Rif1 (replication timing regulatory factor 1) - Rat Genome Database

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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 and telomere organization. Predicted to act upstream of or within cellular response to leukemia inhibitory factor and somatic stem cell population maintenance. Predicted to be located in several cellular components, including chromosome; nucleus; and spindle midzone. Predicted to be part of chromatin. 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
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8356,963,840 - 57,017,106 (+)NCBIGRCr8
mRatBN7.2336,554,689 - 36,607,961 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl336,554,697 - 36,603,617 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0337,599,540 - 37,648,818 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl337,599,728 - 37,647,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0342,697,416 - 42,746,743 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4333,574,934 - 33,624,794 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera334,698,698 - 34,747,822 (+)NCBICelera
Cytogenetic Map3q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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)
biochanin A  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (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)
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)

Molecular Pathway Annotations     Click to see Annotation Detail View
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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8356,963,840 - 57,017,106 (+)NCBIGRCr8
mRatBN7.2336,554,689 - 36,607,961 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl336,554,697 - 36,603,617 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0337,599,540 - 37,648,818 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl337,599,728 - 37,647,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0342,697,416 - 42,746,743 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4333,574,934 - 33,624,794 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera334,698,698 - 34,747,822 (+)NCBICelera
Cytogenetic Map3q12NCBI
RIF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382151,409,902 - 151,534,435 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2151,409,883 - 151,508,013 (+)EnsemblGRCh38hg38GRCh38
GRCh372152,266,416 - 152,338,686 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362151,974,674 - 152,040,665 (+)NCBINCBI36Build 36hg18NCBI36
Build 342152,091,935 - 152,157,927NCBI
Celera2145,880,663 - 145,948,138 (+)NCBICelera
Cytogenetic Map2q23.3NCBI
HuRef2144,162,934 - 144,230,323 (+)NCBIHuRef
CHM1_12152,272,265 - 152,339,750 (+)NCBICHM1_1
T2T-CHM13v2.02151,861,663 - 151,986,225 (+)NCBIT2T-CHM13v2.0
Rif1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39251,962,725 - 52,016,781 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl251,962,844 - 52,012,395 (+)EnsemblGRCm39 Ensembl
GRCm38252,072,815 - 52,126,769 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl252,072,832 - 52,122,383 (+)EnsemblGRCm38mm10GRCm38
MGSCv37251,928,357 - 51,977,901 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36251,894,841 - 51,944,069 (+)NCBIMGSCv36mm8
Celera253,801,434 - 53,849,273 (+)NCBICelera
Cytogenetic Map2C1.1NCBI
cM Map229.98NCBI
Rif1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544016,979,042 - 17,041,748 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544016,977,710 - 17,047,809 (+)NCBIChiLan1.0ChiLan1.0
RIF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21354,099,763 - 54,260,321 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B54,114,717 - 54,275,309 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B38,721,658 - 38,818,488 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B155,985,960 - 156,109,726 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B155,985,960 - 156,052,926 (+)Ensemblpanpan1.1panPan2
RIF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11952,661,278 - 52,711,969 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1952,661,155 - 52,709,279 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1952,823,853 - 52,876,461 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01954,171,299 - 54,224,157 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1954,170,503 - 54,220,826 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11952,884,821 - 52,937,353 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01952,956,937 - 53,009,549 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01954,422,620 - 54,475,318 (+)NCBIUU_Cfam_GSD_1.0
Rif1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303115,511,724 - 115,575,000 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493646926,048,953 - 26,105,997 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493646926,045,500 - 26,105,980 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RIF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15774,191 - 832,010 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115769,518 - 832,036 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215157,039,785 - 157,101,592 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RIF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11036,845,751 - 36,937,040 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1036,845,777 - 36,907,015 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040162,606,462 - 162,698,978 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rif1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248665,619,758 - 5,680,165 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rif1
132 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298073Cm13Cardiac mass QTL 132.5heart mass (VT:0007028)heart wet weight (CMO:0000069)32501391138192233Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
631832Sach1Saccharin preference QTL 12.70.02consumption behavior trait (VT:0002069)calculated saccharin drink intake volume (CMO:0001600)32749462144188411Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32824968773249687Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2313093Bmd77Bone mineral density QTL 772.20.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)32749462150302886Rat
12879852Cm93Cardiac mass QTL 930.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)31831145447233430Rat
12879853Am5Aortic mass QTL 50.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)31831145447233430Rat
12879854Kidm63Kidney mass QTL 630.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)31831145447233430Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33068464275684642Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
12879849Bw180Body weight QTL 1800.037body mass (VT:0001259)body weight (CMO:0000012)31831145447233430Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
12879850Cm91Cardiac mass QTL 910.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)31831145447233430Rat
2313101Bmd76Bone mineral density QTL 763.60.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)32749462150302886Rat
731172Bp151Blood pressure QTL 1510.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31831145447233430Rat
12879851Cm92Cardiac mass QTL 920.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)31831145447233430Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32824968773249687Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33142640370668733Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33142640370668733Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33142640370668733Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33142640370668733Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33142640370668733Rat
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32793691972936919Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32846857173468571Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32846857173468571Rat
2313079Bss73Bone structure and strength QTL 731.5tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)32749462150302886Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33068464275684642Rat
2313076Bss74Bone structure and strength QTL 7420.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)32749462150302886Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33370334761017857Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32824968773249687Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)32824968773249687Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32824968773249687Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
2313049Bss72Bone structure and strength QTL 722.60.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)32749462150302886Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33142640370668733Rat

Markers in Region
AU016181  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2336,603,316 - 36,603,457 (+)MAPPERmRatBN7.2
Rnor_6.0337,648,189 - 37,648,329NCBIRnor6.0
Rnor_5.0342,746,114 - 42,746,254UniSTSRnor5.0
RGSC_v3.4333,624,165 - 33,624,305UniSTSRGSC3.4
Celera334,747,193 - 34,747,333UniSTS
Cytogenetic Map3q12UniSTS
RH142715  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2336,592,109 - 36,592,225 (+)MAPPERmRatBN7.2
Rnor_6.0337,636,982 - 37,637,097NCBIRnor6.0
Rnor_5.0342,734,907 - 42,735,022UniSTSRnor5.0
RGSC_v3.4333,612,958 - 33,613,073UniSTSRGSC3.4
Celera334,735,992 - 34,736,107UniSTS
RH 3.4 Map3444.8UniSTS
Cytogenetic Map3q12UniSTS
RH142803  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2336,593,110 - 36,593,324 (+)MAPPERmRatBN7.2
Rnor_6.0337,637,983 - 37,638,196NCBIRnor6.0
Rnor_5.0342,735,908 - 42,736,121UniSTSRnor5.0
RGSC_v3.4333,613,959 - 33,614,172UniSTSRGSC3.4
Celera334,736,993 - 34,737,206UniSTS
RH 3.4 Map3443.1UniSTS
Cytogenetic Map3q12UniSTS
RH139990  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2336,603,707 - 36,603,870 (+)MAPPERmRatBN7.2
Rnor_6.0337,648,580 - 37,648,742NCBIRnor6.0
Rnor_5.0342,746,505 - 42,746,667UniSTSRnor5.0
RGSC_v3.4333,624,556 - 33,624,718UniSTSRGSC3.4
Celera334,747,584 - 34,747,746UniSTS
RH 3.4 Map3442.7UniSTS
Cytogenetic Map3q12UniSTS
RH141723  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2336,603,218 - 36,603,438 (+)MAPPERmRatBN7.2
Rnor_6.0337,648,091 - 37,648,310NCBIRnor6.0
Rnor_5.0342,746,016 - 42,746,235UniSTSRnor5.0
RGSC_v3.4333,624,067 - 33,624,286UniSTSRGSC3.4
Celera334,747,095 - 34,747,314UniSTS
Cytogenetic Map3q12UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 23 40 24 17 24 1 1 61 28 41 8 1
Low 3 20 17 17 2 17 7 9 13 7 3 7
Below cutoff 1

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

RefSeq Acc Id: ENSRNOT00000090575   ⟹   ENSRNOP00000075681
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl336,554,956 - 36,603,617 (+)Ensembl
Rnor_6.0 Ensembl337,599,728 - 37,647,631 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094327   ⟹   ENSRNOP00000079724
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl336,554,942 - 36,603,617 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000097817   ⟹   ENSRNOP00000096382
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl336,554,697 - 36,603,617 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109963   ⟹   ENSRNOP00000092899
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl336,554,715 - 36,603,617 (+)Ensembl
RefSeq Acc Id: NM_001427744   ⟹   NP_001414673
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8356,963,854 - 57,017,106 (+)NCBI
RefSeq Acc Id: XM_039106253   ⟹   XP_038962181
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8356,963,858 - 57,017,106 (+)NCBI
mRatBN7.2336,554,693 - 36,607,961 (+)NCBI
RefSeq Acc Id: XM_039106254   ⟹   XP_038962182
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8356,963,840 - 57,017,106 (+)NCBI
mRatBN7.2336,554,689 - 36,607,961 (+)NCBI
RefSeq Acc Id: XM_039106255   ⟹   XP_038962183
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8356,963,841 - 57,017,106 (+)NCBI
mRatBN7.2336,554,690 - 36,607,961 (+)NCBI
RefSeq Acc Id: XM_039106256   ⟹   XP_038962184
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8356,963,840 - 57,017,106 (+)NCBI
mRatBN7.2336,554,689 - 36,607,961 (+)NCBI
RefSeq Acc Id: XM_039106257   ⟹   XP_038962185
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8356,963,840 - 57,017,106 (+)NCBI
mRatBN7.2336,554,690 - 36,607,961 (+)NCBI
RefSeq Acc Id: XM_063283247   ⟹   XP_063139317
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8356,963,858 - 57,017,106 (+)NCBI
RefSeq 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)
RefSeq Acc Id: ENSRNOP00000079724   ⟸   ENSRNOT00000094327
RefSeq Acc Id: ENSRNOP00000092899   ⟸   ENSRNOT00000109963
RefSeq 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 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 AssemblyChrPosition (strand)Source
Rnor_6.0337,599,680 - 37,599,740EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562474 AgrOrtholog
BioCyc Gene G2FUF-49735 BioCyc
Ensembl Genes ENSRNOG00000054901 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000090575.2 UniProtKB/TrEMBL
  ENSRNOT00000094327.1 UniProtKB/TrEMBL
  ENSRNOT00000097817.1 UniProtKB/TrEMBL
  ENSRNOT00000109963.1 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