RAP1 / YNL216W Overview
- Standard Name
- RAP1 1
- Systematic Name
- YNL216W
- SGD ID
- SGD:S000005160
- Aliases
- GRF1 18 , TBA1 , TUF1 , GRC4 19
- Feature Type
- ORF , Verified
- Description
- Essential DNA-binding transcription regulator that binds many loci; involved in transcription activation, repression, chromatin silencing, telomere length maintenance; represses divergent noncoding transcription at highly expressed genes, prevents transcription initiation at cryptic promoters near its binding sites; relocalizes to cytosol under hypoxia; recruits Sir complex to telomeric DNA; present in quiescent cell telomere hyperclusters 2 3 4 5 6 7 8 9 10
- Name Description
- Repressor/Activator site binding Protein 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.)
- 827
- Mol. Weight (Da)
- 92368.2
- Isoelectric Point
- 4.59
- Median Abundance (molecules/cell)
- 4389 +/- 2195
- Half-life (hr)
- 8.3
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 RAP1 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
- Sequence specific DNA-binding RNA polymerase II transcription activator and repressor; activates expression of genes involved in glycolysis; involved in chromatin silencing, establishment of protein localization to chromatin and telomere maintenance; localizes to the cytosol and nucleus
View computational annotations
Molecular Function
- Manually Curated
- enables cis-regulatory region sequence-specific DNA binding (IDA)
- enables DNA binding, bending (IDA)
- enables DNA-binding transcription factor activity (IDA)
- enables DNA-binding transcription factor activity, RNA polymerase II-specific (IDA)
- enables G-quadruplex DNA binding (IDA)
- enables histone binding (IDA)
- enables nucleosomal DNA binding (IDA)
- enables RNA polymerase II-specific DNA-binding transcription factor binding (IDA)
- enables sequence-specific DNA binding (HDA)
- enables TBP-class protein binding (IDA)
- enables telomeric DNA binding (IDA)
- enables telomeric G-quadruplex DNA binding (IDA)
- enables TFIID-class transcription factor complex binding (IDA)
Biological Process
- Manually Curated
- involved in establishment of protein localization to chromatin (IPI)
- involved in establishment of protein localization to telomere (IPI)
- involved in G-quadruplex DNA formation (IDA)
- involved in negative regulation of transcription by RNA polymerase II (IMP)
- involved in positive regulation of transcription by RNA polymerase II (IMP, IGI)
- involved in protection from non-homologous end joining at telomere (IMP)
- involved in regulation of glycolytic process (IGI)
- involved in silent mating-type cassette heterochromatin formation (IGI)
- involved in subtelomeric heterochromatin formation (IPI, IGI)
- involved in telomere maintenance (IMP)
- involved in telomere maintenance via telomere lengthening (IMP, IDA)
Cellular Component
- Manually Curated
- located in chromosome, telomeric region (IDA, IMP)
- located in cytosol (IDA)
- located in nuclear chromosome (IDA)
- located in nucleus (IDA)
- part of shelterin complex (IDA)
Complex
Macromolecular complex annotations are imported from the Complex Portal. These annotations have been derived from physical molecular interaction evidence extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background.
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.
- Summary
- Essential gene; reduced function mutants have decreased fitness, long telomeres increased telomeric silencing, and are sensitive to DNA-damaging agent MMS; overexpression slows growth
Classical Genetics
- null
- overexpression
- reduction of function
- conditional
- repressible
- null
- overexpression
- reduction of function
- conditional
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.
884 total interactions for 712 unique genes
Physical Interactions
- Affinity Capture-MS: 25
- Affinity Capture-RNA: 5
- Affinity Capture-Western: 28
- Biochemical Activity: 2
- Co-crystal Structure: 3
- Co-localization: 3
- Far Western: 2
- PCA: 3
- Proximity Label-MS: 1
- Reconstituted Complex: 27
- Two-hybrid: 23
Genetic Interactions
- Dosage Lethality: 3
- Dosage Rescue: 4
- Negative Genetic: 531
- Phenotypic Enhancement: 3
- Phenotypic Suppression: 10
- Positive Genetic: 183
- Synthetic Growth Defect: 9
- Synthetic Lethality: 2
- Synthetic Rescue: 17
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
- RAP1 encodes a highly conserved helix-turn-helix transcription factor of the MYB superfamily. Rap1p binds sequences of the form 5'-CACCCATACA-3', and controls telomere function, silencing, and the activation of glycolytic and ribosomal protein genes. Rap1p is the major double-stranded telomeric repeat-binding protein in budding yeast and has essential roles in telomere length regulation, subtelomeric gene silencing and chromosome end protection. Rap1p is the only telomere protein that is conserved from budding and fission yeast to mammals. Rap1p and coactivator Gcr1p constitute a complex to recognize the core elements of the upstream activation sequences (UAS) of glycolytic enzyme genes. Rap1p mediates silencing at the mating loci and telomeres by recruiting Sir3p and Sir4p to chromatin. Rap1p further regulates telomere function through recruitment and binding of the telomere length regulators Rif1p and Rif2p to form the telomeric dsDNA end-protection complex. Rap1p exhibits perinuclear localization and activation of target genes occurs at the nuclear periphery.
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.
Summary Paragraph
A summary of the locus, written by SGD Biocurators following a thorough review of the literature. Links to gene names and curated GO terms are included within the Summary Paragraphs.
Last Updated: 2003-01-17
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.