Genome architecture - Number, size and length distributions of exons and introns in six crown eukaryotic genomes

International Journal of Integrative Biology

Volumn 5, Issue 2, 2009, Pages 87-91

  Peng, Li ^a   Sakharkar, Kishore R ^b,c   Sakharkar, Meena K ^a,c  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b OmicsVista ^*  (Singapore)

^c NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

Architecture; Correlation; Distribution; Gene density; Genome design; Genome size; Profiles

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; CHROMOSOME SIZE; DROSOPHILA MELANOGASTER; EUKARYOTE; EXON; GENETIC CORRELATION; GENOME ANALYSIS; HUMAN; HUMAN GENOME; INTRON; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; PAN TROGLODYTES; STRUCTURAL GENOMICS; ZEBRA FISH;

CAENORHABDITIS ELEGANS; DANIO RERIO; DROSOPHILA MELANOGASTER; EUKARYOTA; HOMO SAPIENS; MUS MUSCULUS;

EID: 65549104359     PISSN: 09738363     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (33)

1. Berget SM (1995) Exon recognition in vertebrate splicing. J. Biol. Chem. 270: 2411-2414.
2. Birney E, et al. (2006) Ensembl 2006. Nucleic Acids Res. 34: D556-561.
3. Black DL (1991) Does steric interference between splice sites block the splicing of a short c-src neuron-specific exon in non-neuronal cells? Genes Dev. 5: 389-402.
4. Black DL (1992) Activation of c-src neuron-specific splicing by an unusual RNA element in vivo and in vitro. Cell 69: 795-807.
5. Collins L and Penny D (2006) Investigating the intron recognition mechanism in eukaryotes. Mol. Biol. Evol. 23: 901-910.
6. Coward E, et al. (2002) SpliceNest: visualization of gene structure and alternative splicing based on EST clusters. Trends Genet. 18: 53-55.
7. Croft L, et al. (2000) ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nature Genet. 24: 340-341.
8. Davuluri RV et al. (2001) Computational identification of promoters and first exons in the human genome. Nat. Genet. 29: 412-417.
9. Deutsch M and Long M (1999) Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 27: 3219-3228.
10. Dominski Z and Kole R (1991) Selection of splice sites in pre-mRNAs with short internal exons. Mol. Cell. Biol. 11: 6075-6083.
11. Dominski Z and Kole R (1992) Cooperation of pre-mRNA sequence elements in splice site selection. Mol. Cell. Biol. 12: 2108-2114.
12. Dorit RL, et al. (1990) How big is the universe of exons? Science 250: 1377-1382.
13. Galperin MY, et al. (2006) The Molecular Biology Database Collection: 2006 update. Nucleic Acids Res. 34: D3-D5.
14. Gopalan V, et al. (2004) Xpro: database of eukaryotic protein-encoding genes. Nucleic Acids Res. 32:D59-D63.
15. Gregory TR, et al. (2007) Eukaryotic genome size databases. Nucleic Acids Res. 35: D332-D338.
16. Hawkins JD (1988) A survey on intron and exon lengths. Nucleic Acids Res. 16: 9893-9906.
17. Hinrichs AS, et al. (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34: D590-598.
18. Hughes AL and Hughes MK (1995) Small genomes for better flyers. Nature 377: 391.
19. Lengyel J and Penman S (1975) hnRNA size and processing as related to different DNA content in two dipterans: Drosophila and Aedes. Cell 5: 281-290.
20. Lim LP and Burge CB (2001) A computational analysis of sequence features involved in recognition of short introns. Proc Natl Acad Sci U S A. 98(20): 11193-11198.
21. Maglott D, et al. (2005) Entrez gene: gene-centered information at NCBI. Nucleic Acids Res. 33: D54-D58.
22. McGuire AM et al. (2008) Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol. 9(3):R50.
23. Moriyama EN et al. (1998) Genome size and intron size in Drosophila. Mol. Rol. Evol. 15: 770-773.
24. Robberson BL, et al. (1990) Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol. Cell. Biol. 10: 84-94.
25. Sterner DA and Berget SM (1993) In vivo recognition of a vertebrate mini-exon as an exon-intron-exon unit. Mol. Cell. Biol. 13: 2677-2687.
26. Sakharkar M, et al. (2002) ExInt: an Exon Intron Database. Nucleic Acids Res. 30:191-194.
27. Sakharkar MR, et al. (2004) Distributions of exons and introns in the human genome. In Silico Biol. 4: 0032.
28. Sakharkar MK, et al. (2005) An analysis on gene architecture in human and mouse genomes. In Silico Biol. 5: 0032.
29. Saxonov S. et al. (2000) EID: the Exon-Intron Database: an exhaustive database of proteincoding intron-containing genes. Nucleic Acids Res. 28: 185-190.
30. Sterner DA, et al. (1996) Architectural limits on split genes. Proc. Natl. Acad. Sci. USA 93: 15081-15085.
31. Stormo GD (2000) Gene-finding approaches for eukaryotes. Genome Res. 10: 394-397.
32. Vinogradov AE (1999) Intron-genome size relationship on a large evolutionary scale. J Mol. Evol. 49: 376-384.
33. Zhang MQ (2002) Computational prediction of eukaryotic protein-coding genes. Nat. Rev. Genet. 3: 698-709.