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For: Goren A, Ram O, Amit M, Keren H, Lev-Maor G, Vig I, Pupko T, Ast G. Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. Mol Cell 2006;22:769-781. [PMID: 16793546 DOI: 10.1016/j.molcel.2006.05.008] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Revised: 04/06/2006] [Accepted: 05/03/2006] [Indexed: 12/11/2022]
Number Cited by Other Article(s)
201
Multifactorial interplay controls the splicing profile of Alu-derived exons. Mol Cell Biol 2008;28:3513-25. [PMID: 18332115 DOI: 10.1128/mcb.02279-07] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
202
Abad X, Vera M, Jung SP, Oswald E, Romero I, Amin V, Fortes P, Gunderson SI. Requirements for gene silencing mediated by U1 snRNA binding to a target sequence. Nucleic Acids Res 2008;36:2338-52. [PMID: 18299285 PMCID: PMC2367729 DOI: 10.1093/nar/gkn068] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]  Open
203
Holste D, Ohler U. Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events. PLoS Comput Biol 2008;4:e21. [PMID: 18225947 PMCID: PMC2217580 DOI: 10.1371/journal.pcbi.0040021] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
204
Gal-Mark N, Schwartz S, Ast G. Alternative splicing of Alu exons--two arms are better than one. Nucleic Acids Res 2008;36:2012-23. [PMID: 18276646 PMCID: PMC2330237 DOI: 10.1093/nar/gkn024] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
205
Ke S, Zhang XHF, Chasin LA. Positive selection acting on splicing motifs reflects compensatory evolution. Genome Res 2008;18:533-43. [PMID: 18204002 DOI: 10.1101/gr.070268.107] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
206
Plant SR proteins and their functions. Curr Top Microbiol Immunol 2008;326:83-102. [PMID: 18630748 DOI: 10.1007/978-3-540-76776-3_5] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
207
Goren A, Kim E, Amit M, Bochner R, Lev-Maor G, Ahituv N, Ast G. Alternative approach to a heavy weight problem. Genome Res 2007;18:214-20. [PMID: 18096750 DOI: 10.1101/gr.6661308] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
208
Vela E, Hilari JM, Roca X, Muñoz-Mármol AM, Ariza A, Isamat M. Multisite and bidirectional exonic splicing enhancer in CD44 alternative exon v3. RNA (NEW YORK, N.Y.) 2007;13:2312-2323. [PMID: 17940137 PMCID: PMC2080591 DOI: 10.1261/rna.732807] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
209
Amit M, Sela N, Keren H, Melamed Z, Muler I, Shomron N, Izraeli S, Ast G. Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene. BMC Mol Biol 2007;8:109. [PMID: 18047649 PMCID: PMC2231382 DOI: 10.1186/1471-2199-8-109] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 11/29/2007] [Indexed: 01/21/2023]  Open
210
Ben-Dov C, Hartmann B, Lundgren J, Valcárcel J. Genome-wide analysis of alternative pre-mRNA splicing. J Biol Chem 2007;283:1229-33. [PMID: 18024428 DOI: 10.1074/jbc.r700033200] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
211
U2 snRNP: not just for poly(A) mRNAs. Mol Cell 2007;28:353-4. [PMID: 17996698 DOI: 10.1016/j.molcel.2007.10.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
212
Dogan RI, Getoor L, Wilbur WJ, Mount SM. Features generated for computational splice-site prediction correspond to functional elements. BMC Bioinformatics 2007;8:410. [PMID: 17958908 PMCID: PMC2241647 DOI: 10.1186/1471-2105-8-410] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 10/24/2007] [Indexed: 11/16/2022]  Open
213
Kleino I, Ortiz RM, Huovila APJ. ADAM15 gene structure and differential alternative exon use in human tissues. BMC Mol Biol 2007;8:90. [PMID: 17937806 PMCID: PMC2148059 DOI: 10.1186/1471-2199-8-90] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Accepted: 10/15/2007] [Indexed: 01/21/2023]  Open
214
Královičová J, Vořechovský I. Global control of aberrant splice-site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definition. Nucleic Acids Res 2007;35:6399-413. [PMID: 17881373 PMCID: PMC2095810 DOI: 10.1093/nar/gkm680] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
215
Marinescu V, Loomis PA, Ehmann S, Beales M, Potashkin JA. Regulation of retention of FosB intron 4 by PTB. PLoS One 2007;2:e828. [PMID: 17786200 PMCID: PMC1952174 DOI: 10.1371/journal.pone.0000828] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Accepted: 08/14/2007] [Indexed: 11/19/2022]  Open
216
Wang GS, Cooper TA. Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet 2007;8:749-61. [PMID: 17726481 DOI: 10.1038/nrg2164] [Citation(s) in RCA: 765] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
217
Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T. Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates. ACTA ACUST UNITED AC 2007;23:i319-27. [PMID: 17646313 DOI: 10.1093/bioinformatics/btm176] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
218
Taniguchi I, Masuyama K, Ohno M. Role of purine-rich exonic splicing enhancers in nuclear retention of pre-mRNAs. Proc Natl Acad Sci U S A 2007;104:13684-9. [PMID: 17699631 PMCID: PMC1959442 DOI: 10.1073/pnas.0704922104] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
219
Voelker RB, Berglund JA. A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing. Genes Dev 2007;17:1023-33. [PMID: 17525134 PMCID: PMC1899113 DOI: 10.1101/gr.6017807] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Accepted: 04/12/2007] [Indexed: 11/24/2022]
220
Koren E, Lev-Maor G, Ast G. The emergence of alternative 3' and 5' splice site exons from constitutive exons. PLoS Comput Biol 2007;3:e95. [PMID: 17530917 PMCID: PMC1876488 DOI: 10.1371/journal.pcbi.0030095] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 04/10/2007] [Indexed: 11/19/2022]  Open
221
Dogan RI, Getoor L, Wilbur WJ, Mount SM. SplicePort--an interactive splice-site analysis tool. Nucleic Acids Res 2007;35:W285-91. [PMID: 17576680 PMCID: PMC1933122 DOI: 10.1093/nar/gkm407] [Citation(s) in RCA: 170] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
222
Hull J, Campino S, Rowlands K, Chan MS, Copley RR, Taylor MS, Rockett K, Elvidge G, Keating B, Knight J, Kwiatkowski D. Identification of common genetic variation that modulates alternative splicing. PLoS Genet 2007;3:e99. [PMID: 17571926 PMCID: PMC1904363 DOI: 10.1371/journal.pgen.0030099] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Accepted: 05/04/2007] [Indexed: 01/25/2023]  Open
223
Masuyama K, Taniguchi I, Okawa K, Ohno M. Factors associated with a purine-rich exonic splicing enhancer sequence in Xenopus oocyte nucleus. Biochem Biophys Res Commun 2007;359:580-5. [PMID: 17548051 DOI: 10.1016/j.bbrc.2007.05.144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Accepted: 05/21/2007] [Indexed: 02/05/2023]
224
Pertea M, Mount SM, Salzberg SL. A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics 2007;8:159. [PMID: 17517127 PMCID: PMC1892810 DOI: 10.1186/1471-2105-8-159] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 05/21/2007] [Indexed: 02/05/2023]  Open
225
Yeo GW, Van Nostrand EL, Nostrand ELV, Liang TY. Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements. PLoS Genet 2007;3:e85. [PMID: 17530930 PMCID: PMC1877881 DOI: 10.1371/journal.pgen.0030085] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Accepted: 04/13/2007] [Indexed: 02/05/2023]  Open
226
Lee JA, Xing Y, Nguyen D, Xie J, Lee CJ, Black DL. Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements. PLoS Biol 2007;5:e40. [PMID: 17298178 PMCID: PMC1790950 DOI: 10.1371/journal.pbio.0050040] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 12/08/2006] [Indexed: 12/13/2022]  Open
227
Rätsch G, Sonnenburg S, Srinivasan J, Witte H, Müller KR, Sommer RJ, Schölkopf B. Improving the Caenorhabditis elegans genome annotation using machine learning. PLoS Comput Biol 2007;3:e20. [PMID: 17319737 PMCID: PMC1808025 DOI: 10.1371/journal.pcbi.0030020] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Accepted: 12/20/2006] [Indexed: 11/19/2022]  Open
228
Tian B, Pan Z, Lee JY. Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genes Dev 2007;17:156-65. [PMID: 17210931 PMCID: PMC1781347 DOI: 10.1101/gr.5532707] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2006] [Accepted: 11/20/2006] [Indexed: 12/31/2022]
229
Ule J, Darnell RB. Functional and mechanistic insights from genome-wide studies of splicing regulation in the brain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007;623:148-60. [PMID: 18380345 DOI: 10.1007/978-0-387-77374-2_9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
230
Lev-Maor G, Sorek R, Levanon EY, Paz N, Eisenberg E, Ast G. RNA-editing-mediated exon evolution. Genome Biol 2007;8:R29. [PMID: 17326827 PMCID: PMC1852406 DOI: 10.1186/gb-2007-8-2-r29] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 01/02/2007] [Accepted: 02/27/2007] [Indexed: 02/06/2023]  Open
231
Reddy ASN. Alternative splicing of pre-messenger RNAs in plants in the genomic era. ANNUAL REVIEW OF PLANT BIOLOGY 2007;58:267-94. [PMID: 17222076 DOI: 10.1146/annurev.arplant.58.032806.103754] [Citation(s) in RCA: 372] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
232
Lin S, Fu XD. SR proteins and related factors in alternative splicing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007;623:107-22. [PMID: 18380343 DOI: 10.1007/978-0-387-77374-2_7] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
233
Raponi M, Baralle FE, Pagani F. Reduced splicing efficiency induced by synonymous substitutions may generate a substrate for natural selection of new splicing isoforms: the case of CFTR exon 12. Nucleic Acids Res 2006;35:606-13. [PMID: 17172597 PMCID: PMC1802620 DOI: 10.1093/nar/gkl1087] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2006] [Revised: 11/22/2006] [Accepted: 11/22/2006] [Indexed: 12/19/2022]  Open
234
Ule J, Stefani G, Mele A, Ruggiu M, Wang X, Taneri B, Gaasterland T, Blencowe BJ, Darnell RB. An RNA map predicting Nova-dependent splicing regulation. Nature 2006;444:580-6. [PMID: 17065982 DOI: 10.1038/nature05304] [Citation(s) in RCA: 420] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 10/03/2006] [Indexed: 11/09/2022]
235
Licatalosi DD, Darnell RB. Splicing regulation in neurologic disease. Neuron 2006;52:93-101. [PMID: 17015229 DOI: 10.1016/j.neuron.2006.09.017] [Citation(s) in RCA: 198] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
236
Griffith BN, Walsh CM, Szeszel-Fedorowicz W, Timperman AT, Salati LM. Identification of hnRNPs K, L and A2/B1 as candidate proteins involved in the nutritional regulation of mRNA splicing. ACTA ACUST UNITED AC 2006;1759:552-61. [PMID: 17095106 PMCID: PMC1828878 DOI: 10.1016/j.bbaexp.2006.10.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 09/27/2006] [Accepted: 10/03/2006] [Indexed: 11/24/2022]
237
Stadler MB, Shomron N, Yeo GW, Schneider A, Xiao X, Burge CB. Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS Genet 2006;2:e191. [PMID: 17121466 PMCID: PMC1657047 DOI: 10.1371/journal.pgen.0020191] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Accepted: 09/26/2006] [Indexed: 12/13/2022]  Open
238
Lastella P, Surdo NC, Resta N, Guanti G, Stella A. In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects. BMC Genomics 2006;7:243. [PMID: 16995940 PMCID: PMC1590028 DOI: 10.1186/1471-2164-7-243] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2006] [Accepted: 09/22/2006] [Indexed: 11/10/2022]  Open
239
Guigó R, Valcárcel J. Unweaving the Meanings of Messenger RNA Sequences. Mol Cell 2006;23:150-1. [PMID: 16857580 DOI: 10.1016/j.molcel.2006.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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