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Journal club 06/27/08

Journal club 06/27/08. Non-coding functional regions. Cis-regulation of pre-mRNA splicing Post-splicing (mature mRNA) – degradation, localization Translational efficiency & accuracy – Choice of synonymous codon Secondary structure elements. CRUNCS.

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Journal club 06/27/08

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  1. Journal club 06/27/08

  2. Non-coding functional regions • Cis-regulation of pre-mRNA splicing • Post-splicing (mature mRNA) – degradation, localization • Translational efficiency & accuracy – Choice of synonymous codon Secondary structure elements

  3. CRUNCS • Coding regions under non-coding selection • Are not located in non-functional sequences as are, ex: most known transcription factors binding sites, but rather in coding regions

  4. Mixture selective pressure • Maintain the function of the protein encoded by the gene (AA selecvtive pressure) • Maintain their regulatory role (CRUNCS) – ex: regulatory factors binding sites

  5. Methods • Sequence conservation: • Entropy score • Parsimony score • Conservation p-value (mixture models) • Posterior distributions of conservation scores • Conditional p-values

  6. Fitch’s algorithm

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