Cxcr4 (C-X-C motif chemokine receptor 4) - Rat Genome Database

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Gene: Cxcr4 (C-X-C motif chemokine receptor 4) Rattus norvegicus
Analyze
Symbol: Cxcr4
Name: C-X-C motif chemokine receptor 4
RGD ID: 620465
Description: Predicted to enable several functions, including chemokine receptor activity; cytoskeletal protein binding activity; and ubiquitin protein ligase binding activity. Involved in several processes, including detection of stimulus involved in sensory perception of pain; endothelium development; and nervous system development. Located in endosome; nucleus; and plasma membrane. Used to study pulmonary hypertension and temporal lobe epilepsy. Human ortholog(s) of this gene implicated in WHIM syndrome; hematologic cancer (multiple); leukopenia; osteoporosis; and pancreatic adenocarcinoma. Orthologous to human CXCR4 (C-X-C motif chemokine receptor 4); PARTICIPATES IN ephrin - ephrin receptor bidirectional signaling axis; hypoxia inducible factor pathway; sphingosine 1-phosphate signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: C-X-C chemokine receptor type 4; chemokine (C-X-C motif) receptor 4; Chemokine receptor (LCR1); CXC chemokine receptor; CXC-R4; CXCR-4; fusin; LESTR; leukocyte-derived seven transmembrane domain receptor; MGC108696; SDF-1 receptor; stromal cell-derived factor 1 receptor
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
mRatBN7.21340,077,976 - 40,081,883 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1340,077,976 - 40,081,883 (-)Ensembl
Rnor_6.01345,314,952 - 45,318,856 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1345,314,933 - 45,318,878 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01350,394,128 - 50,398,032 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41341,308,286 - 41,312,190 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11341,322,328 - 41,326,213 (-)NCBI
Celera1340,447,190 - 40,451,093 (-)NCBICelera
Cytogenetic Map13q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-phenylenediamine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-fluoro-2,4-dinitrobenzene  (ISO)
15-acetyldeoxynivalenol  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-acetamidofluorene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,3'-diindolylmethane  (ISO)
3-Nitrobenzanthrone  (ISO)
3-phenylprop-2-enal  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
6-propyl-2-thiouracil  (EXP)
6alpha-methylprednisolone  (ISO)
8'-apo-beta,psi-caroten-8'-al  (ISO)
acetamide  (EXP)
acrylonitrile  (ISO)
aflatoxin B1  (EXP,ISO)
alachlor  (EXP)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha-cyano-4-hydroxycinnamic acid  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (EXP,ISO)
azathioprine  (ISO)
azoxystrobin  (ISO)
Bandrowski's base  (ISO)
benzalkonium chloride  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzyl bromide  (ISO)
beta-carotene  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
cannabidiol  (ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
carfilzomib  (ISO)
chlordecone  (ISO)
chloroprene  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisatracurium  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cyclophosphamide  (EXP,ISO)
cylindrospermopsin  (ISO)
cytarabine  (ISO)
D-glucose  (ISO)
D-penicillamine  (EXP)
dapsone  (ISO)
daunorubicin  (EXP)
deguelin  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dichlorine  (EXP)
dichloromethane  (ISO)
dichromium trioxide  (ISO)
diclofenac  (ISO)
diethylstilbestrol  (ISO)
dihydro-beta-erythroidine  (ISO)
diisononyl phthalate  (ISO)
dinophysistoxin 1  (ISO)
dioxygen  (EXP,ISO)
disulfiram  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
erythromycin A  (ISO)
ethanol  (ISO)
ethylbenzene  (ISO)
etodolac  (ISO)
eugenol  (ISO)
ferric oxide  (ISO)
fingolimod hydrochloride  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
gallic acid  (ISO)
gemcitabine  (ISO)
genistein  (EXP,ISO)
glucose  (ISO)
glyphosate  (EXP)
heparin  (ISO)
hexachlorobenzene  (EXP)
hydrogen peroxide  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
mangiferin  (ISO)
Mecamylamine  (ISO)
mechlorethamine  (ISO)
mercury dibromide  (ISO)
methotrexate  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
methylmercury(1+)  (ISO)
miconazole  (ISO)
mifepristone  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
naproxen  (EXP)
naringin  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
nitric oxide  (ISO)
o-xylene  (ISO)
ochratoxin A  (EXP,ISO)
octadecanoic acid  (ISO)
oleandrin  (ISO)
omeprazole  (ISO)
ozone  (EXP,ISO)
p-chloromercuribenzoic acid  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paraquat  (EXP)
pentanal  (ISO)
pentane-2,3-dione  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
phenformin  (EXP)
phenylmercury acetate  (ISO)
phosgene  (ISO)
picoxystrobin  (ISO)
picrotoxin  (EXP)
pioglitazone  (ISO)
piroxicam  (ISO)
plerixafor  (ISO)
potassium chromate  (ISO)
prednisolone  (ISO)
probucol  (ISO)
progesterone  (EXP,ISO)
propanal  (ISO)
prostaglandin E2  (ISO)
quercetin  (EXP,ISO)
resveratrol  (ISO)
rotenone  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
sarin  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sodium aurothiomalate  (ISO)
sodium dodecyl sulfate  (ISO)
staurosporine  (EXP)
streptozocin  (EXP)
sumatriptan  (EXP)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
tetrathiomolybdate(2-)  (ISO)
thifluzamide  (ISO)
thioacetamide  (EXP)
thymoquinone  (ISO)
titanium dioxide  (ISO)
toluene  (ISO)
toluene 2,4-diisocyanate  (ISO)
tranilast  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (EXP)
Triptolide  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zalcitabine  (EXP)
zinc atom  (EXP,ISO)
zinc(0)  (EXP,ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
ameboidal-type cell migration  (ISO)
aorta development  (ISO)
brain development  (IBA,ISO)
branching involved in blood vessel morphogenesis  (ISO)
calcium-mediated signaling  (IBA,ISO)
cardiac muscle contraction  (IMP)
cell chemotaxis  (IBA)
cell migration  (IMP)
cellular response to cytokine stimulus  (ISO,ISS)
cellular response to xenobiotic stimulus  (IEP)
chemokine-mediated signaling pathway  (IEA)
chemotaxis  (IEA)
CXCL12-activated CXCR4 signaling pathway  (ISO,ISS)
detection of mechanical stimulus involved in sensory perception of pain  (IMP)
detection of temperature stimulus involved in sensory perception of pain  (IMP)
endothelial cell differentiation  (IMP)
endothelial tube morphogenesis  (IMP)
epithelial cell development  (IMP)
G protein-coupled receptor signaling pathway  (IEA,ISO)
generation of neurons  (ISO)
germ cell development  (ISO)
germ cell migration  (ISO)
hematopoietic stem cell migration  (ISO)
immune response  (IBA)
kidney development  (ISO)
motor neuron axon guidance  (ISO)
myelin maintenance  (ISO)
neural precursor cell proliferation  (ISO)
neurogenesis  (IBA,IMP)
neuron migration  (IDA,IMP,ISO)
neuron recognition  (IEP)
positive regulation of calcium ion import  (ISO)
positive regulation of cell migration  (IMP)
positive regulation of chemotaxis  (IMP)
positive regulation of cold-induced thermogenesis  (ISO,ISS)
positive regulation of cytosolic calcium ion concentration  (IBA)
positive regulation of dendrite extension  (IMP)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of macrophage migration inhibitory factor signaling pathway  (ISO)
positive regulation of mesenchymal stem cell migration  (IMP)
positive regulation of neurogenesis  (IMP)
positive regulation of oligodendrocyte differentiation  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of vascular wound healing  (IMP)
regulation of calcium ion transport  (IMP)
regulation of cell adhesion  (ISO)
regulation of cell migration  (ISO)
regulation of chemotaxis  (IMP,ISO)
regulation of programmed cell death  (IMP)
regulation of viral process  (IDA)
response to activity  (IEP)
response to hypoxia  (ISO)
response to morphine  (IEP)
response to organic cyclic compound  (IMP)
response to ultrasound  (IEP)
T cell proliferation  (ISO)
telencephalon cell migration  (IMP)
ventricular septum development  (ISO)

Cellular Component

References

References - curated
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23. MGD data from the GO Consortium
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. OMIM Disease Annotation Pipeline
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30. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
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34. RGD automated data pipeline
35. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
36. RGD automated import pipeline for gene-chemical interactions
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Additional References at PubMed
PMID:8962122   PMID:10521508   PMID:10644702   PMID:12421915   PMID:12477932   PMID:12507773   PMID:12707343   PMID:12900445   PMID:14732474   PMID:15174142   PMID:15467356   PMID:15626744  
PMID:15731012   PMID:16005638   PMID:16129397   PMID:16166380   PMID:16469439   PMID:16553776   PMID:16702540   PMID:16837851   PMID:16841089   PMID:17520275   PMID:17530714   PMID:18031680  
PMID:18064521   PMID:18201717   PMID:18206136   PMID:18308860   PMID:18606818   PMID:18753332   PMID:18850076   PMID:18978811   PMID:19008373   PMID:19024651   PMID:19053768   PMID:19064997  
PMID:19066630   PMID:19106094   PMID:19116316   PMID:19228460   PMID:19285061   PMID:19340530   PMID:19380869   PMID:19586611   PMID:19665027   PMID:19703720   PMID:20026091   PMID:20032115  
PMID:20045921   PMID:20127490   PMID:20133817   PMID:20228059   PMID:20412823   PMID:20458337   PMID:20534485   PMID:20547684   PMID:20586815   PMID:20729750   PMID:20847314   PMID:20882566  
PMID:21171825   PMID:21418513   PMID:21438014   PMID:21540189   PMID:22058039   PMID:22159319   PMID:22166584   PMID:22265737   PMID:22280945   PMID:22345572   PMID:22355073   PMID:22694179  
PMID:22978573   PMID:23029422   PMID:23148226   PMID:23170857   PMID:23223293   PMID:23289420   PMID:23576796   PMID:23620790   PMID:23671625   PMID:23793062   PMID:23832528   PMID:23969990  
PMID:24086760   PMID:24122226   PMID:24312447   PMID:24373940   PMID:24557113   PMID:24581269   PMID:24587052   PMID:24626964   PMID:24637920   PMID:24751384   PMID:24790097   PMID:24912431  
PMID:25032954   PMID:25299045   PMID:25420576   PMID:25492872   PMID:25549045   PMID:25612609   PMID:25807483   PMID:25824297   PMID:25825119   PMID:26164455   PMID:26398409   PMID:26444377  
PMID:26597700   PMID:26818151   PMID:26886751   PMID:27011380   PMID:27269634   PMID:27340942   PMID:28002632   PMID:28233339   PMID:28412763   PMID:28585910   PMID:28903152   PMID:28978524  
PMID:29114002   PMID:29207050   PMID:29476059   PMID:29524405   PMID:29568895   PMID:29693117   PMID:29710553   PMID:30120960   PMID:30195032   PMID:30541517   PMID:30955244   PMID:31177801  
PMID:31437601   PMID:31652450   PMID:31967865   PMID:32006698   PMID:32165091   PMID:32349612   PMID:32751701   PMID:33079278   PMID:33381162   PMID:34260048  


Genomics

Candidate Gene Status
Cxcr4 is a candidate Gene for QTL Bp327
Comparative Map Data
Cxcr4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21340,077,976 - 40,081,883 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1340,077,976 - 40,081,883 (-)Ensembl
Rnor_6.01345,314,952 - 45,318,856 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1345,314,933 - 45,318,878 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01350,394,128 - 50,398,032 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41341,308,286 - 41,312,190 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11341,322,328 - 41,326,213 (-)NCBI
Celera1340,447,190 - 40,451,093 (-)NCBICelera
Cytogenetic Map13q13NCBI
CXCR4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2136,114,349 - 136,118,149 (-)EnsemblGRCh38hg38GRCh38
GRCh382136,114,349 - 136,118,149 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372136,871,919 - 136,875,719 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362136,588,389 - 136,592,195 (-)NCBINCBI36hg18NCBI36
Build 342136,705,651 - 136,709,457NCBI
Celera2130,582,637 - 130,586,442 (-)NCBI
Cytogenetic Map2q22.1NCBI
HuRef2128,864,423 - 128,868,228 (-)NCBIHuRef
CHM1_12136,877,321 - 136,881,126 (-)NCBICHM1_1
Cxcr4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391128,515,936 - 128,520,036 (-)NCBIGRCm39mm39
GRCm39 Ensembl1128,515,936 - 128,520,030 (-)Ensembl
GRCm381128,588,199 - 128,592,299 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1128,588,199 - 128,592,293 (-)EnsemblGRCm38mm10GRCm38
MGSCv371130,484,776 - 130,488,876 (-)NCBIGRCm37mm9NCBIm37
MGSCv361130,415,745 - 130,419,822 (-)NCBImm8
Celera1131,222,729 - 131,226,820 (-)NCBICelera
Cytogenetic Map1E4NCBI
cM Map156.43NCBI
Cxcr4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554403,455,153 - 3,460,109 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554403,456,165 - 3,460,024 (-)NCBIChiLan1.0ChiLan1.0
CXCR4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B140,185,803 - 140,189,626 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B140,181,829 - 140,189,647 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B23,744,271 - 23,748,106 (+)NCBIMhudiblu_PPA_v0panPan3
CXCR4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11938,874,650 - 38,877,740 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1938,874,145 - 38,877,740 (-)EnsemblCanFam3.1canFam3CanFam3.1
Cxcr4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303101,819,271 - 101,823,136 (-)NCBI
SpeTri2.0NW_00493646939,794,613 - 39,798,448 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CXCR4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1515,663,494 - 15,667,233 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11515,663,652 - 15,666,706 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21518,125,415 - 18,128,469 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CXCR4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11020,336,470 - 20,340,308 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1020,336,247 - 20,340,309 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660612,116,532 - 2,120,394 (+)NCBIVero_WHO_p1.0
Cxcr4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473235,473,740 - 35,477,482 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D13Wox18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21340,078,310 - 40,078,623 (+)MAPPERmRatBN7.2
Rnor_6.01345,315,287 - 45,315,599NCBIRnor6.0
Rnor_5.01350,394,463 - 50,394,775UniSTSRnor5.0
RGSC_v3.41341,308,620 - 41,308,933RGDRGSC3.4
RGSC_v3.41341,308,621 - 41,308,933UniSTSRGSC3.4
RGSC_v3.11341,322,663 - 41,322,976RGD
Celera1340,447,525 - 40,447,837UniSTS
RH 2.0 Map11096.8RGD
Cytogenetic Map13q12UniSTS
RH129152  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21340,078,033 - 40,078,248 (+)MAPPERmRatBN7.2
Rnor_6.01345,315,010 - 45,315,224NCBIRnor6.0
Rnor_5.01350,394,186 - 50,394,400UniSTSRnor5.0
RGSC_v3.41341,308,344 - 41,308,558UniSTSRGSC3.4
Celera1340,447,248 - 40,447,462UniSTS
Cytogenetic Map13q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738036Lnnr4Liver neoplastic nodule remodeling QTL 43.64liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)13142356786Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
61339Bp24Blood pressure QTL 240.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)13599466844807491Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)13931346554313465Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)13931346554313465Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
1300163Cardf1Cardiac cell morphology QTL 14.18aorta morphology trait (VT:0000272)artery lesion measurement (CMO:0000975)131192944945417941Rat
2302275Gluco37Glucose level QTL 373.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)131192944946193066Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131491565559915655Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)131515872260158722Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131769443653050594Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132230187567301875Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132320344868203448Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132369296968692969Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132369296968692969Rat
2303030Bp327Blood pressure QTL 327arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133039535141184251Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133124133158363171Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133228447177284471Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133453521879535218Rat
2292232Pur16Proteinuria QTL 1617.2total urine protein amount (VT:0000032)urine protein level (CMO:0000591)133615572341961389Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
4889861Pur29Proteinuria QTL 2913.80.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:88
Interacting mature miRNAs:94
Transcripts:ENSRNOT00000005143
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 2 28 18 2 19 2 4 4 53 21 33 11 4
Low 1 15 39 39 39 4 7 21 14 8 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005143   ⟹   ENSRNOP00000005143
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1340,077,976 - 40,081,883 (-)Ensembl
Rnor_6.0 Ensembl1345,314,933 - 45,318,878 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091514   ⟹   ENSRNOP00000075128
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1345,315,215 - 45,318,822 (-)Ensembl
RefSeq Acc Id: NM_022205   ⟹   NP_071541
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21340,077,976 - 40,081,883 (-)NCBI
Rnor_6.01345,314,952 - 45,318,856 (-)NCBI
Rnor_5.01350,394,128 - 50,398,032 (-)NCBI
RGSC_v3.41341,308,286 - 41,312,190 (-)RGD
Celera1340,447,190 - 40,451,093 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_071541   ⟸   NM_022205
- UniProtKB: Q8VD47 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000005143   ⟸   ENSRNOT00000005143
RefSeq Acc Id: ENSRNOP00000075128   ⟸   ENSRNOT00000091514
Protein Domains
G_PROTEIN_RECEP_F1_2

Transcriptome

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

Promoters
RGD ID:13698797
Promoter ID:EPDNEW_R9307
Type:multiple initiation site
Name:Cxcr4_1
Description:C-X-C motif chemokine receptor 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_6.01345,318,870 - 45,318,930EPDNEW

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)
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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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
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 (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
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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (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
LEXF1C/Stm (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
LEXF2B/Stm (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
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
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)
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
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)
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
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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620465 AgrOrtholog
Ensembl Genes ENSRNOG00000003866 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005143 UniProtKB/Swiss-Prot
  ENSRNOP00000075128 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005143 UniProtKB/Swiss-Prot
  ENSRNOT00000091514 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7380432 IMAGE-MGC_LOAD
InterPro Chemokine_CXCR4_N_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chemokine_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CXCR4/ACKR2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60628 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108696 IMAGE-MGC_LOAD
NCBI Gene 60628 ENTREZGENE
Pfam 7tm_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CXCR4_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB CXCR4 RGD
PhenoGen Cxcr4 PhenoGen
PRINTS CCCHEMOKINER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CXCCHMKINER4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCRRHODOPSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K9U1_RAT UniProtKB/TrEMBL
  A9CMB9_RAT UniProtKB/TrEMBL
  CXCR4_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q8VD47 ENTREZGENE
UniProt Secondary F1LPN8 UniProtKB/Swiss-Prot
  Q8VD47 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-22 Cxcr4  C-X-C motif chemokine receptor 4  Cxcr4  chemokine (C-X-C motif) receptor 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Cxcr4  chemokine (C-X-C motif) receptor 4    Chemokine receptor (LCR1)  Name updated 1299863 APPROVED
2002-08-07 Cxcr4        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in adult brain, glial cells (astrocytes, microglia but not oligodendrocytes) and neurons 632605
gene_expression mRNA expressed in spleen, liver, heart, and brain 632606
gene_expression in brain, expressed at high levels in ependymal layer and lower levels in cerebral cortex, hippocampus, cerebellum, and brainstem 632606