메뉴 건너뛰기




Volumn 7, Issue , 2006, Pages

Fast rate of evolution in alternatively spliced coding regions of mammalian genes

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; RNA;

EID: 33646538440     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-84     Document Type: Article
Times cited : (29)

References (41)
  • 2
    • 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
    • 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, 34:177-180.
    • (2003) Nat Genet , vol.34 , pp. 177-180
    • Modrek, B.1    Lee, C.J.2
  • 3
    • 33646577619 scopus 로고    scopus 로고
    • Computational analysis of alternative splicing
    • Chapman & Hall/CRC Computer & Information Science Series Volume 9. Edited by: Alluru S. New York. Chapman & Hall/CRC
    • Gelfand MS: Computational analysis of alternative splicing. In Handbook of Computational Molecular Biology, Chapman & Hall/CRC Computer & Information Science Series Volume 9. Edited by: Alluru S. New York. Chapman & Hall/CRC; 2005.
    • (2005) Handbook of Computational Molecular Biology
    • Gelfand, M.S.1
  • 4
    • 20044383938 scopus 로고    scopus 로고
    • Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms
    • Kopelman NM, Lancet D, Yanai I: Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms. Nature Genet 2005, 37:588-589.
    • (2005) Nature Genet , vol.37 , pp. 588-589
    • Kopelman, N.M.1    Lancet, D.2    Yanai, I.3
  • 5
    • 32044443159 scopus 로고    scopus 로고
    • Evolution of alternative splicing after gene duplication
    • Su Z, Wang J, Yu J, Huang X, Gu X: Evolution of alternative splicing after gene duplication. Genome Res 2006, 16:182-189.
    • (2006) Genome Res , vol.16 , pp. 182-189
    • Su, Z.1    Wang, J.2    Yu, J.3    Huang, X.4    Gu, X.5
  • 6
    • 0037308625 scopus 로고    scopus 로고
    • Translational control by the 3′-UTR: The ends specify the means
    • Mazumder B, Seshadri V, Fox PL: Translational control by the 3′-UTR: the ends specify the means. Trends Biochem Sci 2003, 28:91-98.
    • (2003) Trends Biochem Sci , vol.28 , pp. 91-98
    • Mazumder, B.1    Seshadri, V.2    Fox, P.L.3
  • 7
    • 1942467065 scopus 로고    scopus 로고
    • Genomic variants in exons and introns: Identifying the splicing spoilers
    • Pagani F, Baralle FE: Genomic variants in exons and introns: identifying the splicing spoilers. Nat Rev Genet 2004, 5:389-396.
    • (2004) Nat Rev Genet , vol.5 , pp. 389-396
    • Pagani, F.1    Baralle, F.E.2
  • 8
    • 16344362654 scopus 로고    scopus 로고
    • The evolution of transcription-initiation sites
    • Lynch M, Scofield DG, Hong X: The evolution of transcription-initiation sites. Mol Biol Evol 2005, 22:1137-1146.
    • (2005) Mol Biol Evol , vol.22 , pp. 1137-1146
    • Lynch, M.1    Scofield, D.G.2    Hong, X.3
  • 9
    • 0342723790 scopus 로고    scopus 로고
    • Frequent alternative splicing of human genes
    • Mironov AA, Fickett JW, Gelfand MS: Frequent alternative splicing of human genes. Genome Res 1999, 9:1288-1293.
    • (1999) Genome Res , vol.9 , pp. 1288-1293
    • Mironov, A.A.1    Fickett, J.W.2    Gelfand, M.S.3
  • 10
    • 0037669010 scopus 로고    scopus 로고
    • Low conservation of alternative splicing patterns in the human and mouse genomes
    • Nurtdinov RN, Artamonova II, Mironov AA, Gelfand MS: Low conservation of alternative splicing patterns in the human and mouse genomes. Hum Mol Genet 2003, 12:1313-1320.
    • (2003) Hum Mol Genet , vol.12 , pp. 1313-1320
    • Nurtdinov, R.N.1    Artamonova, I.I.2    Mironov, A.A.3    Gelfand, M.S.4
  • 11
    • 0037084825 scopus 로고    scopus 로고
    • Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human
    • Clark F, Thanaraj TA: Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human. Hum Mol Genet 2001, 11:451-464.
    • (2001) Hum Mol Genet , vol.11 , pp. 451-464
    • Clark, F.1    Thanaraj, T.A.2
  • 12
    • 0034326362 scopus 로고    scopus 로고
    • Analysis of canonical and non-canonical splice sites in mammalian genomes
    • Burset M, Seledtsov IA, Solovyev VV: Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res 2000, 28:4364-4375.
    • (2000) Nucleic Acids Res , vol.28 , pp. 4364-4375
    • Burset, M.1    Seledtsov, I.A.2    Solovyev, V.V.3
  • 13
    • 0038486897 scopus 로고    scopus 로고
    • Intronic sequences flanking alternatively spliced exons are conserved between human and mouse
    • Sorek R, Ast G: Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res 2003, 13:1631-1637.
    • (2003) Genome Res , vol.13 , pp. 1631-1637
    • Sorek, R.1    Ast, G.2
  • 15
    • 14544277546 scopus 로고    scopus 로고
    • Identification and analysis of alternative splicing events conserved in human and mouse
    • Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB: Identification and analysis of alternative splicing events conserved in human and mouse. Proc Natl Acad Sci U S A 2005, 102:2850-2855.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 2850-2855
    • Yeo, G.W.1    Van Nostrand, E.2    Holste, D.3    Poggio, T.4    Burge, C.B.5
  • 16
    • 27544498768 scopus 로고    scopus 로고
    • Assessing the application of Ka/Ks ratio test to alternatively spliced exons
    • Xing Y, Lee C: Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics 2005, 21:3701-3797.
    • (2005) Bioinformatics , vol.21 , pp. 3701-3797
    • Xing, Y.1    Lee, C.2
  • 17
    • 0034736528 scopus 로고    scopus 로고
    • A test of translational selection at 'silent' sites in the human genome: Base composition comparisons in alternatively spliced genes
    • Iida K, Akashi H: A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes. Gene 2000, 261:93-105.
    • (2000) Gene , vol.261 , pp. 93-105
    • Iida, K.1    Akashi, H.2
  • 18
    • 3242811414 scopus 로고    scopus 로고
    • Rapid evolution by positive Darwinian selection in the extracellular domain of the abundant lymphocyte protein CD45 in primates
    • Filip LC, Mundy NI: Rapid evolution by positive Darwinian selection in the extracellular domain of the abundant lymphocyte protein CD45 in primates. Mol Biol Evol 2004, 21:1504-1511.
    • (2004) Mol Biol Evol , vol.21 , pp. 1504-1511
    • Filip, L.C.1    Mundy, N.I.2
  • 19
    • 0035252561 scopus 로고    scopus 로고
    • Evidence for purifying selection acting on silent sites in BRCAI
    • Hurst LD, Pál C: Evidence for purifying selection acting on silent sites in BRCAI. Trends Genet 2001, 17:62-65.
    • (2001) Trends Genet , vol.17 , pp. 62-65
    • Hurst, L.D.1    Pál, C.2
  • 20
    • 0035340508 scopus 로고    scopus 로고
    • Purifying selection on silent sites - A constraint from splicing regulation?
    • Orban TI, Olah E: Purifying selection on silent sites - a constraint from splicing regulation? Trends Genet 2001, 17:252-253.
    • (2001) Trends Genet , vol.17 , pp. 252-253
    • Orban, T.I.1    Olah, E.2
  • 21
    • 26444593981 scopus 로고    scopus 로고
    • Evidence of functional selection pressure for, alternative splicing events that accelerate evolution of protein subsequences
    • Xing Y, Lee C: Evidence of functional selection pressure for, alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci U S A 2005, 102:13526-13531.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 13526-13531
    • Xing, Y.1    Lee, C.2
  • 22
    • 19344363466 scopus 로고    scopus 로고
    • Preferential duplication of conserved proteins in eukaryotic genomes
    • Davis JC, Petrov DA: Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol 2004, 2:318-326.
    • (2004) PLoS Biol , vol.2 , pp. 318-326
    • Davis, J.C.1    Petrov, D.A.2
  • 24
    • 0141853996 scopus 로고    scopus 로고
    • Asymmetric sequence divergence of duplicate genes
    • Conant GC, Wagner A: Asymmetric sequence divergence of duplicate genes. Genome Res 2003, 13:2052-2058.
    • (2003) Genome Res , vol.13 , pp. 2052-2058
    • Conant, G.C.1    Wagner, A.2
  • 25
    • 0642373709 scopus 로고    scopus 로고
    • Different evolutionary patterns between young duplicate genes in the human genome
    • Zhang P, Gu Z, Li WH: Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol 2003, 4:R56.
    • (2003) Genome Biol , vol.4
    • Zhang, P.1    Gu, Z.2    Li, W.H.3
  • 26
    • 0033977618 scopus 로고    scopus 로고
    • Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
    • Duret L, Mouchiroud D: Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol 2000, 17:68-74.
    • (2000) Mol Biol Evol , vol.17 , pp. 68-74
    • Duret, L.1    Mouchiroud, D.2
  • 27
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • Pal C, Papp B, Hurst LD: Highly expressed genes in yeast evolve slowly. Genetics 2001, 158:927-931.
    • (2001) Genetics , vol.158 , pp. 927-931
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 28
    • 8744268628 scopus 로고    scopus 로고
    • Duplicated genes evolve slower than singletons despite the initial rate increase
    • Jordan IK, Wolf YI, Koonin EV: Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol 2004, 4:22.
    • (2004) BMC Evol Biol , vol.4 , pp. 22
    • Jordan, I.K.1    Wolf, Y.I.2    Koonin, E.V.3
  • 29
    • 55449137900 scopus 로고    scopus 로고
    • Protein Modularity of Alternatively Spliced Exons Is Associated with Tissue-Specific Regulation of Alternative Splicing
    • Xing Y, Lee CJ: Protein Modularity of Alternatively Spliced Exons Is Associated with Tissue-Specific Regulation of Alternative Splicing. PLoS Genet 2005, 1:e34.
    • (2005) PLoS Genet , vol.1
    • Xing, Y.1    Lee, C.J.2
  • 30
    • 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, 23:301-309.
    • (2006) Mol Biol Evol , vol.23 , pp. 301-309
    • Parmley, J.L.1    Chamary, J.V.2    Hurst, L.D.3
  • 31
    • 33644853819 scopus 로고    scopus 로고
    • Can RNA selection pressure distort the measurement of Ka/Ks?
    • in press. Feb 16
    • Xing Y, Lee C: Can RNA selection pressure distort the measurement of Ka/ Ks? Gene in press. 2006, Feb 16
    • (2006) Gene
    • Xing, Y.1    Lee, C.2
  • 32
    • 0028906291 scopus 로고
    • New methods for estimating the numbers of synonymous and nonsynonymous substitutions
    • Ina Y: New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J Mol Evol 1995, 40:190-226.
    • (1995) J Mol Evol , vol.40 , pp. 190-226
    • Ina, Y.1
  • 33
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetics analysis by maximum likelyhood
    • Yang Z: PAML: a program package for phylogenetics analysis by maximum likelyhood. Comput Appl Biosci 1997, 13:555-556.
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 34
    • 84872268583 scopus 로고    scopus 로고
    • Evolutionary differences between alternative and constant protein-coding regions of alternatively spliced Drosophila genes
    • in press
    • Ermakova EO, Malko DB, Gelfand MS: Evolutionary differences between alternative and constant protein-coding regions of alternatively spliced Drosophila genes. Biofizika in press.
    • Biofizika
    • Ermakova, E.O.1    Malko, D.B.2    Gelfand, M.S.3
  • 35
    • 33645521073 scopus 로고    scopus 로고
    • Evolution of the exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes
    • Malko DB, Makeev VJ, Mironov AA, Gelfand MS: Evolution of the exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes. Genome Res 2006, 16(4):505-9.
    • (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
  • 36
    • 26444473715 scopus 로고    scopus 로고
    • Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons
    • Cusack BP, Wolfe KH: Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons. Mol Biol Evol 2005, 22:2198-2208.
    • (2005) Mol Biol Evol , vol.22 , pp. 2198-2208
    • Cusack, B.P.1    Wolfe, K.H.2
  • 38
    • 84872266578 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq)
    • NCBI Reference Sequence (RefSeq) [http://www.ncbi.nlm.nih.gov/RefSeq/]
  • 39
    • 0035748444 scopus 로고    scopus 로고
    • Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins
    • research0053.1-0053.9
    • Jordan IK, Kondrashov FA, Rogozin IB, Tatusov RL, Wolf YI, Koonin EV: Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins. Genome Biol 2001, 2:research0053.1-0053.9.
    • (2001) Genome Biol , vol.2
    • Jordan, I.K.1    Kondrashov, F.A.2    Rogozin, I.B.3    Tatusov, R.L.4    Wolf, Y.I.5    Koonin, E.V.6
  • 40
    • 84872277078 scopus 로고    scopus 로고
    • EDAS: EST-Derived Alternative Splicing Database
    • EDAS: EST-Derived Alternative Splicing Database [http://www.belozersky.msu.ru/edas/]
  • 41
    • 0035113035 scopus 로고    scopus 로고
    • Pro-Frame: Similarity-based gene recognition in eukaryotic DNA sequences with errors
    • Mironov AA, Novichkov PS, Gelfand MS: Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinformatics 2001, 17:13-15.
    • (2001) Bioinformatics , vol.17 , pp. 13-15
    • Mironov, A.A.1    Novichkov, P.S.2    Gelfand, M.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.