Rif1 MGI Mouse Gene Detail - MGI:1098622 - replication timing regulatory factor 1

Symbol

Rif1
Name

replication timing regulatory factor 1
Synonyms

5730435J01Rik, 6530403D07Rik, D2Ertd145e

Feature Type

protein coding gene
IDs

MGI:1098622
NCBI Gene: 51869
Alliance

genome feature page
Transcription Start Sites

16 TSS

Sequence Map

Chr2:51962844-52012395 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 29.98 cM
Mapping Data

4 experiments

SNPs within 2kb

1063 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1098622	protein coding gene	Chr2:51962725-52016781 (+)
129S1/SvImJ	ENSMUSG00200010807	protein coding gene	Chr2:48946783-48995504 (+)
A/J	ENSMUSG00195009894	protein coding gene	Chr2:49095775-49144500 (+)
AKR/J	ENSMUSG00220020090	protein coding gene	Chr2:49228041-49276768 (+)
BALB/cJ	ENSMUSG00180019270	protein coding gene	Chr2:49083822-49133144 (+)
C3H/HeJ	ENSMUSG00175013279	protein coding gene	Chr2:49120130-49168849 (+)
C57BL/6NJ	ENSMUSG00215010289	protein coding gene	Chr2:49129617-49178934 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023555	protein coding gene	Chr2:47388604-47437473 (+)
CAST/EiJ	ENSTCUG00005001512	protein coding gene	Chr2:48629847-48678398 (+)
CBA/J	ENSMUSG00210000695	protein coding gene	Chr2:49133080-49181803 (+)
DBA/2J	ENSMUSG00185002346	protein coding gene	Chr2:49000772-49049489 (+)
FVB/NJ	ENSMUSG00205001567	protein coding gene	Chr2:48797029-48845653 (+)
JF1/MsJ	ENSUMUG00000000469	protein coding gene	Chr2:48823525-48872738 (+)
LP/J	ENSMUSG00230000587	protein coding gene	Chr2:50908406-50957720 (+)
NOD/ShiLtJ	ENSMUSG00190001664	protein coding gene	Chr2:49048327-49097026 (+)
NZO/HlLtJ	ENSMUSG00225000304	protein coding gene	Chr2:58619528-58668844 (+)
PWK/PhJ	ENSLUMG00010004285	protein coding gene	Chr2:48979199-49028474 (+)
SPRET/EiJ	ENSMSPG00010010647	protein coding gene	Chr2:49969744-50023683 (+)
WSB/EiJ	ENSIUOG00005001199	protein coding gene	Chr2:49084304-49132988 (+)

Human Ortholog

RIF1, replication timing regulatory factor 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

RIF1, replication timing regulatory factor 1
Links

HGNC:23207

NCBI Gene ID: 55183

UniProt: Q5UIP0
Chr Location

2q23.3; chr2:151409883-151534435 (+) GRCh38

MGI Vertebrate Homology

Rif1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: RIF1
Gene Tree

Rif1

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Phenotype Summary

23 phenotypes from 6 alleles in 6 genetic backgrounds
1 phenotype from multigenic genotypes
27 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

74
Chemically induced (ENU)

1
Chemically induced (other)

1
Endonuclease-mediated

4
Gene trapped

63
Targeted

5
Genomic Mutations

1 involving Rif1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

172 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit embryonic lethality. Mice homozygous for a gene trap allele exhibit embryonic and postnatal lethality, reduced fertility, and decreased cell proliferation.

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All GO Annotations

54
GO References

15

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

750
Tissues

82
cDNA Data

22
Literature Summary

7

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

Xenbase rif1

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All Sequences

81
RefSeq

16
UniProt

7
CCDS

CCDS50583.1

Ensembl

ENSMUSG00000036202 (Evidence)
NCBI Gene

51869

			Length	Strain/Species	Flank
genomic	ENSMUSG00000036202	Ensembl Gene Model \| MGI Sequence Detail	49552	C57BL/6J	± kb
transcript	ENSMUST00000112693	Ensembl \| MGI Sequence Detail	8509	Not Applicable
polypeptide	ENSMUSP00000108313	Ensembl \| MGI Sequence Detail	2426	Not Applicable

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UniProt

7 Sequences
Protein Ontology

PR:000014000 telomere-associated protein RIF1

(term hierarchy)
InterPro Domains

IPR016024 Armadillo-type fold

IPR022031 Telomere-associated protein Rif1, N-terminal
GlyGen

Q6PR54 1 site

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All nucleic 25

cDNA 22

Primer pair 3

Antibodies 1

Microarray probesets 8

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MGI:1922959, MGI:1923494, MGI:2139159, MGI:2139383

Summaries

All 79

Developmental Gene Expression 7

Gene Ontology 15

Phenotypes 27
Earliest

J:93290 Araki K, et al., Exchangeable gene trap using the Cre/mutated lox system. Cell Mol Biol (Noisy-Le-Grand). 1999 Jul;45(5):737-50
Latest

J:361756 Kabrani E, et al., RIF1 integrates DNA repair and transcriptional requirements during the establishment of humoral immune responses. Nat Commun. 2025 Jan 17;16(1):777

TSS for Rif1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr17707	Chr2:51961521-51961543 (+)	-1,312 bp
Tssr17708	Chr2:51961555-51961564 (+)	-1,284 bp
Tssr17709	Chr2:51961566-51961578 (+)	-1,272 bp
Tssr17710	Chr2:51961583-51961609 (+)	-1,248 bp
Tssr17711	Chr2:51961617-51961629 (+)	-1,221 bp
Tssr17712	Chr2:51961889-51961895 (+)	-952 bp
Tssr17713	Chr2:51962329-51962340 (+)	-509 bp
Tssr17714	Chr2:51962345-51962358 (+)	-492 bp
Tssr17715	Chr2:51962816-51962826 (+)	-23 bp
Tssr17716	Chr2:51962835-51962866 (+)	7 bp
Tssr17717	Chr2:51962873-51962890 (+)	38 bp
Tssr17718	Chr2:51962907-51962918 (+)	69 bp
Tssr17719	Chr2:51963111-51963153 (+)	288 bp
Tssr17720	Chr2:52000199-52000213 (+)	37,362 bp
Tssr17721	Chr2:52010993-52011000 (+)	48,153 bp
Tssr17722	Chr2:52011475-52011489 (+)	48,638 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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