Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES: Initial sequencing and comparative analysis of the mouse genome. Nature 2002,420(6915):520-562. 10.1038/nature01262
Article
CAS
PubMed
Google Scholar
Black DL: Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 2003, 72: 291-336. 10.1146/annurev.biochem.72.121801.161720
Article
CAS
PubMed
Google Scholar
Brosius J: Gene duplication and other evolutionary strategies: from the RNA world to the future. J Struct Funct Genomics 2003,3(1-4):1-17. 10.1023/A:1022627311114
Article
CAS
PubMed
Google Scholar
Brosius J, Gould SJ: On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA". Proc Natl Acad Sci U S A 1992,89(22):10706-10710. 10.1073/pnas.89.22.10706
Article
PubMed Central
CAS
PubMed
Google Scholar
Koch AL: Enzyme evolution. I. The importance of untranslatable intermediates. Genetics 1972,72(2):297-316.
PubMed Central
CAS
PubMed
Google Scholar
Chothia C, Gough J, Vogel C, Teichmann SA: Evolution of the protein repertoire. Science 2003,300(5626):1701-1703. 10.1126/science.1085371
Article
CAS
PubMed
Google Scholar
Talavera D, Vogel C, Orozco M, Teichmann SA, de la Cruz X: The (In)dependence of Alternative Splicing and Gene Duplication. PLoS Comput Biol 2007,3(3):e33. 10.1371/journal.pcbi.0030033
Article
PubMed Central
PubMed
Google Scholar
Ohno S: Evolution by Gene and Genome Duplication . Berlin , Springer-Verlag; 1970.
Chapter
Google Scholar
Lynch M, Katju V: The altered evolutionary trajectories of gene duplicates. Trends Genet 2004,20(11):544-549. 10.1016/j.tig.2004.09.001
Article
CAS
PubMed
Google Scholar
Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J: Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999,151(4):1531-1545.
PubMed Central
CAS
PubMed
Google Scholar
Li WH, Yang J, Gu X: Expression divergence between duplicate genes. Trends Genet 2005,21(11):602-607. 10.1016/j.tig.2005.08.006
Article
PubMed
Google Scholar
Prince VE, Pickett FB: Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet 2002,3(11):827-837. 10.1038/nrg928
Article
CAS
PubMed
Google Scholar
Shakhnovich BE, Koonin EV: Origins and impact of constraints in evolution of gene families. Genome Res 2006,16(12):1529-1536. 10.1101/gr.5346206
Article
PubMed Central
CAS
PubMed
Google Scholar
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, Szustakowki J: Initial sequencing and analysis of the human genome. Nature 2001,409(6822):860-921. 10.1038/35057062
Article
CAS
PubMed
Google Scholar
Zhou Z, Licklider LJ, Gygi SP, Reed R: Comprehensive proteomic analysis of the human spliceosome. Nature 2002,419(6903):182-185. 10.1038/nature01031
Article
CAS
PubMed
Google Scholar
Modrek B, Lee C: A genomic view of alternative splicing. Nat Genet 2002,30(1):13-19. 10.1038/ng0102-13
Article
CAS
PubMed
Google Scholar
Graveley BR: Alternative splicing: increasing diversity in the proteomic world. Trends Genet 2001,17(2):100-107. 10.1016/S0168-9525(00)02176-4
Article
CAS
PubMed
Google Scholar
Kim E, Magen A, Ast G: Different levels of alternative splicing among eukaryotes. Nucleic Acids Res 2007,35(1):125-131. 10.1093/nar/gkl924
Article
PubMed Central
CAS
PubMed
Google Scholar
Mironov AA, Fickett JW, Gelfand MS: Frequent alternative splicing of human genes. Genome Res 1999,9(12):1288-1293. 10.1101/gr.9.12.1288
Article
PubMed Central
CAS
PubMed
Google Scholar
Deininger PL, Moran JV, Batzer MA, Kazazian HH Jr.: Mobile elements and mammalian genome evolution. Curr Opin Genet Dev 2003,13(6):651-658. 10.1016/j.gde.2003.10.013
Article
CAS
PubMed
Google Scholar
Hedges DJ, Batzer MA: From the margins of the genome: mobile elements shape primate evolution. Bioessays 2005,27(8):785-794. 10.1002/bies.20268
Article
CAS
PubMed
Google Scholar
Krull M, Brosius J, Schmitz J: Alu-SINE exonization: en route to protein-coding function. Mol Biol Evol 2005,22(8):1702-1711. 10.1093/molbev/msi164
Article
CAS
PubMed
Google Scholar
Kriegs JO, Churakov G, Jurka J, Brosius J, Schmitz J: Evolutionary history of 7SL RNA-derived SINEs in Supraprimates. Trends Genet 2007,23(4):158-161. 10.1016/j.tig.2007.02.002
Article
CAS
PubMed
Google Scholar
Mighell AJ, Markham AF, Robinson PA: Alu sequences. FEBS Lett 1997,417(1):1-5. 10.1016/S0014-5793(97)01259-3
Article
CAS
PubMed
Google Scholar
Rowold DJ, Herrera RJ: Alu elements and the human genome. Genetica 2000,108(1):57-72. 10.1023/A:1004099605261
Article
CAS
PubMed
Google Scholar
Schmid CW: Alu: structure, origin, evolution, significance and function of one- tenth of human DNA. Prog Nucleic Acid Res Mol Biol 1996, 53: 283-319.
Article
CAS
PubMed
Google Scholar
Onafuwa-Nuga AA, Telesnitsky A, King SR: 7SL RNA, but not the 54-kd signal recognition particle protein, is an abundant component of both infectious HIV-1 and minimal virus-like particles. Rna 2006,12(4):542-546. 10.1261/rna.2306306
Article
PubMed Central
CAS
PubMed
Google Scholar
Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, Ast G: Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol 2007,8(6):R127. 10.1186/gb-2007-8-6-r127
Article
PubMed Central
PubMed
Google Scholar
Sorek R, Lev-Maor G, Reznik M, Dagan T, Belinky F, Graur D, Ast G: Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons. Mol Cell 2004,14(2):221-231. 10.1016/S1097-2765(04)00181-9
Article
CAS
PubMed
Google Scholar
Ast G: How did alternative splicing evolve? Nat Rev Genet 2004,5(10):773-782. 10.1038/nrg1451
Article
CAS
PubMed
Google Scholar
Kopelman NM, Lancet D, Yanai I: Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms. Nat Genet 2005,37(6):588-589. 10.1038/ng1575
Article
CAS
PubMed
Google Scholar
Conant GC, Wagner A: Asymmetric sequence divergence of duplicate genes. Genome Res 2003,13(9):2052-2058. 10.1101/gr.1252603
Article
PubMed Central
CAS
PubMed
Google Scholar
Yu WP, Brenner S, Venkatesh B: Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu. Trends Genet 2003,19(4):180-183. 10.1016/S0168-9525(03)00048-9
Article
CAS
PubMed
Google Scholar
Su Z, Wang J, Yu J, Huang X, Gu X: Evolution of alternative splicing after gene duplication. Genome Res 2006,16(2):182-189. 10.1101/gr.4197006
Article
PubMed Central
CAS
PubMed
Google Scholar
Karni R, de Stanchina E, Lowe SW, Sinha R, Mu D, Krainer AR: The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nat Struct Mol Biol 2007,14(3):185-193. 10.1038/nsmb1209
Article
PubMed Central
CAS
PubMed
Google Scholar
Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV: Selection in the evolution of gene duplications. Genome Biol 2002,3(2):RESEARCH0008. 10.1186/gb-2002-3-2-research0008
Article
PubMed Central
PubMed
Google Scholar
Grover D, Mukerji M, Bhatnagar P, Kannan K, Brahmachari SK: Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics 2004,20(6):813-817. 10.1093/bioinformatics/bth005
Article
CAS
PubMed
Google Scholar
Kuryshev VY, Vorobyov E, Zink D, Schmitz J, Rozhdestvensky TS, Munstermann E, Ernst U, Wellenreuther R, Moosmayer P, Bechtel S, Schupp I, Horst J, Korn B, Poustka A, Wiemann S: An anthropoid-specific segmental duplication on human chromosome 1q22. Genomics 2006,88(2):143-151. 10.1016/j.ygeno.2006.02.002
Article
CAS
PubMed
Google Scholar
Xing J, Wang H, Belancio VP, Cordaux R, Deininger PL, Batzer MA: Emergence of primate genes by retrotransposon-mediated sequence transduction. Proc Natl Acad Sci U S A 2006,103(47):17608-17613. 10.1073/pnas.0603224103
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang CY, Liang YJ, Lin YS, Shih HM, Jou YS, Yu WC: YY1AP, a novel co-activator of YY1. J Biol Chem 2004,279(17):17750-17755. 10.1074/jbc.M310532200
Article
CAS
PubMed
Google Scholar
Grover D, Majumder PP, C BR, Brahmachari SK, Mukerji M: Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22. Mol Biol Evol 2003,20(9):1420-1424. 10.1093/molbev/msg153
Article
CAS
PubMed
Google Scholar
Spurkland A, Sollid LM: Mapping genes and pathways in autoimmune disease. Trends Immunol 2006,27(7):336-342. 10.1016/j.it.2006.05.008
Article
CAS
PubMed
Google Scholar
Vazquez N, Lehrnbecher T, Chen R, Christensen BL, Gallin JI, Malech H, Holland S, Zhu S, Chanock SJ: Mutational analysis of patients with p47-phox-deficient chronic granulomatous disease: The significance of recombination events between the p47-phox gene (NCF1) and its highly homologous pseudogenes. Exp Hematol 2001,29(2):234-243. 10.1016/S0301-472X(00)00646-9
Article
CAS
PubMed
Google Scholar
Mersch B, Sela N, Ast G, Suhai S, Hotz-Wagenblatt A: AluScreen: Identifying tissue or tumor-specific Alu-containing isoforms in DNA. submitted 2007.
Google Scholar
Schnapp A, Pfleiderer C, Rosenbauer H, Grummt I: A growth-dependent transcription initiation factor (TIF-IA) interacting with RNA polymerase I regulates mouse ribosomal RNA synthesis. Embo J 1990,9(9):2857-2863.
PubMed Central
CAS
PubMed
Google Scholar
Yuan X, Zhou Y, Casanova E, Chai M, Kiss E, Grone HJ, Schutz G, Grummt I: Genetic inactivation of the transcription factor TIF-IA leads to nucleolar disruption, cell cycle arrest, and p53-mediated apoptosis. Mol Cell 2005,19(1):77-87. 10.1016/j.molcel.2005.05.023
Article
CAS
PubMed
Google Scholar
Buttgereit D, Pflugfelder G, Grummt I: Growth-dependent regulation of rRNA synthesis is mediated by a transcription initiation factor (TIF-IA). Nucleic Acids Res 1985,13(22):8165-8180. 10.1093/nar/13.22.8165
Article
PubMed Central
CAS
PubMed
Google Scholar
Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent WJ: The UCSC genome browser database: update 2007. Nucleic Acids Res 2007,35(Database issue):D668-73. 10.1093/nar/gkl928
Article
PubMed Central
CAS
PubMed
Google Scholar
Lev-Maor G, Sorek R, Shomron N, Ast G: The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science 2003,300(5623):1288-1291. 10.1126/science.1082588
Article
CAS
PubMed
Google Scholar
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(6):769-781. 10.1016/j.molcel.2006.05.008
Article
CAS
PubMed
Google Scholar
Magen A, Ast G: The importance of being divisible by three in alternative splicing. Nucleic Acids Res 2005,33(17):5574-5582. 10.1093/nar/gki858
Article
PubMed Central
CAS
PubMed
Google Scholar
Sorek R, Ast G: Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res 2003,13(7):1631-1637. 10.1101/gr.1208803
Article
PubMed Central
CAS
PubMed
Google Scholar
Gould SJ, Vrba ES: Exaptation; a missing term in the science of form. Paleobiology 1982,8(1):4-15.
Google Scholar
Zhang XH, Chasin LA: Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. Proc Natl Acad Sci U S A 2006,103(36):13427-13432. 10.1073/pnas.0603042103
Article
PubMed Central
CAS
PubMed
Google Scholar
UCSC genome browser[http://genome.ucsc.edu]
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005,110(1-4):462-467. 10.1159/000084979
Article
CAS
PubMed
Google Scholar