Cx3cr1 (C-X3-C motif chemokine receptor 1) - Rat Genome Database

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Gene: Cx3cr1 (C-X3-C motif chemokine receptor 1) Rattus norvegicus
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Symbol: Cx3cr1
Name: C-X3-C motif chemokine receptor 1
RGD ID: 620137
Description: Enables C-X3-C chemokine receptor activity. Involved in several processes, including negative regulation of apoptotic process; regulation of cell migration; and regulation of gene expression. Located in several cellular components, including cell surface; neuronal cell body membrane; and perinuclear region of cytoplasm. Used to study Parkinsonism; glomerulonephritis; hepatopulmonary syndrome; and status epilepticus. Biomarker of several diseases, including anti-basement membrane glomerulonephritis; artery disease (multiple); borna disease; portal hypertension; and sciatic neuropathy. Human ortholog(s) of this gene implicated in several diseases, including human immunodeficiency virus infectious disease; obesity; pulmonary hypertension; retinal disease (multiple); and systemic scleroderma. Orthologous to human CX3CR1 (C-X3-C motif chemokine receptor 1); PARTICIPATES IN chemokine mediated signaling pathway; cytokine mediated signaling pathway; INTERACTS WITH 6-propyl-2-thiouracil; acetamide; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: C-X3-C CKR-1; chemokine (C-X3-C motif) receptor 1; chemokine (C-X3-C) receptor 1; CX3C chemokine receptor 1; fractalkine receptor; Rbs11
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28119,785,726 - 119,799,431 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl8119,782,595 - 119,800,014 (-)Ensembl
Rnor_6.08128,740,756 - 128,754,514 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8128,740,756 - 128,754,514 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08127,941,653 - 127,955,411 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48125,033,630 - 125,047,335 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18125,053,366 - 125,067,072 (-)NCBI
Celera8118,932,179 - 118,945,873 (-)NCBICelera
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
age related macular degeneration 12  (ISO)
anti-basement membrane glomerulonephritis  (IEP)
arteriosclerosis  (ISO)
arthus reaction  (ISO)
asthma  (ISO)
atherosclerosis  (ISO)
atopic dermatitis  (ISO)
borna disease  (IEP)
Chloracne  (ISO)
Chronic Mesangial Proliferative Glomerulonephritis  (IEP)
congestive heart failure  (IEP)
conjunctivitis  (ISO)
corneal neovascularization  (ISO)
coronary artery disease  (ISS)
Coronary Disease  (ISO)
cystitis  (IEP)
diabetes mellitus  (ISO)
Experimental Arthritis  (IEP)
Experimental Autoimmune Encephalomyelitis  (IEP,IMP)
Experimental Autoimmune Neuritis  (IEP)
Experimental Autoimmune Uveitis  (IEP,ISO)
Experimental Diabetes Mellitus  (IEP)
glaucoma  (ISO)
glomerulonephritis  (IEP,IMP)
Graft vs Host Disease  (ISO)
Hearing Loss  (ISO)
hepatopulmonary syndrome  (IMP)
Herpes Simplex Encephalitis  (ISO)
human immunodeficiency virus infectious disease  (ISO)
Hyperalgesia  (IEP,IMP,ISO)
Inflammation  (IEP,ISO)
Intervertebral Disc Displacement  (IEP)
Intimal Hyperplasia  (ISO)
macular degeneration  (ISO)
Memory Disorders  (IMP)
Microscopic Polyangiitis  (ISO)
Myocardial Reperfusion Injury  (ISO)
Neoplasm Metastasis  (ISO)
nephrosis  (IEP)
obesity  (ISO)
optic nerve glioma  (ISO)
otitis media  (ISO)
Pain  (IMP)
Parkinsonism  (IMP)
portal hypertension  (IEP)
prion disease  (IEP)
psoriasis  (ISO)
pulmonary embolism  (IEP)
pulmonary hypertension  (IEP,ISO)
respiratory syncytial virus infectious disease  (ISO)
retinal degeneration  (ISO)
retinal vasculitis  (ISO)
retinitis  (ISO)
sciatic neuropathy  (IEP,ISO)
Sepsis  (ISO)
status epilepticus  (IMP)
systemic lupus erythematosus  (ISO)
systemic scleroderma  (ISO)
transient cerebral ischemia  (IEP)
uveitis  (IEP)
Viral Bronchiolitis  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-acetyl-1-alkyl-sn-glycero-3-phosphocholine  (ISO)
2-butoxyethanol  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (EXP,ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[ghi]perylene  (ISO)
Benzo[k]fluoranthene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buta-1,3-diene  (ISO)
cadmium atom  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
ceric oxide  (EXP)
choline  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclophosphamide  (EXP)
dextran sulfate  (ISO)
diazinon  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
divanadium pentaoxide  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (ISO)
ferric oxide  (ISO)
folic acid  (ISO)
gamma-hexachlorocyclohexane  (ISO)
GW 501516  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (EXP)
mechlorethamine  (EXP)
methamphetamine  (EXP)
monosodium L-glutamate  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
nickel atom  (ISO)
O-methyleugenol  (ISO)
ochratoxin A  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
pentane-2,3-dione  (EXP)
phenobarbital  (ISO)
quercetin  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
succimer  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
trichloroethene  (ISO)
triptonide  (ISO)
valproic acid  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adaptive immune response  (ISO,ISS)
antifungal innate immune response  (ISO,ISS)
autocrine signaling  (IGI)
brain development  (ISO,ISS)
calcium-mediated signaling  (IBA)
cell adhesion  (ISO)
cell chemotaxis  (IBA,IMP)
cellular response to lipopolysaccharide  (IEP,ISO)
cellular response to transforming growth factor beta stimulus  (IEP)
central nervous system maturation  (ISO)
cerebral cortex cell migration  (ISO)
chemokine-mediated signaling pathway  (IMP)
chemotaxis  (ISO)
cytokine-mediated signaling pathway  (ISO)
host-mediated regulation of intestinal microbiota composition  (ISO,ISS)
immune response  (IBA,ISO,ISS)
inflammatory response  (IEA)
leukocyte chemotaxis  (ISO,ISS)
leukocyte tethering or rolling  (ISO)
macrophage chemotaxis  (ISO)
memory  (IMP)
microglial cell activation  (IMP)
microglial cell activation involved in immune response  (ISO,ISS)
modulation of chemical synaptic transmission  (ISO)
multiple spine synapse organization, single dendrite  (ISO)
negative regulation of angiogenesis  (ISO)
negative regulation of apoptotic signaling pathway  (IGI)
negative regulation of cell migration  (IMP)
negative regulation of chronic inflammatory response to non-antigenic stimulus  (IMP)
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  (ISO)
negative regulation of hippocampal neuron apoptotic process  (IGI)
negative regulation of interleukin-1 beta production  (IMP)
negative regulation of long-term synaptic potentiation  (IMP)
negative regulation of microglial cell mediated cytotoxicity  (ISO,ISS)
phospholipase C-activating G protein-coupled receptor signaling pathway  (ISO)
positive regulation of angiogenesis  (IMP)
positive regulation of cytosolic calcium ion concentration  (IBA)
positive regulation of I-kappaB phosphorylation  (IGI)
positive regulation of microglial cell migration  (IMP)
positive regulation of monocyte chemotaxis  (ISO)
positive regulation of neuroblast proliferation  (IMP)
positive regulation of neurogenesis  (ISO)
positive regulation of NF-kappaB transcription factor activity  (IGI)
positive regulation of protein kinase B signaling  (IGI)
regulation of nitric oxide biosynthetic process  (ISO)
regulation of tumor necrosis factor production  (ISO)
response to ischemia  (IGI)
social behavior  (ISO)
synapse maturation  (ISO)
synapse pruning  (ISO,ISS)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:10187784   PMID:15993821   PMID:16019082   PMID:16732273   PMID:16980051   PMID:17174525   PMID:18292196   PMID:18971423   PMID:20364328   PMID:21131739   PMID:22213034   PMID:22387113  
PMID:22536384   PMID:22613229   PMID:23125415   PMID:23499256   PMID:24175290   PMID:24487234   PMID:24681877   PMID:25461978   PMID:25768734   PMID:26386845   PMID:28612319   PMID:28791023  
PMID:29082919   PMID:30598122   PMID:31726181   PMID:32152663   PMID:32323731   PMID:32423102   PMID:32664639   PMID:32664984   PMID:32819407  


Genomics

Comparative Map Data
Cx3cr1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28119,785,726 - 119,799,431 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl8119,782,595 - 119,800,014 (-)Ensembl
Rnor_6.08128,740,756 - 128,754,514 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8128,740,756 - 128,754,514 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08127,941,653 - 127,955,411 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48125,033,630 - 125,047,335 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.18125,053,366 - 125,067,072 (-)NCBI
Celera8118,932,179 - 118,945,873 (-)NCBICelera
Cytogenetic Map8q32NCBI
CX3CR1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl339,263,495 - 39,281,735 (-)EnsemblGRCh38hg38GRCh38
GRCh38339,263,494 - 39,281,735 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37339,304,985 - 39,323,226 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36339,279,989 - 39,296,531 (-)NCBINCBI36hg18NCBI36
Build 34339,279,990 - 39,296,526NCBI
Celera339,246,596 - 39,264,836 (-)NCBI
Cytogenetic Map3p22.2NCBI
HuRef339,347,466 - 39,365,706 (-)NCBIHuRef
CHM1_1339,256,125 - 39,274,344 (-)NCBICHM1_1
Cx3cr1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,877,749 - 119,897,362 (-)NCBIGRCm39mm39
GRCm39 Ensembl9119,730,682 - 119,898,945 (-)Ensembl
GRCm389120,048,683 - 120,068,296 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9119,901,616 - 120,069,879 (-)EnsemblGRCm38mm10GRCm38
MGSCv379119,957,811 - 119,977,400 (-)NCBIGRCm37mm9NCBIm37
MGSCv369119,897,391 - 119,916,980 (-)NCBImm8
Celera9120,518,248 - 120,537,939 (-)NCBICelera
Cytogenetic Map9F4NCBI
Cx3cr1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542724,701,073 - 24,707,230 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542724,691,206 - 24,705,599 (+)NCBIChiLan1.0ChiLan1.0
CX3CR1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1339,439,009 - 39,456,797 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl339,440,955 - 39,457,219 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0339,158,346 - 39,176,604 (-)NCBIMhudiblu_PPA_v0panPan3
CX3CR1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1238,937,069 - 8,954,738 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl238,938,906 - 8,952,808 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha238,974,330 - 8,988,240 (-)NCBI
ROS_Cfam_1.0239,221,526 - 9,239,150 (-)NCBI
UMICH_Zoey_3.1239,036,770 - 9,050,661 (-)NCBI
UNSW_CanFamBas_1.0239,179,594 - 9,193,497 (-)NCBI
UU_Cfam_GSD_1.0239,172,979 - 9,186,888 (-)NCBI
Cx3cr1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118195,370,137 - 195,397,149 (-)NCBI
SpeTri2.0NW_00493647328,508,726 - 28,535,640 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CX3CR1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1323,944,369 - 23,957,486 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11323,944,386 - 23,957,567 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21326,204,842 - 26,218,014 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CX3CR1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.115136,757 - 153,316 (+)NCBI
ChlSab1.1 Ensembl15150,718 - 151,785 (+)Ensembl
Vero_WHO_p1.0NW_0236660638,861,161 - 8,878,212 (+)NCBI
Cx3cr1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247311,705,953 - 1,719,452 (+)NCBI

Position Markers
D8Wox28  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,785,749 - 119,785,910 (+)MAPPERmRatBN7.2
Rnor_6.08128,740,780 - 128,740,940NCBIRnor6.0
Rnor_5.08127,941,677 - 127,941,837UniSTSRnor5.0
RGSC_v3.48125,033,654 - 125,033,814UniSTSRGSC3.4
Celera8118,932,203 - 118,932,351UniSTS
Cytogenetic Map8q32UniSTS
PMC209384P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,786,211 - 119,786,825 (+)MAPPERmRatBN7.2
Rnor_6.08128,741,242 - 128,741,855NCBIRnor6.0
Rnor_5.08127,942,139 - 127,942,752UniSTSRnor5.0
RGSC_v3.48125,034,116 - 125,034,729UniSTSRGSC3.4
Celera8118,932,653 - 118,933,266UniSTS
Cytogenetic Map8q32UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:113
Count of miRNA genes:91
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000025019
Prediction methods:Microtar, Miranda, Rnahybrid, 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 1 25 3
Low 3 33 37 21 18 21 2 2 49 35 38 11 2
Below cutoff 10 20 20 20 6 9 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025019   ⟹   ENSRNOP00000025019
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,783,208 - 119,800,014 (-)Ensembl
Rnor_6.0 Ensembl8128,740,756 - 128,754,514 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093935   ⟹   ENSRNOP00000097085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,782,595 - 119,799,470 (-)Ensembl
RefSeq Acc Id: NM_133534   ⟹   NP_598218
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,785,726 - 119,799,431 (-)NCBI
Rnor_6.08128,740,756 - 128,754,514 (-)NCBI
Rnor_5.08127,941,653 - 127,955,411 (-)NCBI
RGSC_v3.48125,033,630 - 125,047,335 (-)RGD
Celera8118,932,179 - 118,945,873 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_598218 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB87093 (Get FASTA)   NCBI Sequence Viewer  
  EDL76889 (Get FASTA)   NCBI Sequence Viewer  
  P35411 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_598218   ⟸   NM_133534
- UniProtKB: P35411 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000025019   ⟸   ENSRNOT00000025019
RefSeq Acc Id: ENSRNOP00000097085   ⟸   ENSRNOT00000093935

Transcriptome

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

Promoters
RGD ID:13696381
Promoter ID:EPDNEW_R6904
Type:single initiation site
Name:Cx3cr1_1
Description:C-X3-C motif chemokine receptor 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_6.08128,754,532 - 128,754,592EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/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/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:620137 AgrOrtholog
Ensembl Genes ENSRNOG00000018509 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000025019 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000025019 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Chemokine_CX3CR1 UniProtKB/Swiss-Prot
  GPCR_Rhodpsn UniProtKB/Swiss-Prot
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot
KEGG Report rno:171056 UniProtKB/Swiss-Prot
NCBI Gene 171056 ENTREZGENE
Pfam 7tm_1 UniProtKB/Swiss-Prot
PhenoGen Cx3cr1 PhenoGen
PRINTS FRACTALKINER UniProtKB/Swiss-Prot
  GPCRRHODOPSN UniProtKB/Swiss-Prot
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot
UniProt CX3C1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-22 Cx3cr1  C-X3-C motif chemokine receptor 1  Cx3cr1  chemokine (C-X3-C motif) receptor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Cx3cr1  chemokine (C-X3-C motif) receptor 1  Cx3cr1  chemokine (C-X3-C) receptor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Cx3cr1  chemokine (C-X3-C) receptor 1  Rbs11  Rbs11 protein  Symbol and Name updated 1299863 APPROVED
2002-08-07 Rbs11  Rbs11 protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA is expressed in spinal cord, brainstem, pituitary, brain, kidney, gut, uterus, and testis 633846