RRN3 / YKL125W Overview
- Standard Name
- RRN3 1
- Systematic Name
- YKL125W
- SGD ID
- SGD:S000001608
- Feature Type
- ORF , Verified
- Description
- Protein required for transcription of rDNA by RNA polymerase I; transcription factor independent of DNA template; involved in recruitment of RNA polymerase I to rDNA; structure reveals unique HEAT repeat fold and a surface serine patch; phosphorylation of serine patch impairs cell growth and reduces RNA polymerase I binding in vitro and RNA polymerase I recruitment to the rDNA gene in vivo 2 3 4
- Name Description
- Regulation of RNA polymerase I 1
- Comparative Info
-
Sequence
The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C. Download DNA or protein sequence, view genomic context and coordinates. Click "Sequence Details" to view all sequence information for this locus, including that for other strains.
Analyze Sequence
S288C only
BLASTN | BLASTP | Design Primers | Restriction Fragment Map | Restriction Fragment Sizes | Six-Frame Translation
S288C vs. other species
BLASTN vs. fungi | BLASTP at NCBI | BLASTP vs. fungi
S288C vs. other strains
Protein
Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein.
- Length (a.a.)
- 627
- Mol. Weight (Da)
- 72346.9
- Isoelectric Point
- 4.34
- Median Abundance (molecules/cell)
- 334 +/- 279
- Half-life (hr)
- 1.7
Alleles
Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.
View all RRN3 alleles in SGD search
Gene Ontology
GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes.
- Summary
- rDNA-binding RNA polymerase I transcription factor involved in the assembly of the RNA polymerase I preinitiation complex (PIC) and subsequence synthesis of the nuclear large rRNA transcript; localized to the nucleolus
View computational annotations
Molecular Function
- Manually Curated
- enables rDNA binding (IDA)
- enables RNA polymerase I core binding (IPI, IDA)
- enables RNA polymerase I general transcription initiation factor activity (IDA, IGI, IPI)
- enables RNA polymerase I general transcription initiation factor binding (IPI, IDA)
Biological Process
- Manually Curated
- involved in transcription initiation at RNA polymerase I promoter (IMP)
Phenotype
Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). Whenever possible, allele information and additional details are provided. Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes.
Classical Genetics
- conditional
- null
- reduction of function
- null
- reduction of function
- repressible
- unspecified
- conditional
- overexpression
Large-scale Survey
Interaction
Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g., Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization.
193 total interactions for 161 unique genes
Physical Interactions
- Affinity Capture-MS: 5
- Affinity Capture-RNA: 3
- Affinity Capture-Western: 9
- Co-crystal Structure: 8
- Co-localization: 2
- Co-purification: 3
- Reconstituted Complex: 5
- Two-hybrid: 1
Genetic Interactions
- Dosage Rescue: 2
- Negative Genetic: 136
- Phenotypic Enhancement: 1
- Phenotypic Suppression: 1
- Positive Genetic: 3
- Synthetic Growth Defect: 4
- Synthetic Lethality: 7
- Synthetic Rescue: 3
Regulation
The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. This evidence includes data generated through high-throughput techniques. Click "Regulation Details" to view all regulation annotations, shared GO enrichment among regulation Targets, and a regulator/target diagram for the locus.
- Summary
- RRN3 encodes an evolutionarily-conserved basal transcription factor required for RNA polymerase I (Pol I) transcription initiation. Rrn3p contains a tandem array of HEAT repeats that are on average approximately 40 residues long, encompassing the entire length of Rrn3p. These repeats fold into an elongated and bent conformation that wraps around Pol I. Rrn3p functions as a monomer and its association with Pol I is required to render the polymerase competent for transcription initiation. The level of the initiation competent Rrn3p-Pol I complex likely serves as a key regulatory process affecting the rate of rDNA synthesis in response to nutrient availability. Rrn3p-bound Pol I is recruited to rDNA promoters by the Pol I core factor (CF) complex through interactions between Rrn3p and the CF subunit Rrn6p.
- Regulators
- 3
- Targets
- 0
Expression
Expression data are derived from records contained in the Gene Expression Omnibus (GEO), and are first log2 transformed and normalized. Referenced datasets may contain one or more condition(s), and as a result there may be a greater number of conditions than datasets represented in a single clickable histogram bar. The histogram division at 0.0 separates the down-regulated (green) conditions and datasets from those that are up-regulated (red). Click "Expression Details" to view all expression annotations and details for this locus, including a visualization of genes that share a similar expression pattern.
Literature
All manually curated literature for the specified gene, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review). Click "Literature Details" to view all literature information for this locus, including shared literature between genes.