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Volumn 35, Issue 16, 2007, Pages 5487-5498

Does distance matter? Variations in alternative 3′ splicing regulation

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; POLYPYRIMIDINE TRACT BINDING PROTEIN;

EID: 34548706497     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm603     Document Type: Article
Times cited : (15)

References (40)
  • 1
    • 2442694425 scopus 로고    scopus 로고
    • Transcriptome and genome conservation of alternative splicing events in humans and mice
    • Sugnet,C.W., Kent,W.J., Ares,M.Jr and Haussler,D. (2004) Transcriptome and genome conservation of alternative splicing events in humans and mice. Proc. Symp. Biocomput., 2004, 66-77.
    • (2004) Proc. Symp. Biocomput , vol.2004 , pp. 66-77
    • Sugnet, C.W.1    Kent, W.J.2    Ares Jr, M.3    Haussler, D.4
  • 2
    • 0013394889 scopus 로고    scopus 로고
    • Mechanisms of alternative pre-messenger RNA splicing
    • Black,D.L. (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem., 72, 291-336.
    • (2003) Annu. Rev. Biochem , vol.72 , pp. 291-336
    • Black, D.L.1
  • 3
    • 0023651307 scopus 로고
    • RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression
    • Shapiro,M.B. and Senapathy,P. (1987) RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression. Nucleic Acids Res., 15, 7155-7174.
    • (1987) Nucleic Acids Res , vol.15 , pp. 7155-7174
    • Shapiro, M.B.1    Senapathy, P.2
  • 4
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • Yeo,G. and Burge,C.B. (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol. 11, 377-394.
    • (2004) J. Comput. Biol , vol.11 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2
  • 5
    • 0033118708 scopus 로고    scopus 로고
    • Alternate Pax7 paired box transcripts which include a trinucleotide or a hexanucleotide are generated by use of alternate 3′ intronic splice sites which are not utilized in the ancestral homologue
    • Kay,P.H. and Ziman,M.R. (1999) Alternate Pax7 paired box transcripts which include a trinucleotide or a hexanucleotide are generated by use of alternate 3′ intronic splice sites which are not utilized in the ancestral homologue. Gene, 230, 55-60.
    • (1999) Gene , vol.230 , pp. 55-60
    • Kay, P.H.1    Ziman, M.R.2
  • 6
    • 0027214101 scopus 로고
    • Scanning and competition between AGs are involved in 3′ splice site selection in mammalian introns
    • Smith,C.W., Chu,T.T. and Nadal-Ginard,B. (1993) Scanning and competition between AGs are involved in 3′ splice site selection in mammalian introns. Mol. Cell. Biol., 13, 4939-4952.
    • (1993) Mol. Cell. Biol , vol.13 , pp. 4939-4952
    • Smith, C.W.1    Chu, T.T.2    Nadal-Ginard, B.3
  • 7
    • 0035133535 scopus 로고    scopus 로고
    • An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing
    • Chua,K. and Reed,R. (2001) An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing. Mol. Cell. Biol., 21, 1509-1514.
    • (2001) Mol. Cell. Biol , vol.21 , pp. 1509-1514
    • Chua, K.1    Reed, R.2
  • 8
    • 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
  • 9
    • 33745048938 scopus 로고    scopus 로고
    • A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones
    • Gooding,C., Clark,F., Wollerton,M.C., Grellscheid,S.N., Groom,H. and Smith,C.W. (2006) A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones. Genome Biol., 7, R1.
    • (2006) Genome Biol , vol.7
    • Gooding, C.1    Clark, F.2    Wollerton, M.C.3    Grellscheid, S.N.4    Groom, H.5    Smith, C.W.6
  • 10
    • 31544461505 scopus 로고    scopus 로고
    • Alternative splicing regulation at tandem 3′ splice sites
    • Akerman,M. and Mandel-Gutfreund,Y. (2006) Alternative splicing regulation at tandem 3′ splice sites. Nucleic Acids Res., 34 23-31.
    • (2006) Nucleic Acids Res , vol.34 , pp. 23-31
    • Akerman, M.1    Mandel-Gutfreund, Y.2
  • 11
    • 20444470310 scopus 로고    scopus 로고
    • Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation
    • Kol,G., Lev-Maor,G. and Ast,G. (2005) Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation. Hum. Mol. Genet., 14, 1559-1568.
    • (2005) Hum. Mol. Genet , vol.14 , pp. 1559-1568
    • Kol, G.1    Lev-Maor, G.2    Ast, G.3
  • 12
    • 0025076272 scopus 로고
    • The conserved dinucleotide AG of the 3′ splice site may be recognized twice during in vitro splicing of mammalian mRNA precursors
    • Zhuang,Y. and Weiner,A.M. (1990) The conserved dinucleotide AG of the 3′ splice site may be recognized twice during in vitro splicing of mammalian mRNA precursors. Gene, 90, 263-269.
    • (1990) Gene , vol.90 , pp. 263-269
    • Zhuang, Y.1    Weiner, A.M.2
  • 14
    • 9644278038 scopus 로고    scopus 로고
    • Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity
    • Hiller,M., Huse,K., Szafranski,K., Jahn,N., Hampe,J., Schreiber,S., Backofen,R. and Platzer,M. (2004) Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. Nat. Genet., 36, 1255-1257.
    • (2004) Nat. Genet , vol.36 , pp. 1255-1257
    • Hiller, M.1    Huse, K.2    Szafranski, K.3    Jahn, N.4    Hampe, J.5    Schreiber, S.6    Backofen, R.7    Platzer, M.8
  • 15
    • 0033576626 scopus 로고    scopus 로고
    • Functional recognition of the 3′ splice site AG by the splicing factor U2AF35
    • Wu,S., Romfo,C.M., Nilsen,T.W. and Green,M.R. (1999) Functional recognition of the 3′ splice site AG by the splicing factor U2AF35. Nature, 402, 832-835.
    • (1999) Nature , vol.402 , pp. 832-835
    • Wu, S.1    Romfo, C.M.2    Nilsen, T.W.3    Green, M.R.4
  • 16
    • 0034602779 scopus 로고    scopus 로고
    • Role of adenine functional groups in the recognition of the 3′-splice-site AG during the second step of pre-mRNA splicing
    • Gaur,R.K., Beigelman,L., Haeberli,P. and Maniatis,T. (2000) Role of adenine functional groups in the recognition of the 3′-splice-site AG during the second step of pre-mRNA splicing. Proc. Natl Acad. Sci. USA, 97, 115-120.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 115-120
    • Gaur, R.K.1    Beigelman, L.2    Haeberli, P.3    Maniatis, T.4
  • 17
    • 24744464160 scopus 로고    scopus 로고
    • Biased exon/ intron distribution of cryptic and de novo 3′ splice sites
    • Kralovicova,J., Christensen,M.B. and Vorechovsky,I. (2005) Biased exon/ intron distribution of cryptic and de novo 3′ splice sites. Nucleic Acids Res., 33, 4882-4898.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4882-4898
    • Kralovicova, J.1    Christensen, M.B.2    Vorechovsky, I.3
  • 18
    • 0033547333 scopus 로고    scopus 로고
    • The RNA splicing factor hSlu7 is required for correct 3′ splice-site choice
    • Chua,K. and Reed,R. (1999) The RNA splicing factor hSlu7 is required for correct 3′ splice-site choice. Nature, 402, 207-210.
    • (1999) Nature , vol.402 , pp. 207-210
    • Chua, K.1    Reed, R.2
  • 19
    • 0030857005 scopus 로고    scopus 로고
    • Functional analysis of the polypyrimidine tract in pre-mRNA splicing
    • Coolidge,C.J., Seely,R.J. and Patton,J.G. (1997) Functional analysis of the polypyrimidine tract in pre-mRNA splicing. Nucleic Acids Res., 25, 888-896.
    • (1997) Nucleic Acids Res , vol.25 , pp. 888-896
    • Coolidge, C.J.1    Seely, R.J.2    Patton, J.G.3
  • 20
    • 0029055472 scopus 로고
    • Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins
    • Singh,R., Valcarcel,J. and Green,M.R. (1995) Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. Science, 268, 1173-1176.
    • (1995) Science , vol.268 , pp. 1173-1176
    • Singh, R.1    Valcarcel, J.2    Green, M.R.3
  • 21
    • 0037013195 scopus 로고    scopus 로고
    • Alternative splicing of the adenylyl cyclase stimulatory G-protein G alpha(s) is regulated by SF2/ASF and heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) and involves the use of an unusual TG 3′-splice Site
    • Pollard,A.J., Krainer,A.R., Robson,S.C. and Europe-Finner,G.N. (2002) Alternative splicing of the adenylyl cyclase stimulatory G-protein G alpha(s) is regulated by SF2/ASF and heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) and involves the use of an unusual TG 3′-splice Site. J. Biol. Chem., 277, 15241-15251.
    • (2002) J. Biol. Chem , vol.277 , pp. 15241-15251
    • Pollard, A.J.1    Krainer, A.R.2    Robson, S.C.3    Europe-Finner, G.N.4
  • 22
    • 24644493193 scopus 로고    scopus 로고
    • Sequence conservation, relative isoform. frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing
    • Baek,D. and Green,P. (2005) Sequence conservation, relative isoform. frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc. Natl Acad. Sci. USA, 102, 12813-12918.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 12813-12918
    • Baek, D.1    Green, P.2
  • 23
    • 16344396421 scopus 로고    scopus 로고
    • Accurate identification of alternatively spliced exons using support vector machine
    • Dror,G., Sorek,R. and Shamir,R. (2005) Accurate identification of alternatively spliced exons using support vector machine. Bioinformatics, 21, 897-901.
    • (2005) Bioinformatics , vol.21 , pp. 897-901
    • Dror, G.1    Sorek, R.2    Shamir, R.3
  • 24
    • 32544456772 scopus 로고    scopus 로고
    • Characterization and prediction of alternative splice sites
    • Wang,M. and Marin,A. (2006) Characterization and prediction of alternative splice sites. Gene, 366, 219-227.
    • (2006) Gene , vol.366 , pp. 219-227
    • Wang, M.1    Marin, A.2
  • 25
    • 33845660883 scopus 로고    scopus 로고
    • Identification of alternative 5′/3′ splice sites based on the mechanism of splice site competion
    • Xia,H., Bi,J. and Li,Y. (2006) Identification of alternative 5′/3′ splice sites based on the mechanism of splice site competion. Nucleic Acids Res., 34, 6305-6313.
    • (2006) Nucleic Acids Res , vol.34 , pp. 6305-6313
    • Xia, H.1    Bi, J.2    Li, Y.3
  • 26
    • 0038486897 scopus 로고    scopus 로고
    • Intronic sequences flanking alternatively spliced exons are conserved between human and mouse
    • Sorek,R. and Ast,G. (2003) Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res., 13, 1631-1637.
    • (2003) Genome Res , vol.13 , pp. 1631-1637
    • Sorek, R.1    Ast, G.2
  • 28
    • 24944433166 scopus 로고    scopus 로고
    • Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes
    • Wang,J., Smith,P.J., Krainer,A.R. and Zhang,M.Q. (2005) Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res., 33, 5053-5062.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5053-5062
    • Wang, J.1    Smith, P.J.2    Krainer, A.R.3    Zhang, M.Q.4
  • 29
    • 33745501015 scopus 로고    scopus 로고
    • General and specific functions of exonic splicing silencers in splicing control
    • Wang,Z., Xiao,X., Van Nostrand,E. and Burge,C.B. (2006) General and specific functions of exonic splicing silencers in splicing control. Mol. Cell, 23, 61-70.
    • (2006) Mol. Cell , vol.23 , pp. 61-70
    • Wang, Z.1    Xiao, X.2    Van Nostrand, E.3    Burge, C.B.4
  • 30
    • 0022974809 scopus 로고
    • Sequence requirements for splicing of higher eukaryotic nuclear pre-mRNA
    • Aebi,M., Hornig,H., Padgett,R.A., Reiser,J. and Weissmann,C. (1986) Sequence requirements for splicing of higher eukaryotic nuclear pre-mRNA. Cell, 47, 555-565.
    • (1986) Cell , vol.47 , pp. 555-565
    • Aebi, M.1    Hornig, H.2    Padgett, R.A.3    Reiser, J.4    Weissmann, C.5
  • 31
    • 0035949674 scopus 로고    scopus 로고
    • A computational analysis of sequence features involved in recognition of short introns
    • Lim,L.P. and Burge,C.B. (2001) A computational analysis of sequence features involved in recognition of short introns. Proc. Natl Acad. Sci. USA, 98, 11193-11198.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 11193-11198
    • Lim, L.P.1    Burge, C.B.2
  • 32
    • 0027444808 scopus 로고
    • On adjusting p-values for multiplicity
    • Westfall,P.H. and Young,S.S. (1993) On adjusting p-values for multiplicity. Biometrics, 49, 941-944.
    • (1993) Biometrics , vol.49 , pp. 941-944
    • Westfall, P.H.1    Young, S.S.2
  • 33
    • 0345040882 scopus 로고    scopus 로고
    • Support vector machine applications in bioinformatics
    • Byvatov,E. and Schneider,G. (2003) Support vector machine applications in bioinformatics. Appl. Bioinformatics, 2, 67-77.
    • (2003) Appl. Bioinformatics , vol.2 , pp. 67-77
    • Byvatov, E.1    Schneider, G.2
  • 34
    • 1642473041 scopus 로고    scopus 로고
    • How prevalent is functional alternative splicing in the human genome?
    • Sorek,R., Shamir,R. and Ast,G. (2004) How prevalent is functional alternative splicing in the human genome? Trends Genet., 20, 68-71.
    • (2004) Trends Genet , vol.20 , pp. 68-71
    • Sorek, R.1    Shamir, R.2    Ast, G.3
  • 35
    • 33845225902 scopus 로고    scopus 로고
    • The polypyrimidine tract binding protein (PTB) represses splicing of exon 6B from the beta-tropomyosin pre-mRNA by directly interfering with the binding of the U2AF65 subunit
    • Sauliere,J., Sureau,A., Expert-Bezancon,A. and Marie,J. (2006) The polypyrimidine tract binding protein (PTB) represses splicing of exon 6B from the beta-tropomyosin pre-mRNA by directly interfering with the binding of the U2AF65 subunit. Mol. Cell. Biol., 26, 8755-8769.
    • (2006) Mol. Cell. Biol , vol.26 , pp. 8755-8769
    • Sauliere, J.1    Sureau, A.2    Expert-Bezancon, A.3    Marie, J.4
  • 36
    • 0029295295 scopus 로고
    • Regulation of alternative 3′ splice site selection by constitutive splicing factors
    • Lin,C.H. and Patton,J.G. (1995) Regulation of alternative 3′ splice site selection by constitutive splicing factors. RNA, 1, 234-245.
    • (1995) RNA , vol.1 , pp. 234-245
    • Lin, C.H.1    Patton, J.G.2
  • 39
    • 33845248222 scopus 로고    scopus 로고
    • Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site
    • Dou,Y., Fox-Walsh,K.L., Baldi,P.F. and Hertel,K.J. (2006) Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site. RNA, 12, 2047-2056.
    • (2006) RNA , vol.12 , pp. 2047-2056
    • Dou, Y.1    Fox-Walsh, K.L.2    Baldi, P.F.3    Hertel, K.J.4
  • 40
    • 31544473503 scopus 로고    scopus 로고
    • Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing
    • Hiller,M., Huse,K., Szafranski,K., Jahn,N., Hampe,J., Schreiber,S., Backofen,R. and Platzer,M. (2006) Single-nucleotide polymorphisms in NAGNAG acceptors are highly predictive for variations of alternative splicing. Am. J. Hum. Genet., 78, 291-302.
    • (2006) Am. J. Hum. Genet , vol.78 , pp. 291-302
    • Hiller, M.1    Huse, K.2    Szafranski, K.3    Jahn, N.4    Hampe, J.5    Schreiber, S.6    Backofen, R.7    Platzer, M.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.