DID4 / YKL002W Overview
- Standard Name
- DID4 1
- Systematic Name
- YKL002W
- SGD ID
- SGD:S000001485
- Aliases
- VPS14 12 , GRD7 13 , REN1 2 , VPL2 14 , VPT14 15 , CHM2 16 , VPS2 15 17
- Feature Type
- ORF , Verified
- Description
- Class E Vps protein of the ESCRT-III complex; required for sorting of integral membrane proteins into lumenal vesicles of multivesicular bodies, and for delivery of newly synthesized vacuolar enzymes to the vacuole, involved in endocytosis 1 2 3 4
- Name Description
- Doa4-Independent Degradation 1
- 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
- DID4 is on the left arm of chromosome XI very close to the centromere, between MRP17 mitochondrial ribosomal protein and MET14 adenylylsulfate kinase; coding sequence is 767 nucleotides long with an intron at 61..128, 5 silent SNPs, and 2 SNPs that cause amino acid polymorphisms at residues 204 (Pro/Ala) and 215 (Glu/Asp)
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
- Did4p is 232 amino acids long, shorter-lived, and low in abundance; phosphorylated on 4 serines
- Length (a.a.)
- 232
- Mol. Weight (Da)
- 26286.1
- Isoelectric Point
- 4.96
- Median Abundance (molecules/cell)
- 2857 +/- 1299
- Half-life (hr)
- 8.9
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 DID4 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
- Subunit of ESCRT III complex involved in ATP export, intralumenal vesicle formation and protein retention in golgi apparatus; localizes to cytoplasm
View computational annotations
Molecular Function
- Manually Curated
- enables molecular function unknown (ND)
Biological Process
- Manually Curated
- involved in ATP export (IMP)
- involved in intralumenal vesicle formation (IMP)
- involved in late endosome to vacuole transport (IDA)
- involved in protein retention in Golgi apparatus (IMP)
Cellular Component
- Manually Curated
- located in cytoplasm (IDA)
- part of ESCRT III complex (IDA)
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; null mutant exhibits heat sensitivity, sensitivity to caffeine, Congo Red, and other chemicals, and defects in vacuolar protein targeting; in large-scale studies, null mutant has reduced competitive fitness in several different media, sensitivity to heat shock, desiccation, and osmotic stress, poor utilization of various nitrogen sources, and altered resistance to many chemicals
Classical Genetics
- null
- autophagy: decreased
- biofilm formation: decreased
- endocytosis: decreased
- heat sensitivity: increased
- metal resistance: decreased
- metal resistance: increased
- protein secretion: decreased
- protein/peptide distribution: abnormal
- resistance to chemicals: absent
- resistance to chemicals: decreased
- resistance to chemicals: increased
- telomere length: decreased
- toxin resistance: decreased
- vacuolar transport: abnormal
- reduction of function
- overexpression
- conditional
- null
- acid pH resistance: decreased
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chemical compound excretion: increased
- chromosome/plasmid maintenance: decreased
- chronological lifespan: decreased
- competitive fitness: decreased
- desiccation resistance: decreased
- endocytosis: decreased
- haploinsufficient
- heat sensitivity: increased
- hyperosmotic stress resistance: decreased
- innate thermotolerance: decreased
- metal resistance: decreased
- metal resistance: increased
- oxidative stress resistance: decreased
- oxidative stress resistance: increased
- protein/peptide accumulation: decreased
- protein/peptide distribution: abnormal
- resistance to chemicals: decreased
- resistance to chemicals: increased
- resistance to chemicals: normal
- respiratory growth: absent
- respiratory growth: decreased rate
- reticulophagy: decreased
- sporulation efficiency: decreased
- sporulation: decreased
- toxin resistance: decreased
- toxin resistance: increased
- utilization of carbon source: decreased
- utilization of carbon source: decreased rate
- utilization of nitrogen source: decreased rate
- UV resistance: decreased
- vacuolar morphology: abnormal
- vegetative growth: decreased rate
- viable
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
- DID4 is homologous to human CHMP2B and has been used to study amyotrophic lateral sclerosis type 17, which is now called chromosome 3-linked frontotemporal dementia
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
- Did4p interacts physically with proteins involved in vesicle organization, translation, protein targeting, and RNA catabolism; DID4 interacts genetically with genes involved in transcription
364 total interactions for 237 unique genes
Physical Interactions
- Affinity Capture-MS: 20
- Affinity Capture-RNA: 8
- Affinity Capture-Western: 34
- Co-crystal Structure: 1
- Co-localization: 1
- Far Western: 1
- FRET: 1
- PCA: 6
- Protein-peptide: 1
- Reconstituted Complex: 4
- Two-hybrid: 14
Genetic Interactions
- Dosage Rescue: 1
- Negative Genetic: 196
- Phenotypic Enhancement: 6
- Phenotypic Suppression: 2
- Positive Genetic: 37
- Synthetic Growth Defect: 20
- Synthetic Haploinsufficiency: 1
- Synthetic Lethality: 2
- Synthetic Rescue: 8
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
- 5
- 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.
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: 2006-03-13
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.