CSL4 / YNL232W Overview


Standard Name
CSL4 1
Systematic Name
YNL232W
SGD ID
SGD:S000005176
Aliases
SKI4 15 16
Feature Type
ORF , Verified
Description
Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; predicted to contain an S1 RNA binding domain; human homolog EXOSC1 partially complements yeast csl4 null mutant, and can complement inviability of strain in which expression of CSL4 is repressed 1 2 3 4 5 6
Name Description
Cep1 Synthetic Lethal 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
CSL4 is located on the left arm of Chromosome XIV between BNI4 targeting subunit for Glc7p protein phosphatase and PDR16 phosphatidylinositol transfer protein; coding sequence is 879 nucleotides long with 6 SNPs, 4 of which are silent, 1 of which causes Arg/Lys amino acid polymorphism at residue 65, and 1 of which causes Asp/His polymorphism at position 82
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
Csl4p is 292 amino acids long with exonuclease and nucleic-acid binding domains; subunit of the exosome; shares 2 domains with proteins involved in DNA recombination, DNA repair, and DNA replication; undergoes various post-translational modifications including acetylation and phosphorylation on 15 residues
Length (a.a.)
292
Mol. Weight (Da)
31578.7
Isoelectric Point
4.97
Median Abundance (molecules/cell)
4707 +/- 999
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. Click "YeastMine" to view all alleles in YeastMine.


View all CSL4 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
Component of exosome, which is a ribonuclease complex with 3'-5' processive hydrolytic exoribonuclease activity involved in multiple RNA processing and degradation processes, including rRNA maturation, ncRNA processing, poly(A)-dependent degradation, non-stop and nonsense-mediated mRNA decay; localized to both the nucleus and the cytoplasm

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
Essential gene; reduction-of-function mutations cause increased accumulation of unprocessed mRNA and rRNA species, increased cold and heat sensitivity and decreased competitive fitness
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 CSL4 is homologous to human EXOSC1 and has been used to study mutations found in patients with pontocerebellar hypoplasia type 1F, dilated cardiomyopathy, microcephaly, and scleral abnormalities
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
Interacts physically with proteins involved in rRNA processing; interacts genetically with genes involved in transcription

721 total interactions for 504 unique genes

Physical Interactions

  • Affinity Capture-MS: 263
  • Affinity Capture-RNA: 7
  • Affinity Capture-Western: 18
  • Biochemical Activity: 1
  • Co-purification: 5
  • PCA: 1
  • Reconstituted Complex: 3
  • Two-hybrid: 1

Genetic Interactions

  • Negative Genetic: 309
  • Phenotypic Suppression: 7
  • Positive Genetic: 95
  • Synthetic Lethality: 5
  • Synthetic Rescue: 6
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.


Regulators
4
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: 2009-09-09

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
40
Additional
32
Reviews
39

Resources