608386560 |
---|---|
author | Wakamatsu, Ai Kimura, Kouichi Yamamoto, Jun-ichi Nishikawa, Tetsuo Nomura, Nobuo Sugano, Sumio Isogai, Takao |
author_facet | Wakamatsu, Ai Kimura, Kouichi Yamamoto, Jun-ichi Nishikawa, Tetsuo Nomura, Nobuo Sugano, Sumio Isogai, Takao |
author_sort | Wakamatsu, Ai |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2780955 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-27809552009-11-23 Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing Wakamatsu, Ai Kimura, Kouichi Yamamoto, Jun-ichi Nishikawa, Tetsuo Nomura, Nobuo Sugano, Sumio Isogai, Takao DNA Res Full Papers 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. Oxford University Press 2009-12 2009-10-30 /pmc/articles/PMC2780955/ /pubmed/19880432 http://dx.doi.org/10.1093/dnares/dsp022 Text en © The Author 2009. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Full Papers Wakamatsu, Ai Kimura, Kouichi Yamamoto, Jun-ichi Nishikawa, Tetsuo Nomura, Nobuo Sugano, Sumio Isogai, Takao Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing |
title | Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing |
title_full | Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing |
title_fullStr | Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing |
title_full_unstemmed | Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing |
title_short | Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing |
title_sort | identification and functional analyses of 11 769 full-length human cdnas focused on alternative splicing |
topic | Full Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780955/ https://www.ncbi.nlm.nih.gov/pubmed/19880432 http://dx.doi.org/10.1093/dnares/dsp022 |
work_keys_str_mv | AT wakamatsuai identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing AT kimurakouichi identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing AT yamamotojunichi identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing AT nishikawatetsuo identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing AT nomuranobuo identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing AT suganosumio identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing AT isogaitakao identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing |