XRN1 / YGL173C Overview
- Standard Name
- XRN1 1
- Systematic Name
- YGL173C
- SGD ID
- SGD:S000003141
- Aliases
- KEM1 14 , DST2 15 , RAR5 16 , SEP1 17 , SKI1 18
- Feature Type
- ORF , Verified
- Description
- Evolutionarily-conserved 5'-3' exonuclease; deNADing enzyme that modulates mitochondrial NAD-capped RNA; component of cytoplasmic P-bodies involved in mRNA decay; positively regulates transcription initiation and elongation; involved in microtubule-mediated processes, filamentous growth, rRNA maturation, telomere maintenance, tRNA intron turnover; negative regulator of autophagy; activated by glycolytic flux and scavenger decapping enzyme Dcs1p; role in preventing L-A mycovirus pathogenesis 1 2 3 4 5 6 7 8 9 10 11 12 13
- Name Description
- eXoRiboNuclease 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.
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
- Xrn1p is 1528 amino acids long, longer-lived, moderate in abundance; contains five 5'-3' exoribonuclease 1 domains scattered throughout the protein and disordered regions in the C-terminus; acetylated on 3 lysines, ubiquitinylated on 6 lysines, phosphorylated on 25 residues
- Length (a.a.)
- 1528
- Mol. Weight (Da)
- 175458.4
- Isoelectric Point
- 7.51
- Median Abundance (molecules/cell)
- 12660 +/- 4228
- Half-life (hr)
- 11.0
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 XRN1 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
- Chromatin-binding 5'->3' exoribonuclease that activates transcription initiation and elongation by RNA polymerase II; involved in nuclear mRNA catabolism and decay of nonfunctional rRNAs; role in processing of both rRNA and snoRNA; negative regulator of autophagy; localizes to the nucleus, cytoplasmic stress granules and mRNA P-bodies
View computational annotations
Molecular Function
- Manually Curated
- enables 5'-3' RNA exonuclease activity (IMP, IDA)
- enables chromatin binding (IDA)
- enables eukaryotic initiation factor 4G binding (IDA)
- enables mRNA binding (HDA)
Biological Process
- Manually Curated
- involved in cellular response to nitrogen starvation (IMP)
- involved in mRNA destabilization (IMP)
- involved in NAD-cap decapping (IDA)
- involved in negative regulation of macroautophagy (IMP)
- involved in nonfunctional rRNA decay (IMP)
- involved in nuclear-transcribed mRNA catabolic process (IMP)
- involved in nuclear-transcribed mRNA catabolic process, 5'-3' exonucleolytic nonsense-mediated decay (IMP)
- acts upstream of or within nuclear-transcribed mRNA catabolic process, no-go decay (IMP)
- involved in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (IMP)
- involved in positive regulation of transcription elongation by RNA polymerase II (IMP)
- acts upstream of or within positive regulation of transcription initiation by RNA polymerase II (IMP)
- involved in regulation of telomere maintenance (IMP)
- involved in rRNA processing (IMP, IGI)
- involved in sno(s)RNA processing (IGI)
- involved in translational initiation (IMP)
- involved in traversing start control point of mitotic cell cycle (IMP)
- involved in tRNA decay (IDA)
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 grows slowly, has large cells, abnormal morphology of vacuoles, buds and lipid particles, short telomeres, shortened lifespan, decreased transposition, and is sensitive to antimalarial quinine, various antibiotics, caffeine, metals, heat, osmotic stress; heterozygous diploid nulls are haploinsufficent and sensitive to starvation; overexpression slows growth
Classical Genetics
- null
- autophagy: increased
- cell shape: abnormal
- chromosome/plasmid maintenance: abnormal
- fermentative growth: decreased
- growth in exponential phase: decreased rate
- hyperosmotic stress resistance: decreased
- metal resistance: decreased
- protein/peptide accumulation: decreased
- protein/peptide accumulation: increased
- protein/peptide modification: decreased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- respiratory growth: decreased
- RNA accumulation: increased
- RNA localization: abnormal
- small molecule transport: increased
- vegetative growth: decreased rate
- viability: decreased
- reduction of function
- repressible
- null
- alkaline pH resistance: decreased
- bud morphology: abnormal
- cell size: increased
- 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
- lipid particle morphology: abnormal
- metal resistance: decreased
- mutation frequency: increased
- nutrient utilization: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- resistance to enzymatic treatment: decreased
- respiratory growth: absent
- RNA accumulation: increased
- size of nucleolus: increased
- starvation resistance: decreased
- telomere length: decreased
- toxin resistance: decreased
- toxin resistance: increased
- transposable element transposition: decreased
- transposable element transposition: increased
- utilization of nitrogen source: decreased rate
- vacuolar morphology: abnormal
- vegetative growth: decreased
- viable
- overexpression
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
- Xrn1p interacts physically with proteins involved in rRNA processing; XRN1 interacts genetically with genes involved in transcription
1523 total interactions for 1022 unique genes
Physical Interactions
- Affinity Capture-MS: 366
- Affinity Capture-RNA: 13
- Affinity Capture-Western: 30
- Biochemical Activity: 1
- Co-crystal Structure: 7
- Co-localization: 1
- Co-purification: 3
- PCA: 7
- Proximity Label-MS: 2
- Reconstituted Complex: 4
- Two-hybrid: 12
Genetic Interactions
- Dosage Growth Defect: 1
- Dosage Lethality: 1
- Dosage Rescue: 6
- Negative Genetic: 714
- Phenotypic Enhancement: 25
- Phenotypic Suppression: 33
- Positive Genetic: 183
- Synthetic Growth Defect: 54
- Synthetic Lethality: 39
- Synthetic Rescue: 21
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
- 7
- 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: 2024-11-08
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.