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 several processes, including cellular response to leukemia inhibitory factor; positive regulation of histone H3-K9 methylation; and regulation of nucleobase-containing compound metabolic process. Predicted to localize to several cellular components, including chromosome; nucleus; and spindle midzone. 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: MODEL
Also known as: LOC295602; LOW QUALITY PROTEIN: telomere-associated protein RIF1; 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
Orthologs:
Homo sapiens (human) : RIF1 (replication timing regulatory factor 1)  HGNC  Alliance
Mus musculus (house mouse) : Rif1 (replication timing regulatory factor 1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Rif1 (replication timing regulatory factor 1)
Pan paniscus (bonobo/pygmy chimpanzee) : RIF1 (replication timing regulatory factor 1)
Canis lupus familiaris (dog) : RIF1 (replication timing regulatory factor 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Rif1 (replication timing regulatory factor 1)
Sus scrofa (pig) : RIF1 (replication timing regulatory factor 1)
Chlorocebus sabaeus (African green monkey) : RIF1 (replication timing regulatory factor 1)
Heterocephalus glaber (naked mole-rat) : Rif1 (replication timing regulatory factor 1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
Celera334,698,698 - 34,747,822 (+)NCBICelera
Cytogenetic Map3q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Molecular Pathway Annotations     Click to see Annotation Detail View
References

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
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 (+)NCBIRGSC3.4rn4RGSC3.4
Celera334,698,698 - 34,747,822 (+)NCBICelera
Cytogenetic Map3q12NCBI
RIF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2151,409,883 - 151,508,013 (+)EnsemblGRCh38hg38GRCh38
GRCh382151,409,902 - 151,534,200 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372152,266,397 - 152,333,860 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362151,974,674 - 152,040,665 (+)NCBINCBI36hg18NCBI36
Build 342152,091,935 - 152,157,927NCBI
Celera2145,880,663 - 145,948,138 (+)NCBI
Cytogenetic Map2q23.3NCBI
HuRef2144,162,934 - 144,230,323 (+)NCBIHuRef
CHM1_12152,272,265 - 152,339,750 (+)NCBICHM1_1
Rif1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39251,962,725 - 52,016,781 (+)NCBI
GRCm38252,072,815 - 52,126,769 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl252,072,832 - 52,122,383 (+)EnsemblGRCm38mm10GRCm38
MGSCv37251,928,357 - 51,977,901 (+)NCBIGRCm37mm9NCBIm37
MGSCv36251,894,841 - 51,944,069 (+)NCBImm8
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
PanPan1.12B155,985,960 - 156,109,726 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B155,985,960 - 156,052,926 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B38,721,658 - 38,818,488 (+)NCBIMhudiblu_PPA_v0panPan3
RIF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1952,661,155 - 52,709,279 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11952,661,278 - 52,711,969 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Rif1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493646926,045,500 - 26,105,980 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RIF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15774,189 - 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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl1036,845,777 - 36,907,015 (+)Ensembl
ChlSab1.11036,845,751 - 36,937,040 (+)NCBI
Rif1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248665,619,758 - 5,680,165 (-)NCBI

Position Markers
AU016181  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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
Cytogenetic Map3q12UniSTS
RH 3.4 Map3444.8UniSTS
RH142803  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map3q12UniSTS
RH 3.4 Map3443.1UniSTS
RH139990  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map3q12UniSTS
RH 3.4 Map3442.7UniSTS
RH141723  
Rat AssemblyChrPosition (strand)SourceJBrowse
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3263142148562146Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)3600074851687917Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)3600074851687917Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31009408193415837Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31011931879772001Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31312691441510346Rat
731172Bp151Blood pressure QTL 1510.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31409041148562146Rat
12879849Bw180Body weight QTL 1800.037body mass (VT:0001259)body weight (CMO:0000012)31409041148562146Rat
12879850Cm91Cardiac mass QTL 910.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)31409041148562146Rat
12879851Cm92Cardiac mass QTL 920.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)31409041148562146Rat
12879852Cm93Cardiac mass QTL 930.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)31409041148562146Rat
12879853Am5Aortic mass QTL 50.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)31409041148562146Rat
12879854Kidm63Kidney mass QTL 630.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)31409041148562146Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31802366463023664Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32122380366223803Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32122380366223803Rat
631685Bp118Blood pressure QTL 1183.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)32465522569655225Rat
1298073Cm13Cardiac mass QTL 132.5heart mass (VT:0007028)heart wet weight (CMO:0000069)32563336639248391Rat
631832Sach1Saccharin preference QTL 12.70.02consumption behavior trait (VT:0002069)calculated saccharin drink intake volume (CMO:0001600)32813672845772990Rat
2313049Bss72Bone structure and strength QTL 722.60.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)32813672851687917Rat
2313076Bss74Bone structure and strength QTL 7420.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)32813672851687917Rat
2313079Bss73Bone structure and strength QTL 731.5tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)32813672851687917Rat
2313093Bmd77Bone mineral density QTL 772.20.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)32813672851687917Rat
2313101Bmd76Bone mineral density QTL 763.60.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)32813672851687917Rat
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)32932171474321714Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32968273274682732Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32968273274682732Rat
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)32968273274682732Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32968273274682732Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32968273274682732Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32990825574908255Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32990825574908255Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)330114912123700444Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33110358972989078Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33110358972989078Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33110358972989078Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33110358972989078Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33110358972989078Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33110358972989078Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33213099777130997Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33213099777130997Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33347735462922975Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33347735481136227Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333477354108914061Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)334394121103141944Rat

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.


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000090575   ⟹   ENSRNOP00000075681
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl337,599,728 - 37,647,631 (+)Ensembl
RefSeq Acc Id: XM_003753723   ⟹   XP_003753771
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera334,698,698 - 34,747,822 (+)NCBI
Sequence:
RefSeq Acc Id: XM_003753724   ⟹   XP_003753772
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera334,698,698 - 34,747,822 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006224413   ⟹   XP_006224475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera334,698,698 - 34,747,822 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006224414   ⟹   XP_006224476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera334,698,698 - 34,747,822 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006224415   ⟹   XP_006224477
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera334,698,698 - 34,747,822 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008761831   ⟹   XP_008760053
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0337,599,540 - 37,648,818 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_003753771   ⟸   XM_003753723
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_003753772   ⟸   XM_003753724
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006224476   ⟸   XM_006224414
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006224477   ⟸   XM_006224415
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006224475   ⟸   XM_006224413
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008760053   ⟸   XM_008761831
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000075681   ⟸   ENSRNOT00000090575
Protein Domains
Rif1_N

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562474 AgrOrtholog
Ensembl Genes ENSRNOG00000054901 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000075681 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000090575 ENTREZGENE, UniProtKB/TrEMBL
InterPro ARM-type_fold UniProtKB/TrEMBL
  Rif1_N UniProtKB/TrEMBL
NCBI Gene 295602 ENTREZGENE
Pfam Rif1_N UniProtKB/TrEMBL
PhenoGen Rif1 PhenoGen
Superfamily-SCOP SSF48371 UniProtKB/TrEMBL
UniProt A0A0G2KB73_RAT 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