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Studying Function of Alternative Splicing Products Based on Protein Structure Modeling

Research Project

Project/Area Number 18370061
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biophysics
Research InstitutionOchanomizu University

Principal Investigator

GO Mitiko  Ochanomizu University, バイオサイエンス学部, 特別客員教授 (70037290)

Co-Investigator(Kenkyū-buntansha) SHIONYU Masafumi  長浜バイオ大学, バイオサイエンス学部, 講師 (30345847)
由良 敬  お茶の水女子大学, 大学院・人間文化創成科学研究科, 教授 (50252226)
Co-Investigator(Renkei-kenkyūsha) YURA Kei  お茶の水女子大学, 大学院・人間文化創成科学研究科研究院, 教授 (50252226)
Project Period (FY) 2006 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥18,210,000 (Direct Cost: ¥15,300,000、Indirect Cost: ¥2,910,000)
Fiscal Year 2009: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2008: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2007: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2006: ¥5,600,000 (Direct Cost: ¥5,600,000)
Keywordsタンパク質立体構造 / 選択的スプライシング / ホモロジーモデリング / データベース / RNA編集 / 機能部位 / モジュール / 蛋白質間相互作用 / 理論生物学 / バイオインフォマティクス / RNA / リガンド結合部位
Research Abstract

The number of genes in the genome was turned out to be unexpectedly small and alternative splicing (AS), a mechanism to produce more than one product out of a single gene, is expected to fill the gap in the numbers. It is difficult to experimentally elucidate the mechanisms of functional diversity of proteins produced by alternative splicing of the single genes. We built methods to identify AS products from the measured data, to predict structures of AS products (proteins), and to estimate difference of biochemical function of the products. The methods elucidated the differences in a number of cases.

Report

(6 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report   Self-evaluation Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • Research Products

    (59 results)

All 2010 2009 2008 2007 2006 Other

All Journal Article (17 results) (of which Peer Reviewed: 15 results) Presentation (32 results) Remarks (10 results)

  • [Journal Article] RESOPS : A database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures.2009

    • Author(s)
      Yura, K., Sulaiman, S., Hatta, Y., Shionyu, M., Go, M.
    • Journal Title

      Plant and Cell Physiology 50

      Pages: 1865-1873

    • NAID

      10027344058

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] 陸上植物オルガネラのRNA編集の役割2009

    • Author(s)
      由良敬, 郷通子
    • Journal Title

      生物物理 49

      Pages: 244-245

    • NAID

      10025975899

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] RESOPS : A Database for Analyzing the Correspondence of RNA Editing Sites to Protein Three-Dimensional Structures.2009

    • Author(s)
      Kei Yura, Sintawee Sulaiman, Yosuke Hatta, Masafumi Shionyu, Mitiko Go
    • Journal Title

      Plant and Cell Physiology 50

      Pages: 1865-1873

    • NAID

      10027344058

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 陸上植物オルガネラのRNA編集の役割2009

    • Author(s)
      由良敬、郷通子
    • Journal Title

      生物物理 49

      Pages: 244-245

    • NAID

      10025975899

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Correlation between amino acid residues converted by RNA editing and functional residues in protein three- dimensional structures in plant organelles.2008

    • Author(s)
      Yura, K., Go, M.
    • Journal Title

      BMC Plant Biology 8

      Pages: 79-79

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.2008

    • Author(s)
      Yamasaki, C., Murakami, K., Fujii, Y., Sato, Y., Harada, E.,..., Yura, K.(66th),..., Shionyu, M.(101th),..., Go, M.(107th),..., Gojobori, T.(138th)
    • Journal Title

      Nucleic Acids Research 36

    • NAID

      120004689028

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Correlation between amino acid residues converted by RNA editing and functional residues in protein three- dimensional structures in plant organelles2008

    • Author(s)
      Yura, K., Go, M
    • Journal Title

      BMC Plant Biology 8

      Pages: 79-79

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts2008

    • Author(s)
      Yamasaki, C., Murakami, K., Fujii, Y., Sato, Y., Harada, E., Yura, K. (66th), Shionyu, M. (101th), Go, M. (107th), Gojobori, T. (138th)
    • Journal Title

      Nucleic Acids Research 36

      Pages: 793-799

    • NAID

      120004689028

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles2008

    • Author(s)
      Kei Yura, et al.
    • Journal Title

      BMC Plant Biology 8

      Pages: 79-79

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts2008

    • Author(s)
      Genome Information Integration Project and H-Invitational 2 consortium
    • Journal Title

      Nucleic Acids Research 36

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Contribution of computational biology and structural genomics to understand genome and transcriptome.2007

    • Author(s)
      Go, M., Yura, K., Shionyu, M.
    • Journal Title

      Proceedings of the International Symposium on Frontiers of Computational Science 2005 (ISFCS2005), (eds.Kaneda, Y., Kawamura, H., Sasai, M.)(Springer)

      Pages: 75-80

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Contribution of computational biology and structural genomics to understand genome and transcriptome2007

    • Author(s)
      Go M., Yura K., Shionyu M.
    • Journal Title

      Proceedings of the International Symposium on Frontiers of Computational Science 2005 (ISFCS2005), (eds. Kaneda, Y., Kawamura, H., Sasai, M.), Springer

      Pages: 75-80

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Contribution of computational biology and structural genomics to understand genome and transcriptome.2007

    • Author(s)
      Mitiko Go et al.
    • Journal Title

      Frontiers of Computational Science : Proceedings of the international sysmposium on frontiers of computational science 2005

      Pages: 75-80

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Alternative splicing in human transcriptome : functional and structural influence on proteins.2006

    • Author(s)
      Yura, K., Shionyu, M., Hagino, K., Hijikata, A., Hirashima, Y., Nakahara, T., Eguchi, T., Shinoda, K., Yamaguchi, A., Takahashi, K., Itoh, T., Imanishi, T., Gojobori, T., Go, M.
    • Journal Title

      Gene 380

      Pages: 63-71

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Survey of Conserved Alternative Splicing Events of mRNAs Encoding SR Proteins in Land Plants.2006

    • Author(s)
      Iida, K., Go, M.
    • Journal Title

      Mol.Biol.Evol. 23

      Pages: 1085-1094

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Alternative splicing in human transcriptome : functional and structural influence on proteins2006

    • Author(s)
      Yura, K., Shionyu, M., Hagino, K., Hijikata, A., Hirashima, Y., Nakahara, T., Eguchi, T., Shinoda, K., Yamaguchi, A., Takahashi, K., Itoh, T., Imanishi, T., Gojobori, T., Go, M.
    • Journal Title

      Gene 380

      Pages: 63-71

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Alternative splicing in human transcriptome : functional and structural influence on proteins.2006

    • Author(s)
      Kei Yura et al.
    • Journal Title

      Gene 380・2

      Pages: 3917-3928

    • Related Report
      2006 Annual Research Report
  • [Presentation] Information flow from genes to proteins2010

    • Author(s)
      Go, M.
    • Organizer
      International Symposium : Fifty Years of Biophysics Research at Nagoya University
    • Place of Presentation
      名古屋大学(名古屋市)
    • Year and Date
      2010-03-12
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] AS-ALPS : a database for inferring effects of alternative splicing based on the protein 3D structure2010

    • Author(s)
      Shionyu, M., Takahashi, K., Go, M.
    • Organizer
      Asian Young Researchers Conference on Computational and Omics Biology 2010
    • Place of Presentation
      National Cheng Kung University (Taiwan)
    • Year and Date
      2010-03-10
    • Related Report
      2009 Final Research Report
  • [Presentation] AS-ALPS : a database for inferring effects of alternative splicing based on the protein 3D structure2010

    • Author(s)
      Masafumi Shionyu, Ken-ichi Takahashi, Mitiko Go
    • Organizer
      Asian Young Researchers Conference on Computational and Omics Biology 2010
    • Place of Presentation
      National Cheng Kung University(Taiwan)
    • Year and Date
      2010-03-10
    • Related Report
      2009 Annual Research Report
  • [Presentation] 遺伝情報の流れの複雑性からみる生物進化2010

    • Author(s)
      郷通子
    • Organizer
      「生物進化の持続性と転移」国際高等研究所研究会
    • Place of Presentation
      国際高等研究所(木津川市)
    • Year and Date
      2010-03-02
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] 選択的スプライシングの曖昧さとその意味2010

    • Author(s)
      郷通子
    • Organizer
      大沢文夫研究会
    • Place of Presentation
      名古屋大学(名古屋市)
    • Year and Date
      2010-02-20
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] RNA編集とその生物的意味2010

    • Author(s)
      由良敬
    • Organizer
      大沢文夫研究会
    • Place of Presentation
      名古屋大学(名古屋市)
    • Year and Date
      2010-02-20
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] A web service for functional annotations of protein isoforms produced by alternative splicing2009

    • Author(s)
      Shionyu, M., Takahashi, K., Go, M.
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(横浜市)
    • Year and Date
      2009-12-11
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] RESOPS : A database of RNA editing sites in plant organelle mapped onto protein three-dimensional structures2009

    • Author(s)
      Yura, K., Sulaiman, S., Hatta, Y., Shionyu, M., Go, M.
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(横浜市)
    • Year and Date
      2009-12-10
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] Events during information flow from genomic sequence to protein structure/function in biological system2009

    • Author(s)
      Go, M.
    • Organizer
      The 4th Global COE International Symposium 2009 joint with the 19th Hot Spring Harbor Symposium Molecular Evolution and Bioinformatics
    • Place of Presentation
      九州大学病院キャンパス(福岡市)
    • Year and Date
      2009-11-01
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] 筋蛋白質のモジュールと筋収縮について2009

    • Author(s)
      郷通子
    • Organizer
      生物物理学会サテライトミーティング「筋収縮のメカニズムを考える」
    • Place of Presentation
      徳島文理大学(徳島市)
    • Year and Date
      2009-10-29
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] たくさんの師との巡り会いと海外で学んだ経験2009

    • Author(s)
      郷通子
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテル(熊本市)
    • Year and Date
      2009-05-22
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] Diversification of protein repertoire by alternative splicing2009

    • Author(s)
      Yura, K.
    • Organizer
      The 66th Korean Society for Biochemistry and Molecular Biology Annual Meeting
    • Place of Presentation
      COEX (Korea)
    • Year and Date
      2009-05-13
    • Related Report
      2009 Final Research Report
  • [Presentation] Diversification of protein repertoire by alternative splicing2009

    • Author(s)
      Kei Yura
    • Organizer
      The 66th Korean Society for Biochemistry and Molecular Biology Annual Meeting
    • Place of Presentation
      COEX(Korea)
    • Year and Date
      2009-05-13
    • Related Report
      2009 Annual Research Report
  • [Presentation] Effect of residue substitution by RNA editing on protein three-dimensional structures in plant organelles2008

    • Author(s)
      Yura, K., Go, M.
    • Organizer
      BMB2008(第31回日本分子生物学会年会、第81回日本生化学会年会 合同大会)
    • Place of Presentation
      神戸国際会議場(神戸市)
    • Year and Date
      2008-12-10
    • Related Report
      2009 Final Research Report
  • [Presentation] Effect of residue substitution by RNA editing on protein three-dimensional structures in plant organelles2008

    • Author(s)
      Kei Yura, Mitiko Go
    • Organizer
      BMB2008(第31回日本分子生物学会年会、第81回日本生化学会年会合同大会)
    • Place of Presentation
      神戸国際会議場
    • Year and Date
      2008-12-10
    • Related Report
      2008 Annual Research Report
  • [Presentation] Correlation between RNA editing sites on amino acid residues and protein three-dimensional structures in plant organelles2008

    • Author(s)
      Go, M., Yura, K.
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡国際会議場(福岡市)
    • Year and Date
      2008-12-05
    • Related Report
      2009 Final Research Report
  • [Presentation] Correlation between RNA editing sites on amino acid residues and protein three-dimensional structures in plant organelles2008

    • Author(s)
      Mitiko Go, Kei Yura
    • Organizer
      日本生物物理学会第46回年会
    • Place of Presentation
      福岡国際会議場
    • Year and Date
      2008-12-05
    • Related Report
      2008 Annual Research Report
  • [Presentation] タンパク質の立体構造と遺伝子の構造の進化的起源に関する研究2008

    • Author(s)
      郷通子
    • Organizer
      日本進化学会賞/木村資生記念学術賞受賞講演、第10回日本進化学会大会
    • Place of Presentation
      東京大学駒場キャンパス(東京)
    • Year and Date
      2008-08-23
    • Related Report
      2009 Final Research Report
  • [Presentation] 植物オルガネラにおけるRNAエディティングの部位とタンパク質立体構造の関係2008

    • Author(s)
      郷通子, 由良敬
    • Organizer
      第10回日本進化学会大会
    • Place of Presentation
      東京大学駒場キャンパス(東京)
    • Year and Date
      2008-08-22
    • Related Report
      2009 Final Research Report
  • [Presentation] 植物オルガネラにおけるRNAエディティングの部位とタンパク質立体構造の関係2008

    • Author(s)
      郷通子, 由良敬
    • Organizer
      第10回日本進化学会大会
    • Place of Presentation
      東京大学駒場キャンパス
    • Year and Date
      2008-08-22
    • Related Report
      2008 Annual Research Report
  • [Presentation] 研究は最初から国際舞台で : 男性も女性も輝くために2008

    • Author(s)
      郷通子
    • Organizer
      生物物理若手夏の学校
    • Place of Presentation
      八王子セミナーハウス(八王子市)
    • Year and Date
      2008-07-22
    • Related Report
      2009 Final Research Report
  • [Presentation] Information Flow from DNA Sequence to Protein Function2008

    • Author(s)
      Yura, K., Go, M.
    • Organizer
      Science in Japan Forum 2008 "Interaction of Physics and Biology"
    • Place of Presentation
      JSPS, 米国ワシントンDC
    • Year and Date
      2008-06-20
    • Related Report
      2009 Final Research Report 2008 Annual Research Report
  • [Presentation] Information flow from DNA sequence to protein function2008

    • Author(s)
      Yura, K., Go, M.
    • Organizer
      Science in Japan Forum 2008 : Interaction of Physics and Biology
    • Place of Presentation
      JSPS米国ワシントンDC
    • Year and Date
      2008-06-20
    • Related Report
      2008 Self-evaluation Report
  • [Presentation] シミュレーションが切り開く新しい生物学-夢と発想の展開へ-2007

    • Author(s)
      郷通子
    • Organizer
      次世代生命体統合シミュレーション研究開発プロジェクトシンポジウム2007
    • Place of Presentation
      MY PLAZAホール(東京)
    • Year and Date
      2007-12-25
    • Related Report
      2009 Final Research Report
  • [Presentation] 選択的スプライシングがもたらすタンパク質構造への影響2007

    • Author(s)
      郷通子、由良敬、高橋健一、塩生真史
    • Organizer
      シンポジウム「構造プロテオミクスを支援するバイオインフォマティクス」、生物物理学会年会
    • Place of Presentation
      横浜パシフィコ(横浜)
    • Year and Date
      2007-12-22
    • Related Report
      2009 Final Research Report
  • [Presentation] 真核生物の遺伝子構造とタンパク質立体構造・機能の関係2007

    • Author(s)
      由良敬, 塩生真史, 郷通子
    • Organizer
      日本進化学会第9回京都大会シンポジウム
    • Place of Presentation
      京都大学(京都市)
    • Year and Date
      2007-09-02
    • Related Report
      2009 Final Research Report
  • [Presentation] 真核生物の遺伝子構造とタンパク質立体構造・機能の関係2007

    • Author(s)
      由良敬、塩生真史、郷通子
    • Organizer
      日本進化学会第9回京都大会シンポジウム
    • Place of Presentation
      京都大学
    • Year and Date
      2007-09-02
    • Related Report
      2007 Annual Research Report
  • [Presentation] Computational Biology to Understand Genome and Transcriptome2006

    • Author(s)
      Go, M.
    • Organizer
      5th EABS & 44th Annual Meeting of Biophysical Society of Japan
    • Place of Presentation
      沖縄コンベンションセンター(宜野湾市)
    • Year and Date
      2006-11-12
    • Related Report
      2009 Final Research Report
  • [Presentation] 真核生物遺伝子産物の多様性を生み出している選択的スプライシングのタンパク質立体構造への影響2006

    • Author(s)
      由良敬, 郷通子
    • Organizer
      日本進化学会第8回大会シンポジウム
    • Place of Presentation
      国立オリンピック記念青少年総合センター(東京都渋谷区)
    • Year and Date
      2006-08-30
    • Related Report
      2009 Final Research Report
  • [Presentation] タンパク質の予期せぬ部品モジュール数理と生物の橋渡しをめざして2006

    • Author(s)
      郷通子
    • Organizer
      第27回数理の翼夏季セミナー
    • Place of Presentation
      広島大学西条研修センター(東広島市)
    • Year and Date
      2006-08-10
    • Related Report
      2009 Final Research Report
  • [Presentation] Systematic detection of protein regions affected by alternative splicing2006

    • Author(s)
      Shionyu, M., Yura, K., Hijikata, A., Nakahara, T., Shinoda, K., Yamaguchi, A., Takahashi, K., Go, M.
    • Organizer
      20th International Congress of Biochemistry and Molecular Biology
    • Place of Presentation
      国立京都国際会館(京都市)
    • Year and Date
      2006-06-22
    • Related Report
      2009 Final Research Report
  • [Presentation] A possible effect of alternative splicing on multiple regions of a single protein2006

    • Author(s)
      Shionyu, M., Yura, K., Go, M.
    • Organizer
      5th EABS & 44th Annual Meeting of Biophysical Society of Japan
    • Place of Presentation
      沖縄コンベンションセンター(宜野湾市)
    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://as-alps.nagahama-i-bio.ac.jp/

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://cib.cf.ocha.ac.jp/RNAEDITING/

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://teapot.lib.ocha.ac.jp/ocha/

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://cib.cf.ocha.ac.jp/~yura/present0.html

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://cib.cf.ocha.ac.jp/~yura/present0.html

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://as-alps.nagahama-i-bio.ac.jp/

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://cib.cf.ocha.ac.jp/RNAEDITING/

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://teapot.lib.ocha.ac.jp/ocha/

    • Related Report
      2008 Self-evaluation Report
  • [Remarks]

    • URL

      http://cib.cf.ocha.ac.jp/~yura/present0.html

    • Related Report
      2008 Self-evaluation Report
  • [Remarks]

    • URL

      http://cib.cf.ocha.ac.jp/~yura/present0.html

    • Related Report
      2008 Annual Research Report

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Published: 2006-04-01   Modified: 2016-04-21  

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