Rfc4 (replication factor C subunit 4) - Rat Genome Database

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Gene: Rfc4 (replication factor C subunit 4) Rattus norvegicus
Analyze
Symbol: Rfc4
Name: replication factor C subunit 4
RGD ID: 1310142
Description: Is predicted to contribute to DNA clamp loader activity and single-stranded DNA helicase activity. Predicted to be involved in DNA repair; DNA-dependent DNA replication; and positive regulation of DNA-directed DNA polymerase activity. Predicted to localize to chromosome and nucleoplasm. Orthologous to human RFC4 (replication factor C subunit 4); PARTICIPATES IN mismatch repair pathway; nucleotide excision repair pathway; DNA replication pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC288003; replication factor C (activator 1) 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21177,749,642 - 77,764,123 (+)NCBI
Rnor_6.0 Ensembl1181,358,592 - 81,373,043 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01181,358,592 - 81,373,044 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01184,396,767 - 84,411,362 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41179,935,273 - 79,950,589 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11179,992,852 - 80,008,178 (+)NCBI
Celera1176,622,175 - 76,636,605 (+)NCBICelera
Cytogenetic Map11q23NCBI
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
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2,4-diaminotoluene  (ISO)
2-butoxyethanol  (ISO)
2-methylcholine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dieldrin  (EXP)
dioxygen  (ISO)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
folic acid  (ISO)
furan  (EXP)
glyphosate  (ISO)
heptachlor  (EXP)
hydrogen peroxide  (ISO)
indole-3-methanol  (EXP)
leflunomide  (ISO)
menadione  (ISO)
methotrexate  (ISO)
mirex  (EXP)
mitomycin C  (ISO)
nickel subsulfide  (ISO)
ochratoxin A  (EXP,ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
phenobarbital  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
quercetin  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
sodium dichromate  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
tetrahydropalmatine  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9488738   PMID:12477932   PMID:12930902   PMID:23277426   PMID:24115439  


Genomics

Comparative Map Data
Rfc4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21177,749,642 - 77,764,123 (+)NCBI
Rnor_6.0 Ensembl1181,358,592 - 81,373,043 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01181,358,592 - 81,373,044 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01184,396,767 - 84,411,362 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41179,935,273 - 79,950,589 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11179,992,852 - 80,008,178 (+)NCBI
Celera1176,622,175 - 76,636,605 (+)NCBICelera
Cytogenetic Map11q23NCBI
RFC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3186,789,880 - 186,807,058 (-)EnsemblGRCh38hg38GRCh38
GRCh383186,789,900 - 186,806,482 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373186,507,689 - 186,524,271 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363187,990,375 - 188,006,984 (-)NCBINCBI36hg18NCBI36
Build 343187,990,385 - 188,006,992NCBI
Celera3184,943,843 - 184,960,507 (-)NCBI
Cytogenetic Map3q27.3NCBI
HuRef3183,917,358 - 183,933,324 (-)NCBIHuRef
CHM1_13186,471,258 - 186,488,062 (-)NCBICHM1_1
Rfc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391622,932,698 - 22,946,480 (-)NCBIGRCm39mm39
GRCm39 Ensembl1622,932,693 - 22,946,487 (-)Ensembl
GRCm381623,113,948 - 23,127,730 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1623,113,943 - 23,127,737 (-)EnsemblGRCm38mm10GRCm38
MGSCv371623,114,021 - 23,127,803 (-)NCBIGRCm37mm9NCBIm37
MGSCv361623,029,282 - 23,043,064 (-)NCBImm8
Celera1623,672,554 - 23,686,047 (-)NCBICelera
Cytogenetic Map16B1NCBI
Rfc4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542020,948,549 - 20,967,845 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542020,948,549 - 20,967,845 (+)NCBIChiLan1.0ChiLan1.0
RFC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13192,290,639 - 192,307,478 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3192,290,639 - 192,307,839 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03183,824,865 - 183,841,895 (-)NCBIMhudiblu_PPA_v0panPan3
RFC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13419,361,024 - 19,377,289 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3419,361,044 - 19,377,294 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3423,446,502 - 23,462,817 (-)NCBI
ROS_Cfam_1.03419,272,394 - 19,288,876 (-)NCBI
UMICH_Zoey_3.13419,303,693 - 19,320,012 (-)NCBI
UNSW_CanFamBas_1.03419,303,699 - 19,320,013 (-)NCBI
UU_Cfam_GSD_1.03419,531,570 - 19,547,898 (-)NCBI
Rfc4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602117,112,167 - 117,127,993 (+)NCBI
SpeTri2.0NW_0049365783,204,035 - 3,219,806 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RFC4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13124,589,295 - 124,604,426 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113124,589,292 - 124,604,421 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213133,979,667 - 133,994,796 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RFC4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11581,081,415 - 81,097,599 (-)NCBI
ChlSab1.1 Ensembl1581,081,481 - 81,097,272 (-)Ensembl
Rfc4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473069,979,038 - 69,999,750 (+)NCBI

Position Markers
RH134436  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01181,373,131 - 81,373,311NCBIRnor6.0
Rnor_6.062,979,116 - 2,979,297NCBIRnor6.0
Rnor_5.01184,411,449 - 84,411,629UniSTSRnor5.0
RGSC_v3.41179,950,676 - 79,950,856UniSTSRGSC3.4
Celera1176,636,692 - 76,636,872UniSTS
Celera614,390,529 - 14,390,709UniSTS
Cytogenetic Map6q11UniSTS
Cytogenetic Map11q23UniSTS
D20S1005  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01181,373,449 - 81,373,528NCBIRnor6.0
Rnor_5.01184,411,767 - 84,411,846UniSTSRnor5.0
RGSC_v3.41179,950,994 - 79,951,073UniSTSRGSC3.4
Celera1176,637,010 - 76,637,089UniSTS
Cytogenetic Map11q23UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113215552082443118Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114658320986714631Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115994302390463843Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116010984287141948Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)116265336586714475Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116265336586714483Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116449467190463843Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116934231986312439Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116964970890463843Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)117272002986994795Rat
10450831Scl80Serum cholesterol level QTL 804.70.01blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)118035840887200449Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:13
Count of miRNA genes:13
Interacting mature miRNAs:13
Transcripts:ENSRNOT00000002487
Prediction methods:Miranda, Rnahybrid
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 3 28 40 27 19 27 1 1 73 27 41 11 1
Low 15 17 14 14 7 10 1 8 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002487   ⟹   ENSRNOP00000002487
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1181,358,592 - 81,373,043 (+)Ensembl
RefSeq Acc Id: NM_001105869   ⟹   NP_001099339
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21177,749,670 - 77,764,123 (+)NCBI
Rnor_6.01181,358,592 - 81,373,044 (+)NCBI
Rnor_5.01184,396,767 - 84,411,362 (+)NCBI
RGSC_v3.41179,935,273 - 79,950,589 (+)RGD
Celera1176,622,175 - 76,636,605 (+)RGD
Sequence:
RefSeq Acc Id: XM_039088096   ⟹   XP_038944024
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21177,749,642 - 77,764,123 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001099339 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944024 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68166 (Get FASTA)   NCBI Sequence Viewer  
  EDL78078 (Get FASTA)   NCBI Sequence Viewer  
  EDL78079 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099339   ⟸   NM_001105869
- UniProtKB: B4F778 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002487   ⟸   ENSRNOT00000002487
RefSeq Acc Id: XP_038944024   ⟸   XM_039088096
- Peptide Label: isoform X1
Protein Domains
AAA

Transcriptome

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

Promoters
RGD ID:13698245
Promoter ID:EPDNEW_R8770
Type:multiple initiation site
Name:Rfc4_1
Description:replication factor C subunit 4
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_6.01181,358,562 - 81,358,622EPDNEW

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)
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
F344/NRrrc (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
FHH/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)
FHH/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
FHL/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)
FHL/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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
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)
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
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:1310142 AgrOrtholog
Ensembl Genes ENSRNOG00000001816 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002487 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002487 ENTREZGENE, UniProtKB/TrEMBL
InterPro ATPase_AAA+_core UniProtKB/TrEMBL
  ATPase_AAA_core UniProtKB/TrEMBL
  DNA_pol3_clamp-load_cplx_C UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  Replication_factor_C UniProtKB/TrEMBL
KEGG Report rno:288003 UniProtKB/TrEMBL
NCBI Gene 288003 ENTREZGENE
Pfam AAA UniProtKB/TrEMBL
  Rep_fac_C UniProtKB/TrEMBL
PhenoGen Rfc4 PhenoGen
SMART AAA UniProtKB/TrEMBL
Superfamily-SCOP Pol_clamp_load_C UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt B4F778 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-16 Rfc4  replication factor C subunit 4  Rfc4  replication factor C (activator 1) 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Rfc4  replication factor C (activator 1) 4   Rfc4_predicted  replication factor C (activator 1) 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Rfc4_predicted  replication factor C (activator 1) 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED