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Volumn 62, Issue 5, 2006, Pages 511-522

Processed pseudogenes, processed genes, and spontaneous mutations in the Arabidopsis genome

Author keywords

Arabidopsis thaliana; Processed genes; Processed pseudogenes; Spontaneous mutations; Substitutions

Indexed keywords

COMPLEMENTARY DNA; CYTOSINE; ENZYME; HYDROLASE; NUCLEIC ACID; NUCLEOTIDE; PHOSPHOTRANSFERASE; RNA; TRANSFERASE;

EID: 33745644047     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-005-0045-z     Document Type: Article
Times cited : (29)

References (39)
  • 1
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
    • (2000) Nature , vol.408 , pp. 796-815
  • 2
    • 0032865868 scopus 로고    scopus 로고
    • RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements
    • Brosius J (1999) RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115-134
    • (1999) Gene , vol.238 , pp. 115-134
    • Brosius, J.1
  • 3
    • 0026447994 scopus 로고
    • On "genomenclature": A comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA"
    • USA
    • Brosius J, Gould SJ (1992) On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA". Proc Natl Acad Sci USA 89:10706-10710
    • (1992) Proc Natl Acad Sci , vol.89 , pp. 10706-10710
    • Brosius, J.1    Gould, S.J.2
  • 4
    • 3543107924 scopus 로고    scopus 로고
    • A phylogeny of Caenorhabditis reveals frequent loss of introns during nematode evolution
    • Cho S, Jin SW, Cohen A, Ellis RE (2004) A phylogeny of Caenorhabditis reveals frequent loss of introns during nematode evolution. Genome Res 14:1207-1220
    • (2004) Genome Res , vol.14 , pp. 1207-1220
    • Cho, S.1    Jin, S.W.2    Cohen, A.3    Ellis, R.E.4
  • 5
    • 0018185292 scopus 로고
    • Molecular basis of base substitution hotspots in Escherichia coli
    • Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775-780
    • (1978) Nature , vol.274 , pp. 775-780
    • Coulondre, C.1    Miller, J.H.2    Farabaugh, P.J.3    Gilbert, W.4
  • 6
    • 0023197108 scopus 로고
    • A plant processed pseudogene
    • Drouin G, Dover GA (1987) A plant processed pseudogene. Nature 328:557-558
    • (1987) Nature , vol.328 , pp. 557-558
    • Drouin, G.1    Dover, G.A.2
  • 7
    • 9844238691 scopus 로고    scopus 로고
    • Loss of introns in the pollen-specific actin gene subfamily members of potato and tomato
    • Drouin G, de Moniz Sá M (1997) Loss of introns in the pollen-specific actin gene subfamily members of potato and tomato. J Mol Evol 45:509-513
    • (1997) J Mol Evol , vol.45 , pp. 509-513
    • Drouin, G.1    De Moniz Sá, M.2
  • 8
    • 0023649687 scopus 로고
    • Pseudogenes in yeast?
    • Fink GR (1987) Pseudogenes in yeast? Cell 49:5-6
    • (1987) Cell , vol.49 , pp. 5-6
    • Fink, G.R.1
  • 9
    • 0020317308 scopus 로고
    • Patterns of nucleotide substitution in pseudogenes and functional genes
    • Gojobori T, Li W-H, Graur D (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18:360-369
    • (1982) J Mol Evol , vol.18 , pp. 360-369
    • Gojobori, T.1    Li, W.-H.2    Graur, D.3
  • 10
    • 0342858851 scopus 로고    scopus 로고
    • Nature and structure of human genes that generate retropseudognes
    • Gonçalves I, Duret L, Mouchiroud D (2000) Nature and structure of human genes that generate retropseudognes. Genome Res 10:672-678
    • (2000) Genome Res , vol.10 , pp. 672-678
    • Gonçalves, I.1    Duret, L.2    Mouchiroud, D.3
  • 12
    • 0019417156 scopus 로고
    • Sequence specificity of methylation in higher plant DNA
    • Gruenbaum Y, Naveh-Many T, Cedar H, Razin A (1981) Sequence specificity of methylation in higher plant DNA. Nature 292:860-862
    • (1981) Nature , vol.292 , pp. 860-862
    • Gruenbaum, Y.1    Naveh-Many, T.2    Cedar, H.3    Razin, A.4
  • 13
    • 0035253528 scopus 로고    scopus 로고
    • Digging for dead genes: An analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome
    • Harrison PM, Echols N, Gerstein MB (2001) Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. Nucleic Acids Res 29:818-830
    • (2001) Nucleic Acids Res , vol.29 , pp. 818-830
    • Harrison, P.M.1    Echols, N.2    Gerstein, M.B.3
  • 14
    • 0036300794 scopus 로고    scopus 로고
    • A small reservoir of disabled ORF's in the yeast genome and its implications for the dynamics of proteome evolution
    • Harrison PM, Kumar A, Lan N, Echols N, Snyder M, Gerstein M (2002) A small reservoir of disabled ORF's in the yeast genome and its implications for the dynamics of proteome evolution. J Mol Biol 316:409-419
    • (2002) J Mol Biol , vol.316 , pp. 409-419
    • Harrison, P.M.1    Kumar, A.2    Lan, N.3    Echols, N.4    Snyder, M.5    Gerstein, M.6
  • 16
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotides sequences
    • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotides sequences. J Mol Evol 16:111-120
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 18
    • 0029168659 scopus 로고
    • A cdc2 homologue and closely related processed retropseudogenes from Norway spruce
    • Kvarnheden A, Tandre K, Engstrom P (1995) A cdc2 homologue and closely related processed retropseudogenes from Norway spruce. Plant Mol Biol 27:391-403
    • (1995) Plant Mol Biol , vol.27 , pp. 391-403
    • Kvarnheden, A.1    Tandre, K.2    Engstrom, P.3
  • 19
    • 0027403961 scopus 로고
    • Unbiased estimation of the rates of synonymous and nonsynonymous substitution
    • Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36:96-99
    • (1993) J Mol Evol , vol.36 , pp. 96-99
    • Li, W.-H.1
  • 20
    • 0019726330 scopus 로고
    • Pseudogenes as a paradigm of neutral evolution
    • Li W-H, Gojobori T, Nei M (1981) Pseudogenes as a paradigm of neutral evolution. Nature 292:237-239
    • (1981) Nature , vol.292 , pp. 237-239
    • Li, W.-H.1    Gojobori, T.2    Nei, M.3
  • 21
    • 0021710490 scopus 로고
    • Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications
    • Li W-H, Wu CI, Luo CC (1984) Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J Mol Evol 21:58-71
    • (1984) J Mol Evol , vol.21 , pp. 58-71
    • Li, W.-H.1    Wu, C.I.2    Luo, C.C.3
  • 22
    • 0030019558 scopus 로고    scopus 로고
    • Structure and evolution of the actin gene family in Arabidopsis thaliana
    • McDowell JM, Huang S, McKinney EC, An YQ, Meagher RB (1996) Structure and evolution of the actin gene family in Arabidopsis thaliana. Genetics 142:587-602
    • (1996) Genetics , vol.142 , pp. 587-602
    • McDowell, J.M.1    Huang, S.2    McKinney, E.C.3    An, Y.Q.4    Meagher, R.B.5
  • 23
    • 0037252518 scopus 로고    scopus 로고
    • Identification and characterization of the ARIADNE gene family in Arabidopsis. A group of putative E3 ligases
    • Mladek C, Guger K, Hauser MT (2003) Identification and characterization of the ARIADNE gene family in Arabidopsis. A group of putative E3 ligases. Plant Physiol 131:27-40
    • (2003) Plant Physiol , vol.131 , pp. 27-40
    • Mladek, C.1    Guger, K.2    Hauser, M.T.3
  • 25
    • 1542682570 scopus 로고    scopus 로고
    • Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
    • Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, Okada N (2003) Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol 4:R74
    • (2003) Genome Biol , vol.4
    • Ohshima, K.1    Hattori, M.2    Yada, T.3    Gojobori, T.4    Sakaki, Y.5    Okada, N.6
  • 26
    • 0031593238 scopus 로고    scopus 로고
    • Patterns and rates of indel evolution in processed pseudogenes from humans and murids
    • Ophir R, Graur D (1997) Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene 205:191-202
    • (1997) Gene , vol.205 , pp. 191-202
    • Ophir, R.1    Graur, D.2
  • 27
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • USA
    • Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444-2448
    • (1988) Proc Natl Acad Sci , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 28
    • 0033573925 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution in Drosophila and mammalian genomes
    • USA
    • Petrov DA, Hard DL (1999) Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc Natl Acad Sci USA 96:1475-1479
    • (1999) Proc Natl Acad Sci , vol.96 , pp. 1475-1479
    • Petrov, D.A.1    Hard, D.L.2
  • 29
    • 0019318994 scopus 로고
    • DNA methylation and gene function
    • Razin A, Riggs AD (1980) DNA methylation and gene function. Science 210:604-610
    • (1980) Science , vol.210 , pp. 604-610
    • Razin, A.1    Riggs, A.D.2
  • 32
    • 0020476276 scopus 로고
    • The absence of detectable methylated bases in Drosophila melanogaster DNA
    • Urieli-Shoval S, Gruenbaum Y, Sedat J, Razin A (1982) The absence of detectable methylated bases in Drosophila melanogaster DNA. FEBS Lett 146:148-152
    • (1982) FEBS Lett , vol.146 , pp. 148-152
    • Urieli-Shoval, S.1    Gruenbaum, Y.2    Sedat, J.3    Razin, A.4
  • 33
    • 0022293979 scopus 로고
    • Processed pseudogenes: Characteristics and evolution
    • Vanin EF (1985) Processed pseudogenes: characteristics and evolution. Annu Rev Genet 19:253-272
    • (1985) Annu Rev Genet , vol.19 , pp. 253-272
    • Vanin, E.F.1
  • 34
    • 0022555861 scopus 로고
    • Nonviral retroposons: Genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information
    • Weiner AM, Deininger PL, Efstratiadis A (1986) Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem 55:631-661
    • (1986) Annu Rev Biochem , vol.55 , pp. 631-661
    • Weiner, A.M.1    Deininger, P.L.2    Efstratiadis, A.3
  • 36
    • 0345306317 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes
    • Zhang Z, Gerstein M (2003) Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res 31:5338-5348
    • (2003) Nucleic Acids Res , vol.31 , pp. 5338-5348
    • Zhang, Z.1    Gerstein, M.2
  • 37
    • 0036796620 scopus 로고    scopus 로고
    • Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome
    • Zhang Z, Harrison P, Gerstein M (2002) Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res 12:1466-1482
    • (2002) Genome Res , vol.12 , pp. 1466-1482
    • Zhang, Z.1    Harrison, P.2    Gerstein, M.3
  • 38
    • 0346752110 scopus 로고    scopus 로고
    • Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human genome
    • Zhang Z, Harrison PM, Liu L, Gerstein M (2003) Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res 13:2541-2558
    • (2003) Genome Res , vol.13 , pp. 2541-2558
    • Zhang, Z.1    Harrison, P.M.2    Liu, L.3    Gerstein, M.4
  • 39
    • 1642473033 scopus 로고    scopus 로고
    • Comparative analysis of processed pseudogenes in the mouse and human genomes
    • Zhang Z, Carriero N, Gerstein M (2004) Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet 20:62-67
    • (2004) Trends Genet , vol.20 , pp. 62-67
    • Zhang, Z.1    Carriero, N.2    Gerstein, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.