CLN3 / YAL040C Overview
- Standard Name
- CLN3 1
- Systematic Name
- YAL040C
- SGD ID
- SGD:S000000038
- Aliases
- DAF1 12 , FUN10 13 , WHI1 2
- Feature Type
- ORF , Verified
- Description
- G1 cyclin involved in cell cycle progression; activates Cdc28p kinase to promote G1 to S phase transition; plays a role in regulating transcription of other G1 cyclins, CLN1 and CLN2; regulated by phosphorylation and proteolysis; acetyl-CoA induces CLN3 transcription in response to nutrient repletion to promote cell-cycle entry; cell cycle arrest phenotype of the cln1 cln2 cln3 triple null mutant is complemented by any of human cyclins CCNA2, CCNB1, CCNC, CCND1, or CCNE1 2 3 4 5 6
- Name Description
- CycLiN
- 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.
- Summary
- CLN3 is located on the left arm of chromosome I between CDC24 guanine nucleotide exchange factor and CYC3 cytochrome c heme lyase; coding sequence is 1743 nucleotides long with 10 nonsynonymous SNPs, 17 synonymous SNPs
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.
- Summary
- Cln3p is 580 amino acids long, very low in abundance; contains cyclin domain, phosphorylated on 2 serines toward C-terminus
- Length (a.a.)
- 580
- Mol. Weight (Da)
- 65007.7
- Isoelectric Point
- 9.45
- Median Abundance (molecules/cell)
- 873
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 CLN3 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
- Cyclin-dependent protein kinase (CDK) regulatory subunit; regulates cell cycle passage through START by regulating transcription at the G1/S phase transcription; regulates non-autophagic vacuole fusion; localizes to the nucleus
View computational annotations
Molecular Function
- Manually Curated
Biological Process
- Manually Curated
- involved in G1/S transition of mitotic cell cycle (IGI, IMP)
- involved in regulation of protein phosphorylation (IMP)
- involved in regulation of transcription by RNA polymerase II (IMP, IGI)
- involved in traversing start control point of mitotic cell cycle (IGI, IMP)
- involved in vacuole fusion, non-autophagic (IMP, IDA)
- involved in vacuole organization (IMP)
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
- Non-essential gene; dominant hyperactive alleles result in decreased critical cell size at START, decreased duration of the G1 phase, increased alpha-factor resistance, transient pheromone-induced cell cycle arrest, reduced mating efficiency; null mutants have an increased critical cell size at START, increased duration of the G1 phase, elevated chromosome instability, and increased chronological lifespan; homozygous diploid nulls have an increased sporulation efficiency and enhanced pseudohyphal growth
Classical Genetics
- null
- cell cycle progression in G1 phase: increased duration
- cell size: increased
- chromosome/plasmid maintenance: abnormal
- colony sectoring: increased
- critical cell size at START (G1 cell-size checkpoint): increased
- fermentative metabolism: decreased rate
- metal resistance: increased
- mitochondrial morphology: abnormal
- protein/peptide accumulation: decreased
- protein/peptide accumulation: delayed
- pseudohyphal growth: increased
- resistance to chemicals: decreased
- resistance to chemicals: normal
- RNA accumulation: delayed
- viable
- overexpression
- apoptosis: increased
- cell cycle progression in anaphase: decreased duration
- cell cycle progression in G1 phase: decreased duration
- cell cycle progression in G1 phase: increased
- cell cycle progression in metaphase: decreased duration
- cell size: decreased
- chronological lifespan: decreased
- critical cell size at START (G1 cell-size checkpoint): decreased
- mutation frequency: increased
- pheromone-induced cell cycle arrest: absent
- protein/peptide accumulation: premature
- size of nucleus: decreased
- repressible
- activation
- cell cycle progression in G1 phase: decreased duration
- cell size: decreased
- critical cell size at START (G1 cell-size checkpoint): decreased
- fermentative metabolism: decreased rate
- fermentative metabolism: increased rate
- mating efficiency: decreased
- pheromone sensitivity: abnormal
- pheromone sensitivity: decreased
- pheromone-induced cell cycle arrest: abnormal
- protein/peptide accumulation: increased
- protein/peptide accumulation: premature
- pseudohyphal growth: decreased
- resistance to chemicals: normal
- unspecified
- null
- auxotrophy
- cell size: increased
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chronological lifespan: increased
- colony sectoring: increased
- competitive fitness: decreased
- competitive fitness: increased
- heat sensitivity: decreased
- hyperosmotic stress resistance: decreased
- lipid particle morphology: abnormal
- resistance to chemicals: decreased
- resistance to chemicals: increased
- sporulation efficiency: increased
- stress resistance: decreased
- toxin resistance: decreased
- toxin resistance: increased
- UV resistance: decreased
- viable
- overexpression
Large-scale Survey
Disease
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.
- Summary
- Yeast CLN3 is homologous to human CCNF, and has been used to study frontotemporal dementia and/or amyotrophic lateral sclerosis-5
Manually Curated
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.
- Summary
- Cln3p interacts physically with proteins involved in mitotic cell cycle regulation; CLN3 interacts genetically with genes involved in mitotic cell cycle regulation.
473 total interactions for 296 unique genes
Physical Interactions
- Affinity Capture-MS: 5
- Affinity Capture-RNA: 11
- Affinity Capture-Western: 22
- Biochemical Activity: 6
- PCA: 1
- Protein-RNA: 1
- Reconstituted Complex: 1
- Two-hybrid: 2
Genetic Interactions
- Dosage Growth Defect: 5
- Dosage Lethality: 6
- Dosage Rescue: 30
- Negative Genetic: 211
- Phenotypic Enhancement: 30
- Phenotypic Suppression: 30
- Positive Genetic: 45
- Synthetic Growth Defect: 17
- Synthetic Lethality: 23
- Synthetic Rescue: 27
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.
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: 1999-12-17
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.