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Rif1 replication timing regulatory factor 1 [ Mus musculus (house mouse) ]

Gene ID: 51869, updated on 21-Apr-2024

Summary

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Official Symbol
Rif1provided by MGI
Official Full Name
replication timing regulatory factor 1provided by MGI
Primary source
MGI:MGI:1098622
See related
Ensembl:ENSMUSG00000036202 AllianceGenome:MGI:1098622
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
D2Ertd145e; 5730435J01Rik; 6530403D07Rik
Summary
Involved in positive regulation of histone H3-K9 methylation; regulation of nucleobase-containing compound metabolic process; and telomere organization. Acts upstream of or within cellular response to leukemia inhibitory factor and stem cell population maintenance. Located in chromosome and pronucleus. Is expressed in several structures, including early conceptus; hindgut epithelium; primordial germ cell; reproductive system; and urinary system. Orthologous to human RIF1 (replication timing regulatory factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in CNS E11.5 (RPKM 5.0), cerebellum adult (RPKM 4.1) and 23 other tissues See more
Orthologs
human all
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Genomic context

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Location:
2 C1.1; 2 29.98 cM
Exon count:
35
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (51962725..52016781)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (52072815..52126769)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene N-myc (and STAT) interactor Neighboring gene STARR-seq mESC enhancer starr_04475 Neighboring gene tumor necrosis factor alpha induced protein 6 Neighboring gene STARR-seq mESC enhancer starr_04477 Neighboring gene nebulin Neighboring gene STARR-seq mESC enhancer starr_04479 Neighboring gene RIKEN cDNA 4930573O16 gene Neighboring gene STARR-seq mESC enhancer starr_04480 Neighboring gene predicted gene 13521

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Loss of full-length DNA replication regulator Rif1 in two-cell embryos is associated with zygotic transcriptional activation. Yoshizawa-Sugata N, et al. J Biol Chem, 2021 Dec. PMID 34736895, Free PMC Article
  2. Characterization of Interaction of the MBP-Tagged MuRif1-C-Terminal Domain with G-Quadruplex DNA by SPR. Ghadiri H, et al. Biochemistry (Mosc), 2021 Jul. PMID 34284714
  3. RIF1 promotes replication fork protection and efficient restart to maintain genome stability. Mukherjee C, et al. Nat Commun, 2019 Jul 23. PMID 31337767, Free PMC Article
  4. Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture. Moriyama K, et al. J Biol Chem, 2018 Mar 9. PMID 29348174, Free PMC Article
  5. Rif1 promotes a repressive chromatin state to safeguard against endogenous retrovirus activation. Li P, et al. Nucleic Acids Res, 2017 Dec 15. PMID 29040764, Free PMC Article

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RIF1 regulates early replication timing in murine B cells.
    Title: RIF1 regulates early replication timing in murine B cells.
  2. Rif1 Regulates Self-Renewal and Impedes Mesendodermal Differentiation of Mouse Embryonic Stem Cells.
    Title: Rif1 Regulates Self-Renewal and Impedes Mesendodermal Differentiation of Mouse Embryonic Stem Cells.
  3. Rif1 and Hmgn3 regulate the conversion of murine trophoblast stem cells.
    Title: Rif1 and Hmgn3 regulate the conversion of murine trophoblast stem cells.
  4. Elevated RIF1 participates in the epigenetic abnormalities of zygotes by regulating histone modifications on MuERV-L in obese mice.
    Title: Elevated RIF1 participates in the epigenetic abnormalities of zygotes by regulating histone modifications on MuERV-L in obese mice.
  5. Loss of full-length DNA replication regulator Rif1 in two-cell embryos is associated with zygotic transcriptional activation.
    Title: Loss of full-length DNA replication regulator Rif1 in two-cell embryos is associated with zygotic transcriptional activation.
  6. Characterization of Interaction of the MBP-Tagged MuRif1-C-Terminal Domain with G-Quadruplex DNA by SPR.
    Title: Characterization of Interaction of the MBP-Tagged MuRif1-C-Terminal Domain with G-Quadruplex DNA by SPR.
  7. Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction.
    Title: Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction.
  8. RIF1 is an essential factor for replication fork protection.
    Title: RIF1 promotes replication fork protection and efficient restart to maintain genome stability.
  9. data suggest that CST-Polalpha-mediated fill-in helps to control the repair of double-strand breaks by 53BP1, RIF1 and shieldin
    Title: 53BP1-RIF1-shieldin counteracts DSB resection through CST- and Polα-dependent fill-in.
  10. Data support model in which Rif1 modulates chromatin loop structures through binding to multiple G-quadruplex assemblies and by holding chromatin fibers together.
    Title: Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture.
Submit: New GeneRIF Correction See all GeneRIFs (24)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (2) 
  • Targeted (3)  1 citation
  • Chemically induced (ENU) (1)  1 citation
  • Endonuclease-mediated (3) 

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within DNA repair IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cell cycle IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in negative regulation of double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of double-strand break repair via homologous recombination ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of gene expression, epigenetic IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of isotype switching IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within somatic stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in subtelomeric heterochromatin formation 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 
involved_in telomere maintenance in response to DNA damage ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of chromatin IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in chromosome, telomeric repeat region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in condensed chromosome ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in female pronucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in male pronucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear membrane ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 
located_in site of double-strand break IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
  
located_in spindle midzone ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
telomere-associated protein RIF1
Names
Rap1 interacting factor 1 homolog
mRif1
rap1-interacting factor 1 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001355414.1 → NP_001342343.1  telomere-associated protein RIF1 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AL844571, AL929138
    Consensus CDS
    CCDS50583.1
    UniProtKB/TrEMBL
    J7I1C3
    Conserved Domains (1) summary
    pfam12231
    Location:25 → 368
    Rif1_N; Rap1-interacting factor 1 N terminal

  2. NM_001355415.1 → NP_001342344.1  telomere-associated protein RIF1 isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AL844571, AL929138
    UniProtKB/Swiss-Prot
    Q6PR54, Q6T8D9, Q7TPD8, Q8BTU2, Q8C408, Q9CS77
    UniProtKB/TrEMBL
    J7I1C3
    Conserved Domains (1) summary
    pfam12231
    Location:25 → 361
    Rif1_N; Rap1-interacting factor 1 N terminal

  3. NM_175238.6 → NP_780447.4  telomere-associated protein RIF1 isoform a

    See identical proteins and their annotated locations for NP_780447.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AL844571, AL929138
    Consensus CDS
    CCDS50583.1
    UniProtKB/TrEMBL
    J7I1C3
    Related
    ENSMUSP00000108313.3, ENSMUST00000112693.10
    Conserved Domains (1) summary
    pfam12231
    Location:25 → 368
    Rif1_N; Rap1-interacting factor 1 N terminal

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    51962725..52016781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036162373.1 → XP_036018266.1  telomere-associated protein RIF1 isoform X4

    UniProtKB/TrEMBL
    J7I1C3
    Conserved Domains (2) summary
    cd14267
    Location:2125 → 2172
    Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
    pfam12231
    Location:1 → 226
    Rif1_N; Rap1-interacting factor 1 N terminal

  2. XM_011239136.3 → XP_011237438.1  telomere-associated protein RIF1 isoform X2

    UniProtKB/TrEMBL
    J7I1C3
    Conserved Domains (2) summary
    cd14267
    Location:2234 → 2281
    Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
    pfam12231
    Location:25 → 361
    Rif1_N; Rap1-interacting factor 1 N terminal

  3. XM_011239135.3 → XP_011237437.1  telomere-associated protein RIF1 isoform X1

    UniProtKB/TrEMBL
    J7I1C3
    Conserved Domains (2) summary
    cd14267
    Location:2252 → 2299
    Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
    pfam12231
    Location:25 → 361
    Rif1_N; Rap1-interacting factor 1 N terminal

  4. XM_030251862.1 → XP_030107722.1  telomere-associated protein RIF1 isoform X3

    UniProtKB/TrEMBL
    J7I1C3
    Conserved Domains (2) summary
    cd14267
    Location:2117 → 2164
    Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
    pfam12231
    Location:1 → 226
    Rif1_N; Rap1-interacting factor 1 N terminal

  5. XM_011239137.4 → XP_011237439.1  telomere-associated protein RIF1 isoform X5

    Conserved Domains (1) summary
    cd14267
    Location:1241 → 1288
    Rif1_CTD_C-II_like; Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6PR54.2 GenPept UniProtKB/Swiss-Prot:Q6PR54

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