CDC39 / YCR093W Overview
- Standard Name
- CDC39 1 2
- Systematic Name
- YCR093W
- SGD ID
- SGD:S000000689
- Aliases
- NOT1 9 , ROS1 10 , SMD6
- Feature Type
- ORF , Verified
- Description
- Subunit of the CCR4-NOT1 core complex; this complex has multiple roles in the regulation of mRNA levels including regulation of transcription and destabilization of mRNA by deadenylation; basal transcription factor that increases initiation and elongation; activates the ATPase activity of Dhh1p, resulting in processing body disassembly 3 4 6 7 8
- Name Description
- Cell Division Cycle 5
- 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.)
- 2108
- Mol. Weight (Da)
- 240261.3
- Isoelectric Point
- 6.39
- Median Abundance (molecules/cell)
- 6644 +/- 2379
- Half-life (hr)
- 10.0
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 CDC39 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
- ATPase activator subunit of CCR4-NOT core complex; involved in transcription regulation, cell cycle regulation, pheromone response, pseudohyphal growth, mRNA catabolism, and negative regulation of cytoplasmic mRNA processing body assembly; localizes to both nucleus and cytoplasm
View computational annotations
Molecular Function
- Manually Curated
- enables ATPase activator activity (IDA)
Biological Process
- Manually Curated
- involved in negative regulation of cytoplasmic mRNA processing body assembly (IDA, IMP)
- involved in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (IDA, IMP)
- involved in nuclear-transcribed mRNA poly(A) tail shortening (IDA)
- involved in positive regulation of transcription elongation by RNA polymerase II (IDA)
- involved in pseudohyphal growth (IMP)
- involved in regulation of cell cycle (IMP)
- involved in regulation of transcription by RNA polymerase II (IPI)
- involved in response to pheromone triggering conjugation with cellular fusion (IMP)
- involved in transcription elongation by RNA polymerase II (IMP, IGI)
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; conditional mutant arrests in the G1 phase at START, as conjugation-competent, unbudded cells with single, undivided nuclei and pear-shaped morphology; conditional mutant displays elevated colony sectoring indicative of chromosomal instability and increased nucleolar size; homozygous diploid transposon insertion mutant is unable to undergo nitrogen-starvation induced pseudohyphal growth; heterozygous diploid null mutant has increased innate thermotolerance; overexpression results in an accumulation of cells with a 2C DNA content and an increased percentage of large-budded cells indicative of a G2 or M phase delay or arrest
Classical Genetics
- unspecified
- null
- conditional
- reduction of function
- 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.
579 total interactions for 372 unique genes
Physical Interactions
- Affinity Capture-MS: 109
- Affinity Capture-RNA: 12
- Affinity Capture-Western: 58
- Co-crystal Structure: 2
- Co-fractionation: 1
- Co-localization: 1
- Co-purification: 20
- Cross-Linking-MS (XL-MS): 1
- PCA: 21
- Proximity Label-MS: 1
- Reconstituted Complex: 7
- Two-hybrid: 24
Genetic Interactions
- Dosage Lethality: 1
- Dosage Rescue: 8
- Negative Genetic: 251
- Phenotypic Enhancement: 1
- Phenotypic Suppression: 3
- Positive Genetic: 31
- Synthetic Growth Defect: 1
- Synthetic Haploinsufficiency: 2
- Synthetic Lethality: 10
- Synthetic Rescue: 14
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.
- Regulators
- 9
- Targets
- 0
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.
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.