메뉴 건너뛰기




Volumn 136, Issue 9, 2017, Pages 1059-1078

Estimating the prevalence of functional exonic splice regulatory information

Author keywords

[No Author keywords available]

Indexed keywords

CONSERVATION GENETICS; EXON; FUNCTIONAL GENOMICS; GENETIC CONSERVATION; GENETIC REGULATION; HUMAN; INTRON; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA SPLICING; ANIMAL; MOLECULAR EVOLUTION; PHYSIOLOGY; RNA SPLICE SITE;

EID: 85017454441     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-017-1798-3     Document Type: Review
Times cited : (21)

References (188)
  • 1
    • 84964575593 scopus 로고    scopus 로고
    • Disentangling sources of selection on exonic transcriptional enhancers
    • COI: 1:CAS:528:DC%2BC28XhtlantL7M, PID: 26500252
    • Agoglia RM, Fraser HB (2016) Disentangling sources of selection on exonic transcriptional enhancers. Mol Biol Evol 33:585–590
    • (2016) Mol Biol Evol , vol.33 , pp. 585-590
    • Agoglia, R.M.1    Fraser, H.B.2
  • 2
    • 64849109747 scopus 로고    scopus 로고
    • A computational approach for genome-wide mapping of splicing factor binding sites
    • PID: 19296853
    • Akerman M, David-Eden H, Pinter RY, Mandel-Gutfreund Y (2009) A computational approach for genome-wide mapping of splicing factor binding sites. Genome Biol 10:R30
    • (2009) Genome Biol , vol.10 , pp. R30
    • Akerman, M.1    David-Eden, H.2    Pinter, R.Y.3    Mandel-Gutfreund, Y.4
  • 3
    • 34247360831 scopus 로고    scopus 로고
    • Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes
    • COI: 1:CAS:528:DC%2BD2sXltVakur8%3D, PID: 17369312
    • Alekseyenko AV, Kim N, Lee CJ (2007) Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. RNA 13:661–670
    • (2007) RNA , vol.13 , pp. 661-670
    • Alekseyenko, A.V.1    Kim, N.2    Lee, C.J.3
  • 4
    • 84861694712 scopus 로고    scopus 로고
    • Differential GC content between exons and introns establishes distinct strategies of splice-site recognition
    • COI: 1:CAS:528:DC%2BC38XotlWlu7g%3D, PID: 22832277
    • Amit M et al (2012) Differential GC content between exons and introns establishes distinct strategies of splice-site recognition. Cell Rep 1:543–556
    • (2012) Cell Rep , vol.1 , pp. 543-556
    • Amit, M.1
  • 5
    • 0001553024 scopus 로고
    • Function without purpose: the uses of causal role function in evolutionary biology
    • Amundson R, Lauder GV (1994) Function without purpose: the uses of causal role function in evolutionary biology. Biol Philos 9:443–469
    • (1994) Biol Philos , vol.9 , pp. 443-469
    • Amundson, R.1    Lauder, G.V.2
  • 6
    • 70349333201 scopus 로고    scopus 로고
    • Nucleosomes are well positioned in exons and carry characteristic histone modifications
    • COI: 1:CAS:528:DC%2BD1MXht1GjtbzL, PID: 19687145
    • Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J (2009) Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res 19:1732–1741
    • (2009) Genome Res , vol.19 , pp. 1732-1741
    • Andersson, R.1    Enroth, S.2    Rada-Iglesias, A.3    Wadelius, C.4    Komorowski, J.5
  • 7
    • 84904469265 scopus 로고    scopus 로고
    • Regulation of gene expression programmes by serine-arginine rich splicing factors
    • PID: 24657192
    • Änkö ML (2014) Regulation of gene expression programmes by serine-arginine rich splicing factors. Semin Cell Dev Biol 32:11–21
    • (2014) Semin Cell Dev Biol , vol.32 , pp. 11-21
    • Änkö, M.L.1
  • 8
    • 0038744296 scopus 로고    scopus 로고
    • Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case Series unselected for family history: a combined analysis of 22 studies
    • COI: 1:CAS:528:DC%2BD3sXjslagtbg%3D, PID: 12677558
    • Antoniou A et al (2003) Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case Series unselected for family history: a combined analysis of 22 studies. Am J Hum Genet 72:1117–1130
    • (2003) Am J Hum Genet , vol.72 , pp. 1117-1130
    • Antoniou, A.1
  • 9
    • 84879684637 scopus 로고    scopus 로고
    • Genome-wide inference of natural selection on human transcription factor binding sites
    • COI: 1:CAS:528:DC%2BC3sXptVagt7o%3D, PID: 23749186
    • Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A (2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet 45:723–729
    • (2013) Nat Genet , vol.45 , pp. 723-729
    • Arbiza, L.1    Gronau, I.2    Aksoy, B.A.3    Hubisz, M.J.4    Gulko, B.5    Keinan, A.6    Siepel, A.7
  • 10
    • 32244436130 scopus 로고    scopus 로고
    • Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p
    • COI: 1:CAS:528:DC%2BD28XhtFajtrw%3D, PID: 16429151
    • Aviv T, Lin Z, Ben-Ari G, Smibert CA, Sicheri F (2006) Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat Struct Mol Biol 13:168–176
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 168-176
    • Aviv, T.1    Lin, Z.2    Ben-Ari, G.3    Smibert, C.A.4    Sicheri, F.5
  • 11
    • 17344363640 scopus 로고    scopus 로고
    • A gene related to Caenorhabditis elegans spermatogenesis factor fer-1 is mutated in limb-girdle muscular dystrophy type 2B
    • COI: 1:CAS:528:DyaK1cXmtVOmt7Y%3D, PID: 9731527
    • Bashir R et al (1998) A gene related to Caenorhabditis elegans spermatogenesis factor fer-1 is mutated in limb-girdle muscular dystrophy type 2B. Nat Genet 20:37–42
    • (1998) Nat Genet , vol.20 , pp. 37-42
    • Bashir, R.1
  • 12
    • 84908332907 scopus 로고    scopus 로고
    • Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation
    • PID: 25340400
    • Birnbaum RY et al (2014) Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. PLoS Genet 10:e1004592
    • (2014) PLoS Genet , vol.10
    • Birnbaum, R.Y.1
  • 13
    • 0038101450 scopus 로고    scopus 로고
    • Haemophilias A and B
    • COI: 1:CAS:528:DC%2BD3sXktVOns7Y%3D, PID: 12781551
    • Bolton-Maggs PHB, Pasi KJ (2003) Haemophilias A and B. Lancet 361:1801–1809
    • (2003) Lancet , vol.361 , pp. 1801-1809
    • Bolton-Maggs, P.H.B.1    Pasi, K.J.2
  • 14
    • 79958071334 scopus 로고    scopus 로고
    • Cancer risks associated with germline mutations in MLH1, MSH2, and MSH6 genes in Lynch syndrome
    • COI: 1:CAS:528:DC%2BC3MXntlyksLk%3D, PID: 21642682
    • Bonadona V et al (2011) Cancer risks associated with germline mutations in MLH1, MSH2, and MSH6 genes in Lynch syndrome. JAMA 305:2304–2310
    • (2011) JAMA , vol.305 , pp. 2304-2310
    • Bonadona, V.1
  • 15
    • 47149083097 scopus 로고    scopus 로고
    • Screening BRCA1 and BRCA2 unclassified variants for splicing mutations using reverse transcription PCR on patient RNA and an ex vivo assay based on a splicing reporter minigene
    • COI: 1:CAS:528:DC%2BD1cXpsFOqtbc%3D, PID: 18424508
    • Bonnet C et al (2008) Screening BRCA1 and BRCA2 unclassified variants for splicing mutations using reverse transcription PCR on patient RNA and an ex vivo assay based on a splicing reporter minigene. J Med Genet 45:438–446
    • (2008) J Med Genet , vol.45 , pp. 438-446
    • Bonnet, C.1
  • 16
    • 44949129000 scopus 로고    scopus 로고
    • Assessing the evolutionary impact of amino acid mutations in the human genome
    • PID: 18516229
    • Boyko AR et al (2008) Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet 4:e1000083
    • (2008) PLoS Genet , vol.4
    • Boyko, A.R.1
  • 17
    • 84967225586 scopus 로고    scopus 로고
    • The Meaning of NMD: translate or Perish
    • COI: 1:CAS:528:DC%2BC28XnslansL4%3D, PID: 27185236
    • Brogna S, McLeod T, Petric M (2016) The Meaning of NMD: translate or Perish. Trends Genet 32:395–407
    • (2016) Trends Genet , vol.32 , pp. 395-407
    • Brogna, S.1    McLeod, T.2    Petric, M.3
  • 19
    • 84890527710 scopus 로고    scopus 로고
    • The evolution, impact and properties of exonic splice enhancers
    • Cáceres EF, Hurst LD (2013) The evolution, impact and properties of exonic splice enhancers. Genome Biol 14:1–18
    • (2013) Genome Biol , vol.14 , pp. 1-18
    • Cáceres, E.F.1    Hurst, L.D.2
  • 20
    • 84991281534 scopus 로고    scopus 로고
    • Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation
    • COI: 1:CAS:528:DC%2BC28XhvFClsrzM, PID: 27492286
    • Cakiroglu SA, Zaugg JB, Luscombe NM (2016) Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation. Nucleic Acids Res 44:8065–8072
    • (2016) Nucleic Acids Res , vol.44 , pp. 8065-8072
    • Cakiroglu, S.A.1    Zaugg, J.B.2    Luscombe, N.M.3
  • 21
    • 31844449496 scopus 로고    scopus 로고
    • Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers
    • COI: 1:CAS:528:DC%2BD28XhtFWms70%3D, PID: 16320116
    • Carlini DB, Genut JE (2006) Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers. J Mol Evol 62:89–98
    • (2006) J Mol Evol , vol.62 , pp. 89-98
    • Carlini, D.B.1    Genut, J.E.2
  • 22
    • 60349093708 scopus 로고    scopus 로고
    • Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation
    • COI: 1:CAS:528:DC%2BD1MXhvFGlu7s%3D, PID: 19204717
    • Charlesworth B (2009) Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat Rev Genet 10:195–205
    • (2009) Nat Rev Genet , vol.10 , pp. 195-205
    • Charlesworth, B.1
  • 23
    • 0025242929 scopus 로고
    • Defective intracellular transport and processing of CFTR is the molecular basis of most cystic fibrosis
    • COI: 1:CAS:528:DyaK3MXnvFKguw%3D%3D, PID: 1699669
    • Cheng SH et al (1990) Defective intracellular transport and processing of CFTR is the molecular basis of most cystic fibrosis. Cell 63:827–834
    • (1990) Cell , vol.63 , pp. 827-834
    • Cheng, S.H.1
  • 24
    • 0028274042 scopus 로고
    • Protection from Fas-mediated apoptosis by a soluble form of the Fas molecule
    • COI: 1:CAS:528:DyaK2cXktVentL8%3D, PID: 7510905
    • Cheng J et al (1994) Protection from Fas-mediated apoptosis by a soluble form of the Fas molecule. Science 263:1759–1762
    • (1994) Science , vol.263 , pp. 1759-1762
    • Cheng, J.1
  • 25
    • 77954659099 scopus 로고    scopus 로고
    • Relationship between nucleosome positioning and DNA methylation
    • COI: 1:CAS:528:DC%2BC3cXmslWmu78%3D, PID: 20512117
    • Chodavarapu RK et al (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466:388–392
    • (2010) Nature , vol.466 , pp. 388-392
    • Chodavarapu, R.K.1
  • 26
    • 56749117987 scopus 로고    scopus 로고
    • Mid-frequency DFNA8/12 hearing loss caused by a synonymous TECTA mutation that affects an exonic splice enhancer
    • COI: 1:CAS:528:DC%2BD1cXhsVSjs7jK, PID: 18575463
    • Collin RW et al (2008) Mid-frequency DFNA8/12 hearing loss caused by a synonymous TECTA mutation that affects an exonic splice enhancer. Eur J Hum Genet 16:1430–1436
    • (2008) Eur J Hum Genet , vol.16 , pp. 1430-1436
    • Collin, R.W.1
  • 27
    • 84922454174 scopus 로고    scopus 로고
    • High-throughput characterization of protein-RNA interactions
    • Cook KB, Hughes TR, Morris QD (2015) High-throughput characterization of protein-RNA interactions. Brief Funct Genom 14:74–89
    • (2015) Brief Funct Genom , vol.14 , pp. 74-89
    • Cook, K.B.1    Hughes, T.R.2    Morris, Q.D.3
  • 28
    • 27944439248 scopus 로고    scopus 로고
    • Use of minigene systems to dissect alternative splicing elements
    • COI: 1:CAS:528:DC%2BD2MXht1OnurrN, PID: 16314262
    • Cooper TA (2005) Use of minigene systems to dissect alternative splicing elements. Methods 37:331–340
    • (2005) Methods , vol.37 , pp. 331-340
    • Cooper, T.A.1
  • 29
    • 0000798871 scopus 로고
    • Functional Analysis
    • Cummins R (1975) Functional Analysis. J Philos 72:741–765
    • (1975) J Philos , vol.72 , pp. 741-765
    • Cummins, R.1
  • 30
    • 84904462273 scopus 로고    scopus 로고
    • Reciprocal regulatory links between cotranscriptional splicing and chromatin
    • PID: 24657193
    • de Almeida SF, Carmo-Fonseca M (2014) Reciprocal regulatory links between cotranscriptional splicing and chromatin. Semin Cell Dev Biol 32:2–10
    • (2014) Semin Cell Dev Biol , vol.32 , pp. 2-10
    • de Almeida, S.F.1    Carmo-Fonseca, M.2
  • 31
    • 33845895301 scopus 로고    scopus 로고
    • Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns
    • Dewey CN, Rogozin IB, Koonin EV (2006) Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns. BMC Genom 7:311
    • (2006) BMC Genom , vol.7 , pp. 311
    • Dewey, C.N.1    Rogozin, I.B.2    Koonin, E.V.3
  • 32
    • 84885434679 scopus 로고    scopus 로고
    • Functional analysis of a large set of BRCA2 exon 7 variants highlights the predictive value of hexamer scores in detecting alterations of exonic splicing regulatory elements
    • PID: 23983145
    • Di Giacomo D, Gaildrat P, Abuli A, Abdat J, Frebourg T, Tosi M, Martins A (2013) Functional analysis of a large set of BRCA2 exon 7 variants highlights the predictive value of hexamer scores in detecting alterations of exonic splicing regulatory elements. Hum Mutat 34:1547–1557
    • (2013) Hum Mutat , vol.34 , pp. 1547-1557
    • Di Giacomo, D.1    Gaildrat, P.2    Abuli, A.3    Abdat, J.4    Frebourg, T.5    Tosi, M.6    Martins, A.7
  • 33
    • 84875847924 scopus 로고    scopus 로고
    • Is junk DNA bunk? A critique of ENCODE
    • COI: 1:CAS:528:DC%2BC3sXntVehtLg%3D, PID: 23479647
    • Doolittle WF (2013) Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA 110:5294–5300
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 5294-5300
    • Doolittle, W.F.1
  • 34
    • 0027433563 scopus 로고
    • Genetic linkage analysis in familial breast and ovarian cancer: results from 214 families
    • COI: 1:CAS:528:DyaK2cXhtVemurs%3D, PID: 8460634
    • Easton DF, Bishop DT, Ford D, Crockford GP, The Breast Cancer Linkage Consortium (1993) Genetic linkage analysis in familial breast and ovarian cancer: results from 214 families. Am J Hum Genet 52:678–701
    • (1993) Am J Hum Genet , vol.52 , pp. 678-701
    • Easton, D.F.1    Bishop, D.T.2    Ford, D.3    Crockford, G.P.4
  • 35
    • 84868550433 scopus 로고    scopus 로고
    • The C-value paradox, junk DNA and ENCODE
    • COI: 1:CAS:528:DC%2BC38Xhs1aqtrnK, PID: 23137679
    • Eddy SR (2012) The C-value paradox, junk DNA and ENCODE. Curr Biol 22:R898–R899
    • (2012) Curr Biol , vol.22 , pp. R898-R899
    • Eddy, S.R.1
  • 36
    • 84876031068 scopus 로고    scopus 로고
    • The ENCODE project: missteps overshadowing a success
    • COI: 1:CAS:528:DC%2BC3sXlsFChu7Y%3D, PID: 23578867
    • Eddy SR (2013) The ENCODE project: missteps overshadowing a success. Curr Biol 23:R259–R261
    • (2013) Curr Biol , vol.23 , pp. R259-R261
    • Eddy, S.R.1
  • 37
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74
    • (2012) Nature , vol.489 , pp. 57-74
  • 38
    • 72649102150 scopus 로고    scopus 로고
    • Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes
    • COI: 1:CAS:528:DC%2BD1MXhsFykt7%2FN, PID: 19759235
    • Eory L, Halligan DL, Keightley PD (2010) Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Mol Biol Evol 27:177–192
    • (2010) Mol Biol Evol , vol.27 , pp. 177-192
    • Eory, L.1    Halligan, D.L.2    Keightley, P.D.3
  • 39
    • 34447546660 scopus 로고    scopus 로고
    • The distribution of fitness effects of new mutations
    • COI: 1:CAS:528:DC%2BD2sXnvVekt7s%3D, PID: 17637733
    • Eyre-Walker A, Keightley PD (2007) The distribution of fitness effects of new mutations. Nat Rev Genet 8:610–618
    • (2007) Nat Rev Genet , vol.8 , pp. 610-618
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 40
    • 33745347447 scopus 로고    scopus 로고
    • The distribution of fitness effects of new deleterious amino acid mutations in humans
    • COI: 1:CAS:528:DC%2BD28Xns12qs7Y%3D, PID: 16547091
    • Eyre-Walker A, Woolfit M, Phelps T (2006) The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics 173:891–900
    • (2006) Genetics , vol.173 , pp. 891-900
    • Eyre-Walker, A.1    Woolfit, M.2    Phelps, T.3
  • 41
    • 0037047644 scopus 로고    scopus 로고
    • Predictive identification of exonic splicing enhancers in human genes
    • COI: 1:CAS:528:DC%2BD38Xmt1Ckt74%3D, PID: 12114529
    • Fairbrother WG, Yeh R-F, Sharp PA, Burge CB (2002) Predictive identification of exonic splicing enhancers in human genes. Science 297:1007–1013
    • (2002) Science , vol.297 , pp. 1007-1013
    • Fairbrother, W.G.1    Yeh, R.-F.2    Sharp, P.A.3    Burge, C.B.4
  • 42
    • 19344367734 scopus 로고    scopus 로고
    • Single nucleotide polymorphism-based validation of exonic splicing enhancers
    • PID: 15340491
    • Fairbrother WG, Holste D, Burge CB, Sharp PA (2004) Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol 2:E268
    • (2004) PLoS Biol , vol.2 , pp. E268
    • Fairbrother, W.G.1    Holste, D.2    Burge, C.B.3    Sharp, P.A.4
  • 43
    • 79952907985 scopus 로고    scopus 로고
    • The impact of miRNA target sites in coding sequences and in 3′UTRs
    • COI: 1:CAS:528:DC%2BC3MXktlChtbg%3D, PID: 21445367
    • Fang Z, Rajewski N (2011) The impact of miRNA target sites in coding sequences and in 3′UTRs. PloS One 6:e18067
    • (2011) PloS One , vol.6
    • Fang, Z.1    Rajewski, N.2
  • 44
    • 0027742295 scopus 로고
    • The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer
    • COI: 1:CAS:528:DyaK2cXktVaitr8%3D, PID: 8252616
    • Fishel R et al (1993) The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer. Cell 75:1027–1038
    • (1993) Cell , vol.75 , pp. 1027-1038
    • Fishel, R.1
  • 45
    • 0029025441 scopus 로고
    • Dominant interfering Fas gene mutations impair apoptosis in a human autoimmune lymphoproliferative syndrome
    • COI: 1:CAS:528:DyaK2MXmsVagt7w%3D, PID: 7540117
    • Fisher GH et al (1995) Dominant interfering Fas gene mutations impair apoptosis in a human autoimmune lymphoproliferative syndrome. Cell 81:935–946
    • (1995) Cell , vol.81 , pp. 935-946
    • Fisher, G.H.1
  • 46
    • 84914173890 scopus 로고    scopus 로고
    • Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate
    • PID: 25452276
    • Fong N et al (2014) Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev 28:2663–2676
    • (2014) Genes Dev , vol.28 , pp. 2663-2676
    • Fong, N.1
  • 47
    • 54449097149 scopus 로고    scopus 로고
    • A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence
    • COI: 1:CAS:528:DC%2BD1cXht1aqur7J, PID: 18812516
    • Forman JJ, Legesse-Miller A, Coller HA (2008) A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci USA 105:14879–14884
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 14879-14884
    • Forman, J.J.1    Legesse-Miller, A.2    Coller, H.A.3
  • 48
    • 28044455878 scopus 로고    scopus 로고
    • The architecture of pre-mRNAs affects mechanisms of splice-site pairing
    • COI: 1:CAS:528:DC%2BD2MXht1CgurzO, PID: 16260721
    • Fox-Walsh KL, Dou Y, Lam BJ, Hung SP, Baldi PF, Hertel KJ (2005) The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci USA 102:16176–16181
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 16176-16181
    • Fox-Walsh, K.L.1    Dou, Y.2    Lam, B.J.3    Hung, S.P.4    Baldi, P.F.5    Hertel, K.J.6
  • 49
    • 84922255144 scopus 로고    scopus 로고
    • Context-dependent control of alternative splicing by RNA-binding proteins
    • COI: 1:CAS:528:DC%2BC2cXhtlarurfK, PID: 25112293
    • Fu XD, Ares M Jr (2014) Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet 15:689–701
    • (2014) Nat Rev Genet , vol.15 , pp. 689-701
    • Fu, X.D.1    Ares, M.2
  • 50
    • 0028062781 scopus 로고
    • Cystic fibrosis heterozygote resistance to cholera toxin in the cystic fibrosis mouse model
    • COI: 1:CAS:528:DyaK2cXmsFejsbo%3D, PID: 7524148
    • Gabriel SE, Brigman KN, Koller BH, Boucher RC, Stutts MJ (1994) Cystic fibrosis heterozygote resistance to cholera toxin in the cystic fibrosis mouse model. Science 266:107–109
    • (1994) Science , vol.266 , pp. 107-109
    • Gabriel, S.E.1    Brigman, K.N.2    Koller, B.H.3    Boucher, R.C.4    Stutts, M.J.5
  • 51
    • 77953690065 scopus 로고    scopus 로고
    • Use of splicing reporter minigene assay to evaluate the effect on splicing of unclassified genetic variants
    • COI: 1:CAS:528:DC%2BC3cXht1KmtLrP, PID: 20721748
    • Gaildrat P, Killian A, Martins A, Tournier I, Frébourg T, Tosi M (2010) Use of splicing reporter minigene assay to evaluate the effect on splicing of unclassified genetic variants. Methods Mol Biol 653:249–257
    • (2010) Methods Mol Biol , vol.653 , pp. 249-257
    • Gaildrat, P.1    Killian, A.2    Martins, A.3    Tournier, I.4    Frébourg, T.5    Tosi, M.6
  • 52
    • 84870293904 scopus 로고    scopus 로고
    • Multiple sequence variants of BRCA2 exon 7 alter splicing regulation
    • COI: 1:CAS:528:DC%2BC38XhvVWhur%2FP, PID: 22962691
    • Gaildrat P et al (2012) Multiple sequence variants of BRCA2 exon 7 alter splicing regulation. J Med Genet 49:609–617
    • (2012) J Med Genet , vol.49 , pp. 609-617
    • Gaildrat, P.1
  • 53
    • 79957992453 scopus 로고    scopus 로고
    • Selected effects and causal role functions in the brain: the case for an etiological approach to neuroscience
    • Garson J (2011) Selected effects and causal role functions in the brain: the case for an etiological approach to neuroscience. Biol Philos 26:547–565
    • (2011) Biol Philos , vol.26 , pp. 547-565
    • Garson, J.1
  • 54
    • 84911006514 scopus 로고    scopus 로고
    • Junk or functional DNA? ENCODE and the function controversy
    • Germain P-L, Ratti E, Boem F (2014) Junk or functional DNA? ENCODE and the function controversy. Biol Philos 29:807–831
    • (2014) Biol Philos , vol.29 , pp. 807-831
    • Germain, P.-L.1    Ratti, E.2    Boem, F.3
  • 55
    • 0000103250 scopus 로고
    • A modern history theory of functions
    • Godfrey-Smith P (1994) A modern history theory of functions. Noûs 28:344–362
    • (1994) Noûs , vol.28 , pp. 344-362
    • Godfrey-Smith, P.1
  • 57
    • 84875275808 scopus 로고    scopus 로고
    • On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE
    • PID: 23431001
    • Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E (2013) On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 5:578–590
    • (2013) Genome Biol Evol , vol.5 , pp. 578-590
    • Graur, D.1    Zheng, Y.2    Price, N.3    Azevedo, R.B.4    Zufall, R.A.5    Elhaik, E.6
  • 58
    • 84940107361 scopus 로고    scopus 로고
    • An evolutionary classification of genomic function
    • COI: 1:CAS:528:DC%2BC2MXlvFKjtbg%3D, PID: 25635041
    • Graur D, Zheng Y, Azevedo RB (2015) An evolutionary classification of genomic function. Genome Biol Evol 7:642–645
    • (2015) Genome Biol Evol , vol.7 , pp. 642-645
    • Graur, D.1    Zheng, Y.2    Azevedo, R.B.3
  • 59
    • 0032538791 scopus 로고    scopus 로고
    • A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers
    • COI: 1:CAS:528:DyaK1cXnvF2jtL0%3D, PID: 9822617
    • Graveley BR, Hertel KJ, Maniatis T (1998) A systematic analysis of the factors that determine the strength of pre-mRNA splicing enhancers. EMBO J 17:6747–6756
    • (1998) EMBO J , vol.17 , pp. 6747-6756
    • Graveley, B.R.1    Hertel, K.J.2    Maniatis, T.3
  • 60
    • 84876561639 scopus 로고    scopus 로고
    • Inference of natural selection from interspersed genomic elements based on polymorphism and divergence
    • COI: 1:CAS:528:DC%2BC3sXlvFWgs7w%3D, PID: 23386628
    • Gronau I, Arbiza L, Mohammed J, Siepel A (2013) Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. Mol Biol Evol 30:1159–1171
    • (2013) Mol Biol Evol , vol.30 , pp. 1159-1171
    • Gronau, I.1    Arbiza, L.2    Mohammed, J.3    Siepel, A.4
  • 61
    • 84875992976 scopus 로고    scopus 로고
    • Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation
    • COI: 1:CAS:528:DC%2BC3sXlslGlsrs%3D, PID: 23335364
    • Hausser J, Syed AP, Bilen B, Zavolan M (2013) Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome Res 23:604–615
    • (2013) Genome Res , vol.23 , pp. 604-615
    • Hausser, J.1    Syed, A.P.2    Bilen, B.3    Zavolan, M.4
  • 62
    • 37349056702 scopus 로고    scopus 로고
    • Pre-mRNA secondary structures influence exon recognition
    • Hiller M, Zhang Z, Backofen R, Stamm S (2007) Pre-mRNA secondary structures influence exon recognition. PLoS Genet 3:2148–2155
    • (2007) PLoS Genet , vol.3 , pp. 2148-2155
    • Hiller, M.1    Zhang, Z.2    Backofen, R.3    Stamm, S.4
  • 63
    • 84991112173 scopus 로고    scopus 로고
    • How are short exons flanked by long introns defined and committed to splicing?
    • COI: 1:CAS:528:DC%2BC28Xht1KlsrfO, PID: 27507607
    • Hollander D, Naftelberg S, Lev-Maor G, Kornblihtt AR, Ast G (2016) How are short exons flanked by long introns defined and committed to splicing? Trends Genet 32:596–606
    • (2016) Trends Genet , vol.32 , pp. 596-606
    • Hollander, D.1    Naftelberg, S.2    Lev-Maor, G.3    Kornblihtt, A.R.4    Ast, G.5
  • 64
    • 84916640509 scopus 로고    scopus 로고
    • The RNAissance family: SR proteins as multifaceted regulators of gene expression
    • COI: 1:CAS:528:DC%2BC2cXitFSnsLbO, PID: 25155147
    • Howard JM, Sanford JR (2015) The RNAissance family: SR proteins as multifaceted regulators of gene expression. Wiley Interdiscip Rev RNA 6:93–110
    • (2015) Wiley Interdiscip Rev RNA , vol.6 , pp. 93-110
    • Howard, J.M.1    Sanford, J.R.2
  • 65
    • 18444362122 scopus 로고    scopus 로고
    • Biallelic inactivation of BRCA2 in Fanconi anemia
    • COI: 1:CAS:528:DC%2BD38XlslWrs7k%3D, PID: 12065746
    • Howlett NG et al (2002) Biallelic inactivation of BRCA2 in Fanconi anemia. Science 297:606–609
    • (2002) Science , vol.297 , pp. 606-609
    • Howlett, N.G.1
  • 66
    • 0344211508 scopus 로고    scopus 로고
    • SR splicing factors serve as adapter proteins for TAP-dependent mRNA export
    • COI: 1:CAS:528:DC%2BD3sXjtVWktLY%3D, PID: 12667464
    • Huang Y, Gattoni R, Stévenin J, Steitz JA (2003) SR splicing factors serve as adapter proteins for TAP-dependent mRNA export. Mol Cell 11:837–843
    • (2003) Mol Cell , vol.11 , pp. 837-843
    • Huang, Y.1    Gattoni, R.2    Stévenin, J.3    Steitz, J.A.4
  • 67
    • 33746435693 scopus 로고    scopus 로고
    • Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals
    • COI: 1:CAS:528:DC%2BD28Xnt1yisrY%3D, PID: 16786435
    • Hurst LD (2006) Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals. J Mol Evol 63:174–182
    • (2006) J Mol Evol , vol.63 , pp. 174-182
    • Hurst, L.D.1
  • 68
    • 84878357990 scopus 로고    scopus 로고
    • Open questions: a logic (or lack thereof) of genome organization
    • PID: 23714162
    • Hurst LD (2013) Open questions: a logic (or lack thereof) of genome organization. BMC Biol 11:58
    • (2013) BMC Biol , vol.11 , pp. 58
    • Hurst, L.D.1
  • 69
    • 77958082013 scopus 로고    scopus 로고
    • Overlapping codes within protein-coding sequences
    • COI: 1:CAS:528:DC%2BC3cXhsVGqu73N, PID: 20841429
    • Itzkovitz S, Hodis E, Segal E (2010) Overlapping codes within protein-coding sequences. Genome Res 20:1582–1589
    • (2010) Genome Res , vol.20 , pp. 1582-1589
    • Itzkovitz, S.1    Hodis, E.2    Segal, E.3
  • 70
    • 84940435596 scopus 로고    scopus 로고
    • Specificity and nonspecificity in RNA-protein interactions
    • COI: 1:CAS:528:DC%2BC2MXhtlKntrbM, PID: 26285679
    • Jankowsky E, Harris ME (2015) Specificity and nonspecificity in RNA-protein interactions. Nat Rev Mol Cell Biol 16:533–544
    • (2015) Nat Rev Mol Cell Biol , vol.16 , pp. 533-544
    • Jankowsky, E.1    Harris, M.E.2
  • 71
    • 84877721757 scopus 로고    scopus 로고
    • SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase
    • COI: 1:CAS:528:DC%2BC3sXnsFSmtbo%3D, PID: 23663783
    • Ji X et al (2013) SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell 153:855–868
    • (2013) Cell , vol.153 , pp. 855-868
    • Ji, X.1
  • 72
    • 84879619070 scopus 로고    scopus 로고
    • Latent effects of Hsp90 mutants revealed at reduced expression levels
    • COI: 1:CAS:528:DC%2BC3sXhtFGjsL3E, PID: 23825969
    • Jiang L, Mishra P, Hietpas RT, Zeldovich KB, Bolon DN (2013) Latent effects of Hsp90 mutants revealed at reduced expression levels. PLoS Genet 9:e1003600
    • (2013) PLoS Genet , vol.9
    • Jiang, L.1    Mishra, P.2    Hietpas, R.T.3    Zeldovich, K.B.4    Bolon, D.N.5
  • 73
    • 79956067688 scopus 로고    scopus 로고
    • New insights into RNA secondary structure in the alternative splicing of pre-mRNAs
    • Jin Y, Yang Y, Zhang P (2014) New insights into RNA secondary structure in the alternative splicing of pre-mRNAs. RNA Biol 8:450–457
    • (2014) RNA Biol , vol.8 , pp. 450-457
    • Jin, Y.1    Yang, Y.2    Zhang, P.3
  • 74
    • 84968547785 scopus 로고    scopus 로고
    • The complete local genotype-phenotype landscape for the alternative splicing of a human exon
    • COI: 1:CAS:528:DC%2BC28Xnslamtr0%3D, PID: 27161764
    • Julien P, Minana B, Baeza-Centurion P, Valcarcel J, Lehner B (2016) The complete local genotype-phenotype landscape for the alternative splicing of a human exon. Nature communications 7:11558
    • (2016) Nature communications , vol.7 , pp. 11558
    • Julien, P.1    Minana, B.2    Baeza-Centurion, P.3    Valcarcel, J.4    Lehner, B.5
  • 75
    • 0019869334 scopus 로고
    • The molecular basis of dominance
    • COI: 1:CAS:528:DyaL3MXlvVahurY%3D, PID: 7297851
    • Kacser H, Burns JA (1981) The molecular basis of dominance. Genetics 97:639–666
    • (1981) Genetics , vol.97 , pp. 639-666
    • Kacser, H.1    Burns, J.A.2
  • 76
    • 37249042614 scopus 로고    scopus 로고
    • Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
    • COI: 1:CAS:528:DC%2BD1cXhtlCjs78%3D, PID: 18073430
    • Keightley PD, Eyre-Walker A (2007) Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177:2251–2261
    • (2007) Genetics , vol.177 , pp. 2251-2261
    • Keightley, P.D.1    Eyre-Walker, A.2
  • 77
    • 80051532482 scopus 로고    scopus 로고
    • Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans
    • PID: 21596896
    • Keightley PD, Halligan DL (2011) Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans. Genetics 188:931–940
    • (2011) Genetics , vol.188 , pp. 931-940
    • Keightley, P.D.1    Halligan, D.L.2
  • 78
    • 79955442386 scopus 로고    scopus 로고
    • Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation
    • COI: 1:CAS:528:DC%2BC3MXmsVSgsbs%3D, PID: 21288873
    • Keightley PD, Eory L, Halligan DL, Kirkpatrick M (2011) Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation. Genetics 187:1153–1161
    • (2011) Genetics , vol.187 , pp. 1153-1161
    • Keightley, P.D.1    Eory, L.2    Halligan, D.L.3    Kirkpatrick, M.4
  • 79
    • 84899633396 scopus 로고    scopus 로고
    • Defining functional DNA elements in the human genome
    • COI: 1:CAS:528:DC%2BC2cXmslaqs7g%3D, PID: 24753594
    • Kellis M et al (2014) Defining functional DNA elements in the human genome. Proc Natl Acad Sci USA 111:6131–6138
    • (2014) Proc Natl Acad Sci USA , vol.111 , pp. 6131-6138
    • Kellis, M.1
  • 80
    • 84983762697 scopus 로고    scopus 로고
    • Massively parallel interrogation of the effects of gene expression levels on fitness
    • Keren L et al (2016) Massively parallel interrogation of the effects of gene expression levels on fitness. Cell 166(1282–1294):e1218
    • (2016) Cell , vol.166 , Issue.1282-1294
    • Keren, L.1
  • 81
    • 84911382071 scopus 로고    scopus 로고
    • Identification of splicing defects caused by mutations in the dysferlin gene
    • COI: 1:CAS:528:DC%2BC2cXitVektb%2FP, PID: 25312915
    • Kergourlay V et al (2014) Identification of splicing defects caused by mutations in the dysferlin gene. Hum Mutat 35:1532–1541
    • (2014) Hum Mutat , vol.35 , pp. 1532-1541
    • Kergourlay, V.1
  • 82
    • 0022423415 scopus 로고
    • Size and position of intervening sequences are critical for the splicing efficiency of pre-mRNA in the yeast Saccharomyces cerevisiae
    • COI: 1:CAS:528:DyaL2MXksV2jtLk%3D, PID: 3892483
    • Klinz F-J, Gallwitz D (1985) Size and position of intervening sequences are critical for the splicing efficiency of pre-mRNA in the yeast Saccharomyces cerevisiae. Nucleic Acids Res 13:3791–3804
    • (1985) Nucleic Acids Res , vol.13 , pp. 3791-3804
    • Klinz, F.-J.1    Gallwitz, D.2
  • 83
    • 61349098460 scopus 로고    scopus 로고
    • Differential chromatin marking of introns and expressed exons by H3K36me3
    • COI: 1:CAS:528:DC%2BD1MXht1ehur8%3D, PID: 19182803
    • Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J (2009) Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41:376–381
    • (2009) Nat Genet , vol.41 , pp. 376-381
    • Kolasinska-Zwierz, P.1    Down, T.2    Latorre, I.3    Liu, T.4    Liu, X.S.5    Ahringer, J.6
  • 84
    • 84876350995 scopus 로고    scopus 로고
    • A comparison of models to infer the distribution of fitness effects of new mutations
    • PID: 23341416
    • Kousathanas A, Keightley PD (2013) A comparison of models to infer the distribution of fitness effects of new mutations. Genetics 193:1197–1208
    • (2013) Genetics , vol.193 , pp. 1197-1208
    • Kousathanas, A.1    Keightley, P.D.2
  • 85
    • 77649267695 scopus 로고    scopus 로고
    • Dynamic changes in the human methylome during differentiation
    • COI: 1:CAS:528:DC%2BC3cXjtlCktbo%3D, PID: 20133333
    • Laurent L et al (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20:320–331
    • (2010) Genome Res , vol.20 , pp. 320-331
    • Laurent, L.1
  • 86
    • 84878486976 scopus 로고    scopus 로고
    • Strong purifying selection at synonymous sites in D. melanogaster
    • COI: 1:CAS:528:DC%2BC3sXpsFelu7o%3D, PID: 23737754
    • Lawrie DS, Messer PW, Hershberg R, Petrov DA (2013) Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genet 9:e1003527
    • (2013) PLoS Genet , vol.9
    • Lawrie, D.S.1    Messer, P.W.2    Hershberg, R.3    Petrov, D.A.4
  • 87
    • 0024522826 scopus 로고
    • A novel member of the thyroid/steroid hormone receptor family is encoded by the opposite strand of the rat c-erbAα transcriptional unit
    • COI: 1:CAS:528:DyaK3cXhs1Wn, PID: 2542765
    • Lazar MA, Hodin RA, Darling DS, Chin WW (1989) A novel member of the thyroid/steroid hormone receptor family is encoded by the opposite strand of the rat c-erbAα transcriptional unit. Mol Cell Biol 9:1128–1136
    • (1989) Mol Cell Biol , vol.9 , pp. 1128-1136
    • Lazar, M.A.1    Hodin, R.A.2    Darling, D.S.3    Chin, W.W.4
  • 88
    • 84930691710 scopus 로고    scopus 로고
    • Mechanisms and regulation of alternative pre-mRNA splicing
    • COI: 1:CAS:528:DC%2BC2MXhsVyrt7zN, PID: 25784052
    • Lee Y, Rio DC (2015) Mechanisms and regulation of alternative pre-mRNA splicing. Annu Rev Biochem 84:291–323
    • (2015) Annu Rev Biochem , vol.84 , pp. 291-323
    • Lee, Y.1    Rio, D.C.2
  • 89
    • 0028797783 scopus 로고
    • Identification and characterization of a spinal muscular atrophy-determining gene
    • COI: 1:CAS:528:DyaK2MXjtFegu74%3D, PID: 7813012
    • Lefebvre S et al (1995) Identification and characterization of a spinal muscular atrophy-determining gene. Cell 80:155–165
    • (1995) Cell , vol.80 , pp. 155-165
    • Lefebvre, S.1
  • 90
    • 84928761297 scopus 로고    scopus 로고
    • The alternative role of DNA methylation in splicing regulation
    • COI: 1:CAS:528:DC%2BC2MXltFWiu7o%3D, PID: 25837375
    • Lev Maor G, Yearim A, Ast G (2015) The alternative role of DNA methylation in splicing regulation. Trends Genet 31:274–280
    • (2015) Trends Genet , vol.31 , pp. 274-280
    • Lev Maor, G.1    Yearim, A.2    Ast, G.3
  • 91
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA Targets
    • COI: 1:CAS:528:DC%2BD2MXot1ChsA%3D%3D, PID: 15652477
    • Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA Targets. Cell 120:15–20
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 92
    • 23744455164 scopus 로고    scopus 로고
    • Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability
    • COI: 1:CAS:528:DC%2BD2MXovV2qsrk%3D, PID: 16096057
    • Li X, Manley JL (2005) Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 122:365–378
    • (2005) Cell , vol.122 , pp. 365-378
    • Li, X.1    Manley, J.L.2
  • 93
    • 77952687104 scopus 로고    scopus 로고
    • Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure
    • COI: 1:CAS:528:DC%2BC3cXntV2iu78%3D, PID: 20418358
    • Li X, Quon G, Lipshitz HD, Morris Q (2010) Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. RNA 16:1096–1107
    • (2010) RNA , vol.16 , pp. 1096-1107
    • Li, X.1    Quon, G.2    Lipshitz, H.D.3    Morris, Q.4
  • 94
    • 84890294599 scopus 로고    scopus 로고
    • Finding the target sites of RNA-binding proteins
    • COI: 1:CAS:528:DC%2BC3sXhvFKqu7nE, PID: 24217996
    • Li X, Kazan H, Lipshitz HD, Morris QD (2014) Finding the target sites of RNA-binding proteins. Wiley Interdiscip Rev RNA 5:111–130
    • (2014) Wiley Interdiscip Rev RNA , vol.5 , pp. 111-130
    • Li, X.1    Kazan, H.2    Lipshitz, H.D.3    Morris, Q.D.4
  • 95
    • 79960594889 scopus 로고    scopus 로고
    • Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes
    • COI: 1:CAS:528:DC%2BC3MXptV2htb4%3D, PID: 21685335
    • Lim KH, Ferraris L, Filloux ME, Raphael BJ, Fairbrother WG (2011) Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc Natl Acad Sci USA 108:11093–11098
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 11093-11098
    • Lim, K.H.1    Ferraris, L.2    Filloux, M.E.3    Raphael, B.J.4    Fairbrother, W.G.5
  • 96
    • 49449116959 scopus 로고    scopus 로고
    • The splicing factor SC35 has an active role in transcriptional elongation
    • COI: 1:CAS:528:DC%2BD1cXptlOisrg%3D, PID: 18641664
    • Lin S, Coutinho-Mansfield G, Wang D, Pandit S, Fu X-D (2008) The splicing factor SC35 has an active role in transcriptional elongation. Nat Struct Mol Biol 15:819–826
    • (2008) Nat Struct Mol Biol , vol.15 , pp. 819-826
    • Lin, S.1    Coutinho-Mansfield, G.2    Wang, D.3    Pandit, S.4    Fu, X.-D.5
  • 97
    • 80055024376 scopus 로고    scopus 로고
    • Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
    • COI: 1:CAS:528:DC%2BC3MXhsVKjsLzE, PID: 21994248
    • Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M (2011) Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res 21:1916–1928
    • (2011) Genome Res , vol.21 , pp. 1916-1928
    • Lin, M.F.1    Kheradpour, P.2    Washietl, S.3    Parker, B.J.4    Pedersen, J.S.5    Kellis, M.6
  • 98
    • 17344365600 scopus 로고    scopus 로고
    • Dysferlin, a novel skeletal muscle gene, is mutated in Miyoshi myopathy and limb girdle muscular dystrophy
    • COI: 1:CAS:528:DyaK1cXmtVOmt7s%3D, PID: 9731526
    • Liu J et al (1998) Dysferlin, a novel skeletal muscle gene, is mutated in Miyoshi myopathy and limb girdle muscular dystrophy. Nat Genet 20:31–36
    • (1998) Nat Genet , vol.20 , pp. 31-36
    • Liu, J.1
  • 99
    • 78049248013 scopus 로고    scopus 로고
    • Regulation of splicing enhancer activities by RNA secondary structures
    • COI: 1:CAS:528:DC%2BC3cXhtlKrsrnI, PID: 20888818
    • Liu W, Zhou Y, Hu Z, Sun T, Denise A, Fu XD, Zhang Y (2010) Regulation of splicing enhancer activities by RNA secondary structures. FEBS Lett 584:4401–4407
    • (2010) FEBS Lett , vol.584 , pp. 4401-4407
    • Liu, W.1    Zhou, Y.2    Hu, Z.3    Sun, T.4    Denise, A.5    Fu, X.D.6    Zhang, Y.7
  • 100
    • 84965093239 scopus 로고    scopus 로고
    • Functional conservation of both CDS- and 3′-UTR-located microRNA binding sites between species
    • COI: 1:CAS:528:DC%2BC28Xht1KqtrvM, PID: 25414126
    • Liu G, Zhang R, Xu J, Wu CI, Lu X (2015) Functional conservation of both CDS- and 3′-UTR-located microRNA binding sites between species. Mol Biol Evol 32:623–628
    • (2015) Mol Biol Evol , vol.32 , pp. 623-628
    • Liu, G.1    Zhang, R.2    Xu, J.3    Wu, C.I.4    Lu, X.5
  • 101
    • 33644764039 scopus 로고    scopus 로고
    • Estimating selection on nonsynonymous mutations
    • COI: 1:CAS:528:DC%2BD28XivFCkurs%3D, PID: 16299397
    • Loewe L, Charlesworth B, Bartolome C, Noel V (2006) Estimating selection on nonsynonymous mutations. Genetics 172:1079–1092
    • (2006) Genetics , vol.172 , pp. 1079-1092
    • Loewe, L.1    Charlesworth, B.2    Bartolome, C.3    Noel, V.4
  • 102
    • 15544379277 scopus 로고    scopus 로고
    • Are splicing mutations the most frequent cause of hereditary disease?
    • COI: 1:CAS:528:DC%2BD2MXisFGqurY%3D, PID: 15792793
    • Lopez-Bigas N, Audit B, Ouzounis C, Parra G, Guigo R (2005) Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett 579:1900–1903
    • (2005) FEBS Lett , vol.579 , pp. 1900-1903
    • Lopez-Bigas, N.1    Audit, B.2    Ouzounis, C.3    Parra, G.4    Guigo, R.5
  • 103
    • 84901675912 scopus 로고    scopus 로고
    • Synonymous constraint elements show a tendency to encode intrinsically disordered protein segments
    • PID: 24809503
    • Macossay-Castillo M, Kosol S, Tompa P, Pancsa R (2014) Synonymous constraint elements show a tendency to encode intrinsically disordered protein segments. PLoS Comput Biol 10:e1003607
    • (2014) PLoS Comput Biol , vol.10
    • Macossay-Castillo, M.1    Kosol, S.2    Tompa, P.3    Pancsa, R.4
  • 104
    • 0036911605 scopus 로고    scopus 로고
    • Distribution and characterization of regulatory elements in the human genome
    • COI: 1:CAS:528:DC%2BD38XpsVOqtbo%3D, PID: 12466286
    • Majewski J, Ott J (2002) Distribution and characterization of regulatory elements in the human genome. Genome Res 12:1827–1836
    • (2002) Genome Res , vol.12 , pp. 1827-1836
    • Majewski, J.1    Ott, J.2
  • 105
    • 12444259766 scopus 로고    scopus 로고
    • Overlapping genes in vertebrate genomes
    • COI: 1:CAS:528:DC%2BD2MXos12qtQ%3D%3D, PID: 15680581
    • Makalowska I, Lin CF, Makalowski W (2005) Overlapping genes in vertebrate genomes. Comput Biol Chem 29:1–12
    • (2005) Comput Biol Chem , vol.29 , pp. 1-12
    • Makalowska, I.1    Lin, C.F.2    Makalowski, W.3
  • 106
    • 84899845940 scopus 로고    scopus 로고
    • The translational landscape of the splicing factor SRSF1 and its role in mitosis
    • Maslon MM, Heras SR, Bellora N, Eyras E, Caceres JF (2014) The translational landscape of the splicing factor SRSF1 and its role in mitosis. eLife 3:e02028
    • (2014) eLife , vol.3
    • Maslon, M.M.1    Heras, S.R.2    Bellora, N.3    Eyras, E.4    Caceres, J.F.5
  • 107
    • 84899637780 scopus 로고    scopus 로고
    • The extent of functionality in the human genome
    • Mattick JS, Dinger ME (2013) The extent of functionality in the human genome. HUGO J 7:2
    • (2013) HUGO J , vol.7 , pp. 2
    • Mattick, J.S.1    Dinger, M.E.2
  • 108
    • 79960918747 scopus 로고    scopus 로고
    • RNA structure and the mechanisms of alternative splicing
    • COI: 1:CAS:528:DC%2BC3MXps1ejsbc%3D, PID: 21530232
    • McManus CJ, Graveley BR (2011) RNA structure and the mechanisms of alternative splicing. Curr Opin Genet Dev 21:373–379
    • (2011) Curr Opin Genet Dev , vol.21 , pp. 373-379
    • McManus, C.J.1    Graveley, B.R.2
  • 109
    • 28544440092 scopus 로고    scopus 로고
    • Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs
    • COI: 1:CAS:528:DC%2BD2MXht1entLjL, PID: 16275783
    • Meyer IM, Miklos I (2005) Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs. Nucleic Acids Res 33:6338–6348
    • (2005) Nucleic Acids Res , vol.33 , pp. 6338-6348
    • Meyer, I.M.1    Miklos, I.2
  • 110
    • 84868324214 scopus 로고    scopus 로고
    • Observation of dually decoded regions of the human genome using ribosome profiling data
    • COI: 1:CAS:528:DC%2BC38Xhs1ektr7J, PID: 22593554
    • Michel AM, Choudhury KR, Firth AE, Ingolia NT, Atkins JF, Baranov PV (2012) Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res 22:2219–2229
    • (2012) Genome Res , vol.22 , pp. 2219-2229
    • Michel, A.M.1    Choudhury, K.R.2    Firth, A.E.3    Ingolia, N.T.4    Atkins, J.F.5    Baranov, P.V.6
  • 111
    • 42949109848 scopus 로고    scopus 로고
    • The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1
    • COI: 1:CAS:528:DC%2BD1cXlsFentb0%3D, PID: 18439897
    • Michlewski G, Sanford JR, Caceres JF (2008) The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1. Mol Cell 30:179–189
    • (2008) Mol Cell , vol.30 , pp. 179-189
    • Michlewski, G.1    Sanford, J.R.2    Caceres, J.F.3
  • 112
    • 0001410504 scopus 로고
    • In defense of proper functions
    • Millikan RG (1989) In defense of proper functions. Philos Sci 56:288–302
    • (1989) Philos Sci , vol.56 , pp. 288-302
    • Millikan, R.G.1
  • 113
    • 0024511936 scopus 로고
    • Two erbA homologs encoding proteins with different T 3 binding capacities are transcribed from opposite DNA strands of the same genetic locus
    • COI: 1:CAS:528:DyaK3cXkvFKktg%3D%3D, PID: 2539258
    • Miyajima N, Horiuchi R, Shibuya Y, S-i Fukushige, K-i Matsubara, Toyoshima K, Yamamoto T (1989) Two erbA homologs encoding proteins with different T 3 binding capacities are transcribed from opposite DNA strands of the same genetic locus. Cell 57:31–39
    • (1989) Cell , vol.57 , pp. 31-39
    • Miyajima, N.1    Horiuchi, R.2    Shibuya, Y.3    S-i, F.4    K-i, M.5    Toyoshima, K.6    Yamamoto, T.7
  • 114
    • 0036171787 scopus 로고    scopus 로고
    • An exon splice enhancer mutation causes autosomal dominant GH deficiency
    • COI: 1:CAS:528:DC%2BD38XhsVSisb4%3D
    • Moseley CT, Mullis PE, Prince MA, Phillips JA III (2002) An exon splice enhancer mutation causes autosomal dominant GH deficiency. J Clin Endocrionol Metab 87:847–852
    • (2002) J Clin Endocrionol Metab , vol.87 , pp. 847-852
    • Moseley, C.T.1    Mullis, P.E.2    Prince, M.A.3    Phillips, J.A.4
  • 115
    • 84946962573 scopus 로고    scopus 로고
    • The silent sway of splicing by synonymous substitutions
    • COI: 1:CAS:528:DC%2BC2MXhvVeqt7vO, PID: 26424794
    • Mueller WF, Larsen LS, Garibaldi A, Hatfield GW, Hertel KJ (2015) The silent sway of splicing by synonymous substitutions. J Biol Chem 290:27700–27711
    • (2015) J Biol Chem , vol.290 , pp. 27700-27711
    • Mueller, W.F.1    Larsen, L.S.2    Garibaldi, A.3    Hatfield, G.W.4    Hertel, K.J.5
  • 116
    • 0001261899 scopus 로고
    • Functions as selected effects: the conceptual analyst’s defense
    • Neander K (1991) Functions as selected effects: the conceptual analyst’s defense. Philos Sci 58:168–184
    • (1991) Philos Sci , vol.58 , pp. 168-184
    • Neander, K.1
  • 117
    • 0042354654 scopus 로고    scopus 로고
    • Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA
    • COI: 1:CAS:528:DC%2BD3sXms1Wks7o%3D, PID: 12777508
    • Nielsen R, Yang Z (2003) Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol Biol Evol 20:1231–1239
    • (2003) Mol Biol Evol , vol.20 , pp. 1231-1239
    • Nielsen, R.1    Yang, Z.2
  • 118
    • 84872861423 scopus 로고    scopus 로고
    • Can ENCODE tell us how much junk DNA we carry in our genome?
    • COI: 1:CAS:528:DC%2BC3sXovFCrsQ%3D%3D, PID: 23268340
    • Niu DK, Jiang L (2013) Can ENCODE tell us how much junk DNA we carry in our genome? Biochem Biophys Res Commun 430:1340–1343
    • (2013) Biochem Biophys Res Commun , vol.430 , pp. 1340-1343
    • Niu, D.K.1    Jiang, L.2
  • 119
    • 84928386012 scopus 로고    scopus 로고
    • Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing
    • COI: 1:CAS:528:DC%2BC2MXnt1eqsrs%3D, PID: 25910207
    • Nojima T et al (2015) Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing. Cell 161:526–540
    • (2015) Cell , vol.161 , pp. 526-540
    • Nojima, T.1
  • 120
    • 0037669010 scopus 로고    scopus 로고
    • Low conservation of alternative splicing patterns in the human and mouse genomes
    • COI: 1:CAS:528:DC%2BD3sXkt1WrurY%3D, PID: 12761046
    • Nurtdinov RN (2003) Low conservation of alternative splicing patterns in the human and mouse genomes. Hum Mol Genet 12:1313–1320
    • (2003) Hum Mol Genet , vol.12 , pp. 1313-1320
    • Nurtdinov, R.N.1
  • 121
    • 75649108241 scopus 로고    scopus 로고
    • Entropic contributions to the splicing process
    • PID: 19934491
    • Osella M, Caselle M (2009) Entropic contributions to the splicing process. Phys Biol 6:046018
    • (2009) Phys Biol , vol.6 , pp. 046018
    • Osella, M.1    Caselle, M.2
  • 122
    • 0038712558 scopus 로고    scopus 로고
    • Missense, nonsense, and neutral mutations define juxtaposed regulatory elements of splicing in cystic fibrosis transmembrane regulator exon 9
    • COI: 1:CAS:528:DC%2BD3sXltlKqsL8%3D, PID: 12732620
    • Pagani F, Buratti E, Stuani C, Baralle FE (2003) Missense, nonsense, and neutral mutations define juxtaposed regulatory elements of splicing in cystic fibrosis transmembrane regulator exon 9. J Biol Chem 278:26580–26588
    • (2003) J Biol Chem , vol.278 , pp. 26580-26588
    • Pagani, F.1    Buratti, E.2    Stuani, C.3    Baralle, F.E.4
  • 123
    • 18144386947 scopus 로고    scopus 로고
    • Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution
    • COI: 1:CAS:528:DC%2BD2MXktlygtrg%3D, PID: 15840711
    • Pagani F, Raponi M, Baralle FE (2005) Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proc Natl Acad Sci USA 102:6368–6372
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6368-6372
    • Pagani, F.1    Raponi, M.2    Baralle, F.E.3
  • 124
    • 10944245056 scopus 로고    scopus 로고
    • Alternative splicing of conserved exons is frequently species-specific in human and mouse
    • COI: 1:CAS:528:DC%2BD2MXmslKhtg%3D%3D, PID: 15661351
    • Pan Q, Bakowski MA, Morris Q, Zhang W, Frey BJ, Hughes TR, Blencowe BJ (2005) Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet 21:73–77
    • (2005) Trends Genet , vol.21 , pp. 73-77
    • Pan, Q.1    Bakowski, M.A.2    Morris, Q.3    Zhang, W.4    Frey, B.J.5    Hughes, T.R.6    Blencowe, B.J.7
  • 125
    • 84994545646 scopus 로고    scopus 로고
    • Coding regions of intrinsic disorder accommodate parallel functions
    • COI: 1:CAS:528:DC%2BC28XhsVels7fJ, PID: 27647212
    • Pancsa R, Tompa P (2016) Coding regions of intrinsic disorder accommodate parallel functions. Trends Biochem Sci 41:898–906
    • (2016) Trends Biochem Sci , vol.41 , pp. 898-906
    • Pancsa, R.1    Tompa, P.2
  • 126
    • 84876839218 scopus 로고    scopus 로고
    • Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing
    • COI: 1:CAS:528:DC%2BC3sXlsFalurk%3D, PID: 23562324
    • Pandit S et al (2013) Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell 50:223–235
    • (2013) Mol Cell , vol.50 , pp. 223-235
    • Pandit, S.1
  • 127
    • 34547709593 scopus 로고    scopus 로고
    • Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals
    • COI: 1:CAS:528:DC%2BD2sXpsVGrsLw%3D, PID: 17525472
    • Parmley JL, Hurst LD (2007) Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Mol Biol Evol 24:1600–1603
    • (2007) Mol Biol Evol , vol.24 , pp. 1600-1603
    • Parmley, J.L.1    Hurst, L.D.2
  • 128
    • 30744469841 scopus 로고    scopus 로고
    • Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers
    • COI: 1:CAS:528:DC%2BD28XntValtw%3D%3D, PID: 16221894
    • Parmley JL, Chamary JV, Hurst LD (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol 23:301–309
    • (2006) Mol Biol Evol , vol.23 , pp. 301-309
    • Parmley, J.L.1    Chamary, J.V.2    Hurst, L.D.3
  • 130
  • 131
    • 0032492855 scopus 로고    scopus 로고
    • Salmonella typhi uses CFTR to enter intestinal epithelial cells
    • COI: 1:CAS:528:DyaK1cXjt1anu7s%3D, PID: 9590693
    • Pier GB et al (1998) Salmonella typhi uses CFTR to enter intestinal epithelial cells. Nature 393:79–82
    • (1998) Nature , vol.393 , pp. 79-82
    • Pier, G.B.1
  • 132
    • 0041836283 scopus 로고    scopus 로고
    • Estimating the distribution of fitness effects from DNA sequence data: implications for the molecular clock
    • COI: 1:CAS:528:DC%2BD3sXntFygu7k%3D, PID: 12925735
    • Piganeau G, Eyre-Walker A (2003) Estimating the distribution of fitness effects from DNA sequence data: implications for the molecular clock. Proc Natl Acad Sci USA 100:10335–10340
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 10335-10340
    • Piganeau, G.1    Eyre-Walker, A.2
  • 133
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • COI: 1:CAS:528:DC%2BC3cXls1OlsQ%3D%3D, PID: 19858363
    • Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20:110–121
    • (2010) Genome Res , vol.20 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 134
    • 80555142991 scopus 로고    scopus 로고
    • What fraction of the human genome is functional?
    • COI: 1:CAS:528:DC%2BC3MXhsVKjs7fL, PID: 21875934
    • Ponting CP, Hardison RC (2011) What fraction of the human genome is functional? Genome Res 21:1769–1776
    • (2011) Genome Res , vol.21 , pp. 1769-1776
    • Ponting, C.P.1    Hardison, R.C.2
  • 135
    • 6044239562 scopus 로고    scopus 로고
    • Over-representation of exonic splicing enhancers in human intronless genes suggests multiple functions in mRNA processing
    • COI: 1:CAS:528:DC%2BD2cXmvFeksr8%3D, PID: 15325254
    • Pozzoli U et al (2004) Over-representation of exonic splicing enhancers in human intronless genes suggests multiple functions in mRNA processing. Biochem Biophys Res Commun 322:470–476
    • (2004) Biochem Biophys Res Commun , vol.322 , pp. 470-476
    • Pozzoli, U.1
  • 136
    • 84954380474 scopus 로고    scopus 로고
    • Are synonymous sites in primates and rodents functionally constrained?
    • COI: 1:CAS:528:DC%2BC2MXhvVehtr7L, PID: 26563252
    • Price N, Graur D (2016) Are synonymous sites in primates and rodents functionally constrained? J Mol Evol 82:51–64
    • (2016) J Mol Evol , vol.82 , pp. 51-64
    • Price, N.1    Graur, D.2
  • 137
    • 84912075546 scopus 로고    scopus 로고
    • Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms
    • PID: 25375159
    • Racimo F, Schraiber JG (2014) Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms. PLoS Genet 10:e1004697
    • (2014) PLoS Genet , vol.10
    • Racimo, F.1    Schraiber, J.G.2
  • 138
    • 20244369597 scopus 로고    scopus 로고
    • A unique exonic splice enhancer mutation in a family with X-linked mental retardation and epilepsy points to a novel role of the renin receptor
    • COI: 1:CAS:528:DC%2BD2MXjtlensrw%3D, PID: 15746149
    • Ramser J et al (2005) A unique exonic splice enhancer mutation in a family with X-linked mental retardation and epilepsy points to a novel role of the renin receptor. Hum Mol Genet 14:1019–1027
    • (2005) Hum Mol Genet , vol.14 , pp. 1019-1027
    • Ramser, J.1
  • 139
    • 0031037337 scopus 로고    scopus 로고
    • The molecular basis of partial penetrance of splicing mutations in cystic fibrosis
    • COI: 1:CAS:528:DyaK2sXlvFKksQ%3D%3D, PID: 8981951
    • Rave-Harel N et al (1997) The molecular basis of partial penetrance of splicing mutations in cystic fibrosis. Am J Hum Genet 60:87
    • (1997) Am J Hum Genet , vol.60 , pp. 87
    • Rave-Harel, N.1
  • 140
    • 84964597654 scopus 로고    scopus 로고
    • Coupling of RNA polymerase II transcription elongation with pre-mRNA splicing
    • COI: 1:CAS:528:DC%2BC28XmslSgsLY%3D, PID: 27107644
    • Saldi T, Cortazar MA, Sheridan RM, Bentley DL (2016) Coupling of RNA polymerase II transcription elongation with pre-mRNA splicing. J Mol Biol 428:2623–2635
    • (2016) J Mol Biol , vol.428 , pp. 2623-2635
    • Saldi, T.1    Cortazar, M.A.2    Sheridan, R.M.3    Bentley, D.L.4
  • 141
    • 1842632326 scopus 로고    scopus 로고
    • A novel role for shuttling SR proteins in mRNA translation
    • COI: 1:CAS:528:DC%2BD2cXjsVGksb0%3D, PID: 15082528
    • Sanford JR, Gray NK, Beckmann K, Cáceres JF (2004) A novel role for shuttling SR proteins in mRNA translation. Genes Dev 18:755–768
    • (2004) Genes Dev , vol.18 , pp. 755-768
    • Sanford, J.R.1    Gray, N.K.2    Beckmann, K.3    Cáceres, J.F.4
  • 142
    • 42549092747 scopus 로고    scopus 로고
    • Overlapping genes in the human and mouse genomes
    • PID: 18410680
    • Sanna CR, Li WH, Zhang L (2008) Overlapping genes in the human and mouse genomes. BMC Genomics 9:169
    • (2008) BMC Genomics , vol.9 , pp. 169
    • Sanna, C.R.1    Li, W.H.2    Zhang, L.3
  • 143
    • 64749099643 scopus 로고    scopus 로고
    • SR protein family members display diverse activities in the formation of nascent and mature mRNPs in vivo
    • COI: 1:CAS:528:DC%2BD1MXlvVCltL8%3D, PID: 19394295
    • Sapra AK et al (2009) SR protein family members display diverse activities in the formation of nascent and mature mRNPs in vivo. Mol Cell 34:179–190
    • (2009) Mol Cell , vol.34 , pp. 179-190
    • Sapra, A.K.1
  • 144
    • 84973311523 scopus 로고    scopus 로고
    • Purifying selection on exonic splice enhancers in intronless genes
    • COI: 1:CAS:528:DC%2BC28XhslaqsbrN, PID: 26802218
    • Savisaar R, Hurst LD (2016) Purifying selection on exonic splice enhancers in intronless genes. Mol Biol Evol 33:1396–1418
    • (2016) Mol Biol Evol , vol.33 , pp. 1396-1418
    • Savisaar, R.1    Hurst, L.D.2
  • 145
    • 85019136599 scopus 로고    scopus 로고
    • Both maintenance and avoidance of RNA-binding protein interactions constrain coding sequence evolution
    • PID: 28138077
    • Savisaar R, Hurst LD (2017) Both maintenance and avoidance of RNA-binding protein interactions constrain coding sequence evolution. Mol Biol Evol. doi:10.1093/molbev/msx061
    • (2017) Mol Biol Evol
    • Savisaar, R.1    Hurst, L.D.2
  • 146
    • 0347380978 scopus 로고    scopus 로고
    • Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection
    • COI: 1:CAS:528:DC%2BD2cXjsVeitw%3D%3D, PID: 15008412
    • Sawyer SA, Kulathinal RJ, Bustamante CD, Hartl DL (2003) Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. J Mol Evol 57:S154–S164
    • (2003) J Mol Evol , vol.57 , pp. S154-S164
    • Sawyer, S.A.1    Kulathinal, R.J.2    Bustamante, C.D.3    Hartl, D.L.4
  • 147
    • 83455176994 scopus 로고    scopus 로고
    • A method for inferring the rate of occurrence and fitness effects of advantageous mutations
    • COI: 1:CAS:528:DC%2BC38XltlGit7s%3D, PID: 21954160
    • Schneider A, Charlesworth B, Eyre-Walker A, Keightley PD (2011) A method for inferring the rate of occurrence and fitness effects of advantageous mutations. Genetics 189:1427–1437
    • (2011) Genetics , vol.189 , pp. 1427-1437
    • Schneider, A.1    Charlesworth, B.2    Eyre-Walker, A.3    Keightley, P.D.4
  • 148
    • 84964315393 scopus 로고    scopus 로고
    • Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs
    • PID: 25158797
    • Schüler A, Ghanbarian AT, Hurst LD (2014) Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs. Mol Biol Evol 31:3164–3183
    • (2014) Mol Biol Evol , vol.31 , pp. 3164-3183
    • Schüler, A.1    Ghanbarian, A.T.2    Hurst, L.D.3
  • 149
    • 84877818178 scopus 로고    scopus 로고
    • Nonsense-mediated mRNA decay—mechanisms of substrate mRNA recognition and degradation in mammalian cells
    • COI: 1:CAS:528:DC%2BC3sXktVOrs7o%3D, PID: 23435113
    • Schweingruber C, Rufener SC, Zund D, Yamashita A, Muhlemann O (2013) Nonsense-mediated mRNA decay—mechanisms of substrate mRNA recognition and degradation in mammalian cells. Biochem Biophys Acta 1829:612–623
    • (2013) Biochem Biophys Acta , vol.1829 , pp. 612-623
    • Schweingruber, C.1    Rufener, S.C.2    Zund, D.3    Yamashita, A.4    Muhlemann, O.5
  • 150
    • 84876348105 scopus 로고    scopus 로고
    • Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity
    • COI: 1:CAS:528:DC%2BC3sXjtVahs78%3D, PID: 23293005
    • Shabalina SA, Spiridonov NA, Kashina A (2013) Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res 41:2073–2094
    • (2013) Nucleic Acids Res , vol.41 , pp. 2073-2094
    • Shabalina, S.A.1    Spiridonov, N.A.2    Kashina, A.3
  • 151
    • 47949120992 scopus 로고    scopus 로고
    • Conserved RNA secondary structures promote alternative splicing
    • COI: 1:CAS:528:DC%2BD1cXpsVyisbg%3D, PID: 18579871
    • Shepard PJ, Hertel KJ (2008) Conserved RNA secondary structures promote alternative splicing. RNA 14:1463–1469
    • (2008) RNA , vol.14 , pp. 1463-1469
    • Shepard, P.J.1    Hertel, K.J.2
  • 152
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • COI: 1:CAS:528:DC%2BD2MXotFaht7o%3D, PID: 16024819
    • Siepel A et al (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15:1034–1050
    • (2005) Genome Res , vol.15 , pp. 1034-1050
    • Siepel, A.1
  • 153
    • 0842289003 scopus 로고    scopus 로고
    • An extended inhibitory context causes skipping of exon 7 of SMN2 in spinal muscular atrophy
    • COI: 1:CAS:528:DC%2BD2cXps1Ogug%3D%3D, PID: 14766219
    • Singh NN, Androphy EJ, Singh RN (2004) An extended inhibitory context causes skipping of exon 7 of SMN2 in spinal muscular atrophy. Biochem Biophys Res Commun 315:381–388
    • (2004) Biochem Biophys Res Commun , vol.315 , pp. 381-388
    • Singh, N.N.1    Androphy, E.J.2    Singh, R.N.3
  • 154
    • 0026800854 scopus 로고
    • Omission of exon 12 in cystic fibrosis transmembrane conductance regulator (CFTR) gene transcripts
    • COI: 1:CAS:528:DyaK3sXpvFKqsA%3D%3D, PID: 1380942
    • Slomski R, Schloesser M, Berg L-P, Wagner M, Kakkar VV, Cooper DN, Reiss J (1992) Omission of exon 12 in cystic fibrosis transmembrane conductance regulator (CFTR) gene transcripts. Hum Genet 89:615–619
    • (1992) Hum Genet , vol.89 , pp. 615-619
    • Slomski, R.1    Schloesser, M.2    Berg, L.-P.3    Wagner, M.4    Kakkar, V.V.5    Cooper, D.N.6    Reiss, J.7
  • 155
    • 84931275197 scopus 로고    scopus 로고
    • Splice junctions are constrained by protein disorder
    • COI: 1:CAS:528:DC%2BC2MXhsFegsL7O, PID: 25934802
    • Smithers B, Oates ME, Gough J (2015) Splice junctions are constrained by protein disorder. Nucleic Acids Res 43:4814–4822
    • (2015) Nucleic Acids Res , vol.43 , pp. 4814-4822
    • Smithers, B.1    Oates, M.E.2    Gough, J.3
  • 156
    • 84958729894 scopus 로고    scopus 로고
    • exonic splicing mutations are more prevalent than currently estimated and can be predicted by using in silico tools
    • PID: 26761715
    • Soukarieh O et al (2016) exonic splicing mutations are more prevalent than currently estimated and can be predicted by using in silico tools. PLoS Genet 12:e1005756
    • (2016) PLoS Genet , vol.12
    • Soukarieh, O.1
  • 157
    • 0033364822 scopus 로고    scopus 로고
    • Human molybdopterin synthase gene: identification of a bicistronic transcript with overlapping reading frames
    • COI: 1:CAS:528:DyaK1MXitFChtrc%3D, PID: 10053003
    • Stallmeyer B, Drugeon G, Reiss J, Haenni AL, Mendel RR (1999) Human molybdopterin synthase gene: identification of a bicistronic transcript with overlapping reading frames. Am J Hum Genet 64:698–705
    • (1999) Am J Hum Genet , vol.64 , pp. 698-705
    • Stallmeyer, B.1    Drugeon, G.2    Reiss, J.3    Haenni, A.L.4    Mendel, R.R.5
  • 158
    • 84865859048 scopus 로고    scopus 로고
    • What does our genome encode?
    • COI: 1:CAS:528:DC%2BC38XhtlentL3K, PID: 22955972
    • Stamatoyannopoulos JA (2012) What does our genome encode? Genome Res 22:1602–1611
    • (2012) Genome Res , vol.22 , pp. 1602-1611
    • Stamatoyannopoulos, J.A.1
  • 159
    • 84890072854 scopus 로고    scopus 로고
    • Exonic transcription factor binding directs codon choice and affects protein evolution
    • COI: 1:CAS:528:DC%2BC3sXhvV2lsLvL, PID: 24337295
    • Stergachis AB et al (2013) Exonic transcription factor binding directs codon choice and affects protein evolution. Science 342:1367–1372
    • (2013) Science , vol.342 , pp. 1367-1372
    • Stergachis, A.B.1
  • 160
    • 0030473462 scopus 로고    scopus 로고
    • Architectural limits on split genes
    • COI: 1:CAS:528:DyaK2sXmvVam, PID: 8986767
    • Sterner DA, Carlo T, Berget SM (1996) Architectural limits on split genes. Proc Natl Acad Sci USA 93:15081–15085
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 15081-15085
    • Sterner, D.A.1    Carlo, T.2    Berget, S.M.3
  • 161
    • 79960607075 scopus 로고    scopus 로고
    • Loss of exon identity is a common mechanism of human inherited disease
    • COI: 1:CAS:528:DC%2BC3MXhtlSrurfE, PID: 21750108
    • Sterne-Weiler T, Howard J, Mort M, Cooper DN, Sanford JR (2011) Loss of exon identity is a common mechanism of human inherited disease. Genome Res 21:1563–1571
    • (2011) Genome Res , vol.21 , pp. 1563-1571
    • Sterne-Weiler, T.1    Howard, J.2    Mort, M.3    Cooper, D.N.4    Sanford, J.R.5
  • 162
    • 33846984935 scopus 로고    scopus 로고
    • Transcriptional noise and the fidelity of initiation by RNA polymerase II
    • COI: 1:CAS:528:DC%2BD2sXht1Gqurs%3D, PID: 17277804
    • Struhl K (2007) Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat Struct Mol Biol 14:103–105
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 103-105
    • Struhl, K.1
  • 163
    • 34547119966 scopus 로고    scopus 로고
    • The shuttling SR protein 9G8 plays a role in translation of unspliced mRNA containing a constitutive transport element
    • COI: 1:CAS:528:DC%2BD2sXntFWqsr8%3D, PID: 17513303
    • Swartz JE, Bor YC, Misawa Y, Rekosh D, Hammarskjold ML (2007) The shuttling SR protein 9G8 plays a role in translation of unspliced mRNA containing a constitutive transport element. J Biol Chem 282:19844–19853
    • (2007) J Biol Chem , vol.282 , pp. 19844-19853
    • Swartz, J.E.1    Bor, Y.C.2    Misawa, Y.3    Rekosh, D.4    Hammarskjold, M.L.5
  • 164
    • 84974530326 scopus 로고    scopus 로고
    • Molecular basis and therapeutic strategies to rescue factor IX variants that affect splicing and protein function
    • PID: 27227676
    • Tajnik M, Rogalska ME, Bussani E, Barbon E, Balestra D, Pinotti M, Pagani F (2016) Molecular basis and therapeutic strategies to rescue factor IX variants that affect splicing and protein function. PLoS Genet 12:e1006082
    • (2016) PLoS Genet , vol.12
    • Tajnik, M.1    Rogalska, M.E.2    Bussani, E.3    Barbon, E.4    Balestra, D.5    Pinotti, M.6    Pagani, F.7
  • 165
    • 35348897138 scopus 로고    scopus 로고
    • Role of purine-rich exonic splicing enhancers in nuclear retention of pre-mRNAs
    • COI: 1:CAS:528:DC%2BD2sXpvVOjsLY%3D, PID: 17699631
    • Taniguchi I, Masuyama K, Ohno M (2007) Role of purine-rich exonic splicing enhancers in nuclear retention of pre-mRNAs. Proc Natl Acad Sci USA 104:13684–13689
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 13684-13689
    • Taniguchi, I.1    Masuyama, K.2    Ohno, M.3
  • 167
    • 80053052971 scopus 로고    scopus 로고
    • Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes
    • COI: 1:CAS:528:DC%2BC3MXht1ajtLjE, PID: 21673748
    • Thery JC et al (2011) Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes. Eur J Hum Genet 19:1052–1058
    • (2011) Eur J Hum Genet , vol.19 , pp. 1052-1058
    • Thery, J.C.1
  • 168
    • 47149097787 scopus 로고    scopus 로고
    • A large fraction of unclassified variants of the mismatch repair genes MLH1 and MSH2 is associated with splicing defects
    • COI: 1:CAS:528:DC%2BD1MXhtVGgsLc%3D, PID: 18561205
    • Tournier I et al (2008) A large fraction of unclassified variants of the mismatch repair genes MLH1 and MSH2 is associated with splicing defects. Hum Mutat 29:1412–1424
    • (2008) Hum Mutat , vol.29 , pp. 1412-1424
    • Tournier, I.1
  • 169
    • 10744227931 scopus 로고    scopus 로고
    • Mammalian overlapping genes: the comparative perspective
    • COI: 1:CAS:528:DC%2BD2cXhsFKhs7o%3D, PID: 14762064
    • Veeramachaneni V, Makalowski W, Galdzicki M, Sood R, Makalowska I (2004) Mammalian overlapping genes: the comparative perspective. Genome Res 14:280–286
    • (2004) Genome Res , vol.14 , pp. 280-286
    • Veeramachaneni, V.1    Makalowski, W.2    Galdzicki, M.3    Sood, R.4    Makalowska, I.5
  • 170
    • 84885909715 scopus 로고    scopus 로고
    • Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs
    • COI: 1:CAS:528:DC%2BC3sXhsFOksLjO, PID: 23887936
    • Wan J, Oliver VF, Zhu H, Zack DJ, Qian J, Merbs SL (2013) Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs. Nucleic Acids Res 41:8503–8514
    • (2013) Nucleic Acids Res , vol.41 , pp. 8503-8514
    • Wan, J.1    Oliver, V.F.2    Zhu, H.3    Zack, D.J.4    Qian, J.5    Merbs, S.L.6
  • 171
    • 57149100569 scopus 로고    scopus 로고
    • The impact of the nucleosome code on protein-coding sequence evolution in yeast
    • PID: 18989456
    • Warnecke T, Batada NN, Hurst LD (2008a) The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet 4:e1000250
    • (2008) PLoS Genet , vol.4
    • Warnecke, T.1    Batada, N.N.2    Hurst, L.D.3
  • 172
    • 43549084386 scopus 로고    scopus 로고
    • Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes
    • PID: 18257921
    • Warnecke T, Parmley JL, Hurst LD (2008b) Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes. Genome Biol 9:R29
    • (2008) Genome Biol , vol.9 , pp. R29
    • Warnecke, T.1    Parmley, J.L.2    Hurst, L.D.3
  • 173
    • 84976520941 scopus 로고    scopus 로고
    • dbDSM: a manually curated database for deleterious synonymous mutations
    • COI: 1:CAS:528:DC%2BC28XhsF2lsbzP, PID: 27153700
    • Wen P, Xiao P, Xia J (2016) dbDSM: a manually curated database for deleterious synonymous mutations. Bioinformatics 32:1914–1916
    • (2016) Bioinformatics , vol.32 , pp. 1914-1916
    • Wen, P.1    Xiao, P.2    Xia, J.3
  • 174
    • 84855266301 scopus 로고    scopus 로고
    • A population genetics-phylogenetics approach to inferring natural selection in coding sequences
    • COI: 1:CAS:528:DC%2BC3MXhs1Ggur3K, PID: 22144911
    • Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M (2011) A population genetics-phylogenetics approach to inferring natural selection in coding sequences. PLoS Genet 7:e1002395
    • (2011) PLoS Genet , vol.7
    • Wilson, D.J.1    Hernandez, R.D.2    Andolfatto, P.3    Przeworski, M.4
  • 175
    • 77949480756 scopus 로고    scopus 로고
    • Genomic features defining exonic variants that modulate splicing
    • PID: 20158892
    • Woolfe A, Mullikin JC, Elnitski L (2010) Genomic features defining exonic variants that modulate splicing. Genome Biol 11:R20
    • (2010) Genome Biol , vol.11 , pp. R20
    • Woolfe, A.1    Mullikin, J.C.2    Elnitski, L.3
  • 176
    • 0006713602 scopus 로고
    • Identification of the breast cancer susceptibility gene BRCA2
    • COI: 1:CAS:528:DyaK28XltFWi, PID: 8524414
    • Wooster R et al (1995) Identification of the breast cancer susceptibility gene BRCA2. Nature 378:789–792
    • (1995) Nature , vol.378 , pp. 789-792
    • Wooster, R.1
  • 177
    • 0002878320 scopus 로고
    • Physiological and evolutionary theories of dominance
    • Wright S (1934) Physiological and evolutionary theories of dominance. Am Nat 68:24–53
    • (1934) Am Nat , vol.68 , pp. 24-53
    • Wright, S.1
  • 178
    • 84931289173 scopus 로고    scopus 로고
    • Why selection might be stronger when populations are small: intron size and density predict within and between-species usage of exonic splice associated cis-motifs
    • PID: 25771198
    • Wu X, Hurst LD (2015) Why selection might be stronger when populations are small: intron size and density predict within and between-species usage of exonic splice associated cis-motifs. Mol Biol Evol 32:1847–1861
    • (2015) Mol Biol Evol , vol.32 , pp. 1847-1861
    • Wu, X.1    Hurst, L.D.2
  • 179
    • 84964608718 scopus 로고    scopus 로고
    • Determinants of the usage of splice-associated cis-motifs predict the distribution of human pathogenic SNPs
    • COI: 1:CAS:528:DC%2BC28XhslWksrfF, PID: 26545919
    • Wu X, Hurst LD (2016) Determinants of the usage of splice-associated cis-motifs predict the distribution of human pathogenic SNPs. Mol Biol Evol 33:518–529
    • (2016) Mol Biol Evol , vol.33 , pp. 518-529
    • Wu, X.1    Hurst, L.D.2
  • 180
    • 23244443123 scopus 로고    scopus 로고
    • Distribution of exonic splicing enhancer elements in human genes
    • COI: 1:CAS:528:DC%2BD2MXmvFCrtLg%3D, PID: 16005179
    • Wu Y, Zhang Y, Zhang J (2005) Distribution of exonic splicing enhancer elements in human genes. Genomics 86:329–336
    • (2005) Genomics , vol.86 , pp. 329-336
    • Wu, Y.1    Zhang, Y.2    Zhang, J.3
  • 181
    • 77950357450 scopus 로고    scopus 로고
    • A splicing-independent function of SF2/ASF in microRNA processing
    • COI: 1:CAS:528:DC%2BC3cXlvFynsbo%3D, PID: 20385090
    • Wu H, Sun S, Tu K, Gao Y, Xie B, Krainer AR, Zhu J (2010) A splicing-independent function of SF2/ASF in microRNA processing. Mol Cell 38:67–77
    • (2010) Mol Cell , vol.38 , pp. 67-77
    • Wu, H.1    Sun, S.2    Tu, K.3    Gao, Y.4    Xie, B.5    Krainer, A.R.6    Zhu, J.7
  • 182
    • 84926652259 scopus 로고    scopus 로고
    • Reassessing the “duon” hypothesis of protein evolution
    • COI: 1:CAS:528:DC%2BC28Xhs12rsLjO, PID: 25582593
    • Xing K, He X (2015) Reassessing the “duon” hypothesis of protein evolution. Mol Biol Evol 32:1056–1062
    • (2015) Mol Biol Evol , vol.32 , pp. 1056-1062
    • Xing, K.1    He, X.2
  • 183
    • 26444593981 scopus 로고    scopus 로고
    • Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences
    • COI: 1:CAS:528:DC%2BD2MXhtVygtr7M, PID: 16157889
    • Xing Y, Lee C (2005) Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci USA 102:13526–13531
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 13526-13531
    • Xing, Y.1    Lee, C.2
  • 184
    • 84976870685 scopus 로고    scopus 로고
    • Ensembl 2016
    • COI: 1:CAS:528:DC%2BC2sXhtV2gu7fP, PID: 26687719
    • Yates A et al (2016) Ensembl 2016. Nucleic Acids Res 44:D710–D716
    • (2016) Nucleic Acids Res , vol.44 , pp. D710-D716
    • Yates, A.1
  • 185
    • 84924578243 scopus 로고    scopus 로고
    • HP1 is involved in regulating the global impact of DNA methylation on alternative splicing
    • COI: 1:CAS:528:DC%2BC2MXjtlSqtLw%3D, PID: 25704815
    • Yearim A et al (2015) HP1 is involved in regulating the global impact of DNA methylation on alternative splicing. Cell reports 10:1122–1134
    • (2015) Cell reports , vol.10 , pp. 1122-1134
    • Yearim, A.1
  • 186
    • 84873323035 scopus 로고    scopus 로고
    • Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements
    • COI: 1:CAS:528:DC%2BC3sXhvFSrsrg%3D, PID: 23374342
    • Zarnack K et al (2013) Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 152:453–466
    • (2013) Cell , vol.152 , pp. 453-466
    • Zarnack, K.1
  • 187
    • 79251564926 scopus 로고    scopus 로고
    • GC content around splice sites affects splicing through pre-mRNA secondary structures
    • COI: 1:CAS:528:DC%2BC3MXhvFagt7w%3D, PID: 21281513
    • Zhang J, Kuo CJ, Chen L (2011) GC content around splice sites affects splicing through pre-mRNA secondary structures. BMC genomics 12:90
    • (2011) BMC genomics , vol.12 , pp. 90
    • Zhang, J.1    Kuo, C.J.2    Chen, L.3
  • 188
    • 84881493949 scopus 로고    scopus 로고
    • Prediction of clustered RNA-binding protein motif sites in the mammalian genome
    • COI: 1:CAS:528:DC%2BC3sXht1Cktb%2FN, PID: 23685613
    • Zhang C, Lee KY, Swanson MS, Darnell RB (2013) Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res 41:6793–6807
    • (2013) Nucleic Acids Res , vol.41 , pp. 6793-6807
    • Zhang, C.1    Lee, K.Y.2    Swanson, M.S.3    Darnell, R.B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.