TY - JOUR AU - Clay, O. AU - Cacciò, S. AU - Zoubak, S. AU - Mouchiroud, D. AU - Bernardi, G. PY - 1996 DA - 1996// TI - Human coding and noncoding DNA: compositional correlations. JO - Mol Phylogenet Evol VL - 5 UR - https://doi.org/10.1006/mpev.1996.0002 DO - 10.1006/mpev.1996.0002 ID - Clay1996 ER - TY - JOUR AU - Parmley, J. L. AU - Urrutia, A. O. AU - Potrzebowski, L. AU - Kaessmann, H. AU - Hurst, L. D. PY - 2007 DA - 2007// TI - Splicing and the evolution of proteins in mammals. JO - PLoS Biol VL - 5 UR - https://doi.org/10.1371/journal.pbio.0050014 DO - 10.1371/journal.pbio.0050014 ID - Parmley2007 ER - TY - JOUR AU - Blencowe, B. J. PY - 2000 DA - 2000// TI - Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. JO - Trends Biochem Sci VL - 25 UR - https://doi.org/10.1016/S0968-0004(00)01549-8 DO - 10.1016/S0968-0004(00)01549-8 ID - Blencowe2000 ER - TY - JOUR AU - Zheng, Z. M. PY - 2004 DA - 2004// TI - Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression. JO - J Biomed Sci VL - 11 UR - https://doi.org/10.1007/BF02254432 DO - 10.1007/BF02254432 ID - Zheng2004 ER - TY - JOUR AU - Ram, O. AU - Ast, G. PY - 2007 DA - 2007// TI - SR proteins: a foot on the exon before the transition from intron to exon definition. JO - Trends Genet VL - 23 UR - https://doi.org/10.1016/j.tig.2006.10.002 DO - 10.1016/j.tig.2006.10.002 ID - Ram2007 ER - TY - JOUR AU - Berget, S. M. PY - 1995 DA - 1995// TI - Exon recognition in vertebrate splicing. JO - J Biol Chem VL - 270 UR - https://doi.org/10.1074/jbc.270.6.2411 DO - 10.1074/jbc.270.6.2411 ID - Berget1995 ER - TY - JOUR AU - Irimia, M. AU - Penny, D. AU - Roy, S. W. PY - 2007 DA - 2007// TI - Coevolution of genomic intron number and splice sites. JO - Trends Genet VL - 23 UR - https://doi.org/10.1016/j.tig.2007.04.001 DO - 10.1016/j.tig.2007.04.001 ID - Irimia2007 ER - TY - JOUR AU - Hertel, K. J. AU - Maniatis, T. PY - 1998 DA - 1998// TI - The function of multisite splicing enhancers. JO - Mol Cell VL - 1 UR - https://doi.org/10.1016/S1097-2765(00)80045-3 DO - 10.1016/S1097-2765(00)80045-3 ID - Hertel1998 ER - TY - JOUR AU - Graveley, B. R. AU - Hertel, K. J. AU - Maniatis, T. PY - 1998 DA - 1998// TI - A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers. JO - EMBO J VL - 17 UR - https://doi.org/10.1093/emboj/17.22.6747 DO - 10.1093/emboj/17.22.6747 ID - Graveley1998 ER - TY - JOUR AU - Willie, E. AU - Majewski, J. PY - 2004 DA - 2004// TI - Evidence for codon bias selection at the pre-mRNA level in eukaryotes. JO - Trends Genet VL - 20 UR - https://doi.org/10.1016/j.tig.2004.08.014 DO - 10.1016/j.tig.2004.08.014 ID - Willie2004 ER - TY - JOUR AU - Chamary, J. V. AU - Hurst, L. D. PY - 2005 DA - 2005// TI - Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else? JO - Trends Genet VL - 21 UR - https://doi.org/10.1016/j.tig.2005.03.001 DO - 10.1016/j.tig.2005.03.001 ID - Chamary2005 ER - TY - JOUR AU - Parmley, J. L. AU - Hurst, L. D. PY - 2007 DA - 2007// TI - Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm104 DO - 10.1093/molbev/msm104 ID - Parmley2007 ER - TY - JOUR AU - Barbosa-Morais, N. L. AU - Carmo-Fonseca, M. AU - Aparicio, S. PY - 2006 DA - 2006// TI - Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion. JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.3936206 DO - 10.1101/gr.3936206 ID - Barbosa-Morais2006 ER - TY - JOUR AU - Graveley, B. R. PY - 2000 DA - 2000// TI - Sorting out the complexity of SR protein functions. JO - RNA VL - 6 UR - https://doi.org/10.1017/S1355838200000960 DO - 10.1017/S1355838200000960 ID - Graveley2000 ER - TY - JOUR AU - Fox-Walsh, K. L. AU - Dou, Y. AU - Lam, B. J. AU - Hung, S. P. AU - Baldi, P. F. AU - Hertel, K. J. PY - 2005 DA - 2005// TI - The architecture of pre-mRNAs affects mechanisms of splice-site pairing. JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0508489102 DO - 10.1073/pnas.0508489102 ID - Fox-Walsh2005 ER - TY - JOUR AU - Collins, L. AU - Penny, D. PY - 2006 DA - 2006// TI - Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Investigating the intron recognition mechanism in eukaryotes. JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msj084 DO - 10.1093/molbev/msj084 ID - Collins2006 ER - TY - JOUR AU - Fahey, M. E. AU - Higgins, D. G. PY - 2007 DA - 2007// TI - Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis. JO - J Mol Evol VL - 65 UR - https://doi.org/10.1007/s00239-007-9015-y DO - 10.1007/s00239-007-9015-y ID - Fahey2007 ER - TY - JOUR AU - Mount, S. M. AU - Burks, C. AU - Hertz, G. AU - Stormo, G. D. AU - White, O. AU - Fields, C. PY - 1992 DA - 1992// TI - Splicing signals in Drosophila: intron size, information content, and consensus sequences. JO - Nucleic Acids Res VL - 20 UR - https://doi.org/10.1093/nar/20.16.4255 DO - 10.1093/nar/20.16.4255 ID - Mount1992 ER - TY - JOUR AU - Fields, C. PY - 1990 DA - 1990// TI - Information content of Caenorhabditis eleganssplice site sequences varies with intron length. JO - Nucleic Acids Res VL - 18 UR - https://doi.org/10.1093/nar/18.6.1509 DO - 10.1093/nar/18.6.1509 ID - Fields1990 ER - TY - JOUR AU - Loftus, B. J. AU - Fung, E. AU - Roncaglia, P. AU - Rowley, D. AU - Amedeo, P. AU - Bruno, D. AU - Vamathevan, J. AU - Miranda, M. AU - Anderson, I. J. AU - Fraser, J. A. AU - Allen, J. E. AU - Bosdet, I. E. AU - Brent, M. R. AU - Chiu, R. AU - Doering, T. L. AU - Donlin, M. J. AU - D'Souza, C. A. AU - Fox, D. S. AU - Grinberg, V. AU - Fu, J. AU - Fukushima, M. AU - Haas, B. J. AU - Huang, J. C. AU - Janbon, G. AU - Jones, S. J. AU - Koo, H. L. AU - Krzywinski, M. I. AU - Kwon-Chung, J. K. AU - Lengeler, K. B. AU - Maiti, R. PY - 2005 DA - 2005// TI - The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. JO - Science VL - 307 UR - https://doi.org/10.1126/science.1103773 DO - 10.1126/science.1103773 ID - Loftus2005 ER - TY - JOUR AU - Warton, D. I. AU - Weber, N. C. PY - 2002 DA - 2002// TI - Common slope tests for bivariate errors-in-variables models. JO - Biom J VL - 44 UR - https://doi.org/3.0.CO;2-N DO - 3.0.CO;2-N ID - Warton2002 ER - TY - JOUR AU - Warton, D. I. AU - Wright, I. J. AU - Falster, D. S. AU - Westoby, M. PY - 2006 DA - 2006// TI - Bivariate line-fitting methods for allometry. JO - Biol Rev Camb Philos Soc VL - 81 UR - https://doi.org/10.1017/S1464793106007007 DO - 10.1017/S1464793106007007 ID - Warton2006 ER - TY - CHAP AU - Robinson, R. M. PY - 2005 DA - 2005// TI - Splicing signals in Caenorhabditis elegans: candidate exonic splicing enhancer motifs. BT - PhD thesis ID - Robinson2005 ER - TY - STD TI - RESCUE-ESE Web Server. [http://genes.mit.edu/burgelab/rescue-ese/] UR - http://genes.mit.edu/burgelab/rescue-ese/ ID - ref24 ER - TY - JOUR AU - Yeo, G. AU - Hoon, S. AU - Venkatesh, B. AU - Burge, C. B. PY - 2004 DA - 2004// TI - Variation in sequence and organization of splicing regulatory elements in vertebrate genes. JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0404901101 DO - 10.1073/pnas.0404901101 ID - Yeo2004 ER - TY - JOUR AU - Parmley, J. L. AU - Chamary, J. V. AU - Hurst, L. D. PY - 2006 DA - 2006// TI - Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msj035 DO - 10.1093/molbev/msj035 ID - Parmley2006 ER - TY - JOUR AU - Eskesen, S. T. AU - Eskesen, F. N. AU - Ruvinsky, A. PY - 2004 DA - 2004// TI - Natural selection affects frequencies of AG and GT dinucleotides at the 5' and 3' ends of exons. JO - Genetics VL - 167 UR - https://doi.org/10.1534/genetics.167.1.543 DO - 10.1534/genetics.167.1.543 ID - Eskesen2004 ER - TY - JOUR AU - Whamond, G. S. AU - Thornton, J. M. PY - 2006 DA - 2006// TI - An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure. JO - J Mol Biol VL - 359 UR - https://doi.org/10.1016/j.jmb.2006.03.029 DO - 10.1016/j.jmb.2006.03.029 ID - Whamond2006 ER - TY - JOUR AU - Blencowe, B. J. PY - 2006 DA - 2006// TI - Alternative splicing: New insights from global analyses. JO - Cell VL - 126 UR - https://doi.org/10.1016/j.cell.2006.06.023 DO - 10.1016/j.cell.2006.06.023 ID - Blencowe2006 ER - TY - JOUR AU - Fairbrother, W. G. AU - Yeh, R. F. AU - Sharp, P. A. AU - Burge, C. B. PY - 2002 DA - 2002// TI - Predictive identification of exonic splicing enhancers in human genes. JO - Science VL - 297 UR - https://doi.org/10.1126/science.1073774 DO - 10.1126/science.1073774 ID - Fairbrother2002 ER - TY - JOUR AU - Wang, Z. F. AU - Xiao, X. S. AU - Van Nostrand, E. AU - Burge, C. B. PY - 2006 DA - 2006// TI - General and specific functions of exonic splicing silencers in splicing control. JO - Mol Cell VL - 23 UR - https://doi.org/10.1016/j.molcel.2006.05.018 DO - 10.1016/j.molcel.2006.05.018 ID - Wang2006 ER - TY - JOUR AU - Siebel, C. W. AU - Feng, L. N. AU - Guthrie, C. AU - Fu, X. D. PY - 1999 DA - 1999// TI - Conservation in budding yeast of a kinase specific for SR splicing factors. JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.10.5440 DO - 10.1073/pnas.96.10.5440 ID - Siebel1999 ER - TY - JOUR AU - Ares, M. AU - Grate, L. AU - Pauling, M. H. PY - 1999 DA - 1999// TI - A handful of intron-containing genes produces the lion's share of yeast mRNA. JO - RNA VL - 5 UR - https://doi.org/10.1017/S1355838299991379 DO - 10.1017/S1355838299991379 ID - Ares1999 ER - TY - JOUR AU - Wood, V. AU - Gwilliam, R. AU - Rajandream, M. A. AU - Lyne, M. AU - Lyne, R. AU - Stewart, A. AU - Sgouros, J. AU - Peat, N. AU - Hayles, J. AU - Baker, S. AU - Basham, D. AU - Bowman, S. AU - Brooks, K. AU - Brown, D. AU - Brown, S. AU - Chillingworth, T. AU - Churcher, C. AU - Collins, M. AU - Connor, R. AU - Cronin, A. AU - Davis, P. AU - Feltwell, T. AU - Fraser, A. AU - Gentles, S. AU - Goble, A. AU - Hamlin, N. AU - Harris, D. AU - Hidalgo, J. AU - Hodgson, G. AU - Holroyd, S. PY - 2002 DA - 2002// TI - The genome sequence of Schizosaccharomyces pombe. JO - Nature VL - 415 UR - https://doi.org/10.1038/nature724 DO - 10.1038/nature724 ID - Wood2002 ER - TY - JOUR AU - Gross, T. AU - Richert, K. AU - Mierke, C. AU - Lutzelberger, M. AU - Kaufer, N. F. PY - 1998 DA - 1998// TI - Identification and characterization of srp1, a gene of fission yeast encoding a RNA binding domain and a RS domain typical of SR splicing factors. JO - Nucleic Acids Res VL - 26 UR - https://doi.org/10.1093/nar/26.2.505 DO - 10.1093/nar/26.2.505 ID - Gross1998 ER - TY - JOUR AU - Lützelberger, M. AU - Gross, T. AU - Käufer, N. F. PY - 1999 DA - 1999// TI - Srp2, an SR protein family member of fission yeast: in vivocharacterization of its modular domains. JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.13.2618 DO - 10.1093/nar/27.13.2618 ID - Lützelberger1999 ER - TY - JOUR AU - Kuhn, A. N. AU - Käufer, N. F. PY - 2003 DA - 2003// TI - Pre-mRNA splicing in Schizosaccharomyces pombe: regulatory role of a kinase conserved from fission yeast to mammals. JO - Curr Genet VL - 42 ID - Kuhn2003 ER - TY - JOUR AU - Webb, C. J. AU - Romfo, C. M. AU - van Heeckeren, W. J. AU - Wise, J. A. PY - 2005 DA - 2005// TI - Exonic splicing enhancers in fission yeast: functional conservation demonstrates an early evolutionary origin. JO - Genes Dev VL - 19 UR - https://doi.org/10.1101/gad.1265905 DO - 10.1101/gad.1265905 ID - Webb2005 ER - TY - JOUR AU - Davis, C. A. AU - Grate, L. AU - Spingola, M. AU - Ares, M. PY - 2000 DA - 2000// TI - Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.8.1700 DO - 10.1093/nar/28.8.1700 ID - Davis2000 ER - TY - JOUR AU - Okazaki, K. AU - Niwa, O. PY - 2000 DA - 2000// TI - mRNAs encoding zinc finger protein isoforms are expressed by alternative splicing of an in-frame intron in fission yeast. JO - DNA Res VL - 7 UR - https://doi.org/10.1093/dnares/7.1.27 DO - 10.1093/dnares/7.1.27 ID - Okazaki2000 ER - TY - JOUR AU - Ast, G. PY - 2004 DA - 2004// TI - How did alternative splicing evolve? JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1451 DO - 10.1038/nrg1451 ID - Ast2004 ER - TY - JOUR AU - Xing, Y. AU - Lee, C. PY - 2006 DA - 2006// TI - Alternative splicing and RNA selection pressure - evolutionary consequences for eukaryotic genomes. JO - Nat Rev Genet VL - 7 UR - https://doi.org/10.1038/nrg1896 DO - 10.1038/nrg1896 ID - Xing2006 ER - TY - JOUR AU - Sanford, J. R. AU - Bruzik, J. P. PY - 1999 DA - 1999// TI - SR proteins are required for nematode trans-splicing in vitro. JO - RNA VL - 5 UR - https://doi.org/10.1017/S1355838299990234 DO - 10.1017/S1355838299990234 ID - Sanford1999 ER - TY - JOUR AU - Longman, D. AU - Johnstone, I. L. AU - Cáceres, J. F. PY - 2000 DA - 2000// TI - Functional characterization of SR and SR-related genes in Caenorhabditis elegans. JO - EMBO J VL - 19 UR - https://doi.org/10.1093/emboj/19.7.1625 DO - 10.1093/emboj/19.7.1625 ID - Longman2000 ER - TY - STD TI - Blumenthal T: WormBook: Trans-splicing and operons. [http://www.wormbook.org/chapters/www_transsplicingoperons/transsplicingoperons.html] UR - http://www.wormbook.org/chapters/www_transsplicingoperons/transsplicingoperons.html ID - ref45 ER - TY - JOUR AU - Hastings, K. E. PY - 2005 DA - 2005// TI - SL trans-splicing: easy come or easy go? JO - Trends Genet VL - 21 UR - https://doi.org/10.1016/j.tig.2005.02.005 DO - 10.1016/j.tig.2005.02.005 ID - Hastings2005 ER - TY - JOUR AU - Sheth, N. AU - Roca, X. AU - Hastings, M. L. AU - Roeder, T. AU - Krainer, A. R. AU - Sachidanandam, R. PY - 2006 DA - 2006// TI - Comprehensive splice-site analysis using comparative genomics. JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl556 DO - 10.1093/nar/gkl556 ID - Sheth2006 ER - TY - JOUR AU - Furuyama, S. AU - Bruzik, J. P. PY - 2002 DA - 2002// TI - Multiple roles for SR proteins in trans splicing. JO - Mol Cell Biol VL - 22 UR - https://doi.org/10.1128/MCB.22.15.5337-5346.2002 DO - 10.1128/MCB.22.15.5337-5346.2002 ID - Furuyama2002 ER - TY - JOUR AU - Huang, T. AU - Kuersten, S. AU - Deshpande, A. M. AU - Spieth, J. AU - MacMorris, M. AU - Blumenthal, T. PY - 2001 DA - 2001// TI - Intercistronic region required for polycistronic pre-mRNA processing in Caenorhabditis elegans. JO - Mol Cell Biol VL - 21 UR - https://doi.org/10.1128/MCB.21.4.1111-1120.2001 DO - 10.1128/MCB.21.4.1111-1120.2001 ID - Huang2001 ER - TY - STD TI - Yeast Gene Order Browser. [http://wolfe.gen.tcd.ie/ygob/] UR - http://wolfe.gen.tcd.ie/ygob/ ID - ref50 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput. JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - STD TI - Inparanoid Dm-Dps Orthologues. [http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.flyDROPS.fa-modDROME.fa] UR - http://inparanoid.sbc.su.se/download/current/sqltables/sqltable.flyDROPS.fa-modDROME.fa ID - ref52 ER - TY - STD TI - UCSC Genome Browser: Table Browser. [http://genome.ucsc.edu/cgi-bin/hgTables] UR - http://genome.ucsc.edu/cgi-bin/hgTables ID - ref53 ER - TY - JOUR AU - Carmel, L. AU - Wolf, Y. I. AU - Rogozin, I. B. AU - Koonin, E. V. PY - 2007 DA - 2007// TI - Three distinct modes of intron dynamics in the evolution of eukaryotes. JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.6438607 DO - 10.1101/gr.6438607 ID - Carmel2007 ER - TY - JOUR AU - Newman, A. J. PY - 1997 DA - 1997// TI - The role of U5 snRNP in pre-mRNA splicing. JO - EMBO J VL - 16 UR - https://doi.org/10.1093/emboj/16.19.5797 DO - 10.1093/emboj/16.19.5797 ID - Newman1997 ER - TY - JOUR AU - O'Keefe, R. T. AU - Newman, A. J. PY - 1998 DA - 1998// TI - Functional analysis of the U5 snRNA loop 1 in the second catalytic step of yeast pre-mRNA splicing. JO - EMBO J VL - 17 UR - https://doi.org/10.1093/emboj/17.2.565 DO - 10.1093/emboj/17.2.565 ID - O'Keefe1998 ER - TY - JOUR AU - Newman, A. J. AU - Norman, C. PY - 1992 DA - 1992// TI - U5 snRNA interacts with exon sequences at 5' and 3' splice sites. JO - Cell VL - 68 UR - https://doi.org/10.1016/0092-8674(92)90149-7 DO - 10.1016/0092-8674(92)90149-7 ID - Newman1992 ER - TY - STD TI - Rfam: Seed Alignment for U5. [http://www.sanger.ac.uk/cgi-bin/Rfam/getalignment.pl?acc=RF00020&type=seed&format=link] UR - http://www.sanger.ac.uk/cgi-bin/Rfam/getalignment.pl?acc=RF00020&type=seed&format=link ID - ref58 ER - TY - JOUR AU - Finn, R. D. AU - Mistry, J. AU - Schuster-Böckler, B. AU - Griffiths-Jones, S. AU - Hollich, V. AU - Lassmann, T. AU - Moxon, S. AU - Marshall, M. AU - Khanna, A. AU - Durbin, R. AU - Eddy, S. R. AU - Sonnhammer, E. L. AU - Bateman, A. PY - 2006 DA - 2006// TI - Pfam: clans, web tools and services. JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj149 DO - 10.1093/nar/gkj149 ID - Finn2006 ER -