LCB5 / YLR260W Overview
- Standard Name
- LCB5 1
- Systematic Name
- YLR260W
- SGD ID
- SGD:S000004250
- Feature Type
- ORF , Verified
- Description
- Minor sphingoid long-chain base kinase; possibly involved in synthesis of long-chain base phosphates, which function as signaling molecules; LCB5 has a paralog, LCB4, that arose from the whole genome duplication 1 2
- Name Description
- Long-Chain Base 1
- Paralog
- LCB4 2
- 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
- LCB5 has a paralog, LCB4, that arose from the whole genome duplication
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.)
- 687
- Mol. Weight (Da)
- 77561.5
- Isoelectric Point
- 6.86
- Median Abundance (molecules/cell)
- 1235 +/- 437
- Half-life (hr)
- 7.7
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 LCB5 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
- Sphingosine kinase, phosphorylates dihydrosphingosine to form dihydrosphingosine-1-phosphate; involved in sphingolipid metabolism; localizes to Golgi membranes
View computational annotations
Molecular Function
- Manually Curated
- enables D-erythro-sphingosine kinase activity (IDA)
Biological Process
- Manually Curated
- involved in calcium-mediated signaling (IMP)
- involved in response to heat (IDA)
- involved in sphingolipid metabolic process (IDA)
Pathways
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.
Classical Genetics
- null
- null
- cell size: decreased
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chronological lifespan: decreased
- competitive fitness: decreased
- haploinsufficient
- heat sensitivity: increased
- hyperosmotic stress resistance: decreased
- innate thermotolerance: decreased
- mitochondrial genome maintenance: absent
- protein/peptide accumulation: increased
- replicative lifespan: decreased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- respiratory growth: absent
- respiratory growth: decreased
- respiratory growth: decreased rate
- utilization of carbon source: decreased
- vegetative growth: decreased rate
- viable
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.
- Summary
- The lcb5 null mutant is viable; the null mutant of paralog lcb4 is viable; the lcb5 lcb4 double mutant displays a synthetic growth defect.
252 total interactions for 187 unique genes
Physical Interactions
- Affinity Capture-MS: 26
- Affinity Capture-RNA: 4
- Co-purification: 1
- PCA: 1
Genetic Interactions
- Dosage Lethality: 1
- Negative Genetic: 185
- Phenotypic Enhancement: 1
- Positive Genetic: 27
- Synthetic Growth Defect: 4
- Synthetic Lethality: 1
- Synthetic Rescue: 1
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.
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: 2007-10-05
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.