SLM5 / YCR024C Overview


Standard Name
SLM5 1
Systematic Name
YCR024C
SGD ID
SGD:S000000618
Feature Type
ORF , Verified
Description
Mitochondrial asparaginyl-tRNA synthetase 2
Name Description
Synthetic Lethal with Mss4 1
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
SLM5/YCR024C is located on the right arm of chromosome III between YCR023C vacuolar membrane protein and YCR024C-B protein of unknown function; coding sequence is 1479 nucleotides long with 3 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
Slm5p is 492 amino acids long, of average half-life, low in abundance; contains 4 aspartyl/asparaginyl-tRNA synthetase class IIb domains
Length (a.a.)
492
Mol. Weight (Da)
56791.5
Isoelectric Point
8.64
Median Abundance (molecules/cell)
1501 +/- 965
Half-life (hr)
9.5

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 SLM5 alleles in SGD search

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
Mitochondrial asparaginyl-tRNA synthetase that performs asparaginyl-tRNA aminoacylation by coupling asparagine to asparaginyl-tRNA

View computational annotations

Molecular Function

Manually Curated

Biological Process

Manually Curated

Cellular Component

Manually Curated
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
SLM5/YCR024C is a non-essential gene; null mutants are viable but exhibit a range of phenotypic changes including abnormal or absent mitochondrial genome maintenance, abnormal mitochondrial morphology, decreased mitophagy, decreased acid pH resistance, decreased chronological lifespan, decreased competitive fitness, decreased desiccation resistance, increased heat sensitivity, increased metal resistance, decreased oxidative stress resistance, altered resistance to chemicals (both increased and decreased), absent or decreased respiratory growth, decreased toxin resistance, decreased utilization of various carbon sources, decreased UV resistance, and decreased vegetative growth rate.
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 SLM5 is homologous to human NARS2 and has been used to study mutations found in patients with mitochondrial disease presenting as developmental delay, epilepsy, and complex I deficiency
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
Slm5p interacts physically with proteins involved in rRNA processing and ribosomal small subunit biogenesis; SLM5 interacts genetically with genes involved in transcription

183 total interactions for 180 unique genes

Physical Interactions

  • Affinity Capture-MS: 29
  • Affinity Capture-RNA: 3
  • Biochemical Activity: 2
  • Protein-peptide: 1
  • Reconstituted Complex: 2
  • Two-hybrid: 4

Genetic Interactions

  • Dosage Growth Defect: 1
  • Negative Genetic: 119
  • Positive Genetic: 12
  • Synthetic Growth Defect: 3
  • Synthetic Lethality: 7
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
SLM5 promoter is bound by Srb5p during heat response and Fkh2p during starvation response
Regulators
6
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: 2008-07-14

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
8
Additional
20
Reviews
1

Resources