-
1
-
-
2442694425
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
13
-
-
33646491292
-
A simple physical model predicts small exon length variations
-
Chern,T.M., van Nimwegen,E., Kai,C., Kawai,J., Carninci,P., Hayashizaki,Y. and Zavolan,M. (2006) A simple physical model predicts small exon length variations. PLoS Genet., 2, e45.
-
(2006)
PLoS Genet
, vol.2
-
-
Chern, T.M.1
van Nimwegen, E.2
Kai, C.3
Kawai, J.4
Carninci, P.5
Hayashizaki, Y.6
Zavolan, M.7
-
14
-
-
9644278038
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
27
-
-
33645760966
-
Unusual intron conservation near tissue-regulated exons found by splicing microarrays
-
Sugnet,C.W., Srinivasan,K., Clark,T.A., O'Brien,G., Cline,M.S., Wang,H., Williams,A., Kulp,D., Blume,J.E. et al. (2006) Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput. Biol., 2, e4.
-
(2006)
PLoS Comput. Biol
, vol.2
-
-
Sugnet, C.W.1
Srinivasan, K.2
Clark, T.A.3
O'Brien, G.4
Cline, M.S.5
Wang, H.6
Williams, A.7
Kulp, D.8
Blume, J.E.9
-
28
-
-
24944433166
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
37
-
-
17844406887
-
Exon repression by polypyrimidine tract binding protein
-
Amir-Ahmady,B., Boutz,P.L., Markovtsov,V., Phillips,M.L. and Black,D.L. (2005) Exon repression by polypyrimidine tract binding protein. RNA 11, 699-716.
-
(2005)
RNA
, vol.11
, pp. 699-716
-
-
Amir-Ahmady, B.1
Boutz, P.L.2
Markovtsov, V.3
Phillips, M.L.4
Black, D.L.5
-
38
-
-
25444486174
-
Structure of PTB bound to RNA: Specific binding and implications for splicing regulation
-
Oberstrass,F.C., Auweter,S.D., Erat,M., Hargous,Y., Henning,A., Wenter,P., Reymond,L., Amir-Ahmady,B., Pitsch,S. et al. (2005) Structure of PTB bound to RNA: Specific binding and implications for splicing regulation. Science, 309, 2054-2057.
-
(2005)
Science
, vol.309
, pp. 2054-2057
-
-
Oberstrass, F.C.1
Auweter, S.D.2
Erat, M.3
Hargous, Y.4
Henning, A.5
Wenter, P.6
Reymond, L.7
Amir-Ahmady, B.8
Pitsch, S.9
-
39
-
-
33845248222
-
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
-
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
|