Discovery and Analysis of Evolutionarily Conserved Intronic Splicing Regulatory Elements

2005, Understanding alternative splicing: Towards a cellular code., Nat Rev Mol Cell Biol, 6, 386, 10.1038/nrm1645

2002, Finding signals that regulate alternative splicing in the post-genomic era., Genome Biol, 3, reviews0008

2002, Listening to silence and understanding nonsense: Exonic mutations that affect splicing., Nat Rev Genet, 3, 285, 10.1038/nrg775

2004, Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression., J Biomed Sci, 11, 278, 10.1007/BF02254432

2003, Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays., Science, 302, 2141, 10.1126/science.1090100

1992, The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: Causes and consequences., Hum Genet, 90, 41

2004, Alternative splicing in disease and therapy., Nat Biotechnol, 22, 535, 10.1038/nbt964

2006, Alternative splicing: New insights from global analyses., Cell, 126, 37, 10.1016/j.cell.2006.06.023

2002, Predictive identification of exonic splicing enhancers in human genes., Science, 297, 1007, 10.1126/science.1073774

2004, Computational definition of sequence motifs governing constitutive exon splicing., Genes Dev, 18, 1241, 10.1101/gad.1195304

2004, Systematic identification and analysis of exonic splicing silencers., Cell, 119, 831, 10.1016/j.cell.2004.11.010

2006, General and specific functions of exonic splicing silencers in splicing control., Mol Cell, 23, 61, 10.1016/j.molcel.2006.05.018

2004, Variation in sequence and organization of splicing regulatory elements in vertebrate genes., Proc Natl Acad Sci U S A, 101, 15700, 10.1073/pnas.0404901101

2003, Nucleotide frequency variation across human genes., Genome Res, 13, 2594, 10.1101/gr.1317703

2003, Sequence information for the splicing of human pre-mRNA identified by support vector machine classification., Genome Res, 13, 2637, 10.1101/gr.1679003

2006, Comparative analysis identifies exonic splicing regulatory sequences—the complex definition of enhancers and silencers., Mol Cell, 22, 769, 10.1016/j.molcel.2006.05.008

2006, Intronic alternative splicing regulators identified by comparative genomics in nematodes., PLoS Comput Biol, 2

2006, Unusual intron conservation near tissue-regulated exons found by splicing microarrays., PLoS Comput Biol, 2

2004, Variation in alternative splicing across human tissues., Genome Biol, 5, R74, 10.1186/gb-2004-5-10-r74

2001, Genome-wide detection of alternative splicing in expressed sequences of human genes., Nucleic Acids Res, 29, 2850, 10.1093/nar/29.13.2850

2002, Genome-wide detection of tissue-specific alternative splicing in the human transcriptome., Nucleic Acids Res, 30, 3754, 10.1093/nar/gkf492

2004, Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform., Mol Cell, 16, 929, 10.1016/j.molcel.2004.12.004

2003, Sequencing and comparison of yeast species to identify genes and regulatory elements., Nature, 423, 241, 10.1038/nature01644

2005, Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals., Nature, 434, 338, 10.1038/nature03441

2003, Intronic sequences flanking alternatively spliced exons are conserved between human and mouse., Genome Res, 13, 1631, 10.1101/gr.1208803

SugnetCWKentWJAresMJr.HausslerD 2004 Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput 66 77

2005, Identification and analysis of alternative splicing events conserved in human and mouse., Proc Natl Acad Sci U S A, 102, 2850, 10.1073/pnas.0409742102

2003, The UCSC Genome Browser Database., Nucleic Acids Res, 31, 51, 10.1093/nar/gkg129

2004, Aligning multiple genomic sequences with the threaded blockset aligner., Genome Res, 14, 708, 10.1101/gr.1933104

2001, Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex., Mol Cell Biol, 21, 5232, 10.1128/MCB.21.15.5232-5241.2001

2006, Inference of splicing regulatory activities by sequence neighborhood analysis., PLoS Genet, 2

2005, Nova autoregulation reveals dual functions in neuronal splicing., EMBO J, 24, 1608, 10.1038/sj.emboj.7600630

2003, CLIP identifies Nova-regulated RNA networks in the brain., Science, 302, 1212, 10.1126/science.1090095

1997, G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection., Mol Cell Biol, 17, 4562, 10.1128/MCB.17.8.4562

1994, Regulation of alternative pre-mRNA splicing by a novel repeated hexanucleotide element., Genes Dev, 8, 1561, 10.1101/gad.8.13.1561

1997, Control of alternative pre-mRNA splicing by distributed pentameric repeats., Proc Natl Acad Sci U S A, 94, 12343, 10.1073/pnas.94.23.12343

1998, Alternative splicing of the fibronectin EIIIB exon depends on specific TGCATG repeats., Mol Cell Biol, 18, 3900, 10.1128/MCB.18.7.3900

2003, A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG., EMBO J, 22, 905, 10.1093/emboj/cdg089

1997, A neuron-specific splicing switch mediated by an array of pre-mRNA repressor sites: Evidence of a regulatory role for the polypyrimidine tract binding protein and a brain-specific PTB counterpart., RNA, 3, 996

2006, An RNA map predicting Nova-dependent splicing regulation., Nature, 444, 580, 10.1038/nature05304

2004, Muscleblind proteins regulate alternative splicing., EMBO J, 23, 3103, 10.1038/sj.emboj.7600300

2000, Recruitment of human muscleblind proteins to (CUG)(n) expansions associated with myotonic dystrophy., EMBO J, 19, 4439, 10.1093/emboj/19.17.4439

2002, Three proteins, MBNL, MBLL and MBXL, co-localize in vivo with nuclear foci of expanded-repeat transcripts in DM1 and DM2 cells., Hum Mol Genet, 11, 805, 10.1093/hmg/11.7.805

1992, The mechanism of somatic inhibition of Drosophila P-element pre-mRNA splicing: Multiprotein complexes at an exon pseudo-5′ splice site control U1 snRNP binding., Genes Dev, 6, 1386, 10.1101/gad.6.8.1386

2000, Human genomic sequences that inhibit splicing., Mol Cell Biol, 20, 6816, 10.1128/MCB.20.18.6816-6825.2000

2001, A computational analysis of sequence features involved in recognition of short introns., Proc Natl Acad Sci U S A, 98, 11193, 10.1073/pnas.201407298

2005, Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals., Mol Cell Biol, 25, 10005, 10.1128/MCB.25.22.10005-10016.2005

1993, Nova, the paraneoplastic Ri antigen, is homologous to an RNA-binding protein and is specifically expressed in the developing motor system., Neuron, 11, 657, 10.1016/0896-6273(93)90077-5

1997, Conserved intron elements repress splicing of a neuron-specific c-src exon in vitro., Mol Cell Biol, 17, 2970, 10.1128/MCB.17.5.2970

1995, Conserved intron elements repress splicing of a neuron-specific c-src exon in vitro., Mol Cell Biol, 15, 6377, 10.1128/MCB.15.11.6377

2005, Identification of putative new splicing targets for ETR-3 using sequences identified by systematic evolution of ligands by exponential enrichment., Mol Cell Biol, 25, 879, 10.1128/MCB.25.3.879-887.2005

2005, Nova regulates brain-specific splicing to shape the synapse., Nat Genet, 37, 844, 10.1038/ng1610

2005, Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences., Hum Mol Genet, 14, 2533, 10.1093/hmg/ddi257

2004, A gene atlas of the mouse and human protein-encoding transcriptomes., Proc Natl Acad Sci U S A, 101, 6062, 10.1073/pnas.0400782101

2000, Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein., Mol Cell Biol, 20, 7463, 10.1128/MCB.20.20.7463-7479.2000

2006, Fox-2 mediates epithelial cell-specific fibroblast growth factor receptor 2 exon choice., Mol Cell Biol, 26, 1209, 10.1128/MCB.26.4.1209-1222.2006

1999, Modulation of exon skipping by high-affinity hnRNP A1-binding sites and by intron elements that repress splice site utilization., EMBO J, 18, 1939, 10.1093/emboj/18.7.1939

1997, The splicing factor SRp20 modifies splicing of its own mRNA and ASF/SF2 antagonizes this regulation., EMBO J, 16, 5077, 10.1093/emboj/16.16.5077

2001, TIA-1 and TIAR activate splicing of alternative exons with weak 5′ splice sites followed by a U-rich stretch on their own pre-mRNAs., J Biol Chem, 276, 40638, 10.1074/jbc.M105642200

1999, Regulation of alternative splicing by RNA editing., Nature, 399, 75, 10.1038/19992

2001, SC35 autoregulates its expression by promoting splicing events that destabilize its mRNAs., EMBO J, 20, 1785, 10.1093/emboj/20.7.1785

2004, Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay., Mol Cell, 13, 91, 10.1016/S1097-2765(03)00502-1

2004, A non-EST-based method for exon-skipping prediction., Genome Res, 14, 1617, 10.1101/gr.2572604

2004, Ultraconserved elements in the human genome., Science, 304, 1321, 10.1126/science.1098119

2005, Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities., Nucleic Acids Res, 33, 2078, 10.1093/nar/gki338

2002, Alternative splicing of brain-specific PTB defines a tissue-specific isoform pattern that predicts distinct functional roles., Genomics, 80, 245, 10.1006/geno.2002.6826

1994, The determinants of RNA-binding specificity of the heterogeneous nuclear ribonucleoprotein C proteins., J Biol Chem, 269, 23074, 10.1016/S0021-9258(17)31621-6