Advanced Search (OLGA)

Gene: Rif1 (replication timing regulatory factor 1) Rattus norvegicus

Analyze

Symbol:

Rif1

Name:

replication timing regulatory factor 1

RGD ID:

1562474

Description:

Predicted to be involved in regulation of nucleobase-containing compound metabolic process; subtelomeric heterochromatin formation; and telomere maintenance in response to DNA damage. Predicted to act upstream of or within cellular response to leukemia inhibitory factor and somatic stem cell population maintenance. Predicted to be located in chromosome; pronucleus; and spindle midzone. Predicted to be active in chromosome, telomeric repeat region and nucleus. Orthologous to human RIF1 (replication timing regulatory factor 1); PARTICIPATES IN ataxia telangiectasia-mutated (ATM) signaling pathway; non-homologous end joining pathway of double-strand break repair; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; bisphenol A.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC295602; Rap1 interacting factor 1 homolog; Rap1 interacting factor 1 homolog (yeast); RAP1 interacting factor homolog; RAP1 interacting factor homolog (yeast); RGD1562474; similar to Rap1-interacting factor 1; telomere-associated protein RIF1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	RIF1 (replication timing regulatory factor 1)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther
Mus musculus (house mouse):	Rif1 (replication timing regulatory factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Rif1 (replication timing regulatory factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RIF1 (replication timing regulatory factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RIF1 (replication timing regulatory factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rif1 (replication timing regulatory factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RIF1 (replication timing regulatory factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	RIF1 (replication timing regulatory factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rif1 (replication timing regulatory factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Rif1 (replication timing regulatory factor 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RIF1 (replication timing regulatory factor 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Rif1 (replication timing regulatory factor 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	rif1 (replication timing regulatory factor 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	F11E6.7	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Drosophila melanogaster (fruit fly):	Rif1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	Rif1	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	F19H6.3	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	rif1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	rif1	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	56,963,840 - 57,017,106 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	56,963,854 - 57,017,106 (+)	Ensembl				GRCr8
mRatBN7.2	3	36,554,689 - 36,607,961 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	36,554,697 - 36,603,617 (+)	Ensembl				mRatBN7.2
Rnor_6.0	3	37,599,540 - 37,648,818 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	37,599,728 - 37,647,631 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	42,697,416 - 42,746,743 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	3	33,574,934 - 33,624,794 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	3	34,698,698 - 34,747,822 (+)	NCBI		Celera
Cytogenetic Map	3	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

nemaline myopathy 2 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-demecolcine (ISO)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,6-di-tert-butyl-4-methylphenol (ISO)

2-butoxyethanol (ISO)

2-hydroxypropanoic acid (ISO)

2-methylcholine (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

acrolein (ISO)

acrylamide (ISO)

aflatoxin B1 (ISO)

aflatoxin M1 (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

amphetamine (EXP)

anthracene-1,8,9-triol (ISO)

aristolochic acid A (ISO)

arsenite(3-) (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

beta-lapachone (ISO)

biochanin A (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

Bisphenol A diglycidyl ether (ISO)

bisphenol AF (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

caffeine (ISO)

chloroprene (EXP)

chlorpyrifos (ISO)

cholic acid (ISO)

cisplatin (ISO)

clofibrate (ISO)

cobalt dichloride (ISO)

corosolic acid (ISO)

coumarin (ISO)

cyclosporin A (ISO)

decabromodiphenyl ether (ISO)

dibutyl phthalate (EXP)

diuron (EXP)

doxorubicin (ISO)

enzyme inhibitor (ISO)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

FR900359 (ISO)

hydrogen peroxide (ISO)

iron dichloride (ISO)

Mezerein (ISO)

oxaliplatin (EXP)

ozone (ISO)

palytoxin (ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

phenobarbital (ISO)

phorbol 13-acetate 12-myristate (ISO)

progesterone (ISO)

rac-lactic acid (ISO)

resveratrol (ISO)

saccharin (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenate (ISO)

succimer (ISO)

tamibarotene (ISO)

testosterone (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

topotecan (EXP)

torcetrapib (ISO)

trichostatin A (ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (ISO)

triptonide (ISO)

troglitazone (ISO)

tungsten (ISO)

urethane (ISO)

valproic acid (EXP,ISO)

vincristine (ISO)

zinc dichloride (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

cellular response to leukemia inhibitory factor (ISO)

DNA damage response (IEA,ISO)

DNA repair (IEA)

negative regulation of double-strand break repair via homologous recombination (IEA,ISO)

negative regulation of gene expression, epigenetic (IEA,ISO)

negative regulation of transcription by RNA polymerase II (IEA,ISO)

positive regulation of double-strand break repair via nonhomologous end joining (IEA,ISO)

positive regulation of isotype switching (IEA,ISO)

stem cell population maintenance (ISO)

subtelomeric heterochromatin formation (IEA,ISO)

telomere maintenance (IBA,IEA,ISO)

telomere maintenance in response to DNA damage (IEA,ISO)

Cellular Component

chromatin (IEA,ISO)

chromosome, telomeric region (IEA,ISO)

chromosome, telomeric repeat region (IBA,IEA,ISO)

condensed chromosome (IEA,ISO)

female pronucleus (IEA,ISO)

male pronucleus (IEA,ISO)

nuclear membrane (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (IBA,IEA,ISO)

site of double-strand break (IEA,ISO)

spindle (IEA)

spindle midzone (IEA,ISO)

Molecular Function

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

ataxia telangiectasia-mutated (ATM) signaling pathway (ISO)

non-homologous end joining pathway of double-strand break repair (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Double-strand break repair: 53BP1 comes into focus.	Panier S and Boulton SJ, Nat Rev Mol Cell Biol. 2014 Jan;15(1):7-18. doi: 10.1038/nrm3719. Epub 2013 Dec 11.
3.	GOA pipeline	RGD automated data pipeline
4.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
6.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:15042697	PMID:15583028	PMID:16518401	PMID:20439489	PMID:23306437	PMID:23306439	PMID:23333305	PMID:23333306	PMID:24735877	PMID:28241136

Genomics

Comparative Map Data

Rif1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	56,963,840 - 57,017,106 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	3	56,963,854 - 57,017,106 (+)	Ensembl				GRCr8
mRatBN7.2	3	36,554,689 - 36,607,961 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	36,554,697 - 36,603,617 (+)	Ensembl				mRatBN7.2
Rnor_6.0	3	37,599,540 - 37,648,818 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	37,599,728 - 37,647,631 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	3	42,697,416 - 42,746,743 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	3	33,574,934 - 33,624,794 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	3	34,698,698 - 34,747,822 (+)	NCBI		Celera
Cytogenetic Map	3	q12	NCBI

RIF1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	151,409,902 - 151,534,435 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	151,409,883 - 151,508,013 (+)	Ensembl			hg38	GRCh38
GRCh37	2	152,266,416 - 152,338,686 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	151,974,674 - 152,040,665 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	2	152,091,935 - 152,157,927	NCBI
Celera	2	145,880,663 - 145,948,138 (+)	NCBI		Celera
Cytogenetic Map	2	q23.3	NCBI
HuRef	2	144,162,934 - 144,230,323 (+)	NCBI		HuRef
CHM1_1	2	152,272,265 - 152,339,750 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	151,861,663 - 151,986,225 (+)	NCBI		T2T-CHM13v2.0

Rif1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	51,962,725 - 52,016,781 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	51,962,844 - 52,012,395 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	2	52,072,815 - 52,126,769 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	52,072,832 - 52,122,383 (+)	Ensembl			mm10	GRCm38
MGSCv37	2	51,928,357 - 51,977,901 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	2	51,894,841 - 51,944,069 (+)	NCBI		MGSCv36	mm8
Celera	2	53,801,434 - 53,849,273 (+)	NCBI		Celera
Cytogenetic Map	2	C1.1	NCBI
cM Map	2	29.98	NCBI

Rif1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955440	16,979,042 - 17,041,748 (+)	Ensembl
ChiLan1.0	NW_004955440	16,977,710 - 17,047,809 (+)	NCBI	ChiLan1.0	ChiLan1.0

RIF1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	13	54,099,763 - 54,260,321 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2B	54,114,717 - 54,275,309 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2B	38,721,658 - 38,818,488 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2B	155,985,960 - 156,109,726 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2B	155,985,960 - 156,052,926 (+)	Ensembl			panPan2	panpan1.1

RIF1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	19	52,661,278 - 52,711,969 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	19	52,661,155 - 52,709,279 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	19	52,823,853 - 52,876,461 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	19	54,171,299 - 54,224,157 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	19	54,170,503 - 54,220,826 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	19	52,884,821 - 52,937,353 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	19	52,956,937 - 53,009,549 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	19	54,422,620 - 54,475,318 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Rif1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405303	115,511,724 - 115,575,000 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936469	26,048,953 - 26,105,997 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936469	26,045,500 - 26,105,980 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RIF1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	774,191 - 832,010 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	15	769,518 - 832,036 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	157,039,785 - 157,101,592 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RIF1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	10	36,845,751 - 36,937,040 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	10	36,845,777 - 36,907,015 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666040	162,606,462 - 162,698,978 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Rif1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624866	5,619,758 - 5,680,165 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Rif1
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	5	29,864,927 - 29,913,417 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Rif1
384 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	129
Count of miRNA genes:	90
Interacting mature miRNAs:	93
Transcripts:	ENSRNOT00000008201, ENSRNOT00000008240
Prediction methods:	Microtar, Miranda, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1300178	Hrtrt4	Heart rate QTL 4	3.74		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	51490129	111359995	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	51581665	184004958	Rat
1354589	Bw31	Body weight QTL 31	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	3	53651826	98651826	Rat
1298073	Cm13	Cardiac mass QTL 13	2.5		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	45423609	58601291	Rat
2303593	Gluco46	Glucose level QTL 46	3		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	48876619	93876619	Rat
1354590	Despr11	Despair related QTL 11		0.000031	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	3	48876619	93876619	Rat
10401810	Kidm53	Kidney mass QTL 53			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	28625339	67641995	Rat
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	35403199	97383526	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	49872657	138829559	Rat
631832	Sach1	Saccharin preference QTL 1	2.7	0.02	consumption behavior trait (VT:0002069)	calculated saccharin drink intake volume (CMO:0001600)	3	47904172	92904172	Rat
2313079	Bss73	Bone structure and strength QTL 73	1.5		tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	3	47904172	70710963	Rat
631647	Bp122	Blood pressure QTL 122	6.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	51092561	96092561	Rat
2313076	Bss74	Bone structure and strength QTL 74	2	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	3	47904172	70710963	Rat
631568	Bp92	Blood pressure QTL 92	2.2	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	15272348	60272348	Rat
1300169	Bp177	Blood pressure QTL 177	2.96		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	3	36425116	81425116	Rat
9590286	Uminl1	Urine mineral level QTL 1	3.5	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	3	48657744	93657744	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	37796919	82796919	Rat
2313093	Bmd77	Bone mineral density QTL 77	2.2	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	3	47904172	70710963	Rat
12879852	Cm93	Cardiac mass QTL 93		0.001	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	3	38708931	67641995	Rat
12879853	Am5	Aortic mass QTL 5		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	3	38708931	67641995	Rat
9590136	Scort3	Serum corticosterone level QTL 3	23.37	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	48657744	93657744	Rat
12879854	Kidm63	Kidney mass QTL 63		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	38708931	67641995	Rat
61419	Cia11	Collagen induced arthritis QTL 11	5.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	3	50766145	95766145	Rat
61356	Bp37	Blood pressure QTL 37	3		blood pressure trait (VT:0000183)	systolic blood pressure (CMO:0000004)	3	51092561	96092561	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	50766145	95766145	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	36721849	110333156	Rat
12879849	Bw180	Body weight QTL 180		0.037	body mass (VT:0001259)	body weight (CMO:0000012)	3	38708931	67641995	Rat
2313101	Bmd76	Bone mineral density QTL 76	3.6	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	3	47904172	70710963	Rat
12879850	Cm91	Cardiac mass QTL 91		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	3	38708931	67641995	Rat
731172	Bp151	Blood pressure QTL 151		0.04	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	38708931	67641995	Rat
12879851	Cm92	Cardiac mass QTL 92		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	38708931	67641995	Rat
8694196	Abfw2	Abdominal fat weight QTL 2	16.58	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	3	48657744	93657744	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	42158111	124558371	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	1	141509147	Rat
2325840	Bp345	Blood pressure QTL 345		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	38708931	83708931	Rat
8552950	Pigfal12	Plasma insulin-like growth factor 1 level QTL 12	7.3		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	3	48657744	93657744	Rat
631676	Cm8	Cardiac mass QTL 8	7.03	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	3	37363734	82363734	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	36101403	81101403	Rat
8694386	Bw159	Body weight QTL 159	4.52	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	3	48657744	93657744	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	42158111	124558371	Rat
2313049	Bss72	Bone structure and strength QTL 72	2.6	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	3	47904172	70710963	Rat
2312664	Scl62	Serum cholesterol level QTL 62		0.05	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	37796919	59119581	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	5675975	141509147	Rat

Markers in Region

AU016181

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	36,603,316 - 36,603,457 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	37,648,189 - 37,648,329	NCBI	Rnor6.0
Rnor_5.0	3	42,746,114 - 42,746,254	UniSTS	Rnor5.0
RGSC_v3.4	3	33,624,165 - 33,624,305	UniSTS	RGSC3.4
Celera	3	34,747,193 - 34,747,333	UniSTS
Cytogenetic Map	3	q12	UniSTS

RH142715

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	36,592,109 - 36,592,225 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	37,636,982 - 37,637,097	NCBI	Rnor6.0
Rnor_5.0	3	42,734,907 - 42,735,022	UniSTS	Rnor5.0
RGSC_v3.4	3	33,612,958 - 33,613,073	UniSTS	RGSC3.4
Celera	3	34,735,992 - 34,736,107	UniSTS
RH 3.4 Map	3	444.8	UniSTS
Cytogenetic Map	3	q12	UniSTS

RH142803

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	36,593,110 - 36,593,324 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	37,637,983 - 37,638,196	NCBI	Rnor6.0
Rnor_5.0	3	42,735,908 - 42,736,121	UniSTS	Rnor5.0
RGSC_v3.4	3	33,613,959 - 33,614,172	UniSTS	RGSC3.4
Celera	3	34,736,993 - 34,737,206	UniSTS
RH 3.4 Map	3	443.1	UniSTS
Cytogenetic Map	3	q12	UniSTS

RH139990

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	36,603,707 - 36,603,870 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	37,648,580 - 37,648,742	NCBI	Rnor6.0
Rnor_5.0	3	42,746,505 - 42,746,667	UniSTS	Rnor5.0
RGSC_v3.4	3	33,624,556 - 33,624,718	UniSTS	RGSC3.4
Celera	3	34,747,584 - 34,747,746	UniSTS
RH 3.4 Map	3	442.7	UniSTS
Cytogenetic Map	3	q12	UniSTS

RH141723

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	36,603,218 - 36,603,438 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	37,648,091 - 37,648,310	NCBI	Rnor6.0
Rnor_5.0	3	42,746,016 - 42,746,235	UniSTS	Rnor5.0
RGSC_v3.4	3	33,624,067 - 33,624,286	UniSTS	RGSC3.4
Celera	3	34,747,095 - 34,747,314	UniSTS
Cytogenetic Map	3	q12	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001427744	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_001429786	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003753723	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_003753724	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006224413	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006224414	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006224415	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008761831	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039106253	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039106254	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039106255	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039106256	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039106257	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_063283247	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473983	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000090575 ⟹ ENSRNOP00000075681

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	3	56,963,854 - 57,017,106 (+)	Ensembl
mRatBN7.2 Ensembl	3	36,554,956 - 36,603,617 (+)	Ensembl
Rnor_6.0 Ensembl	3	37,599,728 - 37,647,631 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000094327 ⟹ ENSRNOP00000079724

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	3	56,963,854 - 57,017,106 (+)	Ensembl
mRatBN7.2 Ensembl	3	36,554,942 - 36,603,617 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000097817 ⟹ ENSRNOP00000096382

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	3	56,963,854 - 57,017,106 (+)	Ensembl
mRatBN7.2 Ensembl	3	36,554,697 - 36,603,617 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000109963 ⟹ ENSRNOP00000092899

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	3	56,963,854 - 57,017,106 (+)	Ensembl
mRatBN7.2 Ensembl	3	36,554,715 - 36,603,617 (+)	Ensembl

RefSeq Acc Id:

NM_001427744 ⟹ NP_001414673

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	56,963,854 - 57,017,106 (+)	NCBI

RefSeq Acc Id:

XM_039106253 ⟹ XP_038962181

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	56,963,858 - 57,017,106 (+)	NCBI
mRatBN7.2	3	36,554,693 - 36,607,961 (+)	NCBI

RefSeq Acc Id:

XM_039106254 ⟹ XP_038962182

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	56,963,840 - 57,017,106 (+)	NCBI
mRatBN7.2	3	36,554,689 - 36,607,961 (+)	NCBI

RefSeq Acc Id:

XM_039106255 ⟹ XP_038962183

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	56,963,841 - 57,017,106 (+)	NCBI
mRatBN7.2	3	36,554,690 - 36,607,961 (+)	NCBI

RefSeq Acc Id:

XM_039106256 ⟹ XP_038962184

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	56,963,840 - 57,017,106 (+)	NCBI
mRatBN7.2	3	36,554,689 - 36,607,961 (+)	NCBI

RefSeq Acc Id:

XM_039106257 ⟹ XP_038962185

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	56,963,840 - 57,017,106 (+)	NCBI
mRatBN7.2	3	36,554,690 - 36,607,961 (+)	NCBI

RefSeq Acc Id:

XM_063283247 ⟹ XP_063139317

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	56,963,858 - 57,017,106 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001414673	(Get FASTA)	NCBI Sequence Viewer
	NP_001416715	(Get FASTA)	NCBI Sequence Viewer
	XP_038962181	(Get FASTA)	NCBI Sequence Viewer
	XP_038962182	(Get FASTA)	NCBI Sequence Viewer
	XP_038962183	(Get FASTA)	NCBI Sequence Viewer
	XP_038962184	(Get FASTA)	NCBI Sequence Viewer
	XP_038962185	(Get FASTA)	NCBI Sequence Viewer
	XP_063139317	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM00442	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000075681
	ENSRNOP00000075681.3
	ENSRNOP00000079724
	ENSRNOP00000079724.2
	ENSRNOP00000092899
	ENSRNOP00000092899.1
	ENSRNOP00000096382
	ENSRNOP00000096382.1

Ensembl Acc Id:

ENSRNOP00000075681 ⟸ ENSRNOT00000090575

RefSeq Acc Id:	XP_038962184 ⟸ XM_039106256
- Peptide Label:	isoform X4
- UniProtKB:	A0A8I5ZP39 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038962182 ⟸ XM_039106254
- Peptide Label:	isoform X2
- UniProtKB:	A0A8I6AHX2 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038962183 ⟸ XM_039106255
- Peptide Label:	isoform X3
- UniProtKB:	A0A8I6AQP3 (UniProtKB/TrEMBL), A0A8I6AHX2 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038962185 ⟸ XM_039106257
- Peptide Label:	isoform X5

RefSeq Acc Id:	XP_038962181 ⟸ XM_039106253
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I6AHX2 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSRNOP00000079724 ⟸ ENSRNOT00000094327

Ensembl Acc Id:

ENSRNOP00000092899 ⟸ ENSRNOT00000109963

Ensembl Acc Id:

ENSRNOP00000096382 ⟸ ENSRNOT00000097817

RefSeq Acc Id:	NP_001414673 ⟸ NM_001427744
- UniProtKB:	A0A8I6AHX2 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_063139317 ⟸ XM_063283247
- Peptide Label:	isoform X2
- UniProtKB:	A0A8I6AHX2 (UniProtKB/TrEMBL)

Protein Domains

Telomere-associated protein Rif1 N-terminal

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-A0A0G2KB73-F1-model_v2	AlphaFold	A0A0G2KB73	1-2416	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13692091

Promoter ID:

EPDNEW_R2601

Type:

single initiation site

Name:

Rif1_1

Description:

replication timing regulatory factor 1

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	37,599,680 - 37,599,740	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1562474	AgrOrtholog
BioCyc Gene	G2FUF-49735	BioCyc
Ensembl Genes	ENSRNOG00000054901	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000090575	ENTREZGENE
	ENSRNOT00000090575.3	UniProtKB/TrEMBL
	ENSRNOT00000094327	ENTREZGENE
	ENSRNOT00000094327.2	UniProtKB/TrEMBL
	ENSRNOT00000097817	ENTREZGENE
	ENSRNOT00000097817.2	UniProtKB/TrEMBL
	ENSRNOT00000109963	ENTREZGENE
	ENSRNOT00000109963.2	UniProtKB/TrEMBL
InterPro	ARM-type_fold	UniProtKB/TrEMBL
	Rif1_N	UniProtKB/TrEMBL
NCBI Gene	295602	ENTREZGENE
PANTHER	PTHR22928	UniProtKB/TrEMBL
	TELOMERE-ASSOCIATED PROTEIN RIF1	UniProtKB/TrEMBL
Pfam	Rif1_N	UniProtKB/TrEMBL
PhenoGen	Rif1	PhenoGen
RatGTEx	ENSRNOG00000054901	RatGTEx
Superfamily-SCOP	SSF48371	UniProtKB/TrEMBL
UniProt	A0A0G2KB73_RAT	UniProtKB/TrEMBL
	A0A8I5ZP39	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6AHX2	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6AQP3	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2014-12-01	Rif1	replication timing regulatory factor 1	Rif1	Rap1 interacting factor 1 homolog (yeast)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-11-19	Rif1	Rap1 interacting factor 1 homolog (yeast)	Rif1	RAP1 interacting factor homolog (yeast)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-09	Rif1	RAP1 interacting factor homolog (yeast)	Rif1	Rap1 interacting factor 1 homolog (yeast)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-02-29	Rif1	Rap1 interacting factor 1 homolog (yeast)	RGD1562474_predicted	similar to Rap1-interacting factor 1 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1562474_predicted	similar to Rap1-interacting factor 1 (predicted)	LOC295602	similar to Rap1-interacting factor 1	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC295602	similar to Rap1-interacting factor 1			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

RGD Manual Annotations

Send us a Message

Imported Disease Annotations - ClinVar

RGD Manual Annotations