Protein domains correlate strongly with exons in multiple eukaryotic genomes - Evidence of exon shuffling?

Trends in Genetics

Volumn 20, Issue 9, 2004, Pages 399-403

  Liu, Mingyi ^a   Grigoriev, Andrei ^a  

^a GPC Biotech AG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

CORRELATION ANALYSIS; EUKARYOTE; EXON; GENE STRUCTURE; GENETIC ALGORITHM; GENOME; GENOME ANALYSIS; GENOMICS; HUMAN; INTRON; INVERTEBRATE; MOLECULAR EVOLUTION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; REVIEW; SPECIES COMPARISON; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS; THEORETICAL STUDY; VERTEBRATE;

EUKARYOTA; INVERTEBRATA; VERTEBRATA;

EID: 4143069189     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2004.06.013     Document Type: Short Survey

References (23)

1. J-M. Claverie Gene number: what if there are only 30,000 human genes? Science 291 2001 1255 1257
2. D.L. Hartl Molecular melodies in high and low C Nat. Rev. Genet. 1 2000 145 149
3. P.M. Harrison A question of size: the eukaryotic proteome and the problems in defining it Nucleic Acids Res. 30 2002 1083 1090
4. W. Gilbert Why genes in pieces? Nature 271 1978 501
5. M. Long Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila Gene 238 1999 135 141
6. D. Dupuy SCAN domain-containing 2 gene (SCAND2) is a novel nuclear protein derived from the zinc finger family by exon shuffling Gene 289 2002 1 6
7. H. Kaessmann Signatures of domain shuffling in the human genome Genome Res. 12 2002 1642 1650
8. S.J. de Souza Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins Proc. Natl. Acad. Sci. U. S. A. 95 1998 5094 5099
9. M. Long Origin of new genes: evidence from experimental and computational analyses Genetica 118 2003 171 182
10. S. Saxonov, and W. Gilbert The universe of exons revisited Genetica 118 2003 267 278
11. A. Fedorov Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns Proc. Natl. Acad. Sci. U. S. A. 98 2001 13177 13182
12. S.J. de Souza Intron positions correlate with module boundaries in ancient proteins Proc. Natl. Acad. Sci. U. S. A. 93 1996 14632 14636
13. R.F. Doolittle The multiplicity of domains in proteins Annu. Rev. Biochem. 64 1995 287 314
14. R.L. Dorit, and W. Gilbert The limited universe of exons Curr. Opin. Genet. Dev. 1 1991 464 469
15. J.A. Kolkman, and W.P. Stemmer Directed evolution of proteins by exon shuffling Nat. Biotechnol. 19 2001 423 428
16. E. Birney An overview of Ensembl Genome Res. 14 2004 925 928
17. S.R. Eddy Profile hidden Markov models Bioinformatics 14 1998 755 763
18. A. Bateman The Pfam protein families database Nucleic Acids Res. 30 2002 276 280
19. C.C. Blake Do genes-in-pieces imply proteins-in-pieces? Nature 273 1978 267
20. L. Patthy Intron-dependent evolution: preferred types of exons and introns FEBS Lett. 214 1987 1 7
21. A. van Rijk, and H. Bloemendal Molecular mechanisms of exon shuffling: illegitimate recombination Genetica 118 2003 245 249
22. T. Eickbush Exon shuffling in retrospect Science 283 1999 1465 1467
23. S.W. Roy Recent evidence for the exon theory of genes Genetica 118 2003 251 266