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Volumn 7, Issue , 2012, Pages

Origin and evolution of spliceosomal introns

Author keywords

Alternative splicing; Eukaryotic ancestor; Evolution of exon intron structure; Intron gain; Intron loss; Intron sliding; Mobile domains; Phylogenetic trees; Spliceosome; Splicing signals

Indexed keywords

ANIMALIA; EUKARYOTA; METAZOA; PROKARYOTA; PROTISTA; VERTEBRATA;

EID: 84859729407     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-7-11     Document Type: Review
Times cited : (271)

References (287)
  • 1
    • 0018263844 scopus 로고
    • Why genes in pieces?
    • 10.1038/271501a0, 622185
    • Gilbert W. Why genes in pieces?. Nature 1978, 271(5645):501. 10.1038/271501a0, 622185.
    • (1978) Nature , vol.271 , Issue.5645 , pp. 501
    • Gilbert, W.1
  • 2
    • 0042671357 scopus 로고    scopus 로고
    • Pre-mRNA splicing: awash in a sea of proteins
    • 10.1016/S1097-2765(03)00270-3, 12887888
    • Jurica MS, Moore MJ. Pre-mRNA splicing: awash in a sea of proteins. Mol Cell 2003, 12(1):5-14. 10.1016/S1097-2765(03)00270-3, 12887888.
    • (2003) Mol Cell , vol.12 , Issue.1 , pp. 5-14
    • Jurica, M.S.1    Moore, M.J.2
  • 3
    • 0344198459 scopus 로고    scopus 로고
    • The spliceosome: the most complex macromolecular machine in the cell?
    • 10.1002/bies.10394, 14635248
    • Nilsen TW. The spliceosome: the most complex macromolecular machine in the cell?. Bioessays 2003, 25(12):1147-1149. 10.1002/bies.10394, 14635248.
    • (2003) Bioessays , vol.25 , Issue.12 , pp. 1147-1149
    • Nilsen, T.W.1
  • 5
    • 0037136554 scopus 로고    scopus 로고
    • Eukaryotic evolution: early origin of canonical introns
    • 10.1038/419270a, 12239559
    • Simpson AG, MacQuarrie EK, Roger AJ. Eukaryotic evolution: early origin of canonical introns. Nature 2002, 419(6904):270. 10.1038/419270a, 12239559.
    • (2002) Nature , vol.419 , Issue.6904 , pp. 270
    • Simpson, A.G.1    MacQuarrie, E.K.2    Roger, A.J.3
  • 7
    • 38049150492 scopus 로고    scopus 로고
    • Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function
    • 10.1073/pnas.0707419104, 2148396, 18077423
    • Lane CE, van den Heuvel K, Kozera C, Curtis BA, Parsons BJ, Bowman S, Archibald JM. Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function. Proc Natl Acad Sci U S A 2007, 104(50):19908-19913. 10.1073/pnas.0707419104, 2148396, 18077423.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , Issue.50 , pp. 19908-19913
    • Lane, C.E.1    van den Heuvel, K.2    Kozera, C.3    Curtis, B.A.4    Parsons, B.J.5    Bowman, S.6    Archibald, J.M.7
  • 8
    • 16344385067 scopus 로고    scopus 로고
    • Complex spliceosomal organization ancestral to extant eukaryotes
    • 10.1093/molbev/msi091, 15659557
    • Collins L, Penny D. Complex spliceosomal organization ancestral to extant eukaryotes. Mol Biol Evol 2005, 22(4):1053-1066. 10.1093/molbev/msi091, 15659557.
    • (2005) Mol Biol Evol , vol.22 , Issue.4 , pp. 1053-1066
    • Collins, L.1    Penny, D.2
  • 9
    • 0025876808 scopus 로고
    • Who's on first? The U1 snRNP-5' splice site interaction and splicing
    • Rosbash M, Seraphin B. Who's on first? The U1 snRNP-5' splice site interaction and splicing. Trends Biochem Sci 1991, 16(5):187-190.
    • (1991) Trends Biochem Sci , vol.16 , Issue.5 , pp. 187-190
    • Rosbash, M.1    Seraphin, B.2
  • 10
    • 0037026523 scopus 로고    scopus 로고
    • The U1 snRNP protein U1C recognizes the 5' splice site in the absence of base pairing
    • 10.1038/nature00947, 12214237
    • Du H, Rosbash M. The U1 snRNP protein U1C recognizes the 5' splice site in the absence of base pairing. Nature 2002, 419(6902):86-90. 10.1038/nature00947, 12214237.
    • (2002) Nature , vol.419 , Issue.6902 , pp. 86-90
    • Du, H.1    Rosbash, M.2
  • 11
    • 1942469356 scopus 로고    scopus 로고
    • Comparative analysis detects dependencies among the 5' splice-site positions
    • 10.1261/rna.5196404, 1370573, 15100438
    • Carmel I, Tal S, Vig I, Ast G. Comparative analysis detects dependencies among the 5' splice-site positions. RNA 2004, 10(5):828-840. 10.1261/rna.5196404, 1370573, 15100438.
    • (2004) RNA , vol.10 , Issue.5 , pp. 828-840
    • Carmel, I.1    Tal, S.2    Vig, I.3    Ast, G.4
  • 12
    • 0028960809 scopus 로고
    • A novel role for a U5 snRNP protein in 3' splice site selection
    • 10.1101/gad.9.7.855, 7535718
    • Umen JG, Guthrie C. A novel role for a U5 snRNP protein in 3' splice site selection. Genes Dev 1995, 9(7):855-868. 10.1101/gad.9.7.855, 7535718.
    • (1995) Genes Dev , vol.9 , Issue.7 , pp. 855-868
    • Umen, J.G.1    Guthrie, C.2
  • 13
    • 0030750730 scopus 로고    scopus 로고
    • Evidence that U5 snRNP recognizes the 3' splice site for catalytic step II in mammals
    • 10.1093/emboj/16.15.4746, 1170101, 9303319
    • Chiara MD, Palandjian L, Feld Kramer R, Reed R. Evidence that U5 snRNP recognizes the 3' splice site for catalytic step II in mammals. EMBO J 1997, 16(15):4746-4759. 10.1093/emboj/16.15.4746, 1170101, 9303319.
    • (1997) EMBO J , vol.16 , Issue.15 , pp. 4746-4759
    • Chiara, M.D.1    Palandjian, L.2    Feld Kramer, R.3    Reed, R.4
  • 14
    • 0024462103 scopus 로고
    • Evidence that introns arose at proto-splice sites
    • 401080, 2792080
    • Dibb NJ, Newman AJ. Evidence that introns arose at proto-splice sites. EMBO J 1989, 8(7):2015-2021. 401080, 2792080.
    • (1989) EMBO J , vol.8 , Issue.7 , pp. 2015-2021
    • Dibb, N.J.1    Newman, A.J.2
  • 15
    • 0025812574 scopus 로고
    • Proto-splice site model of intron origin
    • Dibb NJ. Proto-splice site model of intron origin. J Theor Biol 1991, 151(7):405-416.
    • (1991) J Theor Biol , vol.151 , Issue.7 , pp. 405-416
    • Dibb, N.J.1
  • 17
    • 50849088978 scopus 로고    scopus 로고
    • Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome
    • 10.1371/journal.pgen.1000148, 2483917, 18688272
    • Irimia M, Roy SW. Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome. PLoS Genet 2008, 4(8):e1000148. 10.1371/journal.pgen.1000148, 2483917, 18688272.
    • (2008) PLoS Genet , vol.4 , Issue.8
    • Irimia, M.1    Roy, S.W.2
  • 18
    • 0030787856 scopus 로고    scopus 로고
    • Analysis of donor splice sites in different eukaryotic organisms
    • 10.1007/PL00006200, 9211734
    • Rogozin IB, Milanesi L. Analysis of donor splice sites in different eukaryotic organisms. J Mol Evol 1997, 45(1):50-59. 10.1007/PL00006200, 9211734.
    • (1997) J Mol Evol , vol.45 , Issue.1 , pp. 50-59
    • Rogozin, I.B.1    Milanesi, L.2
  • 19
    • 33749989756 scopus 로고    scopus 로고
    • Method of predicting splice sites based on signal interactions
    • 10.1186/1745-6150-1-10, 1526722, 16584568
    • Churbanov A, Rogozin IB, Deogun JS, Ali H. Method of predicting splice sites based on signal interactions. Biol Direct 2006, 1:10. 10.1186/1745-6150-1-10, 1526722, 16584568.
    • (2006) Biol Direct , vol.1 , pp. 10
    • Churbanov, A.1    Rogozin, I.B.2    Deogun, J.S.3    Ali, H.4
  • 20
    • 0025836071 scopus 로고
    • A reappraisal of non-consensus mRNA splice sites
    • 10.1093/nar/19.14.3795, 328465, 1713664
    • Jackson IJ. A reappraisal of non-consensus mRNA splice sites. Nucleic Acids Res 1991, 19(14):3795-3798. 10.1093/nar/19.14.3795, 328465, 1713664.
    • (1991) Nucleic Acids Res , vol.19 , Issue.14 , pp. 3795-3798
    • Jackson, I.J.1
  • 21
    • 0028366003 scopus 로고
    • Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites
    • 10.1006/jmbi.1994.1377, 8201617
    • Hall SL, Padgett RA. Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. J Mol Biol 1994, 239(3):357-365. 10.1006/jmbi.1994.1377, 8201617.
    • (1994) J Mol Biol , vol.239 , Issue.3 , pp. 357-365
    • Hall, S.L.1    Padgett, R.A.2
  • 22
    • 0031306509 scopus 로고    scopus 로고
    • Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns
    • 10.1016/S1097-2765(00)80016-7, 9659912
    • Dietrich RC, Incorvaia R, Padgett RA. Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns. Mol Cell 1997, 1(1):151-160. 10.1016/S1097-2765(00)80016-7, 9659912.
    • (1997) Mol Cell , vol.1 , Issue.1 , pp. 151-160
    • Dietrich, R.C.1    Incorvaia, R.2    Padgett, R.A.3
  • 23
    • 0032247416 scopus 로고    scopus 로고
    • Evolutionary fates and origins of U12-type introns
    • 10.1016/S1097-2765(00)80292-0, 9885565
    • Burge CB, Padgett RA, Sharp PA. Evolutionary fates and origins of U12-type introns. Mol Cell 1998, 2(6):773-785. 10.1016/S1097-2765(00)80292-0, 9885565.
    • (1998) Mol Cell , vol.2 , Issue.6 , pp. 773-785
    • Burge, C.B.1    Padgett, R.A.2    Sharp, P.A.3
  • 24
    • 33750336226 scopus 로고    scopus 로고
    • An early evolutionary origin for the minor spliceosome
    • 10.1038/nature05228, 17051219
    • Russell AG, Charette JM, Spencer DF, Gray MW. An early evolutionary origin for the minor spliceosome. Nature 2006, 443(7113):863-866. 10.1038/nature05228, 17051219.
    • (2006) Nature , vol.443 , Issue.7113 , pp. 863-866
    • Russell, A.G.1    Charette, J.M.2    Spencer, D.F.3    Gray, M.W.4
  • 25
    • 44349155377 scopus 로고    scopus 로고
    • Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components
    • 10.1093/nar/gkn142, 2396436, 18390578
    • Davila Lopez M, Rosenblad MA, Samuelsson T. Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. Nucleic Acids Res 2008, 36(9):3001-3010. 10.1093/nar/gkn142, 2396436, 18390578.
    • (2008) Nucleic Acids Res , vol.36 , Issue.9 , pp. 3001-3010
    • Davila Lopez, M.1    Rosenblad, M.A.2    Samuelsson, T.3
  • 26
    • 77749310993 scopus 로고    scopus 로고
    • Evolutionary dynamics of U12-type spliceosomal introns
    • 10.1186/1471-2148-10-47, 2831892, 20163699
    • Lin CF, Mount SM, Jarmolowski A, Makalowski W. Evolutionary dynamics of U12-type spliceosomal introns. BMC Evol Biol 2010, 10:47. 10.1186/1471-2148-10-47, 2831892, 20163699.
    • (2010) BMC Evol Biol , vol.10 , pp. 47
    • Lin, C.F.1    Mount, S.M.2    Jarmolowski, A.3    Makalowski, W.4
  • 27
    • 0037099491 scopus 로고    scopus 로고
    • The splicing of U12-type introns can be a rate-limiting step in gene expression
    • 10.1093/emboj/cdf297, 126102, 12110592
    • Patel AA, McCarthy M, Steitz JA. The splicing of U12-type introns can be a rate-limiting step in gene expression. EMBO J 2002, 21(14):3804-3815. 10.1093/emboj/cdf297, 126102, 12110592.
    • (2002) EMBO J , vol.21 , Issue.14 , pp. 3804-3815
    • Patel, A.A.1    McCarthy, M.2    Steitz, J.A.3
  • 28
    • 0345169036 scopus 로고    scopus 로고
    • Splicing double: insights from the second spliceosome
    • 10.1038/nrm1259, 14685174
    • Patel AA, Steitz JA. Splicing double: insights from the second spliceosome. Nat Rev Mol Cell Biol 2003, 4(12):960-970. 10.1038/nrm1259, 14685174.
    • (2003) Nat Rev Mol Cell Biol , vol.4 , Issue.12 , pp. 960-970
    • Patel, A.A.1    Steitz, J.A.2
  • 29
    • 45549107558 scopus 로고    scopus 로고
    • U12 intron positions are more strongly conserved between animals and plants than U2 intron positions
    • 10.1186/1745-6150-3-19, 2426677, 18479526
    • Basu MK, Makalowski W, Rogozin IB, Koonin EV. U12 intron positions are more strongly conserved between animals and plants than U2 intron positions. Biol Direct 2008, 3:19. 10.1186/1745-6150-3-19, 2426677, 18479526.
    • (2008) Biol Direct , vol.3 , pp. 19
    • Basu, M.K.1    Makalowski, W.2    Rogozin, I.B.3    Koonin, E.V.4
  • 30
    • 54849437046 scopus 로고    scopus 로고
    • Primordial spliceosomal introns were probably U2-type
    • 10.1016/j.tig.2008.09.002, 3381341, 18824272
    • Basu MK, Rogozin IB, Koonin EV. Primordial spliceosomal introns were probably U2-type. Trends Genet 2008, 24(11):525-528. 10.1016/j.tig.2008.09.002, 3381341, 18824272.
    • (2008) Trends Genet , vol.24 , Issue.11 , pp. 525-528
    • Basu, M.K.1    Rogozin, I.B.2    Koonin, E.V.3
  • 31
    • 0028895417 scopus 로고
    • Exon recognition in vertebrate splicing
    • Berget SM. Exon recognition in vertebrate splicing. J Biol Chem 1995, 270(6):2411-2414.
    • (1995) J Biol Chem , vol.270 , Issue.6 , pp. 2411-2414
    • Berget, S.M.1
  • 32
    • 0037041395 scopus 로고    scopus 로고
    • An extensive network of coupling among gene expression machines
    • 10.1038/416499a, 11932736
    • Maniatis T, Reed R. An extensive network of coupling among gene expression machines. Nature 2002, 416(6880):499-506. 10.1038/416499a, 11932736.
    • (2002) Nature , vol.416 , Issue.6880 , pp. 499-506
    • Maniatis, T.1    Reed, R.2
  • 33
    • 5044222204 scopus 로고    scopus 로고
    • How did alternative splicing evolve?
    • Ast G. How did alternative splicing evolve?. Nat Rev Genet 2004, 5(10):773-782.
    • (2004) Nat Rev Genet , vol.5 , Issue.10 , pp. 773-782
    • Ast, G.1
  • 34
    • 44749087058 scopus 로고    scopus 로고
    • Pre-mRNA splicing: a complex picture in higher definition
    • 10.1016/j.tibs.2008.04.004, 18472266
    • Schellenberg MJ, Ritchie DB, MacMillan AM. Pre-mRNA splicing: a complex picture in higher definition. Trends Biochem Sci 2008, 33(6):243-246. 10.1016/j.tibs.2008.04.004, 18472266.
    • (2008) Trends Biochem Sci , vol.33 , Issue.6 , pp. 243-246
    • Schellenberg, M.J.1    Ritchie, D.B.2    MacMillan, A.M.3
  • 35
    • 33646537438 scopus 로고    scopus 로고
    • Pre-messenger RNA processing and its regulation: a genomic perspective
    • Soller M. Pre-messenger RNA processing and its regulation: a genomic perspective. Cell Mol Life Sci 2006, 63(7-8):796-819.
    • (2006) Cell Mol Life Sci , vol.63 , Issue.7-8 , pp. 796-819
    • Soller, M.1
  • 36
    • 0029933504 scopus 로고    scopus 로고
    • Initial splice-site recognition and pairing during pre-mRNA splicing
    • 10.1016/S0959-437X(96)80053-0, 8722179
    • Reed R. Initial splice-site recognition and pairing during pre-mRNA splicing. Curr Opin Genet Dev 1996, 6(2):215-220. 10.1016/S0959-437X(96)80053-0, 8722179.
    • (1996) Curr Opin Genet Dev , vol.6 , Issue.2 , pp. 215-220
    • Reed, R.1
  • 37
    • 58149513315 scopus 로고    scopus 로고
    • Exon definition as a potential negative force against intron losses in evolution
    • 10.1186/1745-6150-3-46, 2614967, 19014515
    • Niu DK. Exon definition as a potential negative force against intron losses in evolution. Biol Direct 2008, 3:46. 10.1186/1745-6150-3-46, 2614967, 19014515.
    • (2008) Biol Direct , vol.3 , pp. 46
    • Niu, D.K.1
  • 38
    • 34547642637 scopus 로고
    • Introns-early
    • Doolittle WF. Introns-early. Nature 1978, 272:581-581.
    • (1978) Nature , vol.272 , pp. 581-581
    • Doolittle, W.F.1
  • 39
    • 0023468862 scopus 로고
    • The exon theory of genes
    • 10.1101/SQB.1987.052.01.098, 2456887
    • Gilbert W. The exon theory of genes. Cold Spring Harb Symp Quant Biol 1987, 52:901-905. 10.1101/SQB.1987.052.01.098, 2456887.
    • (1987) Cold Spring Harb Symp Quant Biol , vol.52 , pp. 901-905
    • Gilbert, W.1
  • 40
    • 0027771868 scopus 로고
    • On the ancient nature of introns
    • Gilbert W, Glynias M. On the ancient nature of introns. Gene 1993, 135(1-2):137-144.
    • (1993) Gene , vol.135 , Issue.1-2 , pp. 137-144
    • Gilbert, W.1    Glynias, M.2
  • 41
    • 0031737389 scopus 로고    scopus 로고
    • The recent origins of spliceosomal introns revisited
    • 10.1016/S0959-437X(98)80031-2, 9914210
    • Logsdon JM. The recent origins of spliceosomal introns revisited. Curr Opin Genet Dev 1998, 8(6):637-648. 10.1016/S0959-437X(98)80031-2, 9914210.
    • (1998) Curr Opin Genet Dev , vol.8 , Issue.6 , pp. 637-648
    • Logsdon, J.M.1
  • 42
    • 0036888952 scopus 로고    scopus 로고
    • The evolution of spliceosomal introns
    • 10.1016/S0959-437X(02)00360-X, 12433585
    • Lynch M, Richardson AO. The evolution of spliceosomal introns. Curr Opin Genet Dev 2002, 12(6):701-710. 10.1016/S0959-437X(02)00360-X, 12433585.
    • (2002) Curr Opin Genet Dev , vol.12 , Issue.6 , pp. 701-710
    • Lynch, M.1    Richardson, A.O.2
  • 43
    • 0028043139 scopus 로고
    • Testing the exon theory of genes: the evidence from protein structure [see comments]
    • 10.1126/science.8023140, 8023140
    • Stoltzfus A, Spencer DF, Zuker M, Logsdon JM, Doolittle WF. Testing the exon theory of genes: the evidence from protein structure [see comments]. Science 1994, 265(5169):202-207. 10.1126/science.8023140, 8023140.
    • (1994) Science , vol.265 , Issue.5169 , pp. 202-207
    • Stoltzfus, A.1    Spencer, D.F.2    Zuker, M.3    Logsdon, J.M.4    Doolittle, W.F.5
  • 44
    • 0030885349 scopus 로고    scopus 로고
    • Intron "sliding" and the diversity of intron positions
    • 10.1073/pnas.94.20.10739, 23469, 9380704
    • Stoltzfus A, Logsdon JM, Palmer JD, Doolittle WF. Intron "sliding" and the diversity of intron positions. Proc Natl Acad Sci U S A 1997, 94(20):10739-10744. 10.1073/pnas.94.20.10739, 23469, 9380704.
    • (1997) Proc Natl Acad Sci U S A , vol.94 , Issue.20 , pp. 10739-10744
    • Stoltzfus, A.1    Logsdon, J.M.2    Palmer, J.D.3    Doolittle, W.F.4
  • 45
    • 0042921194 scopus 로고    scopus 로고
    • Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution
    • 10.1016/S0960-9822(03)00558-X, 12956953
    • Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 2003, 13(17):1512-1517. 10.1016/S0960-9822(03)00558-X, 12956953.
    • (2003) Curr Biol , vol.13 , Issue.17 , pp. 1512-1517
    • Rogozin, I.B.1    Wolf, Y.I.2    Sorokin, A.V.3    Mirkin, B.G.4    Koonin, E.V.5
  • 46
    • 34047175831 scopus 로고    scopus 로고
    • The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?
    • 10.1186/1745-6150-1-22, 1570339, 16907971
    • Koonin EV. The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?. Biol Direct 2006, 1:22. 10.1186/1745-6150-1-22, 1570339, 16907971.
    • (2006) Biol Direct , vol.1 , pp. 22
    • Koonin, E.V.1
  • 47
    • 0031984372 scopus 로고    scopus 로고
    • The path from the RNA world
    • 10.1007/PL00006275, 9419221
    • Poole AM, Jeffares DC, Penny D. The path from the RNA world. J Mol Evol 1998, 46(1):1-17. 10.1007/PL00006275, 9419221.
    • (1998) J Mol Evol , vol.46 , Issue.1 , pp. 1-17
    • Poole, A.M.1    Jeffares, D.C.2    Penny, D.3
  • 48
    • 72449160582 scopus 로고    scopus 로고
    • An overview of the introns-first theory
    • 10.1007/s00239-009-9279-5, 19777149
    • Penny D, Hoeppner MP, Poole AM, Jeffares DC. An overview of the introns-first theory. J Mol Evol 2009, 69(5):527-540. 10.1007/s00239-009-9279-5, 19777149.
    • (2009) J Mol Evol , vol.69 , Issue.5 , pp. 527-540
    • Penny, D.1    Hoeppner, M.P.2    Poole, A.M.3    Jeffares, D.C.4
  • 49
    • 0037197986 scopus 로고    scopus 로고
    • Intron evolution as a population-genetic process
    • 10.1073/pnas.092595699, 122912, 11983904
    • Lynch M. Intron evolution as a population-genetic process. Proc Natl Acad Sci U S A 2002, 99(9):6118-6123. 10.1073/pnas.092595699, 122912, 11983904.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , Issue.9 , pp. 6118-6123
    • Lynch, M.1
  • 50
    • 0345306751 scopus 로고    scopus 로고
    • The origins of genome complexity
    • 10.1126/science.1089370, 14631042
    • Lynch M, Conery JS. The origins of genome complexity. Science 2003, 302(5649):1401-1404. 10.1126/science.1089370, 14631042.
    • (2003) Science , vol.302 , Issue.5649 , pp. 1401-1404
    • Lynch, M.1    Conery, J.S.2
  • 51
    • 34250707188 scopus 로고    scopus 로고
    • Coevolution of genomic intron number and splice sites
    • 10.1016/j.tig.2007.04.001, 17442445
    • Irimia M, Penny D, Roy SW. Coevolution of genomic intron number and splice sites. Trends Genet 2007, 23(7):321-325. 10.1016/j.tig.2007.04.001, 17442445.
    • (2007) Trends Genet , vol.23 , Issue.7 , pp. 321-325
    • Irimia, M.1    Penny, D.2    Roy, S.W.3
  • 52
    • 70350710157 scopus 로고    scopus 로고
    • Complex selection on 5' splice sites in intron-rich organisms
    • 10.1101/gr.089276.108, 2775602, 19745111
    • Irimia M, Roy SW, Neafsey DE, Abril JF, Garcia-Fernandez J, Koonin EV. Complex selection on 5' splice sites in intron-rich organisms. Genome Res 2009, 19(11):2021-2027. 10.1101/gr.089276.108, 2775602, 19745111.
    • (2009) Genome Res , vol.19 , Issue.11 , pp. 2021-2027
    • Irimia, M.1    Roy, S.W.2    Neafsey, D.E.3    Abril, J.F.4    Garcia-Fernandez, J.5    Koonin, E.V.6
  • 53
    • 80053442983 scopus 로고    scopus 로고
    • A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes
    • 10.1371/journal.pcbi.1002150, 3174169, 21935348
    • Csuros M, Rogozin IB, Koonin EV. A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PLoS Comput Biol 2011, 7(9):e1002150. 10.1371/journal.pcbi.1002150, 3174169, 21935348.
    • (2011) PLoS Comput Biol , vol.7 , Issue.9
    • Csuros, M.1    Rogozin, I.B.2    Koonin, E.V.3
  • 55
    • 77955953162 scopus 로고    scopus 로고
    • Constrained intron structures in a microsporidian
    • 10.1093/molbev/msq087, 20360213
    • Lee RC, Gill EE, Roy SW, Fast NM. Constrained intron structures in a microsporidian. Mol Biol Evol 2010, 27(9):1979-1982. 10.1093/molbev/msq087, 20360213.
    • (2010) Mol Biol Evol , vol.27 , Issue.9 , pp. 1979-1982
    • Lee, R.C.1    Gill, E.E.2    Roy, S.W.3    Fast, N.M.4
  • 56
    • 24944446017 scopus 로고    scopus 로고
    • An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia
    • 10.1186/1471-2148-5-45, 1201135, 16109161
    • Russell AG, Shutt TE, Watkins RF, Gray MW. An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia. BMC Evol Biol 2005, 5:45. 10.1186/1471-2148-5-45, 1201135, 16109161.
    • (2005) BMC Evol Biol , vol.5 , pp. 45
    • Russell, A.G.1    Shutt, T.E.2    Watkins, R.F.3    Gray, M.W.4
  • 57
    • 80054680031 scopus 로고    scopus 로고
    • Introns within ribosomal protein genes regulate the production and function of yeast ribosomes
    • 10.1016/j.cell.2011.08.044, 22000012
    • Parenteau J, Durand M, Morin G, Gagnon J, Lucier JF, Wellinger RJ, Chabot B, Elela SA. Introns within ribosomal protein genes regulate the production and function of yeast ribosomes. Cell 2011, 147(2):320-331. 10.1016/j.cell.2011.08.044, 22000012.
    • (2011) Cell , vol.147 , Issue.2 , pp. 320-331
    • Parenteau, J.1    Durand, M.2    Morin, G.3    Gagnon, J.4    Lucier, J.F.5    Wellinger, R.J.6    Chabot, B.7    Elela, S.A.8
  • 58
    • 0029115626 scopus 로고
    • Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory
    • 10.1073/pnas.92.18.8507, 41186, 7667320
    • Logsdon JM, Tyshenko MG, Dixon C, DJ J, Walker VK, Palmer JD. Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory. Proc Natl Acad Sci U S A 1995, 92(18):8507-8511. 10.1073/pnas.92.18.8507, 41186, 7667320.
    • (1995) Proc Natl Acad Sci U S A , vol.92 , Issue.18 , pp. 8507-8511
    • Logsdon, J.M.1    Tyshenko, M.G.2    Dixon, C.3    DJ, J.4    Walker, V.K.5    Palmer, J.D.6
  • 59
    • 0030989167 scopus 로고    scopus 로고
    • Exon/intron structure of aldehyde dehydrogenase genes supports the "introns-late" theory
    • 10.1073/pnas.94.13.6820, 21242, 9192649
    • Rzhetsky A, Ayala FJ, Hsu LC, Chang C, Yoshida A. Exon/intron structure of aldehyde dehydrogenase genes supports the "introns-late" theory. Proc Natl Acad Sci U S A 1997, 94(13):6820-6825. 10.1073/pnas.94.13.6820, 21242, 9192649.
    • (1997) Proc Natl Acad Sci U S A , vol.94 , Issue.13 , pp. 6820-6825
    • Rzhetsky, A.1    Ayala, F.J.2    Hsu, L.C.3    Chang, C.4    Yoshida, A.5
  • 60
    • 0032574738 scopus 로고    scopus 로고
    • Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins
    • 10.1073/pnas.95.9.5094, 20219, 9560234
    • de Souza SJ, Long M, Klein RJ, Roy S, Lin S, Gilbert W. Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins. Proc Natl Acad Sci U S A 1998, 95(9):5094-5099. 10.1073/pnas.95.9.5094, 20219, 9560234.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , Issue.9 , pp. 5094-5099
    • de Souza, S.J.1    Long, M.2    Klein, R.J.3    Roy, S.4    Lin, S.5    Gilbert, W.6
  • 61
    • 56849118754 scopus 로고    scopus 로고
    • Where do introns come from?
    • 10.1371/journal.pbio.0060283, 2586383, 19067485
    • Catania F, Lynch M. Where do introns come from?. PLoS Biol 2008, 6(11):e283. 10.1371/journal.pbio.0060283, 2586383, 19067485.
    • (2008) PLoS Biol , vol.6 , Issue.11
    • Catania, F.1    Lynch, M.2
  • 62
    • 0037058978 scopus 로고    scopus 로고
    • Large-scale comparison of intron positions among animal, plant, and fungal genes
    • 10.1073/pnas.242624899, 138576, 12444254
    • Fedorov A, Merican AF, Gilbert W. Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc Natl Acad Sci U S A 2002, 99(25):16128-16133. 10.1073/pnas.242624899, 138576, 12444254.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , Issue.25 , pp. 16128-16133
    • Fedorov, A.1    Merican, A.F.2    Gilbert, W.3
  • 63
    • 13144253092 scopus 로고    scopus 로고
    • Molecular evolution: recent cases of spliceosomal intron gain?
    • 10.1016/S0960-9822(07)00361-2, 9707398
    • Logsdon JM, Stoltzfus A, Doolittle WF. Molecular evolution: recent cases of spliceosomal intron gain?. Curr Biol 1998, 8(16):R560-R563. 10.1016/S0960-9822(07)00361-2, 9707398.
    • (1998) Curr Biol , vol.8 , Issue.16
    • Logsdon, J.M.1    Stoltzfus, A.2    Doolittle, W.F.3
  • 65
    • 0038780670 scopus 로고    scopus 로고
    • Eukaryotic intron loss
    • 10.1126/science.1080559, 12775832
    • Mourier T, Jeffares DC. Eukaryotic intron loss. Science 2003, 300(5624):1393. 10.1126/science.1080559, 12775832.
    • (2003) Science , vol.300 , Issue.5624 , pp. 1393
    • Mourier, T.1    Jeffares, D.C.2
  • 66
    • 3843113189 scopus 로고    scopus 로고
    • Origins of recently gained introns in Caenorhabditis
    • 10.1073/pnas.0308192101, 509176, 15243155
    • Coghlan A, Wolfe KH. Origins of recently gained introns in Caenorhabditis. Proc Natl Acad Sci U S A 2004, 101(31):11362-11367. 10.1073/pnas.0308192101, 509176, 15243155.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , Issue.31 , pp. 11362-11367
    • Coghlan, A.1    Wolfe, K.H.2
  • 67
    • 33646904207 scopus 로고    scopus 로고
    • Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans
    • 10.1128/EC.5.5.789-793.2006, 1459680, 16682456
    • Stajich JE, Dietrich FS. Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans. Eukaryot Cell 2006, 5(5):789-793. 10.1128/EC.5.5.789-793.2006, 1459680, 16682456.
    • (2006) Eukaryot Cell , vol.5 , Issue.5 , pp. 789-793
    • Stajich, J.E.1    Dietrich, F.S.2
  • 68
    • 37549026866 scopus 로고    scopus 로고
    • Intron loss and gain in Drosophila
    • Coulombe-Huntington J, Majewski J. Intron loss and gain in Drosophila. Mol Biol Evol 2007, 24(12):2842-2850.
    • (2007) Mol Biol Evol , vol.24 , Issue.12 , pp. 2842-2850
    • Coulombe-Huntington, J.1    Majewski, J.2
  • 69
    • 33845868781 scopus 로고    scopus 로고
    • Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana
    • Roy SW, Penny D. Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana. Mol Biol Evol 2007, 24(1):171-181.
    • (2007) Mol Biol Evol , vol.24 , Issue.1 , pp. 171-181
    • Roy, S.W.1    Penny, D.2
  • 70
    • 52449091825 scopus 로고    scopus 로고
    • Intron presence-absence polymorphisms in Daphnia
    • 10.1093/molbev/msn164, 2727387, 18667441
    • Omilian AR, Scofield DG, Lynch M. Intron presence-absence polymorphisms in Daphnia. Mol Biol Evol 2008, 25(10):2129-2139. 10.1093/molbev/msn164, 2727387, 18667441.
    • (2008) Mol Biol Evol , vol.25 , Issue.10 , pp. 2129-2139
    • Omilian, A.R.1    Scofield, D.G.2    Lynch, M.3
  • 71
    • 47249165090 scopus 로고    scopus 로고
    • Origin of introns by 'intronization' of exonic sequences
    • 10.1016/j.tig.2008.05.007, 18597887
    • Irimia M, Rukov JL, Penny D, Vinther J, Garcia-Fernandez J, Roy SW. Origin of introns by 'intronization' of exonic sequences. Trends Genet 2008, 24(8):378-381. 10.1016/j.tig.2008.05.007, 18597887.
    • (2008) Trends Genet , vol.24 , Issue.8 , pp. 378-381
    • Irimia, M.1    Rukov, J.L.2    Penny, D.3    Vinther, J.4    Garcia-Fernandez, J.5    Roy, S.W.6
  • 72
    • 59349107038 scopus 로고    scopus 로고
    • Mystery of intron gain: new data and new models
    • 10.1016/j.tig.2008.11.004, 19070397
    • Roy SW, Irimia M. Mystery of intron gain: new data and new models. Trends Genet 2009, 25(2):67-73. 10.1016/j.tig.2008.11.004, 19070397.
    • (2009) Trends Genet , vol.25 , Issue.2 , pp. 67-73
    • Roy, S.W.1    Irimia, M.2
  • 74
    • 14044252770 scopus 로고    scopus 로고
    • Patterns of intron gain and loss in fungi
    • 10.1371/journal.pbio.0020422, 532390, 15562318
    • Nielsen CB, Friedman B, Birren B, Burge CB, Galagan JE. Patterns of intron gain and loss in fungi. PLoS Biol 2004, 2(12):e422. 10.1371/journal.pbio.0020422, 532390, 15562318.
    • (2004) PLoS Biol , vol.2 , Issue.12
    • Nielsen, C.B.1    Friedman, B.2    Birren, B.3    Burge, C.B.4    Galagan, J.E.5
  • 76
    • 33744789972 scopus 로고    scopus 로고
    • Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number
    • 10.1101/gr.4845406, 1473185, 16702411
    • Roy SW, Hartl DL. Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number. Genome Res 2006, 16(6):750-756. 10.1101/gr.4845406, 1473185, 16702411.
    • (2006) Genome Res , vol.16 , Issue.6 , pp. 750-756
    • Roy, S.W.1    Hartl, D.L.2
  • 77
    • 33748797692 scopus 로고    scopus 로고
    • Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes
    • 10.1093/molbev/msl061, 16847043
    • Roy SW, Irimia M, Penny D. Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes. Mol Biol Evol 2006, 23(10):1824-1827. 10.1093/molbev/msl061, 16847043.
    • (2006) Mol Biol Evol , vol.23 , Issue.10 , pp. 1824-1827
    • Roy, S.W.1    Irimia, M.2    Penny, D.3
  • 78
    • 33749377870 scopus 로고    scopus 로고
    • Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution
    • 10.1101/gr.5410606, 1581436, 16963708
    • Roy SW, Penny D. Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution. Genome Res 2006, 16(10):1270-1275. 10.1101/gr.5410606, 1581436, 16963708.
    • (2006) Genome Res , vol.16 , Issue.10 , pp. 1270-1275
    • Roy, S.W.1    Penny, D.2
  • 79
    • 34547688982 scopus 로고    scopus 로고
    • A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain
    • 10.1093/molbev/msm048, 17350938
    • Roy SW, Penny D. A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain. Mol Biol Evol 2007, 24(7):1447-1457. 10.1093/molbev/msm048, 17350938.
    • (2007) Mol Biol Evol , vol.24 , Issue.7 , pp. 1447-1457
    • Roy, S.W.1    Penny, D.2
  • 80
    • 39749196163 scopus 로고    scopus 로고
    • Investigation of loss and gain of introns in the compact genomes of pufferfishes (Fugu and Tetraodon)
    • 10.1093/molbev/msm278, 18089580
    • Loh YH, Brenner S, Venkatesh B. Investigation of loss and gain of introns in the compact genomes of pufferfishes (Fugu and Tetraodon). Mol Biol Evol 2008, 25(3):526-535. 10.1093/molbev/msm278, 18089580.
    • (2008) Mol Biol Evol , vol.25 , Issue.3 , pp. 526-535
    • Loh, Y.H.1    Brenner, S.2    Venkatesh, B.3
  • 81
    • 77649287495 scopus 로고    scopus 로고
    • Evolution of spliceosomal introns following endosymbiotic gene transfer
    • 10.1186/1471-2148-10-57, 2834692, 20178587
    • Ahmadinejad N, Dagan T, Gruenheit N, Martin W, Gabaldon T. Evolution of spliceosomal introns following endosymbiotic gene transfer. BMC Evol Biol 2010, 10:57. 10.1186/1471-2148-10-57, 2834692, 20178587.
    • (2010) BMC Evol Biol , vol.10 , pp. 57
    • Ahmadinejad, N.1    Dagan, T.2    Gruenheit, N.3    Martin, W.4    Gabaldon, T.5
  • 82
    • 78649999037 scopus 로고    scopus 로고
    • Evaluation of models of the mechanisms underlying intron loss and gain in Aspergillus fungi
    • Zhang LY, Yang YF, Niu DK. Evaluation of models of the mechanisms underlying intron loss and gain in Aspergillus fungi. J Mol Evol 2010, 71(5-6):364-373.
    • (2010) J Mol Evol , vol.71 , Issue.5-6 , pp. 364-373
    • Zhang, L.Y.1    Yang, Y.F.2    Niu, D.K.3
  • 83
    • 3042548834 scopus 로고    scopus 로고
    • The evolutionary gain of spliceosomal introns: sequence and phase preferences
    • 10.1093/molbev/msh120, 15014153
    • Qiu WG, Schisler N, Stoltzfus A. The evolutionary gain of spliceosomal introns: sequence and phase preferences. Mol Biol Evol 2004, 21(7):1252-1263. 10.1093/molbev/msh120, 15014153.
    • (2004) Mol Biol Evol , vol.21 , Issue.7 , pp. 1252-1263
    • Qiu, W.G.1    Schisler, N.2    Stoltzfus, A.3
  • 84
    • 13844309569 scopus 로고    scopus 로고
    • Complex early genes
    • 10.1073/pnas.0408355101, 548548, 15687506
    • Roy SW, Gilbert W. Complex early genes. Proc Natl Acad Sci U S A 2005, 102(6):1986-1991. 10.1073/pnas.0408355101, 548548, 15687506.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.6 , pp. 1986-1991
    • Roy, S.W.1    Gilbert, W.2
  • 86
    • 84872246297 scopus 로고    scopus 로고
    • New maximum likelihood estimators for eukaryotic intron evolution
    • 10.1371/journal.pcbi.0010079, 1323467, 16389300
    • Nguyen HD, Yoshihama M, Kenmochi N. New maximum likelihood estimators for eukaryotic intron evolution. PLoS Comput Biol 2005, 1(7):e79. 10.1371/journal.pcbi.0010079, 1323467, 16389300.
    • (2005) PLoS Comput Biol , vol.1 , Issue.7
    • Nguyen, H.D.1    Yoshihama, M.2    Kenmochi, N.3
  • 87
    • 34347389905 scopus 로고    scopus 로고
    • Three distinct modes of intron dynamics in the evolution of eukaryotes
    • 10.1101/gr.6438607, 1899114, 17495008
    • Carmel L, Wolf YI, Rogozin IB, Koonin EV. Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res 2007, 17(7):1034-1044. 10.1101/gr.6438607, 1899114, 17495008.
    • (2007) Genome Res , vol.17 , Issue.7 , pp. 1034-1044
    • Carmel, L.1    Wolf, Y.I.2    Rogozin, I.B.3    Koonin, E.V.4
  • 88
    • 34547830882 scopus 로고    scopus 로고
    • In search of lost introns
    • 10.1093/bioinformatics/btm190, 17646350
    • Csuros M, Holey JA, Rogozin IB. In search of lost introns. Bioinformatics 2007, 23(13):i87-i96. 10.1093/bioinformatics/btm190, 17646350.
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Csuros, M.1    Holey, J.A.2    Rogozin, I.B.3
  • 89
    • 0037795455 scopus 로고    scopus 로고
    • Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain
    • 10.1073/pnas.1232297100, 165846, 12777620
    • Roy SW, Fedorov A, Gilbert W. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci U S A 2003, 100(12):7158-7162. 10.1073/pnas.1232297100, 165846, 12777620.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , Issue.12 , pp. 7158-7162
    • Roy, S.W.1    Fedorov, A.2    Gilbert, W.3
  • 90
    • 33845982198 scopus 로고    scopus 로고
    • Characterization of intron loss events in mammals
    • 1716263, 17108319
    • Coulombe-Huntington J, Majewski J. Characterization of intron loss events in mammals. Genome Res 2007, 17(1):23-32. 1716263, 17108319.
    • (2007) Genome Res , vol.17 , Issue.1 , pp. 23-32
    • Coulombe-Huntington, J.1    Majewski, J.2
  • 91
    • 3142749596 scopus 로고    scopus 로고
    • Prevalence of intron gain over intron loss in the evolution of paralogous gene families
    • 10.1093/nar/gkh686, 484173, 15254274
    • Babenko VN, Rogozin IB, Mekhedov SL, Koonin EV. Prevalence of intron gain over intron loss in the evolution of paralogous gene families. Nucleic Acids Res 2004, 32(12):3724-3733. 10.1093/nar/gkh686, 484173, 15254274.
    • (2004) Nucleic Acids Res , vol.32 , Issue.12 , pp. 3724-3733
    • Babenko, V.N.1    Rogozin, I.B.2    Mekhedov, S.L.3    Koonin, E.V.4
  • 92
    • 33750938326 scopus 로고    scopus 로고
    • Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses
    • 10.1093/molbev/msl098, 16943250
    • Roy SW, Penny D. Smoke without fire: most reported cases of intron gain in nematodes instead reflect intron losses. Mol Biol Evol 2006, 23(12):2259-2262. 10.1093/molbev/msl098, 16943250.
    • (2006) Mol Biol Evol , vol.23 , Issue.12 , pp. 2259-2262
    • Roy, S.W.1    Penny, D.2
  • 93
    • 33748029468 scopus 로고    scopus 로고
    • High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes
    • 10.1093/molbev/msl017, 16720694
    • Knowles DG, McLysaght A. High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes. Mol Biol Evol 2006, 23(8):1548-1557. 10.1093/molbev/msl017, 16720694.
    • (2006) Mol Biol Evol , vol.23 , Issue.8 , pp. 1548-1557
    • Knowles, D.G.1    McLysaght, A.2
  • 94
    • 38349114864 scopus 로고    scopus 로고
    • Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues
    • Basu MK, Rogozin IB, Deusch O, Dagan T, Martin W, Koonin EV. Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues. Mol Biol Evol 2008, 25(1):111-119.
    • (2008) Mol Biol Evol , vol.25 , Issue.1 , pp. 111-119
    • Basu, M.K.1    Rogozin, I.B.2    Deusch, O.3    Dagan, T.4    Martin, W.5    Koonin, E.V.6
  • 95
    • 45849089569 scopus 로고    scopus 로고
    • Massive horizontal gene transfer in bdelloid rotifers
    • 10.1126/science.1156407, 18511688
    • Gladyshev EA, Meselson M, Arkhipova IR. Massive horizontal gene transfer in bdelloid rotifers. Science 2008, 320(5880):1210-1213. 10.1126/science.1156407, 18511688.
    • (2008) Science , vol.320 , Issue.5880 , pp. 1210-1213
    • Gladyshev, E.A.1    Meselson, M.2    Arkhipova, I.R.3
  • 96
    • 70849137211 scopus 로고    scopus 로고
    • Extensive, recent intron gains in Daphnia populations
    • 10.1126/science.1179302, 19965475
    • Li W, Tucker AE, Sung W, Thomas WK, Lynch M. Extensive, recent intron gains in Daphnia populations. Science 2009, 326(5957):1260-1262. 10.1126/science.1179302, 19965475.
    • (2009) Science , vol.326 , Issue.5957 , pp. 1260-1262
    • Li, W.1    Tucker, A.E.2    Sung, W.3    Thomas, W.K.4    Lynch, M.5
  • 97
    • 33750962013 scopus 로고    scopus 로고
    • Intron size, abundance, and distribution within untranslated regions of genes
    • 10.1093/molbev/msl111, 16980575
    • Hong X, Scofield DG, Lynch M. Intron size, abundance, and distribution within untranslated regions of genes. Mol Biol Evol 2006, 23(12):2392-2404. 10.1093/molbev/msl111, 16980575.
    • (2006) Mol Biol Evol , vol.23 , Issue.12 , pp. 2392-2404
    • Hong, X.1    Scofield, D.G.2    Lynch, M.3
  • 98
    • 33744497802 scopus 로고    scopus 로고
    • Birth of a chimeric primate gene by capture of the transposase gene from a mobile element
    • 10.1073/pnas.0601161103, 1472436, 16672366
    • Cordaux R, Udit S, Batzer MA, Feschotte C. Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc Natl Acad Sci U S A 2006, 103(21):8101-8106. 10.1073/pnas.0601161103, 1472436, 16672366.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , Issue.21 , pp. 8101-8106
    • Cordaux, R.1    Udit, S.2    Batzer, M.A.3    Feschotte, C.4
  • 99
    • 33748596625 scopus 로고    scopus 로고
    • Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons
    • 10.1073/pnas.0603042103, 1569180, 16938881
    • 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, 1569180, 16938881.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , Issue.36 , pp. 13427-13432
    • Zhang, X.H.1    Chasin, L.A.2
  • 100
    • 33846511232 scopus 로고    scopus 로고
    • Modern origin of numerous alternatively spliced human introns from tandem arrays
    • 10.1073/pnas.0604777104, 1783408, 17210920
    • Zhuo D, Madden R, Elela SA, Chabot B. Modern origin of numerous alternatively spliced human introns from tandem arrays. Proc Natl Acad Sci U S A 2007, 104(3):882-886. 10.1073/pnas.0604777104, 1783408, 17210920.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , Issue.3 , pp. 882-886
    • Zhuo, D.1    Madden, R.2    Elela, S.A.3    Chabot, B.4
  • 101
    • 78650460773 scopus 로고    scopus 로고
    • Primate and rodent specific intron gains and the origin of retrogenes with splice variants
    • 10.1093/molbev/msq260, 3002245, 20889727
    • Szczesniak MW, Ciomborowska J, Nowak W, Rogozin IB, Makalowska I. Primate and rodent specific intron gains and the origin of retrogenes with splice variants. Mol Biol Evol 2011, 28(1):33-37. 10.1093/molbev/msq260, 3002245, 20889727.
    • (2011) Mol Biol Evol , vol.28 , Issue.1 , pp. 33-37
    • Szczesniak, M.W.1    Ciomborowska, J.2    Nowak, W.3    Rogozin, I.B.4    Makalowska, I.5
  • 102
    • 60149099385 scopus 로고    scopus 로고
    • Evolution and functions of long noncoding RNAs
    • 10.1016/j.cell.2009.02.006, 19239885
    • Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009, 136(4):629-641. 10.1016/j.cell.2009.02.006, 19239885.
    • (2009) Cell , vol.136 , Issue.4 , pp. 629-641
    • Ponting, C.P.1    Oliver, P.L.2    Reik, W.3
  • 103
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • 10.1101/gad.17446611, 3185964, 21890647
    • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011, 25(18):1915-1927. 10.1101/gad.17446611, 3185964, 21890647.
    • (2011) Genes Dev , vol.25 , Issue.18 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3    Koziol, M.4    Tazon-Vega, B.5    Regev, A.6    Rinn, J.L.7
  • 104
    • 32944461375 scopus 로고    scopus 로고
    • Mechanisms of X-chromosome inactivation
    • 10.2741/1842, 16146776
    • Chang SC, Tucker T, Thorogood NP, Brown CJ. Mechanisms of X-chromosome inactivation. Front Biosci 2006, 11:852-866. 10.2741/1842, 16146776.
    • (2006) Front Biosci , vol.11 , pp. 852-866
    • Chang, S.C.1    Tucker, T.2    Thorogood, N.P.3    Brown, C.J.4
  • 105
    • 49649094943 scopus 로고    scopus 로고
    • A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements
    • 10.1371/journal.pone.0002521, 2430539, 18575625
    • Elisaphenko EA, Kolesnikov NN, Shevchenko AI, Rogozin IB, Nesterova TB, Brockdorff N, Zakian SM. A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements. PLoS One 2008, 3(6):e2521. 10.1371/journal.pone.0002521, 2430539, 18575625.
    • (2008) PLoS One , vol.3 , Issue.6
    • Elisaphenko, E.A.1    Kolesnikov, N.N.2    Shevchenko, A.I.3    Rogozin, I.B.4    Nesterova, T.B.5    Brockdorff, N.6    Zakian, S.M.7
  • 106
    • 34248162440 scopus 로고    scopus 로고
    • Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
    • 10.1101/gr.6036807, 1855172, 17387145
    • Ponjavic J, Ponting CP, Lunter G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 2007, 17(5):556-565. 10.1101/gr.6036807, 1855172, 17387145.
    • (2007) Genome Res , vol.17 , Issue.5 , pp. 556-565
    • Ponjavic, J.1    Ponting, C.P.2    Lunter, G.3
  • 107
    • 0023649687 scopus 로고
    • Pseudogenes in yeast?
    • 10.1016/0092-8674(87)90746-X, 3549000
    • Fink GR. Pseudogenes in yeast?. Cell 1987, 49(1):5-6. 10.1016/0092-8674(87)90746-X, 3549000.
    • (1987) Cell , vol.49 , Issue.1 , pp. 5-6
    • Fink, G.R.1
  • 108
    • 0031968001 scopus 로고    scopus 로고
    • The involvement of cellular recombination and repair genes in RNA-mediated recombination in Saccharomyces cerevisiae
    • 1460045, 9539415
    • Derr LK. The involvement of cellular recombination and repair genes in RNA-mediated recombination in Saccharomyces cerevisiae. Genetics 1998, 148(3):937-945. 1460045, 9539415.
    • (1998) Genetics , vol.148 , Issue.3 , pp. 937-945
    • Derr, L.K.1
  • 109
    • 0036787520 scopus 로고    scopus 로고
    • The evolution of single-copy Drosophila nuclear 4f-rnp genes: spliceosomal intron losses create polymorphic alleles
    • 10.1007/s00239-002-2336-y, 12355261
    • Feiber AL, Rangarajan J, Vaughn JC. The evolution of single-copy Drosophila nuclear 4f-rnp genes: spliceosomal intron losses create polymorphic alleles. J Mol Evol 2002, 55(4):401-413. 10.1007/s00239-002-2336-y, 12355261.
    • (2002) J Mol Evol , vol.55 , Issue.4 , pp. 401-413
    • Feiber, A.L.1    Rangarajan, J.2    Vaughn, J.C.3
  • 110
    • 4143150876 scopus 로고    scopus 로고
    • Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion
    • 10.1016/j.gene.2004.05.027, 15302409
    • Sverdlov AV, Babenko VN, Rogozin IB, Koonin EV. Preferential loss and gain of introns in 3' portions of genes suggests a reverse-transcription mechanism of intron insertion. Gene 2004, 338(1):85-91. 10.1016/j.gene.2004.05.027, 15302409.
    • (2004) Gene , vol.338 , Issue.1 , pp. 85-91
    • Sverdlov, A.V.1    Babenko, V.N.2    Rogozin, I.B.3    Koonin, E.V.4
  • 111
    • 37549021457 scopus 로고    scopus 로고
    • Patterns of intron gain and conservation in eukaryotic genes
    • 10.1186/1471-2148-7-192, 2151770, 17935625
    • Carmel L, Rogozin IB, Wolf YI, Koonin EV. Patterns of intron gain and conservation in eukaryotic genes. BMC Evol Biol 2007, 7:192. 10.1186/1471-2148-7-192, 2151770, 17935625.
    • (2007) BMC Evol Biol , vol.7 , pp. 192
    • Carmel, L.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 112
    • 84855888714 scopus 로고    scopus 로고
    • The Role of Reverse Transcriptase in Intron Gain and Loss Mechanisms
    • Cohen NE, Shen R, Carmel L. The Role of Reverse Transcriptase in Intron Gain and Loss Mechanisms. Mol Biol Evol 2011, 29:179-186.
    • (2011) Mol Biol Evol , vol.29 , pp. 179-186
    • Cohen, N.E.1    Shen, R.2    Carmel, L.3
  • 113
    • 0034307433 scopus 로고    scopus 로고
    • Intron sliding in conserved gene families
    • 10.1016/S0168-9525(00)02096-5, 11050324
    • Rogozin IB, Lyons-Weiler J, Koonin EV. Intron sliding in conserved gene families. Trends Genet 2000, 16(10):430-432. 10.1016/S0168-9525(00)02096-5, 11050324.
    • (2000) Trends Genet , vol.16 , Issue.10 , pp. 430-432
    • Rogozin, I.B.1    Lyons-Weiler, J.2    Koonin, E.V.3
  • 114
    • 44449093240 scopus 로고    scopus 로고
    • Alternative splicing: a missing piece in the puzzle of intron gain
    • 10.1073/pnas.0802941105, 2438231, 18463286
    • Tarrio R, Ayala FJ, Rodriguez-Trelles F. Alternative splicing: a missing piece in the puzzle of intron gain. Proc Natl Acad Sci U S A 2008, 105(20):7223-7228. 10.1073/pnas.0802941105, 2438231, 18463286.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , Issue.20 , pp. 7223-7228
    • Tarrio, R.1    Ayala, F.J.2    Rodriguez-Trelles, F.3
  • 115
    • 77952616845 scopus 로고    scopus 로고
    • Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication
    • 10.1186/1471-2148-10-156, 2891723, 20500887
    • Lehmann J, Eisenhardt C, Stadler PF, Krauss V. Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication. BMC Evol Biol 2010, 10:156. 10.1186/1471-2148-10-156, 2891723, 20500887.
    • (2010) BMC Evol Biol , vol.10 , pp. 156
    • Lehmann, J.1    Eisenhardt, C.2    Stadler, P.F.3    Krauss, V.4
  • 116
    • 38049029652 scopus 로고    scopus 로고
    • Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
    • 2134773, 18032728
    • Schwartz SH, Silva J, Burstein D, Pupko T, Eyras E, Ast G. Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res 2008, 18(1):88-103. 2134773, 18032728.
    • (2008) Genome Res , vol.18 , Issue.1 , pp. 88-103
    • Schwartz, S.H.1    Silva, J.2    Burstein, D.3    Pupko, T.4    Eyras, E.5    Ast, G.6
  • 117
    • 78651503221 scopus 로고    scopus 로고
    • Comparative analysis of information contents relevant to recognition of introns in many species
    • 10.1186/1471-2164-12-45, 3033335, 21247441
    • Iwata H, Gotoh O. Comparative analysis of information contents relevant to recognition of introns in many species. BMC Genomics 2011, 12:45. 10.1186/1471-2164-12-45, 3033335, 21247441.
    • (2011) BMC Genomics , vol.12 , pp. 45
    • Iwata, H.1    Gotoh, O.2
  • 118
    • 0026657738 scopus 로고
    • Splicing signals in Drosophila: intron size, information content, and consensus sequences
    • 10.1093/nar/20.16.4255, 334133, 1508718
    • Mount SM, Burks C, Hertz G, Stormo GD, White O, Fields C. Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res 1992, 20(16):4255-4262. 10.1093/nar/20.16.4255, 334133, 1508718.
    • (1992) Nucleic Acids Res , vol.20 , Issue.16 , pp. 4255-4262
    • Mount, S.M.1    Burks, C.2    Hertz, G.3    Stormo, G.D.4    White, O.5    Fields, C.6
  • 119
    • 33845895301 scopus 로고    scopus 로고
    • Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns
    • 10.1186/1471-2164-7-311, 1713244, 17156453
    • Dewey CN, Rogozin IB, Koonin EV. Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns. BMC Genomics 2006, 7:311. 10.1186/1471-2164-7-311, 1713244, 17156453.
    • (2006) BMC Genomics , vol.7 , pp. 311
    • Dewey, C.N.1    Rogozin, I.B.2    Koonin, E.V.3
  • 120
    • 1842535132 scopus 로고    scopus 로고
    • Exon junction sequences as cryptic splice sites: implications for intron origin
    • Sadusky T, Newman AJ, Dibb NJ. Exon junction sequences as cryptic splice sites: implications for intron origin. Curr Biol 2004, 14(6):505-509.
    • (2004) Curr Biol , vol.14 , Issue.6 , pp. 505-509
    • Sadusky, T.1    Newman, A.J.2    Dibb, N.J.3
  • 121
    • 4344639564 scopus 로고    scopus 로고
    • Reconstruction of ancestral protosplice sites
    • 10.1016/j.cub.2004.08.027, 15324669
    • Sverdlov AV, Rogozin IB, Babenko VN, Koonin EV. Reconstruction of ancestral protosplice sites. Curr Biol 2004, 14(16):1505-1508. 10.1016/j.cub.2004.08.027, 15324669.
    • (2004) Curr Biol , vol.14 , Issue.16 , pp. 1505-1508
    • Sverdlov, A.V.1    Rogozin, I.B.2    Babenko, V.N.3    Koonin, E.V.4
  • 123
    • 79956109930 scopus 로고    scopus 로고
    • Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses
    • 10.1371/journal.pone.0019673, 3096672, 21611157
    • Da Lage JL, Maczkowiak F, Cariou ML. Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses. PLoS One 2011, 6(5):e19673. 10.1371/journal.pone.0019673, 3096672, 21611157.
    • (2011) PLoS One , vol.6 , Issue.5
    • Da Lage, J.L.1    Maczkowiak, F.2    Cariou, M.L.3
  • 124
    • 77954456827 scopus 로고    scopus 로고
    • Does drive toward canonic exonic splicing sites exist in mammals?
    • 10.1007/s00239-010-9336-0, 20336453
    • Babenko V, Ward W, Ruvinsky A. Does drive toward canonic exonic splicing sites exist in mammals?. J Mol Evol 2010, 70(4):387-394. 10.1007/s00239-010-9336-0, 20336453.
    • (2010) J Mol Evol , vol.70 , Issue.4 , pp. 387-394
    • Babenko, V.1    Ward, W.2    Ruvinsky, A.3
  • 125
    • 0345772209 scopus 로고    scopus 로고
    • Evidence of splice signal migration from exon to intron during intron evolution
    • 10.1016/j.cub.2003.12.003, 14680632
    • Sverdlov AV, Rogozin IB, Babenko VN, Koonin EV. Evidence of splice signal migration from exon to intron during intron evolution. Curr Biol 2003, 13(24):2170-2174. 10.1016/j.cub.2003.12.003, 14680632.
    • (2003) Curr Biol , vol.13 , Issue.24 , pp. 2170-2174
    • Sverdlov, A.V.1    Rogozin, I.B.2    Babenko, V.N.3    Koonin, E.V.4
  • 126
    • 0026579475 scopus 로고
    • Analysis of nonuniformity in intron phase distribution
    • 10.1093/nar/20.10.2553, 312392, 1598214
    • Fedorov A, Suboch G, Bujakov M, Fedorova L. Analysis of nonuniformity in intron phase distribution. Nucleic Acids Res 1992, 20(10):2553-2557. 10.1093/nar/20.10.2553, 312392, 1598214.
    • (1992) Nucleic Acids Res , vol.20 , Issue.10 , pp. 2553-2557
    • Fedorov, A.1    Suboch, G.2    Bujakov, M.3    Fedorova, L.4
  • 127
    • 0032753460 scopus 로고    scopus 로고
    • Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns
    • 10.1093/oxfordjournals.molbev.a026065, 10555284
    • Long M, Deutsch M. Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns. Mol Biol Evol 1999, 16(11):1528-1534. 10.1093/oxfordjournals.molbev.a026065, 10555284.
    • (1999) Mol Biol Evol , vol.16 , Issue.11 , pp. 1528-1534
    • Long, M.1    Deutsch, M.2
  • 128
    • 0033637638 scopus 로고    scopus 로고
    • Testing the "proto-splice sites" model of intron origin: evidence from analysis of intron phase correlations
    • 10.1093/oxfordjournals.molbev.a026279, 11110894
    • Long M, Rosenberg C. Testing the "proto-splice sites" model of intron origin: evidence from analysis of intron phase correlations. Mol Biol Evol 2000, 17(12):1789-1796. 10.1093/oxfordjournals.molbev.a026279, 11110894.
    • (2000) Mol Biol Evol , vol.17 , Issue.12 , pp. 1789-1796
    • Long, M.1    Rosenberg, C.2
  • 129
    • 14644402410 scopus 로고    scopus 로고
    • Can codon usage bias explain intron phase distributions and exon symmetry?
    • 10.1007/s00239-004-0032-9, 15696372
    • Ruvinsky A, Eskesen ST, Eskesen FN, Hurst LD. Can codon usage bias explain intron phase distributions and exon symmetry?. J Mol Evol 2005, 60(1):99-104. 10.1007/s00239-004-0032-9, 15696372.
    • (2005) J Mol Evol , vol.60 , Issue.1 , pp. 99-104
    • Ruvinsky, A.1    Eskesen, S.T.2    Eskesen, F.N.3    Hurst, L.D.4
  • 130
    • 33748974763 scopus 로고    scopus 로고
    • Phase distribution of spliceosomal introns: implications for intron origin
    • 10.1186/1471-2148-6-69, 1574350, 16959043
    • Nguyen HD, Yoshihama M, Kenmochi N. Phase distribution of spliceosomal introns: implications for intron origin. BMC Evol Biol 2006, 6:69. 10.1186/1471-2148-6-69, 1574350, 16959043.
    • (2006) BMC Evol Biol , vol.6 , pp. 69
    • Nguyen, H.D.1    Yoshihama, M.2    Kenmochi, N.3
  • 132
    • 15944384932 scopus 로고    scopus 로고
    • Conservation versus parallel gains in intron evolution
    • 10.1093/nar/gki316, 1069513, 15788746
    • Sverdlov AV, Rogozin IB, Babenko VN, Koonin EV. Conservation versus parallel gains in intron evolution. Nucleic Acids Res 2005, 33(6):1741-1748. 10.1093/nar/gki316, 1069513, 15788746.
    • (2005) Nucleic Acids Res , vol.33 , Issue.6 , pp. 1741-1748
    • Sverdlov, A.V.1    Rogozin, I.B.2    Babenko, V.N.3    Koonin, E.V.4
  • 133
    • 0031593151 scopus 로고    scopus 로고
    • A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain
    • Hankeln T, Friedl H, Ebersberger I, Martin J, Schmidt ER. A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain. Gene 1997, 205(1-2):151-160.
    • (1997) Gene , vol.205 , Issue.1-2 , pp. 151-160
    • Hankeln, T.1    Friedl, H.2    Ebersberger, I.3    Martin, J.4    Schmidt, E.R.5
  • 134
    • 0037975529 scopus 로고    scopus 로고
    • A new Drosophila spliceosomal intron position is common in plants
    • 10.1073/pnas.0731952100, 164489, 12750476
    • Tarrio R, Rodriguez-Trelles F, Ayala FJ. A new Drosophila spliceosomal intron position is common in plants. Proc Natl Acad Sci U S A 2003, 100(11):6580-6583. 10.1073/pnas.0731952100, 164489, 12750476.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , Issue.11 , pp. 6580-6583
    • Tarrio, R.1    Rodriguez-Trelles, F.2    Ayala, F.J.3
  • 135
    • 21044447550 scopus 로고    scopus 로고
    • Analysis of evolution of exon-intron structure of eukaryotic genes
    • 10.1093/bib/6.2.118, 15975222
    • Rogozin IB, Sverdlov AV, Babenko VN, Koonin EV. Analysis of evolution of exon-intron structure of eukaryotic genes. Brief Bioinform 2005, 6(2):118-134. 10.1093/bib/6.2.118, 15975222.
    • (2005) Brief Bioinform , vol.6 , Issue.2 , pp. 118-134
    • Rogozin, I.B.1    Sverdlov, A.V.2    Babenko, V.N.3    Koonin, E.V.4
  • 137
    • 33747188649 scopus 로고    scopus 로고
    • Intron-rich ancestors
    • 10.1016/j.tig.2006.07.002, 16857287
    • Roy SW. Intron-rich ancestors. Trends Genet 2006, 22(9):468-471. 10.1016/j.tig.2006.07.002, 16857287.
    • (2006) Trends Genet , vol.22 , Issue.9 , pp. 468-471
    • Roy, S.W.1
  • 138
    • 46249111264 scopus 로고    scopus 로고
    • Malin: maximum likelihood analysis of intron evolution in eukaryotes
    • 10.1093/bioinformatics/btn226, 2718671, 18474506
    • Csuros M. Malin: maximum likelihood analysis of intron evolution in eukaryotes. Bioinformatics 2008, 24(13):1538-1539. 10.1093/bioinformatics/btn226, 2718671, 18474506.
    • (2008) Bioinformatics , vol.24 , Issue.13 , pp. 1538-1539
    • Csuros, M.1
  • 139
    • 34447330054 scopus 로고    scopus 로고
    • A high percentage of introns in human genes were present early in animal evolution: evidence from the basal metazoan Nematostella vectensis
    • Sullivan JC, Reitzel AM, Finnerty JR. A high percentage of introns in human genes were present early in animal evolution: evidence from the basal metazoan Nematostella vectensis. Genome Inform 2006, 17(1):219-229.
    • (2006) Genome Inform , vol.17 , Issue.1 , pp. 219-229
    • Sullivan, J.C.1    Reitzel, A.M.2    Finnerty, J.R.3
  • 141
    • 46249118523 scopus 로고    scopus 로고
    • Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach
    • 10.1093/molbev/msn039, 18296415
    • Csuros M, Rogozin IB, Koonin EV. Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach. Mol Biol Evol 2008, 25(5):903-911. 10.1093/molbev/msn039, 18296415.
    • (2008) Mol Biol Evol , vol.25 , Issue.5 , pp. 903-911
    • Csuros, M.1    Rogozin, I.B.2    Koonin, E.V.3
  • 142
    • 3042599701 scopus 로고    scopus 로고
    • Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites
    • 10.1093/molbev/msh143, 15084679
    • Castillo-Davis CI, Bedford TB, Hartl DL. Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites. Mol Biol Evol 2004, 21(7):1422-1427. 10.1093/molbev/msh143, 15084679.
    • (2004) Mol Biol Evol , vol.21 , Issue.7 , pp. 1422-1427
    • Castillo-Davis, C.I.1    Bedford, T.B.2    Hartl, D.L.3
  • 143
    • 34548316459 scopus 로고    scopus 로고
    • The evolution of spliceosomal introns in alveolates
    • 10.1093/molbev/msm037, 17331959
    • Nguyen HD, Yoshihama M, Kenmochi N. The evolution of spliceosomal introns in alveolates. Mol Biol Evol 2007, 24(5):1093-1096. 10.1093/molbev/msm037, 17331959.
    • (2007) Mol Biol Evol , vol.24 , Issue.5 , pp. 1093-1096
    • Nguyen, H.D.1    Yoshihama, M.2    Kenmochi, N.3
  • 144
    • 34547735995 scopus 로고    scopus 로고
    • On the incidence of intron loss and gain in paralogous gene families
    • 10.1093/molbev/msm082, 17470438
    • Roy SW, Penny D. On the incidence of intron loss and gain in paralogous gene families. Mol Biol Evol 2007, 24(8):1579-1581. 10.1093/molbev/msm082, 17470438.
    • (2007) Mol Biol Evol , vol.24 , Issue.8 , pp. 1579-1581
    • Roy, S.W.1    Penny, D.2
  • 145
    • 33745605777 scopus 로고    scopus 로고
    • Tempo and mode of spliceosomal intron evolution in actin of foraminifera
    • 10.1007/s00239-005-0061-z, 16755352
    • Flakowski J, Bolivar I, Fahrni J, Pawlowski J. Tempo and mode of spliceosomal intron evolution in actin of foraminifera. J Mol Evol 2006, 63(1):30-41. 10.1007/s00239-005-0061-z, 16755352.
    • (2006) J Mol Evol , vol.63 , Issue.1 , pp. 30-41
    • Flakowski, J.1    Bolivar, I.2    Fahrni, J.3    Pawlowski, J.4
  • 146
    • 52949117552 scopus 로고    scopus 로고
    • Ancestry and evolution of a secretory pathway serpin
    • 10.1186/1471-2148-8-250, 2556349, 18793432
    • Kumar A, Ragg H. Ancestry and evolution of a secretory pathway serpin. BMC Evol Biol 2008, 8:250. 10.1186/1471-2148-8-250, 2556349, 18793432.
    • (2008) BMC Evol Biol , vol.8 , pp. 250
    • Kumar, A.1    Ragg, H.2
  • 147
    • 61849175945 scopus 로고    scopus 로고
    • Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins
    • 10.1371/journal.pone.0004680, 2650405, 19262691
    • Garcia-Espana A, Mares R, Sun TT, Desalle R. Intron evolution: testing hypotheses of intron evolution using the phylogenomics of tetraspanins. PLoS One 2009, 4(3):e4680. 10.1371/journal.pone.0004680, 2650405, 19262691.
    • (2009) PLoS One , vol.4 , Issue.3
    • Garcia-Espana, A.1    Mares, R.2    Sun, T.T.3    Desalle, R.4
  • 148
    • 33847031355 scopus 로고    scopus 로고
    • A glimpse of a putative pre-intron phase of eukaryotic evolution
    • 10.1016/j.tig.2007.01.001, 17239982
    • Sverdlov AV, Csuros M, Rogozin IB, Koonin EV. A glimpse of a putative pre-intron phase of eukaryotic evolution. Trends Genet 2007, 23(3):105-108. 10.1016/j.tig.2007.01.001, 17239982.
    • (2007) Trends Genet , vol.23 , Issue.3 , pp. 105-108
    • Sverdlov, A.V.1    Csuros, M.2    Rogozin, I.B.3    Koonin, E.V.4
  • 149
    • 23844497214 scopus 로고    scopus 로고
    • Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
    • 10.1093/nar/gki775, 1187821, 16106042
    • Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res 2005, 33(14):4626-4638. 10.1093/nar/gki775, 1187821, 16106042.
    • (2005) Nucleic Acids Res , vol.33 , Issue.14 , pp. 4626-4638
    • Makarova, K.S.1    Wolf, Y.I.2    Mekhedov, S.L.3    Mirkin, B.G.4    Koonin, E.V.5
  • 150
    • 34548303257 scopus 로고    scopus 로고
    • Intron dynamics in ribosomal protein genes
    • 10.1371/journal.pone.0000141, 1764039, 17206276
    • Yoshihama M, Nguyen HD, Kenmochi N. Intron dynamics in ribosomal protein genes. PLoS One 2007, 2(1):e141. 10.1371/journal.pone.0000141, 1764039, 17206276.
    • (2007) PLoS One , vol.2 , Issue.1
    • Yoshihama, M.1    Nguyen, H.D.2    Kenmochi, N.3
  • 151
    • 0030985059 scopus 로고    scopus 로고
    • Intron distribution in ancient paralogs supports random insertion and not random loss [published erratum appears in J Mol Evol 1997 Aug;45(2):206]
    • 10.1007/PL00006180, 9169549
    • Cho G, Doolittle RF. Intron distribution in ancient paralogs supports random insertion and not random loss [published erratum appears in J Mol Evol 1997 Aug;45(2):206]. J Mol Evol 1997, 44(6):573-584. 10.1007/PL00006180, 9169549.
    • (1997) J Mol Evol , vol.44 , Issue.6 , pp. 573-584
    • Cho, G.1    Doolittle, R.F.2
  • 152
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • 1461684, 11430355
    • Pal C, Papp B, Hurst LD. Highly expressed genes in yeast evolve slowly. Genetics 2001, 158(2):927-931. 1461684, 11430355.
    • (2001) Genetics , vol.158 , Issue.2 , pp. 927-931
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 153
    • 0142124263 scopus 로고    scopus 로고
    • Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    • 10.1101/gr.1589103, 403683, 14525925
    • Krylov DM, Wolf YI, Rogozin IB, Koonin EV. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res 2003, 13(10):2229-2235. 10.1101/gr.1589103, 403683, 14525925.
    • (2003) Genome Res , vol.13 , Issue.10 , pp. 2229-2235
    • Krylov, D.M.1    Wolf, Y.I.2    Rogozin, I.B.3    Koonin, E.V.4
  • 154
    • 70349333227 scopus 로고    scopus 로고
    • The evolutionary consequences of erroneous protein synthesis
    • 10.1038/nrg2662, 2764353, 19763154
    • Drummond DA, Wilke CO. The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet 2009, 10(10):715-724. 10.1038/nrg2662, 2764353, 19763154.
    • (2009) Nat Rev Genet , vol.10 , Issue.10 , pp. 715-724
    • Drummond, D.A.1    Wilke, C.O.2
  • 155
    • 34347398058 scopus 로고    scopus 로고
    • Evolutionarily conserved genes preferentially accumulate introns
    • 10.1101/gr.5978207, 1899115, 17495009
    • Carmel L, Rogozin IB, Wolf YI, Koonin EV. Evolutionarily conserved genes preferentially accumulate introns. Genome Res 2007, 17(7):1045-1050. 10.1101/gr.5978207, 1899115, 17495009.
    • (2007) Genome Res , vol.17 , Issue.7 , pp. 1045-1050
    • Carmel, L.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 157
    • 0038692119 scopus 로고    scopus 로고
    • Human housekeeping genes are compact
    • 10.1016/S0168-9525(03)00140-9, 12850439
    • Eisenberg E, Levanon EY. Human housekeeping genes are compact. Trends Genet 2003, 19(7):362-365. 10.1016/S0168-9525(03)00140-9, 12850439.
    • (2003) Trends Genet , vol.19 , Issue.7 , pp. 362-365
    • Eisenberg, E.1    Levanon, E.Y.2
  • 158
    • 0142092546 scopus 로고    scopus 로고
    • The signature of selection mediated by expression on human genes
    • 10.1101/gr.641103, 403694, 12975314
    • Urrutia AO, Hurst LD. The signature of selection mediated by expression on human genes. Genome Res 2003, 13(10):2260-2264. 10.1101/gr.641103, 403694, 12975314.
    • (2003) Genome Res , vol.13 , Issue.10 , pp. 2260-2264
    • Urrutia, A.O.1    Hurst, L.D.2
  • 159
    • 3843068862 scopus 로고    scopus 로고
    • Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence
    • 10.1534/genetics.104.026351, 1470943, 15280243
    • Comeron JM. Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 2004, 167(3):1293-1304. 10.1534/genetics.104.026351, 1470943, 15280243.
    • (2004) Genetics , vol.167 , Issue.3 , pp. 1293-1304
    • Comeron, J.M.1
  • 160
    • 4744355710 scopus 로고    scopus 로고
    • Compactness of human housekeeping genes: selection for economy or genomic design?
    • 10.1016/j.tig.2004.03.006, 15109779
    • Vinogradov AE. Compactness of human housekeeping genes: selection for economy or genomic design?. Trends Genet 2004, 20(5):248-253. 10.1016/j.tig.2004.03.006, 15109779.
    • (2004) Trends Genet , vol.20 , Issue.5 , pp. 248-253
    • Vinogradov, A.E.1
  • 161
    • 15244364078 scopus 로고    scopus 로고
    • Human antisense genes have unusually short introns: evidence for selection for rapid transcription
    • 10.1016/j.tig.2005.02.003, 15797613
    • Chen J, Sun M, Hurst LD, Carmichael GG, Rowley JD. Human antisense genes have unusually short introns: evidence for selection for rapid transcription. Trends Genet 2005, 21(4):203-207. 10.1016/j.tig.2005.02.003, 15797613.
    • (2005) Trends Genet , vol.21 , Issue.4 , pp. 203-207
    • Chen, J.1    Sun, M.2    Hurst, L.D.3    Carmichael, G.G.4    Rowley, J.D.5
  • 162
    • 34447263110 scopus 로고    scopus 로고
    • Selection for the miniaturization of highly expressed genes
    • 10.1016/j.bbrc.2007.06.085, 17610841
    • Li SW, Feng L, Niu DK. Selection for the miniaturization of highly expressed genes. Biochem Biophys Res Commun 2007, 360(3):586-592. 10.1016/j.bbrc.2007.06.085, 17610841.
    • (2007) Biochem Biophys Res Commun , vol.360 , Issue.3 , pp. 586-592
    • Li, S.W.1    Feng, L.2    Niu, D.K.3
  • 163
    • 35248901812 scopus 로고    scopus 로고
    • Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis
    • 10.1007/s00239-007-9015-y, 17763878
    • Fahey ME, Higgins DG. Gene expression, intron density, and splice site strength in Drosophila and Caenorhabditis. J Mol Evol 2007, 65(3):349-357. 10.1007/s00239-007-9015-y, 17763878.
    • (2007) J Mol Evol , vol.65 , Issue.3 , pp. 349-357
    • Fahey, M.E.1    Higgins, D.G.2
  • 164
    • 33745638358 scopus 로고    scopus 로고
    • Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction
    • 10.1371/journal.pgen.0010013, 1186733, 16110339
    • Seoighe C, Gehring C, Hurst LD. Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction. PLoS Genet 2005, 1(2):e13. 10.1371/journal.pgen.0010013, 1186733, 16110339.
    • (2005) PLoS Genet , vol.1 , Issue.2
    • Seoighe, C.1    Gehring, C.2    Hurst, L.D.3
  • 165
    • 34247516343 scopus 로고    scopus 로고
    • Compact genes are highly expressed in the moss Physcomitrella patens
    • 10.1111/j.1420-9101.2007.01301.x, 17465932
    • Stenoien HK. Compact genes are highly expressed in the moss Physcomitrella patens. J Evol Biol 2007, 20(3):1223-1229. 10.1111/j.1420-9101.2007.01301.x, 17465932.
    • (2007) J Evol Biol , vol.20 , Issue.3 , pp. 1223-1229
    • Stenoien, H.K.1
  • 166
    • 33748552670 scopus 로고    scopus 로고
    • In plants, highly expressed genes are the least compact
    • 10.1016/j.tig.2006.08.008, 16934358
    • Ren XY, Vorst O, Fiers MW, Stiekema WJ, Nap JP. In plants, highly expressed genes are the least compact. Trends Genet 2006, 22(10):528-532. 10.1016/j.tig.2006.08.008, 16934358.
    • (2006) Trends Genet , vol.22 , Issue.10 , pp. 528-532
    • Ren, X.Y.1    Vorst, O.2    Fiers, M.W.3    Stiekema, W.J.4    Nap, J.P.5
  • 167
    • 78149360928 scopus 로고    scopus 로고
    • A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes
    • Carmel L, Koonin EV. A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes. Genome Biol Evol 2009, 1:282-290.
    • (2009) Genome Biol Evol , vol.1 , pp. 282-290
    • Carmel, L.1    Koonin, E.V.2
  • 168
    • 30744475434 scopus 로고    scopus 로고
    • The origins of eukaryotic gene structure
    • Lynch M. The origins of eukaryotic gene structure. Mol Biol Evol 2006, 23(2):450-468.
    • (2006) Mol Biol Evol , vol.23 , Issue.2 , pp. 450-468
    • Lynch, M.1
  • 169
    • 34547396004 scopus 로고    scopus 로고
    • The frailty of adaptive hypotheses for the origins of organismal complexity
    • 1876435, 17494740
    • Lynch M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A 2007, 104(Suppl 1):8597-8604. 1876435, 17494740.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , Issue.SUPPL. 1 , pp. 8597-8604
    • Lynch, M.1
  • 170
    • 60349093708 scopus 로고    scopus 로고
    • Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation
    • 10.1038/nrg2526, 19204717
    • Charlesworth B. Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat Rev Genet 2009, 10(3):195-205. 10.1038/nrg2526, 19204717.
    • (2009) Nat Rev Genet , vol.10 , Issue.3 , pp. 195-205
    • Charlesworth, B.1
  • 171
    • 79955418125 scopus 로고    scopus 로고
    • Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers
    • 10.1093/molbev/msq270, 3080132, 20952500
    • Strasburg JL, Kane NC, Raduski AR, Bonin A, Michelmore R, Rieseberg LH. Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers. Mol Biol Evol 2011, 28(5):1569-1580. 10.1093/molbev/msq270, 3080132, 20952500.
    • (2011) Mol Biol Evol , vol.28 , Issue.5 , pp. 1569-1580
    • Strasburg, J.L.1    Kane, N.C.2    Raduski, A.R.3    Bonin, A.4    Michelmore, R.5    Rieseberg, L.H.6
  • 173
    • 0034721644 scopus 로고    scopus 로고
    • Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology
    • 10.1016/S0092-8674(00)00128-8, 11081623
    • Black DL. Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell 2000, 103(3):367-370. 10.1016/S0092-8674(00)00128-8, 11081623.
    • (2000) Cell , vol.103 , Issue.3 , pp. 367-370
    • Black, D.L.1
  • 174
  • 175
    • 1242352406 scopus 로고    scopus 로고
    • Assessing the impact of alternative splicing on domain interactions in the human proteome
    • 10.1021/pr034064v, 14998166
    • Resch A, Xing Y, Modrek B, Gorlick M, Riley R, Lee C. Assessing the impact of alternative splicing on domain interactions in the human proteome. J Proteome Res 2004, 3(1):76-83. 10.1021/pr034064v, 14998166.
    • (2004) J Proteome Res , vol.3 , Issue.1 , pp. 76-83
    • Resch, A.1    Xing, Y.2    Modrek, B.3    Gorlick, M.4    Riley, R.5    Lee, C.6
  • 176
    • 77951120000 scopus 로고    scopus 로고
    • Alternative splicing and evolution: diversification, exon definition and function
    • 10.1038/nrg2776, 20376054
    • Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 2010, 11(5):345-355. 10.1038/nrg2776, 20376054.
    • (2010) Nat Rev Genet , vol.11 , Issue.5 , pp. 345-355
    • Keren, H.1    Lev-Maor, G.2    Ast, G.3
  • 177
    • 0034716987 scopus 로고    scopus 로고
    • EST comparison indicates 38% of human mRNAs contain possible alternative splice forms
    • 10.1016/S0014-5793(00)01581-7, 10828456
    • Brett D, Hanke J, Lehmann G, Haase S, Delbruck S, Krueger S, Reich J, Bork P. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett 2000, 474(1):83-86. 10.1016/S0014-5793(00)01581-7, 10828456.
    • (2000) FEBS Lett , vol.474 , Issue.1 , pp. 83-86
    • Brett, D.1    Hanke, J.2    Lehmann, G.3    Haase, S.4    Delbruck, S.5    Krueger, S.6    Reich, J.7    Bork, P.8
  • 178
    • 0034029236 scopus 로고    scopus 로고
    • ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome
    • 10.1038/74153, 10742092
    • Croft L, Schandorff S, Clark F, Burrage K, Arctander P, Mattick JS. ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat Genet 2000, 24(4):340-341. 10.1038/74153, 10742092.
    • (2000) Nat Genet , vol.24 , Issue.4 , pp. 340-341
    • Croft, L.1    Schandorff, S.2    Clark, F.3    Burrage, K.4    Arctander, P.5    Mattick, J.S.6
  • 179
    • 0035393343 scopus 로고    scopus 로고
    • Genome-wide detection of alternative splicing in expressed sequences of human genes
    • 10.1093/nar/29.13.2850, 55780, 11433032
    • Modrek B, Resch A, Grasso C, Lee C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res 2001, 29(13):2850-2859. 10.1093/nar/29.13.2850, 55780, 11433032.
    • (2001) Nucleic Acids Res , vol.29 , Issue.13 , pp. 2850-2859
    • Modrek, B.1    Resch, A.2    Grasso, C.3    Lee, C.4
  • 180
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.
    • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40(13):1413-1415.
    • (2008) Nat Genet , vol.40 , Issue.13 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 182
    • 77956277181 scopus 로고    scopus 로고
    • Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
    • 10.1101/gr.106120.110, 2928502, 20627892
    • Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, Guo Y, Huang X, et al. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res 2010, 20(9):1238-1249. 10.1101/gr.106120.110, 2928502, 20627892.
    • (2010) Genome Res , vol.20 , Issue.9 , pp. 1238-1249
    • Lu, T.1    Lu, G.2    Fan, D.3    Zhu, C.4    Li, W.5    Zhao, Q.6    Feng, Q.7    Zhao, Y.8    Guo, Y.9    Huang, X.10
  • 183
    • 79955925635 scopus 로고    scopus 로고
    • Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data
    • 10.1186/1471-2229-11-82, 3118179, 21575182
    • Severing EI, van Dijk AD, van Ham RC. Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data. BMC Plant Biol 2011, 11(1):82. 10.1186/1471-2229-11-82, 3118179, 21575182.
    • (2011) BMC Plant Biol , vol.11 , Issue.1 , pp. 82
    • Severing, E.I.1    van Dijk, A.D.2    van Ham, R.C.3
  • 184
    • 36349026377 scopus 로고    scopus 로고
    • Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
    • 10.1186/1471-2148-7-188, 2082043, 17916237
    • Irimia M, Rukov JL, Penny D, Roy SW. Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evol Biol 2007, 7:188. 10.1186/1471-2148-7-188, 2082043, 17916237.
    • (2007) BMC Evol Biol , vol.7 , pp. 188
    • Irimia, M.1    Rukov, J.L.2    Penny, D.3    Roy, S.W.4
  • 185
    • 13744252347 scopus 로고    scopus 로고
    • Significant expansion of exon-bordering protein domains during animal proteome evolution
    • 10.1093/nar/gki152, 546140, 15640447
    • Liu M, Walch H, Wu S, Grigoriev A. Significant expansion of exon-bordering protein domains during animal proteome evolution. Nucleic Acids Res 2005, 33(1):95-105. 10.1093/nar/gki152, 546140, 15640447.
    • (2005) Nucleic Acids Res , vol.33 , Issue.1 , pp. 95-105
    • Liu, M.1    Walch, H.2    Wu, S.3    Grigoriev, A.4
  • 186
    • 0023646322 scopus 로고
    • Intron-dependent evolution: preferred types of exons and introns
    • 10.1016/0014-5793(87)80002-9, 3552723
    • Patthy L. Intron-dependent evolution: preferred types of exons and introns. FEBS Lett 1987, 214(1):1-7. 10.1016/0014-5793(87)80002-9, 3552723.
    • (1987) FEBS Lett , vol.214 , Issue.1 , pp. 1-7
    • Patthy, L.1
  • 187
    • 0032885169 scopus 로고    scopus 로고
    • Genome evolution and the evolution of exon-shuffling-a review
    • 10.1016/S0378-1119(99)00228-0, 10570989
    • Patthy L. Genome evolution and the evolution of exon-shuffling-a review. Gene 1999, 238(1):103-114. 10.1016/S0378-1119(99)00228-0, 10570989.
    • (1999) Gene , vol.238 , Issue.1 , pp. 103-114
    • Patthy, L.1
  • 188
    • 0038306145 scopus 로고    scopus 로고
    • Modular assembly of genes and the evolution of new functions
    • Patthy L. Modular assembly of genes and the evolution of new functions. Genetica 2003, 118(2-3):217-231.
    • (2003) Genetica , vol.118 , Issue.2-3 , pp. 217-231
    • Patthy, L.1
  • 189
    • 0038617729 scopus 로고    scopus 로고
    • Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss
    • 10.1038/ng1159, 12730695
    • Modrek B, Lee CJ. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat Genet 2003, 34(2):177-180. 10.1038/ng1159, 12730695.
    • (2003) Nat Genet , vol.34 , Issue.2 , pp. 177-180
    • Modrek, B.1    Lee, C.J.2
  • 190
    • 33645521073 scopus 로고    scopus 로고
    • Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes
    • 10.1101/gr.4236606, 1457027, 16520458
    • Malko DB, Makeev VJ, Mironov AA, Gelfand MS. Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes. Genome Res 2006, 16(4):505-509. 10.1101/gr.4236606, 1457027, 16520458.
    • (2006) Genome Res , vol.16 , Issue.4 , pp. 505-509
    • Malko, D.B.1    Makeev, V.J.2    Mironov, A.A.3    Gelfand, M.S.4
  • 191
    • 38849136475 scopus 로고    scopus 로고
    • Conserved and species-specific alternative splicing in mammalian genomes
    • 10.1186/1471-2148-7-249, 2231371, 18154685
    • Nurtdinov RN, Neverov AD, Favorov AV, Mironov AA, Gelfand MS. Conserved and species-specific alternative splicing in mammalian genomes. BMC Evol Biol 2007, 7:249. 10.1186/1471-2148-7-249, 2231371, 18154685.
    • (2007) BMC Evol Biol , vol.7 , pp. 249
    • Nurtdinov, R.N.1    Neverov, A.D.2    Favorov, A.V.3    Mironov, A.A.4    Gelfand, M.S.5
  • 192
    • 56649114578 scopus 로고    scopus 로고
    • Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs
    • 10.1093/nar/gkn677, 2582632, 18838389
    • Takeda J, Suzuki Y, Sakate R, Sato Y, Seki M, Irie T, Takeuchi N, Ueda T, Nakao M, Sugano S, et al. Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs. Nucleic Acids Res 2008, 36(20):6386-6395. 10.1093/nar/gkn677, 2582632, 18838389.
    • (2008) Nucleic Acids Res , vol.36 , Issue.20 , pp. 6386-6395
    • Takeda, J.1    Suzuki, Y.2    Sakate, R.3    Sato, Y.4    Seki, M.5    Irie, T.6    Takeuchi, N.7    Ueda, T.8    Nakao, M.9    Sugano, S.10
  • 194
    • 38949095296 scopus 로고    scopus 로고
    • Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis
    • 10.1093/molbev/msm262, 18048400
    • Irimia M, Rukov JL, Penny D, Garcia-Fernandez J, Vinther J, Roy SW. Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis. Mol Biol Evol 2008, 25(2):375-382. 10.1093/molbev/msm262, 18048400.
    • (2008) Mol Biol Evol , vol.25 , Issue.2 , pp. 375-382
    • Irimia, M.1    Rukov, J.L.2    Penny, D.3    Garcia-Fernandez, J.4    Vinther, J.5    Roy, S.W.6
  • 195
    • 48549085068 scopus 로고    scopus 로고
    • Accumulation of GC donor splice signals in mammals
    • 10.1186/1745-6150-3-30, 2490688, 18613975
    • Churbanov A, Winters-Hilt S, Koonin EV, Rogozin IB. Accumulation of GC donor splice signals in mammals. Biol Direct 2008, 3:30. 10.1186/1745-6150-3-30, 2490688, 18613975.
    • (2008) Biol Direct , vol.3 , pp. 30
    • Churbanov, A.1    Winters-Hilt, S.2    Koonin, E.V.3    Rogozin, I.B.4
  • 196
    • 0035875551 scopus 로고    scopus 로고
    • Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions
    • 10.1093/nar/29.12.2581, 55748, 11410667
    • Thanaraj TA, Clark F. Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions. Nucleic Acids Res 2001, 29(12):2581-2593. 10.1093/nar/29.12.2581, 55748, 11410667.
    • (2001) Nucleic Acids Res , vol.29 , Issue.12 , pp. 2581-2593
    • Thanaraj, T.A.1    Clark, F.2
  • 197
    • 0036682115 scopus 로고    scopus 로고
    • Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing
    • 10.1093/nar/gkf465, 137088, 12140320
    • Farrer T, Roller AB, Kent WJ, Zahler AM. Analysis of the role of Caenorhabditis elegans GC-AG introns in regulated splicing. Nucleic Acids Res 2002, 30(15):3360-3367. 10.1093/nar/gkf465, 137088, 12140320.
    • (2002) Nucleic Acids Res , vol.30 , Issue.15 , pp. 3360-3367
    • Farrer, T.1    Roller, A.B.2    Kent, W.J.3    Zahler, A.M.4
  • 198
    • 33846573830 scopus 로고    scopus 로고
    • Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
    • 10.1186/1471-2164-7-327, 1769492, 17194304
    • Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 2006, 7:327. 10.1186/1471-2164-7-327, 1769492, 17194304.
    • (2006) BMC Genomics , vol.7 , pp. 327
    • Campbell, M.A.1    Haas, B.J.2    Hamilton, J.P.3    Mount, S.M.4    Buell, C.R.5
  • 199
    • 0029959817 scopus 로고    scopus 로고
    • Alternative splicing of exon 3 of the human growth hormone receptor is the result of an unusual genetic polymorphism
    • 10.1073/pnas.93.22.12394, 38002, 8901592
    • Stallings-Mann ML, Ludwiczak RL, Klinger KW, Rottman F. Alternative splicing of exon 3 of the human growth hormone receptor is the result of an unusual genetic polymorphism. Proc Natl Acad Sci U S A 1996, 93(22):12394-12399. 10.1073/pnas.93.22.12394, 38002, 8901592.
    • (1996) Proc Natl Acad Sci U S A , vol.93 , Issue.22 , pp. 12394-12399
    • Stallings-Mann, M.L.1    Ludwiczak, R.L.2    Klinger, K.W.3    Rottman, F.4
  • 200
    • 19344367734 scopus 로고    scopus 로고
    • Single nucleotide polymorphism-based validation of exonic splicing enhancers
    • 10.1371/journal.pbio.0020268, 514884, 15340491
    • Fairbrother WG, Holste D, Burge CB, Sharp PA. Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol 2004, 2(9):E268. 10.1371/journal.pbio.0020268, 514884, 15340491.
    • (2004) PLoS Biol , vol.2 , Issue.9
    • Fairbrother, W.G.1    Holste, D.2    Burge, C.B.3    Sharp, P.A.4
  • 201
    • 20244385671 scopus 로고    scopus 로고
    • A high-frequency polymorphism in exon 6 of the CD45 tyrosine phosphatase gene (PTPRC) resulting in altered isoform expression
    • 10.1073/pnas.0931490100, 156315, 12716971
    • Stanton T, Boxall S, Hirai K, Dawes R, Tonks S, Yasui T, Kanaoka Y, Yuldasheva N, Ishiko O, Bodmer W, et al. A high-frequency polymorphism in exon 6 of the CD45 tyrosine phosphatase gene (PTPRC) resulting in altered isoform expression. Proc Natl Acad Sci U S A 2003, 100(10):5997-6002. 10.1073/pnas.0931490100, 156315, 12716971.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , Issue.10 , pp. 5997-6002
    • Stanton, T.1    Boxall, S.2    Hirai, K.3    Dawes, R.4    Tonks, S.5    Yasui, T.6    Kanaoka, Y.7    Yuldasheva, N.8    Ishiko, O.9    Bodmer, W.10
  • 202
    • 30744469841 scopus 로고    scopus 로고
    • Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
    • Parmley JL, Chamary JV, Hurst LD. Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol 2006, 23(2):301-309.
    • (2006) Mol Biol Evol , vol.23 , Issue.2 , pp. 301-309
    • Parmley, J.L.1    Chamary, J.V.2    Hurst, L.D.3
  • 203
    • 31844449496 scopus 로고    scopus 로고
    • Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers
    • 10.1007/s00239-005-0055-x, 16320116
    • Carlini DB, Genut JE. Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. J Mol Evol 2006, 62(1):89-98. 10.1007/s00239-005-0055-x, 16320116.
    • (2006) J Mol Evol , vol.62 , Issue.1 , pp. 89-98
    • Carlini, D.B.1    Genut, J.E.2
  • 204
    • 41649093631 scopus 로고    scopus 로고
    • Positive selection acting on splicing motifs reflects compensatory evolution
    • 10.1101/gr.070268.107, 2279241, 18204002
    • Ke S, Zhang XH, Chasin LA. Positive selection acting on splicing motifs reflects compensatory evolution. Genome Res 2008, 18(4):533-543. 10.1101/gr.070268.107, 2279241, 18204002.
    • (2008) Genome Res , vol.18 , Issue.4 , pp. 533-543
    • Ke, S.1    Zhang, X.H.2    Chasin, L.A.3
  • 205
    • 67149139310 scopus 로고    scopus 로고
    • Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates
    • 10.1371/journal.pone.0005800, 2686173, 19495418
    • Irimia M, Rukov JL, Roy SW. Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates. PLoS One 2009, 4(6):e5800. 10.1371/journal.pone.0005800, 2686173, 19495418.
    • (2009) PLoS One , vol.4 , Issue.6
    • Irimia, M.1    Rukov, J.L.2    Roy, S.W.3
  • 206
    • 74249100914 scopus 로고    scopus 로고
    • Fine-scale variation and genetic determinants of alternative splicing across individuals
    • 10.1371/journal.pgen.1000766, 2780703, 20011102
    • Coulombe-Huntington J, Lam KC, Dias C, Majewski J. Fine-scale variation and genetic determinants of alternative splicing across individuals. PLoS Genet 2009, 5(12):e1000766. 10.1371/journal.pgen.1000766, 2780703, 20011102.
    • (2009) PLoS Genet , vol.5 , Issue.12
    • Coulombe-Huntington, J.1    Lam, K.C.2    Dias, C.3    Majewski, J.4
  • 207
    • 8544274534 scopus 로고    scopus 로고
    • Translational regulation of angiotensin type 1a receptor expression and signaling by upstream AUGs in the 5' leader sequence
    • 10.1074/jbc.M407261200, 15319432
    • Ji H, Zhang Y, Zheng W, Wu Z, Lee S, Sandberg K. Translational regulation of angiotensin type 1a receptor expression and signaling by upstream AUGs in the 5' leader sequence. J Biol Chem 2004, 279(44):45322-45328. 10.1074/jbc.M407261200, 15319432.
    • (2004) J Biol Chem , vol.279 , Issue.44 , pp. 45322-45328
    • Ji, H.1    Zhang, Y.2    Zheng, W.3    Wu, Z.4    Lee, S.5    Sandberg, K.6
  • 208
    • 33644801773 scopus 로고    scopus 로고
    • Alternative initiation and splicing in dicer gene expression in human breast cells
    • 10.1186/bcr1043, 1175071, 15987463
    • Irvin-Wilson CV, Chaudhuri G. Alternative initiation and splicing in dicer gene expression in human breast cells. Breast Cancer Res 2005, 7(4):R563-R569. 10.1186/bcr1043, 1175071, 15987463.
    • (2005) Breast Cancer Res , vol.7 , Issue.4
    • Irvin-Wilson, C.V.1    Chaudhuri, G.2
  • 209
    • 65449153694 scopus 로고    scopus 로고
    • Evolution of alternative and constitutive regions of mammalian 5'UTRs
    • 10.1186/1471-2164-10-162, 2674463, 19371439
    • Resch AM, Ogurtsov AY, Rogozin IB, Shabalina SA, Koonin EV. Evolution of alternative and constitutive regions of mammalian 5'UTRs. BMC Genomics 2009, 10:162. 10.1186/1471-2164-10-162, 2674463, 19371439.
    • (2009) BMC Genomics , vol.10 , pp. 162
    • Resch, A.M.1    Ogurtsov, A.Y.2    Rogozin, I.B.3    Shabalina, S.A.4    Koonin, E.V.5
  • 210
    • 0345874728 scopus 로고    scopus 로고
    • Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation
    • 314283, 14672974
    • Zhang T, Haws P, Wu Q. Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. Genome Res 2004, 14(1):79-89. 314283, 14672974.
    • (2004) Genome Res , vol.14 , Issue.1 , pp. 79-89
    • Zhang, T.1    Haws, P.2    Wu, Q.3
  • 211
    • 33646866597 scopus 로고    scopus 로고
    • Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns
    • 10.1093/bioinformatics/btl067, 16500940
    • Nagasaki H, Arita M, Nishizawa T, Suwa M, Gotoh O. Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. Bioinformatics 2006, 22(10):1211-1216. 10.1093/bioinformatics/btl067, 16500940.
    • (2006) Bioinformatics , vol.22 , Issue.10 , pp. 1211-1216
    • Nagasaki, H.1    Arita, M.2    Nishizawa, T.3    Suwa, M.4    Gotoh, O.5
  • 212
    • 33846794614 scopus 로고    scopus 로고
    • Estimating the neutral rate of nucleotide substitution using introns
    • Hoffman MM, Birney E. Estimating the neutral rate of nucleotide substitution using introns. Mol Biol Evol 2007, 24(2):522-531.
    • (2007) Mol Biol Evol , vol.24 , Issue.2 , pp. 522-531
    • Hoffman, M.M.1    Birney, E.2
  • 214
    • 0037630627 scopus 로고    scopus 로고
    • Introns in gene evolution
    • Fedorova L, Fedorov A. Introns in gene evolution. Genetica 2003, 118(2-3):123-131.
    • (2003) Genetica , vol.118 , Issue.2-3 , pp. 123-131
    • Fedorova, L.1    Fedorov, A.2
  • 215
    • 33748796735 scopus 로고    scopus 로고
    • Origins and evolution of spliceosomal introns
    • 10.1146/annurev.genet.40.110405.090625, 17094737
    • Rodriguez-Trelles F, Tarrio R, Ayala FJ. Origins and evolution of spliceosomal introns. Annu Rev Genet 2006, 40:47-76. 10.1146/annurev.genet.40.110405.090625, 17094737.
    • (2006) Annu Rev Genet , vol.40 , pp. 47-76
    • Rodriguez-Trelles, F.1    Tarrio, R.2    Ayala, F.J.3
  • 216
    • 0033592896 scopus 로고    scopus 로고
    • Splicing is required for rapid and efficient mRNA export in metazoans
    • 10.1073/pnas.96.26.14937, 24751, 10611316
    • Luo MJ, Reed R. Splicing is required for rapid and efficient mRNA export in metazoans. Proc Natl Acad Sci U S A 1999, 96(26):14937-14942. 10.1073/pnas.96.26.14937, 24751, 10611316.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , Issue.26 , pp. 14937-14942
    • Luo, M.J.1    Reed, R.2
  • 217
    • 0034193569 scopus 로고    scopus 로고
    • Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon-exon junctions
    • 316578, 10809668
    • Le Hir H, Moore MJ, Maquat LE. Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon-exon junctions. Genes Dev 2000, 14(9):1098-1108. 316578, 10809668.
    • (2000) Genes Dev , vol.14 , Issue.9 , pp. 1098-1108
    • Le Hir, H.1    Moore, M.J.2    Maquat, L.E.3
  • 218
    • 0034699472 scopus 로고    scopus 로고
    • The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans
    • 10.1038/35030160, 11014198
    • Zhou Z, Luo MJ, Straesser K, Katahira J, Hurt E, Reed R. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans. Nature 2000, 407(6802):401-405. 10.1038/35030160, 11014198.
    • (2000) Nature , vol.407 , Issue.6802 , pp. 401-405
    • Zhou, Z.1    Luo, M.J.2    Straesser, K.3    Katahira, J.4    Hurt, E.5    Reed, R.6
  • 219
    • 0034672093 scopus 로고    scopus 로고
    • The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions
    • 10.1093/emboj/19.24.6860, 305905, 11118221
    • Le Hir H, Izaurralde E, Maquat LE, Moore MJ. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J 2000, 19(24):6860-6869. 10.1093/emboj/19.24.6860, 305905, 11118221.
    • (2000) EMBO J , vol.19 , Issue.24 , pp. 6860-6869
    • Le Hir, H.1    Izaurralde, E.2    Maquat, L.E.3    Moore, M.J.4
  • 220
    • 0035846138 scopus 로고    scopus 로고
    • Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly
    • 10.1038/35098106, 11675789
    • Luo ML, Zhou Z, Magni K, Christoforides C, Rappsilber J, Mann M, Reed R. Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly. Nature 2001, 413(6856):644-647. 10.1038/35098106, 11675789.
    • (2001) Nature , vol.413 , Issue.6856 , pp. 644-647
    • Luo, M.L.1    Zhou, Z.2    Magni, K.3    Christoforides, C.4    Rappsilber, J.5    Mann, M.6    Reed, R.7
  • 221
    • 0035846109 scopus 로고    scopus 로고
    • Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p
    • 10.1038/35098113, 11675790
    • Strasser K, Hurt E. Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p. Nature 2001, 413(6856):648-652. 10.1038/35098113, 11675790.
    • (2001) Nature , vol.413 , Issue.6856 , pp. 648-652
    • Strasser, K.1    Hurt, E.2
  • 222
    • 0035975942 scopus 로고    scopus 로고
    • The DExH/D box protein HEL/UAP56 is essential for mRNA nuclear export in Drosophila
    • 10.1016/S0960-9822(01)00532-2, 11696332
    • Gatfield D, Le Hir H, Schmitt C, Braun IC, Kocher T, Wilm M, Izaurralde E. The DExH/D box protein HEL/UAP56 is essential for mRNA nuclear export in Drosophila. Curr Biol 2001, 11(21):1716-1721. 10.1016/S0960-9822(01)00532-2, 11696332.
    • (2001) Curr Biol , vol.11 , Issue.21 , pp. 1716-1721
    • Gatfield, D.1    Le Hir, H.2    Schmitt, C.3    Braun, I.C.4    Kocher, T.5    Wilm, M.6    Izaurralde, E.7
  • 223
    • 0034633626 scopus 로고    scopus 로고
    • Lineage-specific loss and divergence of functionally linked genes in eukaryotes
    • 10.1073/pnas.200346997, 17198, 11016957
    • Aravind L, Watanabe H, Lipman DJ, Koonin EV. Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci U S A 2000, 97(21):11319-11324. 10.1073/pnas.200346997, 17198, 11016957.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , Issue.21 , pp. 11319-11324
    • Aravind, L.1    Watanabe, H.2    Lipman, D.J.3    Koonin, E.V.4
  • 224
    • 0035975969 scopus 로고    scopus 로고
    • The DECD box putative ATPase Sub2p is an early mRNA export factor
    • 10.1016/S0960-9822(01)00529-2, 11696331
    • Jensen TH, Boulay J, Rosbash M, Libri D. The DECD box putative ATPase Sub2p is an early mRNA export factor. Curr Biol 2001, 11(21):1711-1715. 10.1016/S0960-9822(01)00529-2, 11696331.
    • (2001) Curr Biol , vol.11 , Issue.21 , pp. 1711-1715
    • Jensen, T.H.1    Boulay, J.2    Rosbash, M.3    Libri, D.4
  • 225
    • 0344211508 scopus 로고    scopus 로고
    • SR splicing factors serve as adapter proteins for TAP-dependent mRNA export
    • 10.1016/S1097-2765(03)00089-3, 12667464
    • Huang Y, Gattoni R, Stevenin J, Steitz JA. SR splicing factors serve as adapter proteins for TAP-dependent mRNA export. Mol Cell 2003, 11(3):837-843. 10.1016/S1097-2765(03)00089-3, 12667464.
    • (2003) Mol Cell , vol.11 , Issue.3 , pp. 837-843
    • Huang, Y.1    Gattoni, R.2    Stevenin, J.3    Steitz, J.A.4
  • 226
    • 14644445227 scopus 로고    scopus 로고
    • SRprises along a messenger's journey
    • 10.1016/j.molcel.2005.02.020, 15749011
    • Huang Y, Steitz JA. SRprises along a messenger's journey. Mol Cell 2005, 17(5):613-615. 10.1016/j.molcel.2005.02.020, 15749011.
    • (2005) Mol Cell , vol.17 , Issue.5 , pp. 613-615
    • Huang, Y.1    Steitz, J.A.2
  • 227
    • 0035807308 scopus 로고    scopus 로고
    • Quality control of mRNA 3'-end processing is linked to the nuclear exosome
    • 10.1038/35097110, 11586364
    • Hilleren P, McCarthy T, Rosbash M, Parker R, Jensen TH. Quality control of mRNA 3'-end processing is linked to the nuclear exosome. Nature 2001, 413(6855):538-542. 10.1038/35097110, 11586364.
    • (2001) Nature , vol.413 , Issue.6855 , pp. 538-542
    • Hilleren, P.1    McCarthy, T.2    Rosbash, M.3    Parker, R.4    Jensen, T.H.5
  • 228
    • 79952227406 scopus 로고    scopus 로고
    • Cytoplasmic intron sequence-retaining transcripts can be dendritically targeted via ID element retrotransposons
    • 10.1016/j.neuron.2011.02.028, 3065018, 21382548
    • Buckley PT, Lee MT, Sul JY, Miyashiro KY, Bell TJ, Fisher SA, Kim J, Eberwine J. Cytoplasmic intron sequence-retaining transcripts can be dendritically targeted via ID element retrotransposons. Neuron 2011, 69(5):877-884. 10.1016/j.neuron.2011.02.028, 3065018, 21382548.
    • (2011) Neuron , vol.69 , Issue.5 , pp. 877-884
    • Buckley, P.T.1    Lee, M.T.2    Sul, J.Y.3    Miyashiro, K.Y.4    Bell, T.J.5    Fisher, S.A.6    Kim, J.7    Eberwine, J.8
  • 229
    • 33846071878 scopus 로고    scopus 로고
    • U12DB: a database of orthologous U12-type spliceosomal introns
    • 1635337, 17082203
    • Alioto TS. U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic Acids Res 2007, 35(Database issue):D110-D115. 1635337, 17082203.
    • (2007) Nucleic Acids Res , vol.35 , Issue.DATABASE ISSUE
    • Alioto, T.S.1
  • 230
    • 34247255773 scopus 로고    scopus 로고
    • Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components
    • 10.1371/journal.pbio.0050090, 1831718, 17388687
    • Pleiss JA, Whitworth GB, Bergkessel M, Guthrie C. Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components. PLoS Biol 2007, 5(4):e90. 10.1371/journal.pbio.0050090, 1831718, 17388687.
    • (2007) PLoS Biol , vol.5 , Issue.4
    • Pleiss, J.A.1    Whitworth, G.B.2    Bergkessel, M.3    Guthrie, C.4
  • 231
    • 0029006062 scopus 로고
    • The multiplicity of domains in proteins
    • 10.1146/annurev.bi.64.070195.001443, 7574483
    • Doolittle RF. The multiplicity of domains in proteins. Annu Rev Biochem 1995, 64:287-314. 10.1146/annurev.bi.64.070195.001443, 7574483.
    • (1995) Annu Rev Biochem , vol.64 , pp. 287-314
    • Doolittle, R.F.1
  • 232
    • 0034625235 scopus 로고    scopus 로고
    • The impact of comparative genomics on our understanding of evolution
    • 10.1016/S0092-8674(00)80867-3, 10892642
    • Koonin EV, Aravind L, Kondrashov AS. The impact of comparative genomics on our understanding of evolution. Cell 2000, 101:573-576. 10.1016/S0092-8674(00)80867-3, 10892642.
    • (2000) Cell , vol.101 , pp. 573-576
    • Koonin, E.V.1    Aravind, L.2    Kondrashov, A.S.3
  • 233
    • 26244442102 scopus 로고    scopus 로고
    • Modules, multidomain proteins and organismic complexity
    • 10.1111/j.1742-4658.2005.04917.x, 16176277
    • Tordai H, Nagy A, Farkas K, Banyai L, Patthy L. Modules, multidomain proteins and organismic complexity. FEBS J 2005, 272(19):5064-5078. 10.1111/j.1742-4658.2005.04917.x, 16176277.
    • (2005) FEBS J , vol.272 , Issue.19 , pp. 5064-5078
    • Tordai, H.1    Nagy, A.2    Farkas, K.3    Banyai, L.4    Patthy, L.5
  • 234
    • 65549111825 scopus 로고    scopus 로고
    • Domain mobility in proteins: functional and evolutionary implications
    • 2722818, 19151098
    • Basu MK, Poliakov E, Rogozin IB. Domain mobility in proteins: functional and evolutionary implications. Brief Bioinform 2009, 10(3):205-216. 2722818, 19151098.
    • (2009) Brief Bioinform , vol.10 , Issue.3 , pp. 205-216
    • Basu, M.K.1    Poliakov, E.2    Rogozin, I.B.3
  • 235
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • 10.1126/science.285.5428.751, 10427000
    • Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285(5428):751-753. 10.1126/science.285.5428.751, 10427000.
    • (1999) Science , vol.285 , Issue.5428 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ng, H.L.3    Rice, D.W.4    Yeates, T.O.5    Eisenberg, D.6
  • 236
    • 0038306163 scopus 로고    scopus 로고
    • The emergence of a synthetic theory of intron evolution
    • de Souza SJ. The emergence of a synthetic theory of intron evolution. Genetica 2003, 118(2-3):117-121.
    • (2003) Genetica , vol.118 , Issue.2-3 , pp. 117-121
    • de Souza, S.J.1
  • 237
    • 0345035503 scopus 로고    scopus 로고
    • Intron size and natural selection
    • 10.1038/43827, 10517631
    • Carvalho AB, Clark AG. Intron size and natural selection. Nature 1999, 401(6751):344. 10.1038/43827, 10517631.
    • (1999) Nature , vol.401 , Issue.6751 , pp. 344
    • Carvalho, A.B.1    Clark, A.G.2
  • 238
    • 0035576933 scopus 로고    scopus 로고
    • Evolutionary origin of SL-addition trans-splicing: still an enigma
    • 10.1016/S0168-9525(01)02499-4, 11718904
    • Nilsen TW. Evolutionary origin of SL-addition trans-splicing: still an enigma. Trends Genet 2001, 17(12):678-680. 10.1016/S0168-9525(01)02499-4, 11718904.
    • (2001) Trends Genet , vol.17 , Issue.12 , pp. 678-680
    • Nilsen, T.W.1
  • 239
    • 0033816026 scopus 로고    scopus 로고
    • Trans splicing of polycistronic Caenorhabditis elegans pre-mRNAs: analysis of the SL2 RNA
    • 10.1128/MCB.20.18.6659-6667.2000, 86170, 10958663
    • Evans D, Blumenthal T. trans splicing of polycistronic Caenorhabditis elegans pre-mRNAs: analysis of the SL2 RNA. Mol Cell Biol 2000, 20(18):6659-6667. 10.1128/MCB.20.18.6659-6667.2000, 86170, 10958663.
    • (2000) Mol Cell Biol , vol.20 , Issue.18 , pp. 6659-6667
    • Evans, D.1    Blumenthal, T.2
  • 241
    • 78751516220 scopus 로고    scopus 로고
    • A global analysis of C. elegans trans-splicing
    • 10.1101/gr.113811.110, 3032929, 21177958
    • Allen MA, Hillier LW, Waterston RH, Blumenthal T. A global analysis of C. elegans trans-splicing. Genome Res 2011, 21(2):255-264. 10.1101/gr.113811.110, 3032929, 21177958.
    • (2011) Genome Res , vol.21 , Issue.2 , pp. 255-264
    • Allen, M.A.1    Hillier, L.W.2    Waterston, R.H.3    Blumenthal, T.4
  • 242
    • 84857710418 scopus 로고    scopus 로고
    • Trans-splicing
    • 10.1002/wrna.71, 21957027
    • Lasda EL, Blumenthal T. Trans-splicing. Wiley Interdiscip Rev RNA 2011, 2(3):417-434. 10.1002/wrna.71, 21957027.
    • (2011) Wiley Interdiscip Rev RNA , vol.2 , Issue.3 , pp. 417-434
    • Lasda, E.L.1    Blumenthal, T.2
  • 243
    • 77249139172 scopus 로고    scopus 로고
    • Evidence for multiple independent origins of trans-splicing in Metazoa
    • 10.1093/molbev/msp286, 19942614
    • Douris V, Telford MJ, Averof M. Evidence for multiple independent origins of trans-splicing in Metazoa. Mol Biol Evol 2010, 27(3):684-693. 10.1093/molbev/msp286, 19942614.
    • (2010) Mol Biol Evol , vol.27 , Issue.3 , pp. 684-693
    • Douris, V.1    Telford, M.J.2    Averof, M.3
  • 244
    • 77950941239 scopus 로고    scopus 로고
    • Detection of human interchromosomal trans-splicing in sequence databanks
    • 10.1093/bib/bbp041, 19955235
    • Herai RH, Yamagishi ME. Detection of human interchromosomal trans-splicing in sequence databanks. Brief Bioinform 2010, 11(2):198-209. 10.1093/bib/bbp041, 19955235.
    • (2010) Brief Bioinform , vol.11 , Issue.2 , pp. 198-209
    • Herai, R.H.1    Yamagishi, M.E.2
  • 245
    • 77955622547 scopus 로고    scopus 로고
    • Global analysis of trans-splicing in Drosophila
    • 10.1073/pnas.1007586107, 2919919, 20615941
    • McManus CJ, Duff MO, Eipper-Mains J, Graveley BR. Global analysis of trans-splicing in Drosophila. Proc Natl Acad Sci U S A 2010, 107(29):12975-12979. 10.1073/pnas.1007586107, 2919919, 20615941.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , Issue.29 , pp. 12975-12979
    • McManus, C.J.1    Duff, M.O.2    Eipper-Mains, J.3    Graveley, B.R.4
  • 246
    • 0037372327 scopus 로고    scopus 로고
    • A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions
    • 10.1016/S0168-9525(03)00016-7, 12615002
    • Glazko GV, Koonin EV, Rogozin IB, Shabalina SA. A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet 2003, 19(3):119-124. 10.1016/S0168-9525(03)00016-7, 12615002.
    • (2003) Trends Genet , vol.19 , Issue.3 , pp. 119-124
    • Glazko, G.V.1    Koonin, E.V.2    Rogozin, I.B.3    Shabalina, S.A.4
  • 247
    • 0034883255 scopus 로고    scopus 로고
    • Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences
    • 10.1101/gr.178701, 11483574
    • Bergman CM, Kreitman M. Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Res 2001, 11(8):1335-1345. 10.1101/gr.178701, 11483574.
    • (2001) Genome Res , vol.11 , Issue.8 , pp. 1335-1345
    • Bergman, C.M.1    Kreitman, M.2
  • 248
    • 0036911605 scopus 로고    scopus 로고
    • Distribution and characterization of regulatory elements in the human genome
    • 10.1101/gr.606402, 187578, 12466286
    • Majewski J, Ott J. Distribution and characterization of regulatory elements in the human genome. Genome Res 2002, 12(12):1827-1836. 10.1101/gr.606402, 187578, 12466286.
    • (2002) Genome Res , vol.12 , Issue.12 , pp. 1827-1836
    • Majewski, J.1    Ott, J.2
  • 249
    • 0347361692 scopus 로고    scopus 로고
    • Selective constraints on intron evolution in Drosophila
    • 1462880, 14704170
    • Parsch J. Selective constraints on intron evolution in Drosophila. Genetics 2003, 165(4):1843-1851. 1462880, 14704170.
    • (2003) Genetics , vol.165 , Issue.4 , pp. 1843-1851
    • Parsch, J.1
  • 250
    • 20444371957 scopus 로고    scopus 로고
    • Intron size and exon evolution in Drosophila
    • 10.1534/genetics.104.037333, 1449718, 15781704
    • Marais G, Nouvellet P, Keightley PD, Charlesworth B. Intron size and exon evolution in Drosophila. Genetics 2005, 170(1):481-485. 10.1534/genetics.104.037333, 1449718, 15781704.
    • (2005) Genetics , vol.170 , Issue.1 , pp. 481-485
    • Marais, G.1    Nouvellet, P.2    Keightley, P.D.3    Charlesworth, B.4
  • 251
    • 25844481290 scopus 로고    scopus 로고
    • Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content
    • 10.1186/gb-2005-6-8-r67, 1273634, 16086849
    • Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P. Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol 2005, 6(8):R67. 10.1186/gb-2005-6-8-r67, 1273634, 16086849.
    • (2005) Genome Biol , vol.6 , Issue.8
    • Haddrill, P.R.1    Charlesworth, B.2    Halligan, D.L.3    Andolfatto, P.4
  • 252
    • 33745612972 scopus 로고    scopus 로고
    • Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
    • 10.1101/gr.5022906, 1484454, 16751341
    • Halligan DL, Keightley PD. Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res 2006, 16(7):875-884. 10.1101/gr.5022906, 1484454, 16751341.
    • (2006) Genome Res , vol.16 , Issue.7 , pp. 875-884
    • Halligan, D.L.1    Keightley, P.D.2
  • 253
    • 77952800173 scopus 로고    scopus 로고
    • On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila
    • 10.1093/molbev/msq046, 2877998, 20150340
    • Parsch J, Novozhilov S, Saminadin-Peter SS, Wong KM, Andolfatto P. On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila. Mol Biol Evol 2010, 27(6):1226-1234. 10.1093/molbev/msq046, 2877998, 20150340.
    • (2010) Mol Biol Evol , vol.27 , Issue.6 , pp. 1226-1234
    • Parsch, J.1    Novozhilov, S.2    Saminadin-Peter, S.S.3    Wong, K.M.4    Andolfatto, P.5
  • 254
    • 0344171940 scopus 로고    scopus 로고
    • Intronic enhancers control expression of zebrafish sonic hedgehog in floor plate and notochord
    • Muller F, Chang B, Albert S, Fischer N, Tora L, Strahle U. Intronic enhancers control expression of zebrafish sonic hedgehog in floor plate and notochord. Development 1999, 126(10):2103-2116.
    • (1999) Development , vol.126 , Issue.10 , pp. 2103-2116
    • Muller, F.1    Chang, B.2    Albert, S.3    Fischer, N.4    Tora, L.5    Strahle, U.6
  • 255
    • 22144473057 scopus 로고    scopus 로고
    • Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
    • 10.1186/1471-2164-5-99, 544600, 15613238
    • Sandelin A, Bailey P, Bruce S, Engstrom PG, Klos JM, Wasserman WW, Ericson J, Lenhard B. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 2004, 5(1):99. 10.1186/1471-2164-5-99, 544600, 15613238.
    • (2004) BMC Genomics , vol.5 , Issue.1 , pp. 99
    • Sandelin, A.1    Bailey, P.2    Bruce, S.3    Engstrom, P.G.4    Klos, J.M.5    Wasserman, W.W.6    Ericson, J.7    Lenhard, B.8
  • 256
    • 34748841064 scopus 로고    scopus 로고
    • Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers
    • 10.1371/journal.pone.0000366, 1838922, 17426814
    • Abbasi AA, Paparidis Z, Malik S, Goode DK, Callaway H, Elgar G, Grzeschik KH. Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers. PLoS One 2007, 2(4):e366. 10.1371/journal.pone.0000366, 1838922, 17426814.
    • (2007) PLoS One , vol.2 , Issue.4
    • Abbasi, A.A.1    Paparidis, Z.2    Malik, S.3    Goode, D.K.4    Callaway, H.5    Elgar, G.6    Grzeschik, K.H.7
  • 257
    • 80054787751 scopus 로고    scopus 로고
    • Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures
    • 10.1093/gbe/evr056, 3140891, 21680890
    • Irimia M, Maeso I, Burguera D, Hidalgo-Sanchez M, Puelles L, Roy SW, Garcia-Fernandez J, Ferran JL. Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures. Genome Biol Evol 2011, 3:551-564. 10.1093/gbe/evr056, 3140891, 21680890.
    • (2011) Genome Biol Evol , vol.3 , pp. 551-564
    • Irimia, M.1    Maeso, I.2    Burguera, D.3    Hidalgo-Sanchez, M.4    Puelles, L.5    Roy, S.W.6    Garcia-Fernandez, J.7    Ferran, J.L.8
  • 259
    • 33645519275 scopus 로고    scopus 로고
    • Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis
    • 10.1101/gr.4143406, 1457030, 16533910
    • McEwen GK, Woolfe A, Goode D, Vavouri T, Callaway H, Elgar G. Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis. Genome Res 2006, 16(4):451-465. 10.1101/gr.4143406, 1457030, 16533910.
    • (2006) Genome Res , vol.16 , Issue.4 , pp. 451-465
    • McEwen, G.K.1    Woolfe, A.2    Goode, D.3    Vavouri, T.4    Callaway, H.5    Elgar, G.6
  • 260
    • 34248153777 scopus 로고    scopus 로고
    • Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
    • 10.1101/gr.6086307, 1855176, 17387144
    • Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engstrom PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res 2007, 17(5):545-555. 10.1101/gr.6086307, 1855176, 17387144.
    • (2007) Genome Res , vol.17 , Issue.5 , pp. 545-555
    • Kikuta, H.1    Laplante, M.2    Navratilova, P.3    Komisarczuk, A.Z.4    Engstrom, P.G.5    Fredman, D.6    Akalin, A.7    Caccamo, M.8    Sealy, I.9    Howe, K.10
  • 261
    • 38849112675 scopus 로고    scopus 로고
    • Genomic regulatory blocks underlie extensive microsynteny conservation in insects
    • 10.1101/gr.6669607, 2099597, 17989259
    • Engstrom PG, Ho Sui SJ, Drivenes O, Becker TS, Lenhard B. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res 2007, 17(12):1898-1908. 10.1101/gr.6669607, 2099597, 17989259.
    • (2007) Genome Res , vol.17 , Issue.12 , pp. 1898-1908
    • Engstrom, P.G.1    Ho Sui, S.J.2    Drivenes, O.3    Becker, T.S.4    Lenhard, B.5
  • 262
    • 0027284266 scopus 로고
    • A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3
    • 10.1101/gad.7.7a.1176, 8319909
    • Tycowski KT, Shu MD, Steitz JA. A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3. Genes Dev 1993, 7(7A):1176-1190. 10.1101/gad.7.7a.1176, 8319909.
    • (1993) Genes Dev , vol.7 , Issue.7 A , pp. 1176-1190
    • Tycowski, K.T.1    Shu, M.D.2    Steitz, J.A.3
  • 263
    • 0030033546 scopus 로고    scopus 로고
    • A mammalian gene with introns instead of exons generating stable RNA products
    • 10.1038/379464a0, 8559254
    • Tycowski KT, Shu MD, Steitz JA. A mammalian gene with introns instead of exons generating stable RNA products. Nature 1996, 379(6564):464-466. 10.1038/379464a0, 8559254.
    • (1996) Nature , vol.379 , Issue.6564 , pp. 464-466
    • Tycowski, K.T.1    Shu, M.D.2    Steitz, J.A.3
  • 264
    • 51449085579 scopus 로고    scopus 로고
    • Origins and evolution of eukaryotic RNA interference
    • 10.1016/j.tree.2008.06.005, 2695246, 18715673
    • Shabalina SA, Koonin EV. Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol 2008, 23(10):578-587. 10.1016/j.tree.2008.06.005, 2695246, 18715673.
    • (2008) Trends Ecol Evol , vol.23 , Issue.10 , pp. 578-587
    • Shabalina, S.A.1    Koonin, E.V.2
  • 266
    • 35348933779 scopus 로고    scopus 로고
    • Mammalian mirtron genes
    • 10.1016/j.molcel.2007.09.028, 2763384, 17964270
    • Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC. Mammalian mirtron genes. Mol Cell 2007, 28(2):328-336. 10.1016/j.molcel.2007.09.028, 2763384, 17964270.
    • (2007) Mol Cell , vol.28 , Issue.2 , pp. 328-336
    • Berezikov, E.1    Chung, W.J.2    Willis, J.3    Cuppen, E.4    Lai, E.C.5
  • 267
    • 77951955175 scopus 로고    scopus 로고
    • Biased hosting of intronic microRNA genes
    • 10.1093/bioinformatics/btq077, 20185406
    • Golan D, Levy C, Friedman B, Shomron N. Biased hosting of intronic microRNA genes. Bioinformatics 2010, 26(8):992-995. 10.1093/bioinformatics/btq077, 20185406.
    • (2010) Bioinformatics , vol.26 , Issue.8 , pp. 992-995
    • Golan, D.1    Levy, C.2    Friedman, B.3    Shomron, N.4
  • 268
    • 80053574171 scopus 로고    scopus 로고
    • Mirtrons: microRNA biogenesis via splicing
    • 10.1016/j.biochi.2011.06.017, 3185189, 21712066
    • Westholm JO, Lai EC. Mirtrons: microRNA biogenesis via splicing. Biochimie 2011, 93(11):1897-1904. 10.1016/j.biochi.2011.06.017, 3185189, 21712066.
    • (2011) Biochimie , vol.93 , Issue.11 , pp. 1897-1904
    • Westholm, J.O.1    Lai, E.C.2
  • 269
    • 58849112575 scopus 로고    scopus 로고
    • Biogenesis of small RNAs in animals
    • 10.1038/nrm2632, 19165215
    • Kim VN, Han J, Siomi MC. Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 2009, 10(2):126-139. 10.1038/nrm2632, 19165215.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , Issue.2 , pp. 126-139
    • Kim, V.N.1    Han, J.2    Siomi, M.C.3
  • 270
    • 69949115558 scopus 로고    scopus 로고
    • An overview of nested genes in eukaryotic genomes
    • 10.1128/EC.00143-09, 2747821, 19542305
    • Kumar A. An overview of nested genes in eukaryotic genomes. Eukaryot Cell 2009, 8(9):1321-1329. 10.1128/EC.00143-09, 2747821, 19542305.
    • (2009) Eukaryot Cell , vol.8 , Issue.9 , pp. 1321-1329
    • Kumar, A.1
  • 271
    • 52949102538 scopus 로고    scopus 로고
    • Nested genes and increasing organizational complexity of metazoan genomes
    • 10.1016/j.tig.2008.08.003, 3380635, 18774620
    • Assis R, Kondrashov AS, Koonin EV, Kondrashov FA. Nested genes and increasing organizational complexity of metazoan genomes. Trends Genet 2008, 24(10):475-478. 10.1016/j.tig.2008.08.003, 3380635, 18774620.
    • (2008) Trends Genet , vol.24 , Issue.10 , pp. 475-478
    • Assis, R.1    Kondrashov, A.S.2    Koonin, E.V.3    Kondrashov, F.A.4
  • 272
    • 0037062440 scopus 로고    scopus 로고
    • Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection
    • 10.1073/pnas.122570299, 123031, 12060758
    • Llopart A, Comeron JM, Brunet FG, Lachaise D, Long M. Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proc Natl Acad Sci U S A 2002, 99(12):8121-8126. 10.1073/pnas.122570299, 123031, 12060758.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , Issue.12 , pp. 8121-8126
    • Llopart, A.1    Comeron, J.M.2    Brunet, F.G.3    Lachaise, D.4    Long, M.5
  • 274
    • 73949123826 scopus 로고    scopus 로고
    • Ubiquitous internal gene duplication and intron creation in eukaryotes
    • 10.1073/pnas.0911093106, 2791625, 19926850
    • Gao X, Lynch M. Ubiquitous internal gene duplication and intron creation in eukaryotes. Proc Natl Acad Sci U S A 2009, 106(49):20818-20823. 10.1073/pnas.0911093106, 2791625, 19926850.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , Issue.49 , pp. 20818-20823
    • Gao, X.1    Lynch, M.2
  • 275
    • 76749130220 scopus 로고    scopus 로고
    • Nonsense-mediated decay enables intron gain in Drosophila
    • 10.1371/journal.pgen.1000819, 2809761, 20107520
    • Farlow A, Meduri E, Dolezal M, Hua L, Schlotterer C. Nonsense-mediated decay enables intron gain in Drosophila. PLoS Genet 2010, 6(1):e1000819. 10.1371/journal.pgen.1000819, 2809761, 20107520.
    • (2010) PLoS Genet , vol.6 , Issue.1
    • Farlow, A.1    Meduri, E.2    Dolezal, M.3    Hua, L.4    Schlotterer, C.5
  • 276
    • 78149334830 scopus 로고    scopus 로고
    • A spliceosomal intron of mitochondrial DNA origin
    • 10.1016/j.cub.2010.09.038, 21056829
    • Curtis BA, Archibald JM. A spliceosomal intron of mitochondrial DNA origin. Curr Biol 2010, 20(21):R919-R920. 10.1016/j.cub.2010.09.038, 21056829.
    • (2010) Curr Biol , vol.20 , Issue.21
    • Curtis, B.A.1    Archibald, J.M.2
  • 277
    • 64849088316 scopus 로고    scopus 로고
    • Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas
    • 10.1126/science.1167222, 19359590
    • Worden AZ, Lee JH, Mock T, Rouze P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, et al. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 2009, 324(5924):268-272. 10.1126/science.1167222, 19359590.
    • (2009) Science , vol.324 , Issue.5924 , pp. 268-272
    • Worden, A.Z.1    Lee, J.H.2    Mock, T.3    Rouze, P.4    Simmons, M.P.5    Aerts, A.L.6    Allen, A.E.7    Cuvelier, M.L.8    Derelle, E.9    Everett, M.V.10
  • 278
    • 0036213311 scopus 로고    scopus 로고
    • The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolution
    • 10.1093/oxfordjournals.molbev.a004097, 11919283
    • Archibald JM, O'Kelly CJ, Doolittle WF. The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolution. Mol Biol Evol 2002, 19(4):422-431. 10.1093/oxfordjournals.molbev.a004097, 11919283.
    • (2002) Mol Biol Evol , vol.19 , Issue.4 , pp. 422-431
    • Archibald, J.M.1    O'Kelly, C.J.2    Doolittle, W.F.3
  • 279
    • 15444370758 scopus 로고    scopus 로고
    • Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis
    • 10.1073/pnas.0407500102, 554003, 15764705
    • Vanacova S, Yan W, Carlton JM, Johnson PJ. Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis. Proc Natl Acad Sci U S A 2005, 102(12):4430-4435. 10.1073/pnas.0407500102, 554003, 15764705.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.12 , pp. 4430-4435
    • Vanacova, S.1    Yan, W.2    Carlton, J.M.3    Johnson, P.J.4
  • 280
    • 33644783626 scopus 로고    scopus 로고
    • Introns and the origin of nucleus-cytosol compartmentalization
    • 10.1038/nature04531, 16511485
    • Martin W, Koonin EV. Introns and the origin of nucleus-cytosol compartmentalization. Nature 2006, 440(7080):41-45. 10.1038/nature04531, 16511485.
    • (2006) Nature , vol.440 , Issue.7080 , pp. 41-45
    • Martin, W.1    Koonin, E.V.2
  • 281
    • 33646360208 scopus 로고    scopus 로고
    • Selective forces for the origin of the eukaryotic nucleus
    • 10.1002/bies.20413, 16615090
    • Lopez-Garcia P, Moreira D. Selective forces for the origin of the eukaryotic nucleus. Bioessays 2006, 28(5):525-533. 10.1002/bies.20413, 16615090.
    • (2006) Bioessays , vol.28 , Issue.5 , pp. 525-533
    • Lopez-Garcia, P.1    Moreira, D.2
  • 283
    • 75649116868 scopus 로고    scopus 로고
    • A structural analysis of the group II intron active site and implications for the spliceosome
    • 10.1261/rna.1791310, 2802019, 19948765
    • Keating KS, Toor N, Perlman PS, Pyle AM. A structural analysis of the group II intron active site and implications for the spliceosome. RNA 2010, 16(1):1-9. 10.1261/rna.1791310, 2802019, 19948765.
    • (2010) RNA , vol.16 , Issue.1 , pp. 1-9
    • Keating, K.S.1    Toor, N.2    Perlman, P.S.3    Pyle, A.M.4
  • 284
    • 70450225451 scopus 로고    scopus 로고
    • A broadscale phylogenetic analysis of group II intron RNAs and intron-encoded reverse transcriptases
    • 10.1093/molbev/msp193, 19713327
    • Simon DM, Kelchner SA, Zimmerly S. A broadscale phylogenetic analysis of group II intron RNAs and intron-encoded reverse transcriptases. Mol Biol Evol 2009, 26(12):2795-2808. 10.1093/molbev/msp193, 19713327.
    • (2009) Mol Biol Evol , vol.26 , Issue.12 , pp. 2795-2808
    • Simon, D.M.1    Kelchner, S.A.2    Zimmerly, S.3
  • 285
    • 3242708809 scopus 로고    scopus 로고
    • Of statistics and genomes
    • 10.1016/j.tig.2004.06.002, 15262405
    • Tautz D, Lassig M. Of statistics and genomes. Trends Genet 2004, 20(8):344-346. 10.1016/j.tig.2004.06.002, 15262405.
    • (2004) Trends Genet , vol.20 , Issue.8 , pp. 344-346
    • Tautz, D.1    Lassig, M.2
  • 286
    • 69249211050 scopus 로고    scopus 로고
    • Intron-dominated genomes of early ancestors of eukaryotes
    • 10.1093/jhered/esp056, 2877545, 19617525
    • Koonin EV. Intron-dominated genomes of early ancestors of eukaryotes. J Hered 2009, 100(5):618-623. 10.1093/jhered/esp056, 2877545, 19617525.
    • (2009) J Hered , vol.100 , Issue.5 , pp. 618-623
    • Koonin, E.V.1
  • 287
    • 33947593126 scopus 로고    scopus 로고
    • The ancient Virus World and evolution of cells
    • 10.1186/1745-6150-1-29, 1594570, 16984643
    • Koonin EV, Senkevich TG, Dolja VV. The ancient Virus World and evolution of cells. Biol Direct 2006, 1:29. 10.1186/1745-6150-1-29, 1594570, 16984643.
    • (2006) Biol Direct , vol.1 , pp. 29
    • Koonin, E.V.1    Senkevich, T.G.2    Dolja, V.V.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.