Crossref journal-article
Public Library of Science (PLoS)
PLoS Genetics (340)
Bibliography

Lev-Maor, G., Goren, A., Sela, N., Kim, E., Keren, H., Doron-Faigenboim, A., Leibman-Barak, S., Pupko, T., & Ast, G. (2007). The “Alternative” Choice of Constitutive Exons throughout Evolution. PLoS Genetics, 3(11), e203.

Authors 9
  1. Galit Lev-Maor (first)
  2. Amir Goren (additional)
  3. Noa Sela (additional)
  4. Eddo Kim (additional)
  5. Hadas Keren (additional)
  6. Adi Doron-Faigenboim (additional)
  7. Shelly Leibman-Barak (additional)
  8. Tal Pupko (additional)
  9. Gil Ast (additional)
References 60 Referenced 55
  1. 10.1146/annurev.biochem.72.121801.161720 / Annu Rev Biochem / Mechanisms of alternative pre-messenger RNA splicing. (2003)
  2. 10.1016/S0168-9525(00)02176-4 / Trends Genet / Alternative splicing: increasing diversity in the proteomic world. (2001)
  3. 10.1016/0168-9525(96)10037-8 / Trends Genet / Directing alternative splicing: cast and scenarios. (1996)
  4. 10.1093/nar/gkl924 / Nucleic Acids Res / Different levels of alternative splicing among eukaryotes. (2007)
  5. SugnetCWKentWJAresMJrHausslerD 2004 Transcriptome and genome conservation of alternative splicing events in humans and mice. Pac Symp Biocomput 66 77 (10.1142/9789812704856_0007)
  6. 10.1038/nrg1451 / Nat Rev Genet / How did alternative splicing evolve? (2004)
  7. 10.1038/sj.emboj.7601023 / EMBO J / The expanding transcriptome: the genome as the ‘Book of Sand'. (2006)
  8. 10.1038/ng1159 / Nat Genet / Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. (2003)
  9. 10.1101/gr.3929705 / Genome Res / Origin and evolution of new exons in rodents. (2005)
  10. 10.1016/j.tig.2004.12.004 / Trends Genet / Alternative splicing of conserved exons is frequently species-specific in human and mouse. (2005)
  11. 10.1073/pnas.0409742102 / Proc Natl Acad Sci U S A / Identification and analysis of alternative splicing events conserved in human and mouse. (2005)
  12. 10.1038/271501a0 / Nature / Why genes in pieces? (1978)
  13. 10.1016/S0168-9525(02)00029-X / Trends Genet / Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences. (2003)
  14. 10.1093/hmg/11.13.1561 / Hum Mol Genet / Common exon duplication in animals and its role in alternative splicing. (2002)
  15. 10.1101/gr.229302 / Genome Res / Alu-containing exons are alternatively spliced. (2002)
  16. 10.1016/0168-9525(94)90254-2 / Trends Genet / Alu sequences in the coding regions of mRNA: a source of protein variability. (1994)
  17. 10.1016/j.jmb.2004.06.070 / J Mol Biol / From “junk” to gene: curriculum vitae of a primate receptor isoform gene. (2004)
  18. 10.1073/pnas.0603042103 / Proc Natl Acad Sci U S A / Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons. (2006)
  19. 10.1186/gb-2007-8-6-r127 / Genome Biol / Comparative analysis of transposed elements' insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. (2007)
  20. {'key': 'pgen-0030203-b020', 'article-title': 'The emergence of alternative 3′ and 5′ splice site exons from constitutive exons.', 'volume': '3', 'year': '2007', 'journal-title': 'PLoS Comput Biol'} / PLoS Comput Biol / The emergence of alternative 3′ and 5′ splice site exons from constitutive exons. (2007)
  21. 10.1261/rna.5196404 / RNA / Comparative analysis detects dependencies among the 5′ splice-site positions. (2004)
  22. 10.1016/j.tig.2003.12.004 / Trends Genet / How prevalent is functional alternative splicing in the human genome? (2004)
  23. 10.1101/gr.2572604 / Genome Res / A non-EST-based method for exon-skipping prediction. (2004)
  24. 10.1038/nrg1896 / Nat Rev Genet / Alternative splicing and RNA selection pressure–evolutionary consequences for eukaryotic genomes. (2006)
  25. 10.1261/rna.2660805 / RNA / Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. (2005)
  26. 10.1101/gr.200901 / Genome Res / The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. (2002)
  27. 10.1093/bioinformatics/bti613 / Bioinformatics / Assessing the application of Ka/Ks ratio test to alternatively spliced exons. (2005)
  28. 10.1101/gr.1208803 / Genome Res / Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. (2003)
  29. 10.1016/j.molcel.2006.05.008 / Mol Cell / Comparative analysis identifies exonic splicing regulatory sequences–The complex definition of enhancers and silencers. (2006)
  30. 10.1093/nar/gkh197 / Nucleic Acids Res / Exon repetition: a major pathway for processing mRNA of some genes is allele-specific. (2004)
  31. 10.1038/nature01262 / Nature / Initial sequencing and comparative analysis of the mouse genome. (2002)
  32. 10.1093/nar/15.17.7155 / Nucleic Acids Res / RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. (1987)
  33. 10.1186/1471-2148-6-50 / BMC Evol Biol / Differentiated evolutionary rates in alternative exons and the implications for splicing regulation. (2006)
  34. 10.1093/nar/gki198 / Nucleic Acids Res / MAFFT version 5: improvement in accuracy of multiple sequence alignment. (2005)
  35. 10.1093/nar/gkg616 / Nucleic Acids Res / ESEfinder: a web resource to identify exonic splicing enhancers. (2003)
  36. 10.1101/gad.1314205 / Genes Dev / Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. (2005)
  37. 10.1073/pnas.0404901101 / Proc Natl Acad Sci U S A / Variation in sequence and organization of splicing regulatory elements in vertebrate genes. (2004)
  38. 10.1074/jbc.M208418200 / J Biol Chem / Transcriptional activators differ in their abilities to control alternative splicing. (2002)
  39. 10.1073/pnas.201407298 / Proc Natl Acad Sci U S A / A computational analysis of sequence features involved in recognition of short introns. (2001)
  40. 10.1126/science.1073774 / Science / Predictive identification of exonic splicing enhancers in human genes. (2002)
  41. 10.1016/j.cell.2004.11.010 / Cell / Systematic identification and analysis of exonic splicing silencers. (2004)
  42. 10.1093/hmg/ddi164 / Hum Mol Genet / Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation. (2005)
  43. 10.1101/gr.926603 / Genome Res / LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. (2003)
  44. 10.1073/pnas.0603797103 / Proc Natl Acad Sci U S A / Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. (2006)
  45. 10.1073/pnas.89.22.10706 / Proc Natl Acad Sci U S A / On “genomenclature”: a comprehensive (and respectful) taxonomy for pseudogenes and other “junk DNA”. (1992)
  46. 10.1016/j.tig.2006.03.006 / Trends Genet / Do transposable elements really contribute to proteomes? (2006)
  47. 10.1074/jbc.M308036200 / J Biol Chem / Smac3, a novel Smac/DIABLO splicing variant, attenuates the stability and apoptosis-inhibiting activity of X-linked inhibitor of apoptosis protein. (2003)
  48. 10.1007/s11033-004-6939-9 / Mol Biol Rep / Molecular cloning and characterization of AAAS-V2, a novel splice variant of human AAAS. (2005)
  49. 10.1073/pnas.0508489102 / Proc Natl Acad Sci U S A / The architecture of pre-mRNAs affects mechanisms of splice-site pairing. (2005)
  50. 10.1016/S1097-2765(04)00181-9 / Mol Cell / Minimal conditions for exonization of intronic sequences: 5′ splice site formation in alu exons. (2004)
  51. 10.1517/14656566.6.4.561 / Expert Opin Pharmacother / Familial dysautonomia: a review of the current pharmacological treatments. (2005)
  52. 10.1101/gr.3936206 / Genome Res / Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion. (2006)
  53. 10.1016/S1097-2765(00)00107-6 / Mol Cell / The apoptosis-promoting factor TIA-1 is a regulator of alternative pre-mRNA splicing. (2000)
  54. {'key': 'pgen-0030203-b054', 'first-page': '555', 'article-title': 'PAML: a program package for phylogenetic analysis by maximum likelihood.', 'volume': '13', 'year': '1997', 'journal-title': 'Comput Appl Biosci'} / Comput Appl Biosci / PAML: a program package for phylogenetic analysis by maximum likelihood. (1997)
  55. 10.1016/S0169-5347(00)01994-7 / Trends Ecol Evol / Statistical methods for detecting molecular adaptation. (2000)
  56. 10.1101/gr.229102 / Genome Res / The human genome browser at UCSC. (2002)
  57. 10.1002/dvdy.10152 / Dev Dyn / Pineal-specific expression of green fluorescent protein under the control of the serotonin-N-acetyltransferase gene regulatory regions in transgenic zebrafish. (2002)
  58. 10.1210/me.2003-0439 / Mol Endocrinol / Zebrafish serotonin-N-acetyltransferase-2 gene regulation: pineal-restrictive downstream module contains a functional E-box and three photoreceptor conserved elements. (2004)
  59. 10.1242/dev.127.17.3645 / Development / The olfactory placodes of the zebrafish form by convergence of cellular fields at the edge of the neural plate. (2000)
  60. 10.1126/science.1082588 / Science / The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. (2003)
Dates
Type When
Created 17 years, 9 months ago (Nov. 13, 2007, 12:03 p.m.)
Deposited 7 months, 2 weeks ago (Jan. 22, 2025, 2:53 a.m.)
Indexed 2 months, 3 weeks ago (June 12, 2025, 7:04 a.m.)
Issued 17 years, 9 months ago (Nov. 16, 2007)
Published 17 years, 9 months ago (Nov. 16, 2007)
Published Online 17 years, 9 months ago (Nov. 16, 2007)
Funders 0

None

@article{Lev_Maor_2007, title={The “Alternative” Choice of Constitutive Exons throughout Evolution}, volume={3}, ISSN={1553-7404}, url={http://dx.doi.org/10.1371/journal.pgen.0030203}, DOI={10.1371/journal.pgen.0030203}, number={11}, journal={PLoS Genetics}, publisher={Public Library of Science (PLoS)}, author={Lev-Maor, Galit and Goren, Amir and Sela, Noa and Kim, Eddo and Keren, Hadas and Doron-Faigenboim, Adi and Leibman-Barak, Shelly and Pupko, Tal and Ast, Gil}, editor={Stubbs, Lisa}, year={2007}, month=nov, pages={e203} }