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 Details

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
Protein Details

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


View all CLN3 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.


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

Cellular Component

Manually Curated

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 Details

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
overexpression
repressible
activation
unspecified
Disease Details

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 Details

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.

470 total interactions for 296 unique genes

Physical Interactions

  • Affinity Capture-MS: 5
  • Affinity Capture-RNA: 10
  • 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: 29
  • Phenotypic Suppression: 29
  • Positive Genetic: 45
  • Synthetic Growth Defect: 17
  • Synthetic Lethality: 23
  • Synthetic Rescue: 27
Regulation Details

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
CLN3 transcription is downregulated by Xbp1p; CLN3 mRNA stability is downregulated by Whi3p; Cln3p translation is downregulated by Rie1p during stress response
Regulators
14
Targets
0
Expression Details

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 Details

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.


Primary
196
Additional
201
Reviews
105

Resources