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Volumn 14, Issue 4, 2004, Pages 517-527

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; GENOMIC DNA; GUANINE; THYMINE;

EID: 1842768391     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1984404     Document Type: Article
Times cited : (68)

References (45)
  • 1
    • 0035028769 scopus 로고    scopus 로고
    • Molecular phylogeny and divergence time estimates for major rodent groups: Evidence from multiple genes
    • Adkins, R., Gelke, E., Rowe, D., and Honeycutt, R. 2001. Molecular phylogeny and divergence time estimates for major rodent groups: Evidence from multiple genes. Mol. Biol. Evol. 18: 777-791.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 777-791
    • Adkins, R.1    Gelke, E.2    Rowe, D.3    Honeycutt, R.4
  • 3
    • 0036250811 scopus 로고    scopus 로고
    • Alu repeats and human genomic diversity
    • Batzer, M.A. and Deininger, P.L. 2002. Alu repeats and human genomic diversity. Nat. Rev. Genet. 3: 370-379.
    • (2002) Nat. Rev. Genet. , vol.3 , pp. 370-379
    • Batzer, M.A.1    Deininger, P.L.2
  • 5
    • 0035807820 scopus 로고    scopus 로고
    • Association between divergence and interspersed repeats in mammalian noncoding genomic DNA
    • Chiaromonte, F., Yang, S., Elnitski, L., Yap, V., Miller, W., and Hardison, R.C. 2001. Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. Proc. Natl. Acad. Sci. 98: 14503-14508.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 14503-14508
    • Chiaromonte, F.1    Yang, S.2    Elnitski, L.3    Yap, V.4    Miller, W.5    Hardison, R.C.6
  • 6
    • 0031982714 scopus 로고    scopus 로고
    • Potential Alu function: Regulation of the activity of double-stranded RNA-activated kinase PKR
    • Chu, W.M., Ballard, R., Carpick, B.W., Williams, B.R., and Schmid, C.W. 1998. Potential Alu function: Regulation of the activity of double-stranded RNA-activated kinase PKR. Mol. Cell. Biol. 18: 58-68.
    • (1998) Mol. Cell Biol. , vol.18 , pp. 58-68
    • Chu, W.M.1    Ballard, R.2    Carpick, B.W.3    Williams, B.R.4    Schmid, C.W.5
  • 7
    • 0036796354 scopus 로고    scopus 로고
    • Mammalian retroelements
    • Deininger, P.L. and Batzer, M.A. 2002. Mammalian retroelements. Genome Res. 12: 1455-1465.
    • (2002) Genome Res. , vol.12 , pp. 1455-1465
    • Deininger, P.L.1    Batzer, M.A.2
  • 8
    • 0041353551 scopus 로고    scopus 로고
    • LINE-mediated retrotransposition of marked Alu sequences
    • Dewannieux, M., Esnault, C., and Heidmann, T. 2003. LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35: 41-48.
    • (2003) Nat. Genet. , vol.35 , pp. 41-48
    • Dewannieux, M.1    Esnault, C.2    Heidmann, T.3
  • 9
    • 0026523850 scopus 로고
    • A human dimorphism resulting from loss of an Alu
    • Edwards, M.C. and Gibbs, R.A. 1992. A human dimorphism resulting from loss of an Alu. Genomics 14: 590-597.
    • (1992) Genomics , vol.14 , pp. 590-597
    • Edwards, M.C.1    Gibbs, R.A.2
  • 12
    • 0038015586 scopus 로고    scopus 로고
    • A neutral explanation for the correlation of diversity with recombination rates in humans
    • Hellmann, I., Ebersberger, I., Ptak, S.E., Paabo, S., and Przeworski, M. 2003. A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72: 1527-1535.
    • (2003) Am. J. Hum. Genet. , vol.72 , pp. 1527-1535
    • Hellmann, I.1    Ebersberger, I.2    Ptak, S.E.3    Paabo, S.4    Przeworski, M.5
  • 13
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 14
    • 0037301560 scopus 로고    scopus 로고
    • Origin of a substantial fraction of human regulatory sequences from transposable elements
    • Jordan, I.K., Rogozin, I.B., Glazko, G.V., and Koonin, E.V. 2003. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 19: 68-72.
    • (2003) Trends Genet. , vol.19 , pp. 68-72
    • Jordan, I.K.1    Rogozin, I.B.2    Glazko, G.V.3    Koonin, E.V.4
  • 15
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • (ed. H.N. Munro), Academic Press, New York
    • Jukes, T.H. and Cantor, C.R. 1969. Evolution of protein molecules. In Mammalian protein metabolism (ed. H.N. Munro), pp. 21-32. Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-32
    • Jukes, T.H.1    Cantor, C.R.2
  • 16
    • 0021731415 scopus 로고
    • Evolutionary constraints and the neutral theory
    • Jukes, T.H. and Kimura, M. 1984. Evolutionary constraints and the neutral theory. J. Mol. Evol. 21: 90-92.
    • (1984) J. Mol. Evol. , vol.21 , pp. 90-92
    • Jukes, T.H.1    Kimura, M.2
  • 17
    • 0031055331 scopus 로고    scopus 로고
    • Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons
    • Jurka, J. 1997. Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons. Proc. Natl. Acad. Sci. 94: 1872-1877.
    • (1997) Proc. Natl. Acad. Sci. , vol.94 , pp. 1872-1877
    • Jurka, J.1
  • 18
    • 0030598975 scopus 로고    scopus 로고
    • Recent amplification of rat ID sequences
    • Kim, J. and Deininger, P.L. 1996. Recent amplification of rat ID sequences. J. Mol. Biol. 261: 322-327.
    • (1996) J. Mol. Biol. , vol.261 , pp. 322-327
    • Kim, J.1    Deininger, P.L.2
  • 20
    • 0036640951 scopus 로고    scopus 로고
    • Human SNP variability and mutation rate are higher in regions of high recombination
    • Lercher, M.J. and Hurst, L.D. 2002. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18: 337-340.
    • (2002) Trends Genet. , vol.18 , pp. 337-340
    • Lercher, M.J.1    Hurst, L.D.2
  • 21
    • 0036613754 scopus 로고    scopus 로고
    • Clustering of housekeeping genes provides a unified model of gene order in the human genome
    • Lercher, M.J., Urrutia, A.O., and Hurst, L.D. 2002. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31: 180-183.
    • (2002) Nat. Genet. , vol.31 , pp. 180-183
    • Lercher, M.J.1    Urrutia, A.O.2    Hurst, L.D.3
  • 22
    • 0036375969 scopus 로고    scopus 로고
    • Significance of interspecies matches when evolutionary rate varies
    • Li, J. and Miller, W. 2002. Significance of interspecies matches when evolutionary rate varies. In RECOMB 2002 216-224.
    • (2002) RECOMB 2002 , pp. 216-224
    • Li, J.1    Miller, W.2
  • 23
    • 0033215140 scopus 로고    scopus 로고
    • Locus control regions: Coming of age at a decade plus
    • Li, Q., Harju, S., and Peterson, K.R. 1999. Locus control regions: Coming of age at a decade plus. Trends Genet. 15: 403-408.
    • (1999) Trends Genet. , vol.15 , pp. 403-408
    • Li, Q.1    Harju, S.2    Peterson, K.R.3
  • 24
    • 0025162768 scopus 로고
    • Recently transposed Alu repeats result from multiple source genes
    • Matera, A.G., Hellmann, U., Hintz, M.F., and Schmid, C.W. 1990. Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res. 18: 6019-6023.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6019-6023
    • Matera, A.G.1    Hellmann, U.2    Hintz, M.F.3    Schmid, C.W.4
  • 25
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Mouse Genome Sequencing Consortium
    • Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
    • (2002) Nature , vol.420 , pp. 520-562
  • 26
    • 0035451450 scopus 로고    scopus 로고
    • Single nucleotide polymorphisms and recombination rate in humans
    • Nachman, M.W. 2001. Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17: 481-485.
    • (2001) Trends Genet. , vol.17 , pp. 481-485
    • Nachman, M.W.1
  • 27
    • 0037371689 scopus 로고    scopus 로고
    • Evidence for co-evolution of gene order and recombination rate
    • Pal, C. and Hurst, L.D. 2003. Evidence for co-evolution of gene order and recombination rate. Nat. Genet. 33: 392-395.
    • (2003) Nat. Genet. , vol.33 , pp. 392-395
    • Pal, C.1    Hurst, L.D.2
  • 28
    • 0035261381 scopus 로고    scopus 로고
    • Genomic strategies to identify mammalian regulatory sequences
    • Pennacchio, L.A. and Rubin, E.M. 2001. Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet. 2: 100-109.
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 100-109
    • Pennacchio, L.A.1    Rubin, E.M.2
  • 29
    • 1842684068 scopus 로고    scopus 로고
    • Genome sequence of the Brown Norway Rat yields insights into mammalian evolution
    • Rat Genome Sequencing Project Consortium (in press)
    • Rat Genome Sequencing Project Consortium. 2004. Genome sequence of the Brown Norway Rat yields insights into mammalian evolution. Nature (in press).
    • (2004) Nature
  • 32
    • 0037100664 scopus 로고    scopus 로고
    • Selective stimulation of translational expression by Alu RNA
    • Rubin, C.M., Kimura, R.H., and Schmid, C.W. 2002. Selective stimulation of translational expression by Alu RNA. Nucleic Acids Res. 30: 3253-3261.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3253-3261
    • Rubin, C.M.1    Kimura, R.H.2    Schmid, C.W.3
  • 35
    • 16544368565 scopus 로고    scopus 로고
    • RepeatMasker at
    • Smit, A. and Green, P. 1999. RepeatMasker at http://ftp.genome.washington.edu/RM/RepeatMasker.html.
    • (1999)
    • Smit, A.1    Green, P.2
  • 36
    • 0027174559 scopus 로고
    • Identification of a new, abundant superfamily of mammalian LTR-transposons
    • Smit, A.F. 1993. Identification of a new, abundant superfamily of mammalian LTR-transposons. Nucleic Acids Res. 21: 1863-1872.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 1863-1872
    • Smit, A.F.1
  • 37
    • 0030479536 scopus 로고    scopus 로고
    • The origin of interspersed repeats in the human genome
    • Smith, A.F. 1996. The origin of interspersed repeats in the human genome. Curr. Opin. Genet. Dev. 6: 743-748.
    • (1996) Curr. Opin. Genet. Dev. , vol.6 , pp. 743-748
    • Smith, A.F.1
  • 38
    • 0028920059 scopus 로고
    • Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences
    • Smit, A.F., Toth, G., Riggs, A.D., and Jurka, J. 1995. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J. Mol. Biol. 246: 401-417.
    • (1995) J. Mol. Biol. , vol.246 , pp. 401-417
    • Smit, A.F.1    Toth, G.2    Riggs, A.D.3    Jurka, J.4
  • 39
    • 0036737595 scopus 로고    scopus 로고
    • Deterministic mutation rate variation in the human genome
    • Smith, N.G., Webster, M.T., and Ellegren, H. 2002. Deterministic mutation rate variation in the human genome. Genome Res. 12: 1350-1356.
    • (2002) Genome Res. , vol.12 , pp. 1350-1356
    • Smith, N.G.1    Webster, M.T.2    Ellegren, H.3
  • 40
    • 0037417891 scopus 로고    scopus 로고
    • Placental mammal diversification and the Cretaceous-Tertiary boundary
    • Springer, M., Murphy, W., Eizirik, E., and O'Brien, S. 2003. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc. Natl. Acad. Sci. 100: 1056-1061.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 1056-1061
    • Springer, M.1    Murphy, W.2    Eizirik, E.3    O'Brien, S.4
  • 41
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • Tavare, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences 17: 57-86.
    • (1986) Lectures on Mathematics in the Life Sciences , vol.17 , pp. 57-86
    • Tavare, S.1
  • 42
    • 0035339920 scopus 로고    scopus 로고
    • Molecular phylogenetics: State-of-the-art methods for looking into the past
    • Whelan, S., Lio, P., and Goldman, N. 2001. Molecular phylogenetics: State-of-the-art methods for looking into the past. Trends Genet. 17: 262-272.
    • (2001) Trends Genet. , vol.17 , pp. 262-272
    • Whelan, S.1    Lio, P.2    Goldman, N.3
  • 43
    • 0024497416 scopus 로고
    • Mutation rates differ among regions of the mammalian genome
    • Wolfe, K.H., Sharp, P.M., and Li, W.H. 1989. Mutation rates differ among regions of the mammalian genome. Nature 337: 283-285.
    • (1989) Nature , vol.337 , pp. 283-285
    • Wolfe, K.H.1    Sharp, P.M.2    Li, W.H.3
  • 44
    • 0028214103 scopus 로고
    • Estimating the pattern of nucleotide substitution
    • Yang, Z. 1994. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39: 105-111.
    • (1994) J. Mol. Evol. , vol.39 , pp. 105-111
    • Yang, Z.1
  • 45
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.