Origin and evolution of spliceosomal introns
暂无分享,去创建一个
Liran Carmel | Eugene V Koonin | Miklos Csuros | E. Koonin | L. Carmel | I. Rogozin | M. Csűros | Igor B Rogozin
[1] D. Penny,et al. Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses. , 2006, Molecular biology and evolution.
[2] E. Koonin,et al. Accumulation of GC donor splice signals in mammals , 2008, Biology Direct.
[3] Junhyong Kim,et al. Cytoplasmic Intron Sequence-Retaining Transcripts Can Be Dendritically Targeted via ID Element Retrotransposons , 2011, Neuron.
[4] J. M. Comeron,et al. Selective and Mutational Patterns Associated With Gene Expression in Humans , 2004, Genetics.
[5] T. Nilsen. Evolutionary origin of SL-addition trans-splicing: still an enigma. , 2001, Trends in genetics : TIG.
[6] M. Kreitman,et al. Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. , 2001, Genome research.
[7] F. Dietrich,et al. Evidence of mRNA-Mediated Intron Loss in the Human-Pathogenic Fungus Cryptococcus neoformans , 2006, Eukaryotic Cell.
[8] D. Carlini,et al. Synonymous SNPs Provide Evidence for Selective Constraint on Human Exonic Splicing Enhancers , 2005, Journal of Molecular Evolution.
[9] Cole Trapnell,et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.
[10] L. Patthy,et al. Intron‐dependent evolution: Preferred types of exons and introns , 1987, FEBS letters.
[11] D. Penny,et al. Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana. , 2006, Molecular biology and evolution.
[12] M. Lynch,et al. Ubiquitous internal gene duplication and intron creation in eukaryotes , 2009, Proceedings of the National Academy of Sciences.
[13] V. Babenko,et al. Does Drive Toward Canonic Exonic Splicing Sites Exist in Mammals? , 2010, Journal of Molecular Evolution.
[14] Scott W Roy,et al. Intron-rich ancestors. , 2006, Trends in genetics : TIG.
[15] T. Köcher,et al. The DExH/D box protein HEL/UAP56 is essential for mRNA nuclear export in Drosophila , 2001, Current Biology.
[16] C Joel McManus,et al. Global analysis of trans-splicing in Drosophila , 2010, Proceedings of the National Academy of Sciences.
[17] Igor B. Rogozin,et al. Reconstruction of Ancestral Protosplice Sites , 2004, Current Biology.
[18] J. Finnerty,et al. A high percentage of introns in human genes were present early in animal evolution: evidence from the basal metazoan Nematostella vectensis. , 2006, Genome informatics. International Conference on Genome Informatics.
[19] A. Grigoriev,et al. Significant expansion of exon-bordering protein domains during animal proteome evolution , 2005, Nucleic acids research.
[20] Miklós Csürös. Malin: maximum likelihood analysis of intron evolution in eukaryotes , 2008, Bioinform..
[21] Marcela Dávila López,et al. Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components , 2008, Nucleic acids research.
[22] K. Howe,et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. , 2007, Genome research.
[23] E. Koonin,et al. Intron sliding in conserved gene families. , 2000, Trends in genetics : TIG.
[24] L. Carmel,et al. The role of reverse transcriptase in intron gain and loss mechanisms. , 2012, Molecular biology and evolution.
[25] Arlin Stoltzfus,et al. Molecular evolution: Recent cases of spliceosomal intron gain? , 1998, Current Biology.
[26] T. Blumenthal,et al. Trans‐splicing , 2011, Wiley interdisciplinary reviews. RNA.
[27] Tyler S. Alioto,et al. U12DB: a database of orthologous U12-type spliceosomal introns , 2006, Nucleic Acids Res..
[28] Stephen M. Mount,et al. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis , 2006, BMC Genomics.
[29] Gil Ast,et al. Comparative analysis detects dependencies among the 5' splice-site positions. , 2004, RNA.
[30] Colin N. Dewey,et al. Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns , 2006, BMC Genomics.
[31] W. Martin,et al. Evolution of spliceosomal introns following endosymbiotic gene transfer , 2010, BMC Evolutionary Biology.
[32] Eric C Lai,et al. Mirtrons: microRNA biogenesis via splicing. , 2011, Biochimie.
[33] Eugene Berezikov,et al. Mammalian mirtron genes. , 2007, Molecular cell.
[34] Luciano Milanesi,et al. Analysis of donor splice sites in different eukaryotic organisms , 1997, Journal of Molecular Evolution.
[35] C. Schlötterer,et al. Nonsense-Mediated Decay Enables Intron Gain in Drosophila , 2010, PLoS genetics.
[36] Hung D. Nguyen,et al. Intron Dynamics in Ribosomal Protein Genes , 2007, PloS one.
[37] Christopher J. Lee,et al. Genome-wide detection of alternative splicing in expressed sequences of human genes , 2001, Nucleic Acids Res..
[38] S. Kelchner,et al. A broadscale phylogenetic analysis of group II intron RNAs and intron-encoded reverse transcriptases. , 2009, Molecular biology and evolution.
[39] T. Maniatis,et al. An extensive network of coupling among gene expression machines , 2002, Nature.
[40] M. Long,et al. Intron presence–absence polymorphism in Drosophila driven by positive Darwinian selection , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[41] Xuehui Huang,et al. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. , 2010, Genome research.
[42] D. Halligan,et al. Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. , 2006, Genome research.
[43] E. Stukenbrock,et al. Evidence for Extensive Recent Intron Transposition in Closely Related Fungi , 2011, Current Biology.
[44] E. Koonin,et al. Evolutionarily conserved genes preferentially accumulate introns. , 2007, Genome research.
[45] K. Klinger,et al. Alternative splicing of exon 3 of the human growth hormone receptor is the result of an unusual genetic polymorphism. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[46] C. Pál,et al. Highly expressed genes in yeast evolve slowly. , 2001, Genetics.
[47] E. Koonin,et al. The Impact of Comparative Genomics on Our Understanding of Evolution , 2000, Cell.
[48] L. Hurst,et al. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. , 2006, Molecular biology and evolution.
[49] Andrew G McArthur,et al. A spliceosomal intron in Giardia lamblia , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[50] Malay Kumar Basu,et al. Domain mobility in proteins: functional and evolutionary implications , 2008, Briefings Bioinform..
[51] Russell F. Doolittle,et al. Intron Distribution in Ancient Paralogs Supports Random Insertion and Not Random Loss , 1997, Journal of Molecular Evolution.
[52] Anuj Kumar,et al. An Overview of Nested Genes in Eukaryotic Genomes , 2009, Eukaryotic Cell.
[53] J. Parsch. Selective constraints on intron evolution in Drosophila. , 2003, Genetics.
[54] Hung D. Nguyen,et al. Phase distribution of spliceosomal introns: implications for intron origin , 2006, BMC Evolutionary Biology.
[55] T. Blumenthal,et al. trans Splicing of PolycistronicCaenorhabditis elegans Pre-mRNAs: Analysis of the SL2 RNA , 2000, Molecular and Cellular Biology.
[56] E. Koonin,et al. The ancient Virus World and evolution of cells , 2006, Biology Direct.
[57] Kevin Burrage,et al. ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome , 2000, Nature Genetics.
[58] E. Hurt,et al. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans , 2000, Nature.
[59] Frédéric Delsuc,et al. Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate , 2010, Science.
[60] I. Ebersberger,et al. A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain. , 1997, Gene.
[61] D. M. Krylov,et al. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. , 2003, Genome research.
[62] Lesley Collins,et al. Complex spliceosomal organization ancestral to extant eukaryotes. , 2005, Molecular biology and evolution.
[63] D. Eisenberg,et al. Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.
[64] A. Lambowitz,et al. Group II introns: mobile ribozymes that invade DNA. , 2011, Cold Spring Harbor perspectives in biology.
[65] D. Niu,et al. Selection for the miniaturization of highly expressed genes. , 2007, Biochemical and biophysical research communications.
[66] S. Brenner,et al. Investigation of loss and gain of introns in the compact genomes of pufferfishes (Fugu and Tetraodon). , 2008, Molecular biology and evolution.
[67] M. Lynch,et al. The Origins of Genome Complexity , 2003, Science.
[68] C. Guthrie,et al. Transcript Specificity in Yeast Pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components , 2007, PLoS biology.
[69] A. Russell,et al. An early evolutionary origin for the minor spliceosome , 2006, Nature.
[70] Eugene V Koonin,et al. A glimpse of a putative pre-intron phase of eukaryotic evolution. , 2007, Trends in genetics : TIG.
[71] C. Wilke,et al. The evolutionary consequences of erroneous protein synthesis , 2009, Nature Reviews Genetics.
[72] L. Patthy. Genome evolution and the evolution of exon-shuffling--a review. , 1999, Gene.
[73] Eugene V Koonin,et al. Evolution of alternative and constitutive regions of mammalian 5'UTRs , 2009, BMC Genomics.
[74] Klaudia Walter,et al. Open access, freely available online PLoS BIOLOGY Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2022 .
[75] P. Perlman,et al. A structural analysis of the group II intron active site and implications for the spliceosome. , 2010, RNA.
[76] Jean Thierry-Mieg,et al. A global analysis of Caenorhabditis elegans operons , 2002, Nature.
[77] B. Birren,et al. Patterns of Intron Gain and Loss in Fungi , 2004, PLoS biology.
[78] Eugene V Koonin,et al. Prevalence of intron gain over intron loss in the evolution of paralogous gene families. , 2004, Nucleic acids research.
[79] G. M. Suboch,et al. Analysis of nonuniformity in intron phase distribution. , 1992, Nucleic acids research.
[80] H. Le Hir,et al. The spliceosome deposits multiple proteins 20–24 nucleotides upstream of mRNA exon–exon junctions , 2000, The EMBO journal.
[81] Henry D. Priest,et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. , 2010, Genome research.
[82] H. Ragg,et al. Ancestry and evolution of a secretory pathway serpin , 2008, BMC Evolutionary Biology.
[83] L. Hurst,et al. Gametophytic Selection in Arabidopsis thaliana Supports the Selective Model of Intron Length Reduction , 2005, PLoS genetics.
[84] Sherif Abou Elela,et al. Modern origin of numerous alternatively spliced human introns from tandem arrays , 2007, Proceedings of the National Academy of Sciences.
[85] E. Koonin. The Logic of Chance: The Nature and Origin of Biological Evolution , 2011 .
[86] H. Lehrach,et al. Hypervariable and Highly Divergent Intron–Exon Organizations in the Chordate Oikopleura dioica , 2004, Journal of Molecular Evolution.
[87] Liran Carmel,et al. An Expectation-Maximization Algorithm for Analysis of Evolution of Exon-Intron Structure of Eukaryotic Genes , 2005, Comparative Genomics.
[88] M. Long,et al. Testing the "proto-splice sites" model of intron origin: evidence from analysis of intron phase correlations. , 2000, Molecular biology and evolution.
[89] Boris Lenhard,et al. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes , 2004, BMC Genomics.
[90] S. J. Souza. The Emergence of a Synthetic Theory of Intron Evolution , 2003, Genetica.
[91] M. Averof,et al. Evidence for multiple independent origins of trans-splicing in Metazoa. , 2010, Molecular biology and evolution.
[92] G. Ast,et al. Alternative splicing and evolution: diversification, exon definition and function , 2010, Nature Reviews Genetics.
[93] R. Reed,et al. Initial splice-site recognition and pairing during pre-mRNA splicing. , 1996, Current opinion in genetics & development.
[94] D. Penny,et al. The Path from the RNA World , 1998, Journal of Molecular Evolution.
[95] L. Chasin,et al. Positive selection acting on splicing motifs reflects compensatory evolution. , 2008, Genome research.
[96] Ed Hurt,et al. Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p , 2001, Nature.
[97] Ewan Birney,et al. Estimating the neutral rate of nucleotide substitution using introns. , 2006, Molecular biology and evolution.
[98] E. Koonin,et al. Origins and evolution of eukaryotic RNA interference. , 2008, Trends in ecology & evolution.
[99] Martin Vingron,et al. Increase of functional diversity by alternative splicing. , 2003, Trends in genetics : TIG.
[100] Igor B. Rogozin,et al. In search of lost introns , 2007, ISMB/ECCB.
[101] Gautam Chaudhuri,et al. Alternative initiation and splicing in dicer gene expression in human breast cells , 2005, Breast Cancer Research.
[102] L. Patthy,et al. Modules, multidomain proteins and organismic complexity , 2005, The FEBS journal.
[103] D. Tautz,et al. Of statistics and genomes. , 2004, Trends in genetics : TIG.
[104] P Bork,et al. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms , 2000, FEBS letters.
[105] I. Bolívar,et al. Tempo and Mode of Spliceosomal Intron Evolution in Actin of Foraminifera , 2006, Journal of Molecular Evolution.
[106] W. Gilbert. Why genes in pieces? , 1978, Nature.
[107] R. Padgett,et al. Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns. , 1997, Molecular cell.
[108] Stephen M. Mount,et al. Splicing signals in Drosophila: intron size, information content, and consensus sequences. , 1992, Nucleic acids research.
[109] C. Ponting,et al. Evolution and Functions of Long Noncoding RNAs , 2009, Cell.
[110] F. Ayala,et al. Origins and evolution of spliceosomal introns. , 2006, Annual review of genetics.
[111] A. Newman,et al. Exon Junction Sequences as Cryptic Splice Sites Implications for Intron Origin , 2004, Current Biology.
[112] J. Coulombe-Huntington,et al. Intron loss and gain in Drosophila. , 2007, Molecular biology and evolution.
[113] F. Ayala,et al. A new Drosophila spliceosomal intron position is common in plants , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[114] M. Mann,et al. Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly , 2001, Nature.
[115] C. Guthrie,et al. A novel role for a U5 snRNP protein in 3' splice site selection. , 1995, Genes & development.
[116] K. Grzeschik,et al. Human GLI3 Intragenic Conserved Non-Coding Sequences Are Tissue-Specific Enhancers , 2007, PloS one.
[117] J. Nap,et al. In plants, highly expressed genes are the least compact. , 2006, Trends in genetics : TIG.
[118] M. Lynch. The origins of eukaryotic gene structure. , 2006, Molecular biology and evolution.
[119] E. Koonin,et al. Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues. , 2007, Molecular biology and evolution.
[120] David Penny,et al. Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing , 2007, BMC Evolutionary Biology.
[121] M. Irimia,et al. Evolution of Alternative Splicing Regulation: Changes in Predicted Exonic Splicing Regulators Are Not Associated with Changes in Alternative Splicing Levels in Primates , 2009, PloS one.
[122] J. Steitz,et al. SR splicing factors serve as adapter proteins for TAP-dependent mRNA export. , 2003, Molecular cell.
[123] D. Penny,et al. A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. , 2007, Molecular biology and evolution.
[124] Douglas G. Scofield,et al. Intron presence-absence polymorphisms in Daphnia. , 2008, Molecular biology and evolution.
[125] Cristian I. Castillo-Davis,et al. Selection for short introns in highly expressed genes , 2002, Nature Genetics.
[126] A. Russell,et al. An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia , 2005, BMC Evolutionary Biology.
[127] E. Koonin,et al. Nested genes and increasing organizational complexity of metazoan genomes. , 2008, Trends in genetics : TIG.
[128] R. Reed,et al. Splicing is required for rapid and efficient mRNA export in metazoans. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[129] Eugene V Koonin,et al. Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion. , 2004, Gene.
[130] Tanya Vavouri,et al. Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis. , 2006, Genome research.
[131] S. Bowman,et al. Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function , 2007, Proceedings of the National Academy of Sciences.
[132] Eugene V Koonin,et al. Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach. , 2008, Molecular biology and evolution.
[133] Igor B. Rogozin,et al. Evidence of Splice Signal Migration from Exon to Intron during Intron Evolution , 2003, Current Biology.
[134] N. Dibb,et al. Proto-splice site model of intron origin. , 1991, Journal of theoretical biology.
[135] N. Brockdorff,et al. A Dual Origin of the Xist Gene from a Protein-Coding Gene and a Set of Transposable Elements , 2008, PloS one.
[136] G. Fink,et al. Pseudogenes in yeast? , 1987, Cell.
[137] P. Stadler,et al. Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication , 2010, BMC Evolutionary Biology.
[138] P. Sharp,et al. Evolutionary fates and origins of U12-type introns. , 1998, Molecular cell.
[139] B. Frey,et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing , 2008, Nature Genetics.
[140] Jackson Ij,et al. A reappraisal of non-consensus mRNA splice sites. , 1991 .
[141] H. Le Hir,et al. Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon-exon junctions. , 2000, Genes & development.
[142] F. Müller,et al. Intronic enhancers control expression of zebrafish sonic hedgehog in floor plate and notochord. , 1999, Development.
[143] Cristian I. Castillo-Davis,et al. Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites. , 2004, Molecular biology and evolution.
[144] J. Vaughn,et al. The Evolution of Single-Copy Drosophila Nuclear 4f-rnp Genes: Spliceosomal Intron Losses Create Polymorphic Alleles , 2002, Journal of Molecular Evolution.
[145] I. Jackson,et al. A reappraisal of non-consensus mRNA splice sites. , 1991, Nucleic acids research.
[146] E. Koonin,et al. Conservation versus parallel gains in intron evolution , 2005, Nucleic acids research.
[147] M. Rosbash,et al. The U1 snRNP protein U1C recognizes the 5′ splice site in the absence of base pairing , 2002, Nature.
[148] J. Coulombe-Huntington,et al. Characterization of intron loss events in mammals. , 2006, Genome research.
[149] E. Koonin,et al. Remarkable Interkingdom Conservation of Intron Positions and Massive, Lineage-Specific Intron Loss and Gain in Eukaryotic Evolution , 2003, Current Biology.
[150] Tracy Farrer,et al. Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing. , 2002, Nucleic acids research.
[151] M. Lynch. The frailty of adaptive hypotheses for the origins of organismal complexity , 2007, Proceedings of the National Academy of Sciences.
[152] Wei Zheng,et al. Translational Regulation of Angiotensin Type 1a Receptor Expression and Signaling by Upstream AUGs in the 5′ Leader Sequence* , 2004, Journal of Biological Chemistry.
[153] A. Salamov,et al. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas , 2009, Science.
[154] Erin E. Gill,et al. Constrained intron structures in a microsporidian. , 2010, Molecular biology and evolution.
[155] Alexei Fedorov,et al. Large-scale comparison of intron positions among animal, plant, and fungal genes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[156] Michel Eduardo Beleza Yamagishi,et al. Detection of human interchromosomal trans-splicing in sequence databanks , 2010, Briefings Bioinform..
[157] Qiang Wu,et al. Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. , 2003, Genome research.
[158] R. Padgett,et al. Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. , 1994, Journal of molecular biology.
[159] T. Tatusova,et al. Cryptic splice sites and split genes , 2011, Nucleic acids research.
[160] Eugene V Koonin,et al. Complex selection on 5' splice sites in intron-rich organisms. , 2009, Genome research.
[161] Noam Shomron,et al. Biased hosting of intronic microRNA genes , 2010, Bioinform..
[162] I. Rogozin,et al. Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants , 2010, Molecular biology and evolution.
[163] Jacek Majewski,et al. Fine-Scale Variation and Genetic Determinants of Alternative Splicing across Individuals , 2009, PLoS genetics.
[164] Yoshiharu Sato,et al. Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs , 2008, Nucleic acids research.
[165] H. Lehrach,et al. Miniature genome in the marine chordate Oikopleura dioica. , 2001, Science.
[166] D. Niu. Exon definition as a potential negative force against intron losses in evolution , 2008, Biology Direct.
[167] B. Charlesworth,et al. Intron Size and Exon Evolution in Drosophila , 2005, Genetics.
[168] S J de Souza,et al. Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[169] L. Patthy. Modular Assembly of Genes and the Evolution of New Functions , 2003, Genetica.
[170] David Penny,et al. Coevolution of genomic intron number and splice sites. , 2007, Trends in genetics : TIG.
[171] D. Hartl,et al. Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number. , 2006, Genome research.
[172] M. Zuker,et al. Testing the exon theory of genes: the evidence from protein structure. , 1994, Science.
[173] M. Batzer,et al. Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[174] M. Cariou,et al. Phylogenetic Distribution of Intron Positions in Alpha-Amylase Genes of Bilateria Suggests Numerous Gains and Losses , 2011, PloS one.
[175] Jurg Ott,et al. Distribution and characterization of regulatory elements in the human genome. , 2002, Genome research.
[176] Hung D. Nguyen,et al. The evolution of spliceosomal introns in alveolates. , 2007, Molecular biology and evolution.
[177] Desmond G. Higgins,et al. Gene Expression, Intron Density, and Splice Site Strength in Drosophila and Caenorhabditis , 2007, Journal of Molecular Evolution.
[178] Miklós Csürös,et al. Likely Scenarios of Intron Evolution , 2005, Comparative Genomics.
[179] Francisco J. Ayala,et al. Alternative splicing: A missing piece in the puzzle of intron gain , 2008, Proceedings of the National Academy of Sciences.
[180] Eugene V Koonin,et al. A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. , 2003, Trends in genetics : TIG.
[181] Liran Carmel,et al. Widespread positive selection in synonymous sites of mammalian genes. , 2007, Molecular biology and evolution.
[182] D. Penny,et al. Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes. , 2006, Molecular biology and evolution.
[183] J. Parsch,et al. On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila. , 2010, Molecular biology and evolution.
[184] Abraham E. Tucker,et al. Extensive, Recent Intron Gains in Daphnia Populations , 2009, Science.
[185] R. Doolittle. The multiplicity of domains in proteins. , 1995, Annual review of biochemistry.
[186] W. Gilbert,et al. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[187] Alexei Fedorov,et al. Introns in Gene Evolution , 2004, Genetica.
[188] L. D. Hurst,et al. Can Codon Usage Bias Explain Intron Phase Distributions and Exon Symmetry? , 2004, Journal of Molecular Evolution.
[189] Shi Lei,et al. Genomic Survey of the Non-Cultivatable Opportunistic Human Pathogen, Enterocytozoon bieneusi , 2009, PLoS pathogens.
[190] M. Lynch,et al. Where Do Introns Come From? , 2008, PLoS biology.
[191] T. Nilsen. The spliceosome: the most complex macromolecular machine in the cell? , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.
[192] N. Yuldasheva,et al. A high-frequency polymorphism in exon 6 of the CD45 tyrosine phosphatase gene (PTPRC) resulting in altered isoform expression , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[193] Eugene V. Koonin,et al. Introns and the origin of nucleus–cytosol compartmentalization , 2006, Nature.
[194] Douglas G Scofield,et al. Intron size, abundance, and distribution within untranslated regions of genes. , 2006, Molecular biology and evolution.
[195] Aalt DJ van Dijk,et al. Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data , 2011, BMC Plant Biology.
[196] B. Charlesworth. Effective population size and patterns of molecular evolution and variation , 2009, Nature Reviews Genetics.
[197] A. Simpson,et al. Eukaryotic evolution: Early origin of canonical introns , 2002, Nature.
[198] R. DeSalle,et al. Intron Evolution: Testing Hypotheses of Intron Evolution Using the Phylogenomics of Tetraspanins , 2009, PloS one.
[199] Lei-Ying Zhang,et al. Evaluation of Models of the Mechanisms Underlying Intron Loss and Gain in Aspergillus Fungi , 2010, Journal of Molecular Evolution.
[200] Walter Gilbert,et al. Complex early genes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[201] Brian Charlesworth,et al. Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content , 2005, Genome Biology.
[202] Dirk Holste,et al. Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers , 2004, PLoS biology.
[203] K. H. Wolfe,et al. Origins of recently gained introns in Caenorhabditis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[204] Tobias Mourier,et al. Eukaryotic Intron Loss , 2003, Science.
[205] L. Hillier,et al. A global analysis of C. elegans trans-splicing. , 2011, Genome research.
[206] W. Gilbert,et al. The exon theory of genes. , 1987, Cold Spring Harbor symposia on quantitative biology.
[207] M. Tomita,et al. On biased distribution of introns in various eukaryotes. , 2002, Gene.
[208] E. Koonin,et al. Three distinct modes of intron dynamics in the evolution of eukaryotes. , 2007, Genome research.
[209] L. Hurst,et al. Human antisense genes have unusually short introns: evidence for selection for rapid transcription. , 2005, Trends in genetics : TIG.
[210] T A Thanaraj,et al. Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions. , 2001, Nucleic acids research.
[211] Yi Xing,et al. Assessing the impact of alternative splicing on domain interactions in the human proteome. , 2004, Journal of proteome research.
[212] Michael Lynch,et al. The evolution of spliceosomal introns. , 2002, Current opinion in genetics & development.
[213] Hank Tu,et al. The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility , 2010, Cell.
[214] Christopher J. Lee,et al. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss , 2003, Nature Genetics.
[215] D J Lipman,et al. Lineage-specific loss and divergence of functionally linked genes in eukaryotes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[216] A. Vinogradov. Compactness of human housekeeping genes: selection for economy or genomic design? , 2004, Trends in genetics : TIG.
[217] Boris G. Mirkin,et al. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell , 2005, Nucleic acids research.
[218] J. Deogun,et al. Method of predicting Splice Sites based on signal interactions , 2006, Biology Direct.
[219] A Yoshida,et al. Exon/intron structure of aldehyde dehydrogenase genes supports the "introns-late" theory. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[220] M. Rosbash,et al. The DECD box putative ATPase Sub2p is an early mRNA export factor , 2001, Current Biology.
[221] D. Moreira,et al. Selective forces for the origin of the eukaryotic nucleus. , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.
[222] A. MacMillan,et al. Pre-mRNA splicing: a complex picture in higher definition. , 2008, Trends in biochemical sciences.
[223] J. Carlton,et al. Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[224] Gil Ast,et al. How did alternative splicing evolve? , 2004, Nature Reviews Genetics.
[225] Hung D. Nguyen,et al. New Maximum Likelihood Estimators for Eukaryotic Intron Evolution , 2005, PLoS Comput. Biol..
[226] Araxi O. Urrutia,et al. The signature of selection mediated by expression on human genes. , 2003, Genome research.
[227] E. Koonin,et al. U12 intron positions are more strongly conserved between animals and plants than U2 intron positions , 2008, Biology Direct.
[228] L. Rieseberg,et al. Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers. , 2011, Molecular biology and evolution.
[229] L K Derr,et al. The involvement of cellular recombination and repair genes in RNA-mediated recombination in Saccharomyces cerevisiae. , 1998, Genetics.
[230] J. Garcia-Fernández,et al. Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis. , 2008, Molecular biology and evolution.
[231] David G. Knowles,et al. High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes. , 2006, Molecular biology and evolution.
[232] Masanori Arita,et al. Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns , 2006, Bioinform..
[233] Igor B. Rogozin,et al. A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes , 2011, PLoS Comput. Biol..
[234] Hans-Werner Mewes,et al. Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns. , 2003, Nucleic acids research.
[235] Samuel S. Shepard,et al. Critical association of ncRNA with introns , 2010, Nucleic acids research.
[236] M. Soller,et al. Pre-messenger RNA processing and its regulation: a genomic perspective , 2006, Cellular and Molecular Life Sciences CMLS.
[237] B. Curtis,et al. A spliceosomal intron of mitochondrial DNA origin , 2010, Current Biology.
[238] Andrey A Mironov,et al. Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes. , 2006, Genome research.
[239] E. Koonin. Intron-dominated genomes of early ancestors of eukaryotes. , 2009, The Journal of heredity.
[240] L. Chasin,et al. Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons , 2006, Proceedings of the National Academy of Sciences.
[241] D. Penny,et al. Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. , 2006, Genome research.
[242] E. Koonin. The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? , 2006, Biology Direct.
[243] Arlin Stoltzfus,et al. The evolutionary gain of spliceosomal introns: sequence and phase preferences. , 2004, Molecular biology and evolution.
[244] C. Ponting,et al. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. , 2007, Genome research.
[245] E. Koonin,et al. Primordial spliceosomal introns were probably U2-type. , 2008, Trends in genetics : TIG.
[246] D. Black. Protein Diversity from Alternative Splicing A Challenge for Bioinformatics and Post-Genome Biology , 2000, Cell.
[247] M. Lynch. Intron evolution as a population-genetic process , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[248] Abhijit A. Patel,et al. The splicing of U12‐type introns can be a rate‐limiting step in gene expression , 2002, The EMBO journal.
[249] J D Palmer,et al. Intron "sliding" and the diversity of intron positions. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[250] D. Penny,et al. An Overview of the Introns-First Theory , 2009, Journal of Molecular Evolution.
[251] E. Koonin,et al. Patterns of intron gain and conservation in eukaryotic genes , 2007, BMC Evolutionary Biology.
[252] M. Rosbash,et al. Quality control of mRNA 3′-end processing is linked to the nuclear exosome , 2001, Nature.
[253] W. Gilbert,et al. On the ancient nature of introns. , 1993, Gene.
[254] V. Kim,et al. Biogenesis of small RNAs in animals , 2009, Nature Reviews Molecular Cell Biology.
[255] J. Logsdon,et al. The recent origins of spliceosomal introns revisited. , 1998, Current opinion in genetics & development.
[256] D. Burstein,et al. Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. , 2007, Genome research.
[257] J. Garcia-Fernández,et al. Contrasting 5' and 3' Evolutionary Histories and Frequent Evolutionary Convergence in Meis/hth Gene Structures , 2011, Genome biology and evolution.
[258] Igor B. Rogozin,et al. Analysis of evolution of exon-intron structure of eukaryotic genes , 2005, Briefings Bioinform..
[259] Stephen M. Mount,et al. Evolutionary dynamics of U12-type spliceosomal introns , 2010, BMC Evolutionary Biology.
[260] R. Reed,et al. Evidence that U5 snRNP recognizes the 3′ splice site for catalytic step II in mammals , 1997, The EMBO journal.
[261] W. Ford Doolittle,et al. Genes in pieces: were they ever together? , 1978, Nature.
[262] M. Irimia,et al. Mystery of intron gain: new data and new models. , 2009, Trends in genetics : TIG.
[263] S. Berget. Exon Recognition in Vertebrate Splicing (*) , 1995, The Journal of Biological Chemistry.
[264] Boris Lenhard,et al. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. , 2007, Genome research.
[265] O. Gotoh,et al. Comparative analysis of information contents relevant to recognition of introns in many species , 2011, BMC Genomics.
[266] J. Garcia-Fernández,et al. Origin of introns by 'intronization' of exonic sequences. , 2008, Trends in genetics : TIG.
[267] Liran Carmel,et al. A Universal Nonmonotonic Relationship between Gene Compactness and Expression Levels in Multicellular Eukaryotes , 2009, Genome biology and evolution.
[268] E. Levanon,et al. Human housekeeping genes are compact. , 2003, Trends in genetics : TIG.
[269] Abhijit A. Patel,et al. Splicing double: insights from the second spliceosome , 2003, Nature Reviews Molecular Cell Biology.
[270] Sherif Abou Elela,et al. Introns within Ribosomal Protein Genes Regulate the Production and Function of Yeast Ribosomes , 2011, Cell.
[271] B. Séraphin,et al. Who's on first? The U1 snRNP-5' splice site interaction and splicing. , 1991, Trends in biochemical sciences.
[272] J. Steitz,et al. A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3. , 1993, Genes & Development.
[273] Melissa S Jurica,et al. Pre-mRNA splicing: awash in a sea of proteins. , 2003, Molecular cell.
[274] J D Palmer,et al. Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[275] J. Steitz,et al. A mammalian gene with introns instead of exons generating stable RNA products , 1996, Nature.
[276] M. Meselson,et al. Massive Horizontal Gene Transfer in Bdelloid Rotifers , 2008, Science.
[277] M. Long,et al. Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns. , 1999, Molecular biology and evolution.
[278] P. Bork,et al. Vertebrate-Type Intron-Rich Genes in the Marine Annelid Platynereis dumerilii , 2005, Science.
[279] Carolyn J. Brown,et al. Mechanisms of X-chromosome inactivation. , 2006, Frontiers in bioscience : a journal and virtual library.
[280] H. Stenøien. Compact genes are highly expressed in the moss Physcomitrella patens. , 2007, Journal of evolutionary biology.
[281] W. Doolittle,et al. The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolution. , 2002, Molecular biology and evolution.
[282] Alexander V. Favorov,et al. Conserved and species-specific alternative splicing in mammalian genomes , 2007, BMC Evolutionary Biology.
[283] Jonathan M. Mudge,et al. The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates , 2011, Molecular biology and evolution.
[284] A. Newman,et al. Evidence that introns arose at proto‐splice sites. , 1989, The EMBO journal.
[285] Manuel Irimia,et al. Evolutionary Convergence on Highly-Conserved 3′ Intron Structures in Intron-Poor Eukaryotes and Insights into the Ancestral Eukaryotic Genome , 2008, PLoS genetics.
[286] D. Penny,et al. On the incidence of intron loss and gain in paralogous gene families. , 2007, Molecular biology and evolution.
[287] J. Steitz,et al. SRprises along a messenger's journey. , 2005, Molecular cell.