CUP9 / YPL177C Overview

Standard Name
CUP9 1
Systematic Name
Feature Type
ORF , Verified
Homeodomain-containing transcriptional repressor; regulates expression of PTR2, which encodes a major peptide transporter; imported peptides activate ubiquitin-dependent proteolysis, resulting in degradation of Cup9p and de-repression of PTR2 transcription; CUP9 has a paralog, TOS8, that arose from the whole genome duplication; protein abundance increases in response to DNA replication stress 1 2 3 4 5
TOS8 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.

CUP9/YPL177C is located on the left arm of chromosome XVI between CBC2 cap binding complex subunit and TRE1 transferrin; coding sequence is 921 nucleotides long with 4 SNPs, 1 of which causes a Thr/Lys polymorphism at residue 258; CUP9 has a paralog, TOS8, that arose from the whole genome duplication
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.

Cup9p is 309 amino acids long, very low in abundance; phosphorylated on S117; protein abundance increases in response to DNA replication stress
Length (a.a.)
Mol. Weight (Da)
Isoelectric Point
Median Abundance (molecules/cell)
506 +/- 239


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 CUP9 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.

A sequence-specific transcription factor involved in the negative regulation of dipeptide transport by negative regulation of transcription from RNA polymerase II promoter; localized to the nucleus

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.

Non-essential gene; null mutation confers sensitivity to copper ions and increases replicative lifespan; in systematic studies, null mutation causes inositol auxotrophy in diploid, and increased competitive fitness and increased lifespan in haploids
Disease Details


Disease Annotations consist of three mandatory components: a gene product, a term from the Disease Ontology (DO) controlled vocabulary and an evidence code. SGD provides manually curated DO Annotations derived from the literature. Click "Disease Details" to view all Disease information and evidence for this locus as well as diseases it shares with other genes.

Yeast CUP9 is homologous to human PKNOX1, PKNOX2, and MEIS1, and has been used to study Down syndrome, substance dependence, restless legs syndrome, and numerous leukemias including acute, myeloid, acute promyelocytic, acute lymphoblasic, and chronic myeloid
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.

Cup9p interacts physically with proteins involved in RNA catabolism; CUP9 interacts genetically with genes involved in transcription; the cup9 null mutant is viable; the null mutant of paralog tos8 is viable; the cup9 tos8 double mutant has not been annotated for phenotype.

176 total interactions for 134 unique genes

Physical Interactions

  • Affinity Capture-MS: 1
  • Affinity Capture-RNA: 4
  • Affinity Capture-Western: 1
  • Biochemical Activity: 4
  • Co-purification: 1
  • Reconstituted Complex: 4

Genetic Interactions

  • Dosage Rescue: 2
  • Negative Genetic: 137
  • Phenotypic Suppression: 2
  • Positive Genetic: 15
  • Synthetic Growth Defect: 2
  • Synthetic Rescue: 3
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.

CUP9 encodes a homeodomain-containing transcriptional repressor. Its most well-characterized target is the PTR2 gene encoding a major dipeptide and tripeptide transporter. Cup9p forms a complex with corepressors Tup1p and Cyc8p (Ssn6p) to repress PTR2 transcription. In strains of W303 background, CUP9 behaves genetically as an activator of DAL5, another transporter whose substrates include dipeptides; however, it is not known whether this effect is direct. Cup9p activity is regulated by ubiquitin-mediated degradation. When dipeptides are present, they enhance the activity of the Ubr1p and Ufd4p E3 ubiquitin ligases, which ubiquitinate Cup9p to target it for degradation. When Cup9p is degraded, PTR2 transcription is derepressed and dipeptide import is induced. Mutations in CUP9 can confer sensitivity to copper, but the mechanism is unknown.
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.

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: 2024-05-23

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.