RIF1 DNA-binding protein RIF1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: RIF1
Official Full Name: DNA-binding protein RIF1
Primary source: SGD:S000000479
Locus tag: YBR275C
See related: AllianceGenome:SGD:S000000479; FungiDB:YBR275C; VEuPathDB:YBR275C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables sequence-specific DNA binding activity. Involved in several processes, including DNA metabolic process; negative regulation of macromolecule metabolic process; and regulation of DNA stability. Located in chromosome, telomeric region. Part of shelterin complex. [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See RIF1 in Genome Data Viewer

Location:: chromosome: II

Exon count:: 1

Sequence:: Chromosome: II; NC_001134.8 (751356..757106, complement)

Chromosome II - NC_001134.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001134.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Checkpoint phosphorylation sites on budding yeast Rif1 protect nascent DNA from degradation by Sgs1-Dna2.
Title: Checkpoint phosphorylation sites on budding yeast Rif1 protect nascent DNA from degradation by Sgs1-Dna2.
A CDK-Dependent Phosphorylation of a Novel Domain of Rif1 Regulates its Function during Telomere Damage and Other Types of Stress.
Title: A CDK-Dependent Phosphorylation of a Novel Domain of Rif1 Regulates its Function during Telomere Damage and Other Types of Stress.
Rif1-Dependent Control of Replication Timing.
Title: Rif1-Dependent Control of Replication Timing.
Telomere length regulation by Rif1 protein from Hansenula polymorpha.
Title: Telomere length regulation by Rif1 protein from Hansenula polymorpha.
Rif1 regulates telomere length through conserved HEAT repeats.
Title: Rif1 regulates telomere length through conserved HEAT repeats.
The role of Rif1 in telomere length regulation is separable from its role in origin firing.
Title: The role of Rif1 in telomere length regulation is separable from its role in origin firing.
results indicate that Rif1 inhibits replication initiation by interacting directly with origins and suggest that Rap1-dependent sequestration of Rif1 increases its effective concentration near telomeres, while limiting its action at chromosome-internal sites.
Title: Rif1 Binding and Control of Chromosome-Internal DNA Replication Origins Is Limited by Telomere Sequestration.
Rif1 controls telomere length by recruiting PP1 to directly suppress telomerase-mediated TG repeat lengthening.
Title: Rif1 acts through Protein Phosphatase 1 but independent of replication timing to suppress telomere extension in budding yeast.
these results indicate that, in addition to controlling DNA replication initiation, budding yeast Rif1 plays an ongoing role after initiation and controls events at blocked replication forks.
Title: Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks.
Rif1 SQ/TQ Cluster Domain (SCD) can modulate Rif1 function. As all Rif1 orthologs have one or more SCD domains, these results for yeast Rif1 have implications for the regulation of Rif1 function in humans and other organisms.
Title: Rif1 phosphorylation site analysis in telomere length regulation and the response to damaged telomeres.

Submit: New GeneRIF Correction See all GeneRIFs (22)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables DNA replication origin binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II core promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables centromeric DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables telomeric DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA double-strand break processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA replication initiation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in DNA replication initiation	IPI Inferred from Physical Interaction more info	PubMed
involved_in negative regulation of DNA-templated DNA replication initiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of mitotic DNA replication initiation from late origin	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to chromosome, telomeric region	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA stability	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in silent mating-type cassette heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomere capping	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomere maintenance	IBA Inferred from Biological aspect of Ancestor more info
involved_in telomere maintenance	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
is_active_in chromosome, telomeric repeat region	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of shelterin complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: DNA-binding protein RIF1

NP_009834.4

Protein involved in control of DNA replication; binds Rap1p C-terminus, telomeres, centromeres, replication origins; contributes to resection of DNA double strand breaks (DSBs); acts synergistically with Rif2p to help control telomere length and establish telomeric silencing; in addition to controlling DNA replication initiation, plays ongoing role after initiation and controls events at blocked replication forks

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001134.8 Reference assembly

Range

751356..757106 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001178623.4 → NP_009834.4 TPA: DNA-binding protein RIF1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_009834.4

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VQS1, P29539, P89507

UniProtKB/TrEMBL

G2W9S9, N1P8V4

Conserved Domains (2) summary

cd14267
Location:1862 → 1907

Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains

pfam12231
Location:241 → 649

Rif1_N; Rap1-interacting factor 1 N terminal