ABF1 / YKL112W Overview
- Standard Name
- ABF1 1
- Systematic Name
- YKL112W
- SGD ID
- SGD:S000001595
- Aliases
- SBF1 , GFI 35 , BAF1 10 , OBF1 36 , REB2 37 , SBF-B 38 39 , EBF2 28
- Feature Type
- ORF , Verified
- Description
- DNA binding protein with possible chromatin-reorganizing activity; involved in transcriptional activation, gene silencing, and DNA replication and repair 2 3 4
- Name Description
- ARS-Binding Factor 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.
- Length (a.a.)
- 731
- Mol. Weight (Da)
- 81693.3
- Isoelectric Point
- 4.67
- Median Abundance (molecules/cell)
- 6206 +/- 1386
- Half-life (hr)
- 6.4
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 ABF1 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
- Sequence specific DNA-binding RNA polymerase II transcription factor; involved in chromatin silencing and remodeling; binds replication origins and is involved in DNA replication; subunit of nucleotide-excision repair factor 4 complex
View computational annotations
Molecular Function
- Manually Curated
- enables DNA replication origin binding (IDA)
- enables DNA-binding transcription activator activity, RNA polymerase II-specific (IDA)
- enables RNA polymerase II cis-regulatory region sequence-specific DNA binding (IDA)
- enables sequence-specific DNA binding (HDA, IDA)
- enables sequence-specific DNA binding, bending (IDA)
- enables zinc ion binding (RCA)
Biological Process
- Manually Curated
- involved in chromatin remodeling (IDA, IGI)
- involved in DNA-templated DNA replication (IDA)
- involved in global genome nucleotide-excision repair (IDA, IMP)
- involved in negative regulation of transcription by RNA polymerase II (IMP)
- involved in positive regulation of transcription by RNA polymerase II (IMP)
- involved in silent mating-type cassette heterochromatin formation (IMP)
Cellular Component
- Manually Curated
- part of nucleotide-excision repair factor 4 complex (IDA)
- located in nucleus (IMP, IDA)
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; overexpression variously reported to cause sensitivity to nocodazol, decreased growth rate, or lethality; conditional mutants show delayed progression through G2 phase
Classical Genetics
- overexpression
- null
- null
- repressible
- overexpression
- reduction of function
- 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.
479 total interactions for 412 unique genes
Physical Interactions
- Affinity Capture-MS: 23
- Affinity Capture-RNA: 9
- Biochemical Activity: 1
- Co-fractionation: 2
- Co-localization: 1
- Proximity Label-MS: 2
- Reconstituted Complex: 7
Genetic Interactions
- Dosage Rescue: 4
- Negative Genetic: 351
- Positive Genetic: 77
- Synthetic Lethality: 2
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
- ABF1 encodes a zinc finger transcription factor that binds the consensus site, 5'-TnnCGTnnnnnnTGAT-3', which is found at various locations throughout the genome including at the silent mating type loci, ARSs, telomeres, and the promoter regions of many genes. Abf1p binding to these sites directly mediates a number of different events in addition to chromatin remodeling and transcriptional regulation such as DNA replication, silencing, and nucleotide excision repair. Abf1p regulates transcription of over 80 genes involved in a diverse range of cellular processes such as sugar and carbohydrate metabolism (ex. ADH1, CDC19, PGK1, ENO1, ENO2), nitrogen utilization (ex. CAR1, CAR2), ascospore formation (ex. SPR3), meiosis (ex. HOP1), ribosomal function (ex. RPL2A, RPL2B), and cellular respiration (ex. COX6). Abf1p contains a bipartite N-terminal DNA-binding domain and a C-terminal activation domain, which is responsible for mediating nuclear localization and chromatin remodeling. Abf1p binding appears to be constitutive and is stimulated by DNA replication protein Cdc6p. Abf1p can repress its own transcription through binding to its own promoter. Abf1p contains multiple phosphorylation sites, with the extent of Abf1p phosphorylation varying in different growth conditions, and regulating its activity.
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: 2005-10-19
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.