Large RNA molecules play important roles in all aspects of cellular metabolism ranging from mRNA splicing and protein biosynthesis to regulation of gene expression. In order to correctly perform its function in the cell, an RNA molecule must fold into a complex tertiary structure. Folding of many large RNAs is slow either due to formation of stable misfolded intermediates or due to high contact order or instability of obligate folding intermediates. Therefore many RNAs use protein cofactors to facilitate their folding in vivo. Folding of the yeast mitochondrial group II intron ai5γ to the native state under physiological conditions is facilitated by the protein cofactor Mss116. This chapter describes the use of Nucleotide Analog Interference Mapping (NAIM) to identify specific substructures within the intron molecule that are directly affected by the protein.
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| Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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| Site | Modification | Modifier | Source | Reference |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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| Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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| Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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