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

Summary

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

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_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RIF1 regulates early replication timing in murine B cells.
Title: RIF1 regulates early replication timing in murine B cells.
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.
Rif1 and Hmgn3 regulate the conversion of murine trophoblast stem cells.
Title: Rif1 and Hmgn3 regulate the conversion of murine trophoblast stem cells.
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.
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.
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.
Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction.
Title: Nuclear organisation and replication timing are coupled through RIF1-PP1 interaction.
RIF1 is an essential factor for replication fork protection.
Title: RIF1 promotes replication fork protection and efficient restart to maintain genome stability.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU016181 (e-PCR)
- UniSTS:164160

NoName (e-PCR)
- UniSTS:234395

AW549474 (e-PCR)
- UniSTS:178621

RH126074 (e-PCR)
- UniSTS:162786

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)

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
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
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

NC_000068.8 Reference GRCm39 C57BL/6J

Range

51962725..52016781

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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