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Evolution of alternative and constitutive regions of mammalian 5'UTRs

By Alissa M Resch, Aleksey Y Ogurtsov, Igor B Rogozin, Svetlana A Shabalina and Eugene V Koonin
Topics: Research Article
Publisher: BioMed Central
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Provided by: PubMed Central
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    1. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA
    2. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
    3. (1996). A: Regulation of RAR beta 2 mRNA expression: evidence for an inhibitory peptide encoded in the 5'-untranslated region.
    4. (2005). Alternative initiation and splicing in dicer gene expression in human breast cells. Breast Cancer Res
    5. (2006). Alternative splicing and RNA selection pressure – evolutionary consequences for eukaryotic genomes. Nat Rev Genet
    6. (2007). Alternatively spliced isoforms of the human elk-1 mRNA within the 5' UTR: implications for ELK-1 expression. Nucleic Acids Res
    7. (1987). An analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucleic Acids Res
    8. (2002). Apobec-1 transcription in rat colon cancer: decreased apobec-1 protein production through alterations in polysome distribution and mRNA translation associated with upstream AUGs. Biochim Biophys Acta
    9. ASD: the Alternative Splicing Database.
    10. (2004). Assessing the impact of alternative splicing on domain interactions in the human proteome.
    11. (2006). Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns. Bioinformatics
    12. (2007). Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse. FEBS Lett
    13. (2000). Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet
    14. (2008). CB: Alternative isoform regulation in human tissue transcriptomes. Nature
    15. (1999). de Serres FJ: Similarity pattern analysis in mutational distributions. Mutat Res
    16. (2005). Diversity and complexity of the mu opioid receptor gene: alternative pre-mRNA splicing and promoters.
    17. (2004). DJ: Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. Nucleic Acids Res
    18. (1994). DR: Initiation codons within 5'-leaders of mRNAs as regulators of translation. Trends Biochem Sci
    19. (2004). E: EnsMart: a generic system for fast and flexible access to biological data. Genome Res
    20. (2005). Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences.
    21. (1993). Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol
    22. (2005). Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes. Nucleic Acids Res
    23. (2009). Expansion of the human mu-opioid receptor gene architecture: novel functional variants. Hum Mol Genet
    24. (2007). Galagan JE: Dual modes of natural selection on upstream open reading frames. Mol Biol Evol
    25. (1999). Geballe AP: Translational control by an upstream open reading frame in the HER-2/neu transcript.
    26. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet
    27. (2001). Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res
    28. (2001). Genome-wide detection of alternative splicing in expressed sequences of human genes.
    29. (2005). Gotoh O: Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes. Gene
    30. (2007). HH: Translational repression of mouse mu opioid receptor expression via leaky scanning. Nucleic Acids Res
    31. (2005). HJ: Expression of axin2 is regulated by the alternative 5'-untranslated regions of its mRNA.
    32. (2005). Hong X: The evolution of transcriptioninitiation sites. Mol Biol Evol
    33. (2003). Identification and functional analysis of human transcriptional promoters. Genome Res
    34. (2007). Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes.
    35. (2000). ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome. Nat Genet
    36. (2002). Kondrashov AS: OWEN: aligning long collinear regions of genomes. Bioinformatics
    37. (2003). Kondrashov AS: Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs. Nucleic Acids Res
    38. (2002). Kondrashov FA: Selection for short introns in highly expressed genes. Nat Genet
    39. (1997). Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res
    40. (2001). Liuni S: Structural and functional features of eukaryotic mRNA untranslated regions. Gene
    41. (2007). MS: Comparative genomics and evolution of alternative splicing: the pessimists' science. Chem Rev
    42. (2006). MS: Fast rate of evolution in alternatively spliced coding regions of mammalian genes.
    43. (1999). MS: Frequent alternative splicing of human genes. Genome Res
    44. (2008). MS: Positive selection in alternatively spliced exons of human genes.
    45. (2004). Multiple variable first exons: a mechanism for cell- and tissue-specific gene regulation. Genome Res
    46. (2000). P: EST comparison indicates 38% of human mRNAs contain possible alternative splice forms. FEBS Lett
    47. (2003). Patterns, mechanisms, and functions of translation regulation in mammalian spermatogenic cells. Cytogenet Genome Res
    48. (2005). Pesole G: uAUG and uORFs in human and rodent 5'untranslated mRNAs. Gene
    49. (2001). Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. Bioinformatics
    50. (2000). Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell
    51. (2002). Pushing the limits of the scanning mechanism for initiation of translation. Gene
    52. (2007). RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science
    53. (2000). Saccone C: Analysis of oligonucleotide AUG start codon context in eukariotic mRNAs. Gene
    54. (2002). Shabalina SA: Classification of common conserved sequences in mammalian intergenic regions. Hum Mol Genet
    55. (1993). Shabalina SA: Intermolecular mRNA-rRNA hybridization and the distribution of potential interaction regions in murine 18S rRNA. Nucleic Acids Res
    56. (2008). Spiridonov NA: Expression patterns of protein kinases correlate with gene architecture and evolutionary rates. PLoS ONE
    57. (2000). Statistical analysis of the 5' untranslated region of human mRNA using "OligoCapped" cDNA libraries. Genomics
    58. (2007). Sugano S: Diversity of translation start sites may define increased complexity of the human short ORFeome. Mol Cell Proteomics
    59. (2007). Sunnerhagen P: Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation.
    60. (2003). Sunyaev S: Increase of functional diversity by alternative splicing. Trends Genet
    61. (2002). T: Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome Res
    62. (2006). The Tie2 5' untranslated region is inhibitory to 5' end-mediated translation initiation. FEBS Lett
    63. (2003). The UCSC Genome Browser Database. Nucleic Acids Res
    64. (2006). TJ: Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol Biol Evol
    65. (2004). Translational regulation of angiotensin type 1a receptor expression and signaling by upstream AUGs in the 5' leader sequence.
    66. (2003). Translational regulation of human neuronal nitric-oxide synthase by an alternatively spliced 5'-untranslated region leader exon.
    67. (2007). Translational regulation of rat multidrug resistance-associated protein 2 expression is mediated by upstream open reading frames in the 5' untranslated region. Mol Pharmacol
    68. (1993). Unbiased estimation of the rates of synonymous and nonsynonymous substitution.
    69. (2008). Y: Stress-induced translation of ATF5 mRNA is regulated by the 5'-untranslated region.
    70. (2000). Zhang MQ: CART classification of human 5' UTR sequences. Genome Res

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