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