Nature and structure of human genes that generate retropseudogenes

Genome Research

Volumn 10, Issue 5, 2000, Pages 672-678

  Gonçalves, Isabelle ^a   Duret, Laurent ^a   Mouchiroud, Dominique ^a  

^a UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA; GUANINE; MESSENGER RNA;

CONTROLLED STUDY; DNA TRANSPOSITION; GENE EXPRESSION; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CONSERVATION; GERM LINE; HUMAN; HUMAN CELL; HUMAN TISSUE; LETTER; PRIORITY JOURNAL; PSEUDOGENE; RETROPOSON; REVERSE TRANSCRIPTION; TISSUE DISTRIBUTION;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, FACTUAL; EVOLUTION, MOLECULAR; GC RICH SEQUENCE; GENE EXPRESSION REGULATION; HUMANS; ORGAN SPECIFICITY; PSEUDOGENES; RETROELEMENTS;

EID: 0342858851     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.10.5.672     Document Type: Letter

References (24)

1. Altschul, S.F., T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Benson, D.A., M.S. Boguski, D.J. Lipman, J. Ostell, and B.F. Ouellette. 1998. GenBank. Nucleic Acids Res. 26: 1-7.
3. Bernardi, G. 1993. The isochore organization of the human genome and its evolutionary history - a review. Gene 135: 57-66.
4. Claverie, J.M. and D.J. States. 1993. Information enhancement methods for large scale sequence analysis. Computers Chem. 17: 191-201.
5. Dhellin, O., J. Maestre, and T. Heidmann. 1997. Functional differences between the human LINE retrotransposon and retroviral reverse transcriptases for in vivo mRNA reverse transcription. EMBO. J. 16: 6590-6602.
6. Dunham, I., N. Shimizu, B.A. Roe, S. Chissoe, A.R. Hunt, J.E. Collins, R. Bruskiewich, D.M. Beare, M. Clamp, L.J. Smink et al. 1999. The DNA sequence of human chromosome 22. Nature 402: 489-495.
7. Duret L. and D. Mouchiroud. 2000. Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17: 68-74.
8. Duret, L., D. Mouchiroud, and M. Gouy. 1994. HOVERGEN: A database of homologous vertebrate genes. Nucleic Acids Res. 22: 2360-2365.
9. Duret, L., D. Mouchiroud, and C. Gautier. 1995. Statistical analysis of vertebrates sequences reveals that long genes are scarce in GC-rich isochores. J. Mol. Evol. 40: 308-317.
10. Duret, L., E. Gasteiger, and G. Perriere. 1996. LALNVIEW: A graphical viewer for pairwise sequence alignments. Comput. Appl. Biosci. 12: 507-510.
11. Fields, C., M.D. Adams, O. White, and J.C. Venter. 1994. How many genes in the human genome? Nature Genet. 7: 345-346.
12. Gojobori, T., W.H. Li, and D. Graur. 1982. Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18: 360-369.
13. Goncalves, I., M. Robinson, G. Perriere, and D. Mouchiroud. 1999. JaDis: Computing distances between nucleic acid sequences. Bioinformatics 15: 424-425.
14. Gouy, M., C. Gautier, M. Attimonelli, C. Lanave, and G. Di Paola. 1985. ACNUC - a portable retrieval system for nucleic acid sequence databases: Logical and physical designs and usage. Comput. Appl. Biosci. 1: 167-172.
15. Graur, D., Y. Shuali, and W.H. Li. 1989. Deletions in processed pseudogenes accumulate faster in rodents than in humans. J. Mol. Evol. 28: 279-285.
16. Gu, X. and W.H. Li. 1995. The size distribution of insertions and deletions in human and rodent pseudogenes suggests the logarithmic gap penalty for sequence alignment. J. Mol. Evol. 40: 464-473.
17. Kazazian, H.H. and J.V. Moran. 1998. The impact of L1 retrotransposons on the human genome. Nature Genet. 19: 19-24.
18. Korenberg, J.R. and M.C. Rykowski. 1988. Human genome organization: Alu, lines, and the molecular structure of metaphase chromosome bands. Cell 53: 391-400.
19. Li, W.H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
20. Makalowski, W. and M.S. Boguski. 1998. Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences. Proc. Natl. Acad. Sci. 95: 9407-9412.
21. Mouchiroud, D., C. Gautier, and G. Bernardi. 1995. Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. J. Mol. Evol. 40: 107-113.
22. Ophir, R. and D. Graur. 1997. Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene 205: 191-202.
23. Vanin, E.F. 1985. Processed pseudogenes: Characteristics and evolution. Annu. Rev. Genet. 19: 253-272.
24. Wolfe, K.H. and P.M. Sharp. 1993. Mammalian gene evolution: Nucleotide sequence divergence between mouse and rat. J. Mol. Evol. 37: 441-456.