RFX1 / YLR176C Overview

Standard Name
RFX1 1
Systematic Name
CRT1 2
Feature Type
ORF , Verified
Major transcriptional repressor of DNA-damage-regulated genes; recruits repressors Tup1p and Cyc8p to their promoters; involved in DNA damage and replication checkpoint pathway; similar to a family of mammalian DNA binding RFX1-4 proteins 1 2 3
Name Description
Regulatory Factor X 4
Comparative Info
Sequence Details


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.

Protein Details


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.)
Mol. Weight (Da)
Isoelectric Point
Median Abundance (molecules/cell)
779 +/- 402
Half-life (hr)


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. Click "YeastMine" to view all alleles in YeastMine.

View all RFX1 alleles in SGD search | YeastMine

Gene Ontology Details

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.

DNA binding protein that binds sequence specific RNA polymerase II cis-regulatory regions; negatively regulates RNA polymerase II transcription; localized to the nucleus and cytoplasm

View computational annotations

Cellular Component

Manually Curated
Phenotype Details


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.

Interaction Details


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.

245 total interactions for 180 unique genes

Physical Interactions

  • Affinity Capture-MS: 16
  • Affinity Capture-RNA: 2
  • Co-localization: 1
  • Reconstituted Complex: 7

Genetic Interactions

  • Dosage Growth Defect: 2
  • Dosage Lethality: 7
  • Dosage Rescue: 3
  • Negative Genetic: 136
  • Phenotypic Enhancement: 18
  • Phenotypic Suppression: 12
  • Positive Genetic: 14
  • Synthetic Growth Defect: 8
  • Synthetic Lethality: 1
  • Synthetic Rescue: 18
Regulation Details


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.

RFX1 encodes a winged helix-turn-helix transcription factor that binds a consensus sequence termed the X box (5'-GTTRCYATG-3'). Multiple X box-related sequences of different strength are in the promoters of the four ribonucleotide-diphosphate reductase genes (RNR1-4). Rfx1p recruits the Tup1p-Ssn6p general repressor complex to suppress the transcription of RNR genes. Upon DNA damage or other replication blocks, activation of the Mec1-Rad53-Dun1 kinase cascade results in phosphorylation of Rfx1p, which abolishes its binding ability, leading to the transcriptional induction of the RNR genes. The transcription of RFX1 is negatively auto-regulated and positively regulated by Crt10p. The expression of RFX1 is low under normal growth conditions, but inducible by DNA-damaging agents. The RFX1 promoter consists of one weak-affinity X box, and one of strong affinity, and RFX1 exhibits 5' untranslated region (UTR) heterogeneity due to alternative transcription start site selection. The long variant of RFX1 contains multiple upstream open reading frames (uORFs) which reduce translation of the main ORF under normal growth conditions. Weak induction of RFX1 may occur immediately following DNA damage, providing a buffer against spurious transcriptional activation of the pathway. It has been speculated that delaying full activation ensures a rapid restoration of the basal repressed state when DNA damage is repaired, which may serve as an autonomous regulatory circuit. Ccr4p influences Rfx1p abundance by controlling RFX1 mRNA stability.
Expression Details


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 Details


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.