NAB3 / YPL190C Overview
- Standard Name
- NAB3 1
- Systematic Name
- YPL190C
- SGD ID
- SGD:S000006111
- Aliases
- HMD1
- Feature Type
- ORF , Verified
- Description
- RNA-binding protein, subunit of Nrd1 complex (Nrd1p-Nab3p-Sen1p); complex interacts with exosome to mediate 3'-end formation of some mRNAs, snRNAs, snoRNAs, and CUTs; required for termination of non-poly(A) transcripts and efficient splicing; Nrd1-Nab3 pathway appears to have a role in rapid suppression of some genes when cells are shifted to poor growth conditions, indicating role for Nrd1-Nab3 in regulating cellular response to nutrient availability 1 2 3 4 5 6
- Name Description
- Nuclear polyAdenylated RNA-Binding 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
- NAB3/YPL190C is located on the left arm of chromosome XVI between cytochrome oxidase assembly factor COA2 and deubiquitinating enzyme MIY2; coding sequence is 2409 nucleotides long with 17 synonymous and 9 nonsynonymous SNPs; several deletions, insertions, and 1 untranslatable variant in some non-S288C 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 | CGD Synteny Browser
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
- Nab3p is 802 amino acids long, low in abundance and short-lived; methylated on K73, K213 and K363, di- and tri- methylated on K363, monoacetylated on K340 and K425, phosphorylated on 12 residues
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 NAB3 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
- RNA-binding subunit of the NRD1 snoRNA termination complex; involved in termination of RNA Pol II transcription, RNA end processing, nuclear mRNA surveillance, and decay of antisense and unstable transcripts
View computational annotations
Molecular Function
- Manually Curated
- enables RNA binding (IDA)
- enables transcription regulatory region RNA binding (IDA)
- High-Throughput
- enables mRNA binding (HDA)
Biological Process
- Manually Curated
- involved in antisense RNA transcript catabolic process (IDA, IMP)
- involved in CUT catabolic process (IMP)
- involved in mRNA 3'-end processing (IMP)
- involved in nuclear mRNA surveillance (IMP)
- involved in sno(s)RNA 3'-end processing (IMP)
- involved in snRNA 3'-end processing (IMP)
- involved in termination of RNA polymerase II transcription, exosome-dependent (IDA)
- involved in tRNA 3'-end processing (IMP)
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
- Essential gene in reference strain S288C; temperature-sensitive mutants display decreased G2/M phase transition, chromosome instability, decreased resistance to DNA-damaging agent camptothecin, decreased silencing at rDNA locus, and decreased nucleolus size; heterozygous diploids have increased chromosome loss and mitotic recombination rates; overexpression causes decreased chromosome/plasmid maintenance, heat sensitivity, decreased competitive fitness, decreased vegetative growth, and decreased resistance to cytoskeleton-damaging agent benomyl and DNA-damaging agent bleomycin; in large-scale studies, displays abnormal RNA accumulation of cryptic unstable transcripts, abnormal redox state, and is haploinsufficient
Classical Genetics
- null
- repressible
- conditional
- null
- overexpression
- conditional
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
- Nab3p interacts physically with proteins involved in rRNA processing; NAB3 interacts genetically with genes involved in transcription by RNA polymerase II
723 total interactions for 627 unique genes
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
- NAB3/YPL190C transcription is regulated by Tfc7p in response to heat
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.
All Curated Literature
All manually curated literature for the specified gene, shown as a count of references by year of publication followed by the most recent papers. Click "Literature Details" or "See all" to view all literature information for this locus, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review).
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