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Volumn 34, Issue 14, 2006, Pages 3917-3928

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

(22)  Takeda, Jun Ichi a,b   Suzuki, Yutaka c   Nakao, Mitsuteru b,d   Barrero, Roberto A e   Koyanagi, Kanako O f   Jin, Lihua e   Motono, Chie b   Hata, Hiroko c   Isogai, Takao g,h   Nagai, Keiichi h,i   Otsuki, Tetsuji h   Kuryshev, Vladimir j   Shionyu, Masafumi k   Yura, Kei l,m   Go, Mitiko j,n   Thierry Mieg, Jean o,p   Thierry Mieg, Danielle o,p   Wiemann, Stefan j   Nomura, Nobuo b   Sugano, Sumio c   more..


Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; CYTOPLASM PROTEIN; HUNTINGTIN; I KAPPA B KINASE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INOSINATE DEHYDROGENASE; NUCLEAR PROTEIN; PROTEIN KINASE; RNA; SEMAPHORIN; TRANSCRIPTOME; MESSENGER RNA; PROTEIN;

EID: 33748550313     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl507     Document Type: Article
Times cited : (35)

References (44)
  • 1
    • 0018263844 scopus 로고
    • Why genes in pieces?
    • Gilbert,W. (1978) Why genes in pieces? Nature, 271, 501.
    • (1978) Nature , vol.271 , pp. 501
    • Gilbert, W.1
  • 2
    • 0032435862 scopus 로고    scopus 로고
    • Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation
    • Lopez,A.J. (1998) Alternative splicing of pre-mRNA: Developmental consequences and mechanisms of regulation. Annu. Rev. Genet., 32, 279-305.
    • (1998) Annu. Rev. Genet. , vol.32 , pp. 279-305
    • Lopez, A.J.1
  • 3
    • 0034256020 scopus 로고    scopus 로고
    • Alternative pre-mRNA splicing: The logic of combinatorial control
    • Smith,C.W. and Valcarcel,J. (2000) Alternative pre-mRNA splicing: The logic of combinatorial control. Trends Biochem. Sci., 25, 381-388.
    • (2000) Trends Biochem. Sci. , vol.25 , pp. 381-388
    • Smith, C.W.1    Valcarcel, J.2
  • 4
    • 5144230220 scopus 로고    scopus 로고
    • Generation of recognition diversity in the nervous system
    • Schmucker,D. and Flanagan,J.G. (2004) Generation of recognition diversity in the nervous system. Neuron, 44, 219-222.
    • (2004) Neuron , vol.44 , pp. 219-222
    • Schmucker, D.1    Flanagan, J.G.2
  • 5
    • 4444318773 scopus 로고    scopus 로고
    • Alternative splicing of Drosophila Dscam generates axon guidance receptors that exhibit isoform-specific homophilic binding
    • Wojtowicz,W.M., Flanagan,J.J., Millard,S.S., Zipursky,S.L. and Clemens,J.C. (2004) Alternative splicing of Drosophila Dscam generates axon guidance receptors that exhibit isoform-specific homophilic binding. Cell, 118, 619-633.
    • (2004) Cell , vol.118 , pp. 619-633
    • Wojtowicz, W.M.1    Flanagan, J.J.2    Millard, S.S.3    Zipursky, S.L.4    Clemens, J.C.5
  • 7
    • 0034084035 scopus 로고    scopus 로고
    • Analysis of expressed sequence tags indicates 35 000 human genes
    • Ewing,B. and Green,P. (2000) Analysis of expressed sequence tags indicates 35 000 human genes. Nature Genet., 25, 232-234.
    • (2000) Nature Genet. , vol.25 , pp. 232-234
    • Ewing, B.1    Green, P.2
  • 8
    • 0036429269 scopus 로고    scopus 로고
    • Finding signals that regulate alternative splicing in the post-genomic era
    • reviews0008.1-0008.16
    • Ladd,A.N. and Cooper,T.A. (2002) Finding signals that regulate alternative splicing in the post-genomic era. Genome Biol., 3, reviews0008.1-0008.16.
    • (2002) Genome Biol. , vol.3
    • Ladd, A.N.1    Cooper, T.A.2
  • 9
    • 0036337915 scopus 로고    scopus 로고
    • A genomic view of alternative splicing
    • Modrek,B. and Lee,C. (2002) A genomic view of alternative splicing. Nature Genet., 30, 13-19.
    • (2002) Nature Genet. , vol.30 , pp. 13-19
    • Modrek, B.1    Lee, C.2
  • 10
    • 0037246718 scopus 로고    scopus 로고
    • ASAP: The Alternative Splicing Annotation Project
    • Lee,C., Atanelov,L., Modrek,B. and Xing,Y. (2003) ASAP: The Alternative Splicing Annotation Project. Nucleic Acids Res., 31, 101-105.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 101-105
    • Lee, C.1    Atanelov, L.2    Modrek, B.3    Xing, Y.4
  • 13
    • 0033782920 scopus 로고    scopus 로고
    • Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells
    • Zhang,Q.H., Ye,M., Wu,X.Y., Ren,S.X., Zhao,M., Zhao,C.J., Fu,G., Shen,Y., Fan,H.Y., Lu,G. et al. (2000) Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. Genome Res., 10, 1546-1560.
    • (2000) Genome Res. , vol.10 , pp. 1546-1560
    • Zhang, Q.H.1    Ye, M.2    Wu, X.Y.3    Ren, S.X.4    Zhao, M.5    Zhao, C.J.6    Fu, G.7    Shen, Y.8    Fan, H.Y.9    Lu, G.10
  • 17
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing,B., Hillier,L., Wendl,M.C. and Green,P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res., 8, 175-185.
    • (1998) Genome Res. , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 18
    • 30044442791 scopus 로고    scopus 로고
    • Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes
    • Kimura,K., Wakamatsu,A., Suzuki,Y., Ota,T., Nishikawa,T., Yamashita,R., Yamamoto,J., Sekine,M., Tsuritani,K., Wakaguri,H. et al. (2006) Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes. Genome Res., 16, 55-65.
    • (2006) Genome Res. , vol.16 , pp. 55-65
    • Kimura, K.1    Wakamatsu, A.2    Suzuki, Y.3    Ota, T.4    Nishikawa, T.5    Yamashita, R.6    Yamamoto, J.7    Sekine, M.8    Tsuritani, K.9    Wakaguri, H.10
  • 19
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • Fairbrother,W.G., Yeh,R.F., Sharp,P.A. and Burge,C.B. (2002) Predictive identification of exonic splicing enhancers in human genes. Science, 297, 1007-1013.
    • (2002) Science , vol.297 , pp. 1007-1013
    • Fairbrother, W.G.1    Yeh, R.F.2    Sharp, P.A.3    Burge, C.B.4
  • 21
    • 33748699034 scopus 로고    scopus 로고
    • Improvement of PSORT II protein sorting prediction for mammalian proteins
    • Nakao,M. and Nakai,K. (2002) Improvement of PSORT II protein sorting prediction for mammalian proteins. Genome Informatics, 13, 441-442.
    • (2002) Genome Informatics , vol.13 , pp. 441-442
    • Nakao, M.1    Nakai, K.2
  • 22
    • 0034326362 scopus 로고    scopus 로고
    • Analysis of canonical and non-canonical splice sites in mammalian genomes
    • Burset,M., Seledtsov,I.A. and Solovyev,V.V. (2000) Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res., 28, 4364-4375.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4364-4375
    • Burset, M.1    Seledtsov, I.A.2    Solovyev, V.V.3
  • 23
    • 0034029236 scopus 로고    scopus 로고
    • ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome
    • Croft,L., Schandorff,S., Clark,F., Burrage,K., Arctander,P. and Mattick,J.S. (2000) ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nature Genet., 24, 340-341.
    • (2000) Nature Genet. , vol.24 , pp. 340-341
    • Croft, L.1    Schandorff, S.2    Clark, F.3    Burrage, K.4    Arctander, P.5    Mattick, J.S.6
  • 24
    • 0035393343 scopus 로고    scopus 로고
    • Genome-wide detection of alternative splicing in expressed sequences of human genes
    • Modrek,B., Resch,A., Grasso,C. and Lee,C. (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res., 29, 2850-2859.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2850-2859
    • Modrek, B.1    Resch, A.2    Grasso, C.3    Lee, C.4
  • 26
    • 0035179257 scopus 로고    scopus 로고
    • The contribution of exon-skipping events on chromosome 22 to protein coding diversity
    • Hide,W.A., Babenko,V.N., van Heusden,P.A., Seoighe,C. and Kelso,J.F. (2001) The contribution of exon-skipping events on chromosome 22 to protein coding diversity. Genome Res., 11, 1848-1853.
    • (2001) Genome Res. , vol.11 , pp. 1848-1853
    • Hide, W.A.1    Babenko, V.N.2    van Heusden, P.A.3    Seoighe, C.4    Kelso, J.F.5
  • 27
    • 19344366251 scopus 로고    scopus 로고
    • Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells
    • Lejeune,F. and Maquat,L.E. (2005) Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr. Opin. Cell Biol., 17, 309-315.
    • (2005) Curr. Opin. Cell Biol. , vol.17 , pp. 309-315
    • Lejeune, F.1    Maquat, L.E.2
  • 28
    • 0038701605 scopus 로고    scopus 로고
    • The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons
    • Lev-Maor,G., Sorek,R., Shomron,N. and Ast,G. (2003) The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science, 300, 1288-1291.
    • (2003) Science , vol.300 , pp. 1288-1291
    • Lev-Maor, G.1    Sorek, R.2    Shomron, N.3    Ast, G.4
  • 29
    • 26844431946 scopus 로고    scopus 로고
    • Splicing of a rare class of introns by the U12-dependent spliceosome
    • Will,C.L. and Luhrmann,R. (2005) Splicing of a rare class of introns by the U12-dependent spliceosome. Biol. Chem., 386, 713-724.
    • (2005) Biol. Chem. , vol.386 , pp. 713-724
    • Will, C.L.1    Luhrmann, R.2
  • 30
    • 0242317345 scopus 로고    scopus 로고
    • Complex controls: The role of alternative promoters in mammalian genomes
    • Landry,J.R., Mager,D.L. and Wilhelm,B.T. (2003) Complex controls: The role of alternative promoters in mammalian genomes. Trends Genet., 19, 640-648.
    • (2003) Trends Genet. , vol.19 , pp. 640-648
    • Landry, J.R.1    Mager, D.L.2    Wilhelm, B.T.3
  • 33
    • 0033595893 scopus 로고    scopus 로고
    • How NF-kappaB is activated: The role of the IkappaB kinase (IKK) complex
    • Karin,M. (1999) How NF-kappaB is activated: The role of the IkappaB kinase (IKK) complex. Oncogene, 18, 6867-6874.
    • (1999) Oncogene , vol.18 , pp. 6867-6874
    • Karin, M.1
  • 34
    • 0033623848 scopus 로고    scopus 로고
    • IKKepsilon is part of a novel PMA-inducible IkappaB kinase complex
    • Peters,R.T., Liao,S.M. and Maniatis,T. (2000) IKKepsilon is part of a novel PMA-inducible IkappaB kinase complex. Mol. Cell, 5, 513-522.
    • (2000) Mol. Cell , vol.5 , pp. 513-522
    • Peters, R.T.1    Liao, S.M.2    Maniatis, T.3
  • 35
    • 1542316923 scopus 로고    scopus 로고
    • The multiassembly problem: Reconstructing multiple transcript isoforms from EST fragment mixtures
    • Xing,Y., Resch,A. and Lee,C. (2004) The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Res., 14, 426-441.
    • (2004) Genome Res. , vol.14 , pp. 426-441
    • Xing, Y.1    Resch, A.2    Lee, C.3
  • 36
    • 17844404583 scopus 로고    scopus 로고
    • Large-scale analysis of human alternative protein isoforms: Pattern classification and correlation with subcellular localization signals
    • Nakao,M., Barrero,R.A., Mukai,Y., Motono,C., Suwa,M. and Nakai,K. (2005) Large-scale analysis of human alternative protein isoforms: Pattern classification and correlation with subcellular localization signals. Nucleic Acids Res., 33, 2355-2363.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2355-2363
    • Nakao, M.1    Barrero, R.A.2    Mukai, Y.3    Motono, C.4    Suwa, M.5    Nakai, K.6
  • 39
    • 17144434438 scopus 로고    scopus 로고
    • Cotranscription and intergenic splicing of human galactose-1-phosphate uridylyltransferase and interleukin-11 receptor alpha-chain genes generate a fusion mRNA in normal cells. Implication for the production of multidomain proteins during evolution
    • Magrangeas,F., Pitiot,G., Dubois,S., Bragado-Nilsson,E., Cherel,M., Jobert,S., Lebeau,B., Boisteau,O., Lethe,B., Mallet,J. et al. (1998) Cotranscription and intergenic splicing of human galactose-1-phosphate uridylyltransferase and interleukin-11 receptor alpha-chain genes generate a fusion mRNA in normal cells. Implication for the production of multidomain proteins during evolution. J. Biol. Chem., 273, 16005-16010.
    • (1998) J. Biol. Chem. , vol.273 , pp. 16005-16010
    • Magrangeas, F.1    Pitiot, G.2    Dubois, S.3    Bragado-Nilsson, E.4    Cherel, M.5    Jobert, S.6    Lebeau, B.7    Boisteau, O.8    Lethe, B.9    Mallet, J.10
  • 41
    • 27544482906 scopus 로고    scopus 로고
    • Alternative pre-mRNA processing regulates cell-type specific expression of the IL411 and NUP62 genes
    • Wiemann,S., Kokocinski,A.K. and Poustka,A. (2005) Alternative pre-mRNA processing regulates cell-type specific expression of the IL411 and NUP62 genes. BMC Biol., 3, 16.
    • (2005) BMC Biol. , vol.3 , pp. 16
    • Wiemann, S.1    Kokocinski, A.K.2    Poustka, A.3
  • 42
    • 7444253965 scopus 로고    scopus 로고
    • Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs
    • Oyama,M., Itagaki,C., Hata,H., Suzuki,Y., Izumi,T., Natsume,T., Isobe,T. and Sugano,S. (2004) Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res., 14, 2048-2052.
    • (2004) Genome Res. , vol.14 , pp. 2048-2052
    • Oyama, M.1    Itagaki, C.2    Hata, H.3    Suzuki, Y.4    Izumi, T.5    Natsume, T.6    Isobe, T.7    Sugano, S.8
  • 43
    • 0038617729 scopus 로고    scopus 로고
    • Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss
    • Modrek,B. and Lee,C.J. (2003) Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nature Genet., 34, 177-180.
    • (2003) Nature Genet. , vol.34 , pp. 177-180
    • Modrek, B.1    Lee, C.J.2
  • 44
    • 14544277546 scopus 로고    scopus 로고
    • Identification and analysis of alternative splicing events conserved in human and mouse
    • Yeo,G.W., Van Nostrand,E., Holste,D., Poggio,T. and Burge,C.B. (2005) Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl Acad. Sci. USA, 102, 2850-2855.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 2850-2855
    • Yeo, G.W.1    Van Nostrand, E.2    Holste, D.3    Poggio, T.4    Burge, C.B.5


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