Csf1r (colony stimulating factor 1 receptor) - Rat Genome Database
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Gene: Csf1r (colony stimulating factor 1 receptor) Rattus norvegicus
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Symbol: Csf1r
Name: colony stimulating factor 1 receptor
RGD ID: 2425
Description: Predicted to have several functions, including macrophage colony-stimulating factor receptor activity; protein homodimerization activity; and protein phosphatase binding activity. Involved in several processes, including positive regulation of osteoclast differentiation; regulation of bone resorption; and skeletal muscle tissue development. Predicted to localize to several cellular components, including CSF1-CSF1R complex; cell surface; and nucleoplasm. Used to study anti-basement membrane glomerulonephritis. Human ortholog(s) of this gene implicated in adult-onset leukoencephalopathy with axonal spheroids and pigmented glia and renal cell carcinoma. Orthologous to human CSF1R (colony stimulating factor 1 receptor); PARTICIPATES IN cytokine mediated signaling pathway; endocytosis pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-diaminodiphenylmethane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: c-fms; CSF-1 receptor; CSF-1-R; CSF-1R; fms proto-oncogene; M-CSF-R; macrophage colony-stimulating factor 1 receptor; MGC125014; mrfms; proto-oncogene c-Fms; proto-oncogene fms
Orthologs:
Homo sapiens (human) : CSF1R (colony stimulating factor 1 receptor)  HGNC  Alliance
Mus musculus (house mouse) : Csf1r (colony stimulating factor 1 receptor)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Csf1r (colony stimulating factor 1 receptor)
Pan paniscus (bonobo/pygmy chimpanzee) : CSF1R (colony stimulating factor 1 receptor)
Canis lupus familiaris (dog) : CSF1R (colony stimulating factor 1 receptor)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Csf1r (colony stimulating factor 1 receptor)
Sus scrofa (pig) : CSF1R (colony stimulating factor 1 receptor)
Chlorocebus sabaeus (African green monkey) : CSF1R (colony stimulating factor 1 receptor)
Heterocephalus glaber (naked mole-rat) : Csf1r (colony stimulating factor 1 receptor)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01856,414,493 - 56,458,300 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1856,414,488 - 56,458,300 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01855,662,670 - 55,689,297 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41857,080,324 - 57,107,295 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1852,716,221 - 52,742,736 (+)NCBICelera
Cytogenetic Map18q12.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
1,4-benzoquinone  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-tert-butylhydroquinone  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nonylphenol  (ISO)
4-tert-Octylphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
benzene  (ISO)
benzene-1,2,4-triol  (ISO)
benzo[a]pyrene  (EXP,ISO)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bucladesine  (ISO)
buspirone  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
crocidolite asbestos  (ISO)
curcumin  (ISO)
D-gluconic acid  (EXP)
deoxycholic acid  (EXP)
dexamethasone  (ISO)
dichlorine  (EXP)
diclofenac  (ISO)
diethylstilbestrol  (ISO)
dimethyl fumarate  (ISO)
dimethyl sulfoxide  (ISO)
doxorubicin  (ISO)
Echimidine  (EXP)
ethanol  (ISO)
fenofibrate  (EXP)
fluoxetine  (EXP)
flutamide  (EXP)
gamma-tocopherol  (ISO)
genistein  (EXP)
GW 4064  (ISO)
Heliotrine  (EXP)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
indoles  (EXP)
isotretinoin  (ISO)
KN-93  (ISO)
Lasiocarpine  (EXP)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
maneb  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-acetyl-L-cysteine  (ISO)
N-nitrosodimethylamine  (EXP)
naringin  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
nitric oxide  (ISO)
ozone  (EXP)
p-tert-Amylphenol  (ISO)
paraquat  (EXP,ISO)
pentanal  (ISO)
phenobarbital  (ISO)
pirinixic acid  (EXP,ISO)
pluronic P-123  (ISO)
Poloxamer  (ISO)
ponatinib  (ISO)
pravastatin  (EXP,ISO)
propanal  (ISO)
raloxifene  (EXP)
resveratrol  (EXP,ISO)
SB 203580  (ISO)
senecionine  (EXP)
Senkirkine  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
Soman  (EXP)
starch  (EXP)
streptozocin  (EXP)
tamoxifen  (EXP)
testosterone  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
tocopherol  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
axon guidance  (IEA,ISO)
cell population proliferation  (IDA,ISO)
cell-cell junction maintenance  (IEA,ISO)
cellular response to cytokine stimulus  (ISO,ISS)
cellular response to macrophage colony-stimulating factor stimulus  (ISO,ISS)
cytokine-mediated signaling pathway  (IEA,ISO)
forebrain neuron differentiation  (IEA,ISO)
hematopoietic progenitor cell differentiation  (IBA)
hemopoiesis  (ISO)
inflammatory response  (IEA)
innate immune response  (IEA)
macrophage colony-stimulating factor signaling pathway  (IEA,ISO)
microglial cell proliferation  (IEA,ISO)
multicellular organism development  (IBA)
negative regulation of apoptotic process  (IEA,ISO)
negative regulation of cell population proliferation  (IEA,ISO)
olfactory bulb development  (IEA,ISO)
osteoclast differentiation  (IBA,IEA,ISO,ISS)
peptidyl-tyrosine phosphorylation  (IEA,ISO,ISS)
phosphatidylinositol metabolic process  (IEA,ISO,ISS)
phosphatidylinositol-mediated signaling  (IEA,ISO,ISS)
positive regulation by host of viral process  (IEA,ISO)
positive regulation of cell migration  (ISO,ISS)
positive regulation of cell motility  (ISO)
positive regulation of cell population proliferation  (ISO,ISS)
positive regulation of chemokine production  (ISO)
positive regulation of ERK1 and ERK2 cascade  (IEA,ISO,ISS)
positive regulation of kinase activity  (IBA)
positive regulation of macrophage chemotaxis  (IEA,ISO)
positive regulation of macrophage proliferation  (IEA,ISO)
positive regulation of osteoclast differentiation  (IMP)
positive regulation of protein phosphorylation  (ISO)
positive regulation of protein serine/threonine kinase activity  (IEA,ISO,ISS)
positive regulation of protein tyrosine kinase activity  (IEA,ISO)
positive regulation of tyrosine phosphorylation of STAT protein  (IEA,ISO,ISS)
protein autophosphorylation  (IEA,ISO,ISS)
regulation of actin cytoskeleton reorganization  (IEA,ISO,ISS)
regulation of bone resorption  (IMP)
regulation of cell shape  (IEA,ISO,ISS)
response to ischemia  (IEA,ISO)
ruffle organization  (IEA,ISO,ISS)
skeletal muscle tissue development  (IEP)
transmembrane receptor protein tyrosine kinase signaling pathway  (IBA,IEA,ISO,ISS)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Borycki AG, etal., Growth Factors 1992;6(3):209-18.
2. Borycki AG, etal., Growth Factors 1992;6(3):209-18.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Hammes LS, etal., Gynecol Oncol. 2008 Jun 18.
6. Ide H, etal., Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14404-9. Epub 2002 Oct 15.
7. Iyoda M, etal., Kidney Int. 2009 May;75(10):1060-70. doi: 10.1038/ki.2009.43. Epub 2009 Feb 25.
8. Jang MH, etal., J Immunol. 2006 Sep 15;177(6):4055-63.
9. Kluger HM, etal., Clin Cancer Res. 2004 Jan 1;10(1 Pt 1):173-7.
10. Lim AK, etal., Diabetologia. 2009 May 23.
11. Menke J, etal., Cancer Res. 2012 Jan 1;72(1):187-200. doi: 10.1158/0008-5472.CAN-11-1232. Epub 2011 Nov 3.
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Ohno H, etal., Mol Cancer Ther. 2006 Nov;5(11):2634-43.
15. OMIM Disease Annotation Pipeline
16. Online Mendelian Inheritance in Man, OMIM (TM).
17. Pipeline to import KEGG annotations from KEGG into RGD
18. RGD automated data pipeline
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. RGD comprehensive gene curation
22. Richardsen E, etal., Histopathology. 2008 May 28;.
23. Shadduck RK, etal., Exp Hematol. 1996 Feb;24(2):314-7.
24. Toma MI, etal., Neoplasia. 2008 Jul;10(7):634-42.
25. Zhang MZ, etal., J Clin Invest. 2012 Dec 3;122(12):4519-32. doi: 10.1172/JCI60363. Epub 2012 Nov 12.
Additional References at PubMed
PMID:2408759   PMID:7681396   PMID:7683918   PMID:8007983   PMID:8262059   PMID:8922060   PMID:12477932   PMID:15117969   PMID:15860730   PMID:16170366   PMID:16705167   PMID:18814279  
PMID:18987110   PMID:19017797   PMID:19100238   PMID:20504948   PMID:20536329   PMID:20829061   PMID:20889566   PMID:21610095   PMID:22451653   PMID:22542597   PMID:23392676   PMID:26754294  
PMID:30249809  


Genomics

Candidate Gene Status
Csf1r is a candidate Gene for QTL Eau7
Comparative Map Data
Csf1r
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01856,414,493 - 56,458,300 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1856,414,488 - 56,458,300 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01855,662,670 - 55,689,297 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41857,080,324 - 57,107,295 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1852,716,221 - 52,742,736 (+)NCBICelera
Cytogenetic Map18q12.1NCBI
CSF1R
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5150,053,291 - 150,113,372 (-)EnsemblGRCh38hg38GRCh38
GRCh385150,053,295 - 150,113,365 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh375149,432,854 - 149,492,935 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365149,413,051 - 149,473,128 (-)NCBINCBI36hg18NCBI36
Build 345149,413,050 - 149,473,128NCBI
Celera5145,514,237 - 145,574,309 (-)NCBI
Cytogenetic Map5q32NCBI
HuRef5144,580,804 - 144,640,914 (-)NCBIHuRef
CHM1_15148,865,545 - 148,925,516 (-)NCBICHM1_1
Csf1r
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391861,238,644 - 61,264,211 (+)NCBI
GRCm381861,105,572 - 61,131,139 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1861,100,598 - 61,132,149 (+)EnsemblGRCm38mm10GRCm38
MGSCv371861,265,226 - 61,290,793 (+)NCBIGRCm37mm9NCBIm37
MGSCv361861,230,941 - 61,256,506 (+)NCBImm8
Celera1862,392,678 - 62,417,929 (+)NCBICelera
Cytogenetic Map18E1NCBI
cM Map1834.41NCBI
Csf1r
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554154,434,453 - 4,461,751 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554154,434,486 - 4,462,505 (+)NCBIChiLan1.0ChiLan1.0
CSF1R
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15151,483,948 - 151,543,128 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5151,483,572 - 151,517,415 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05145,478,725 - 145,537,858 (-)NCBI
CSF1R
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl458,980,788 - 59,010,510 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1458,980,699 - 59,010,683 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Csf1r
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365044,898,947 - 4,927,195 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSF1R
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2151,102,138 - 151,147,634 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12151,102,138 - 151,130,311 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22157,855,536 - 157,882,913 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CSF1R
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2352,664,076 - 52,697,304 (-)Ensembl
ChlSab1.12352,663,290 - 52,723,652 (-)NCBI
Csf1r
(Heterocephalus glaber - naked mole-rat)
No map positions available.

Position Markers
D18Mit140  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01856,431,650 - 56,431,754NCBIRnor6.0
Rnor_5.01855,662,659 - 55,662,763UniSTSRnor5.0
RGSC_v3.41857,080,083 - 57,080,187UniSTSRGSC3.4
Celera1852,715,980 - 52,716,084UniSTS
Cytogenetic Map18q12.1UniSTS
BI288375  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01856,444,563 - 56,444,849NCBIRnor6.0
Rnor_5.01855,675,572 - 55,675,858UniSTSRnor5.0
RGSC_v3.41857,093,038 - 57,093,324UniSTSRGSC3.4
Celera1852,728,892 - 52,729,178UniSTS
Cytogenetic Map18q12.1UniSTS
RH 3.4 Map18520.3UniSTS
RH131310  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01856,458,064 - 56,458,262NCBIRnor6.0
Rnor_5.01855,689,061 - 55,689,259UniSTSRnor5.0
RGSC_v3.41857,107,059 - 57,107,257UniSTSRGSC3.4
Celera1852,742,500 - 52,742,698UniSTS
Cytogenetic Map18q12.1UniSTS
RH 3.4 Map18532.3UniSTS
BI283816  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01856,440,306 - 56,440,542NCBIRnor6.0
Rnor_5.01855,671,315 - 55,671,551UniSTSRnor5.0
RGSC_v3.41857,088,781 - 57,089,017UniSTSRGSC3.4
Celera1852,724,635 - 52,724,871UniSTS
Cytogenetic Map18q12.1UniSTS
RH 3.4 Map18532.2UniSTS
MARC_12115-12116:1004707389:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01856,456,941 - 56,457,362NCBIRnor6.0
Rnor_5.01855,687,938 - 55,688,359UniSTSRnor5.0
RGSC_v3.41857,105,936 - 57,106,357UniSTSRGSC3.4
Celera1852,741,377 - 52,741,798UniSTS
Cytogenetic Map18q12.1UniSTS
Csf1r  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01856,435,737 - 56,436,384NCBIRnor6.0
Rnor_5.01855,666,746 - 55,667,393UniSTSRnor5.0
RGSC_v3.41857,084,212 - 57,084,859UniSTSRGSC3.4
Celera1852,720,066 - 52,720,713UniSTS
Cytogenetic Map18q12.1UniSTS
PMC219482P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01856,434,796 - 56,434,878NCBIRnor6.0
Rnor_5.01855,665,805 - 55,665,887UniSTSRnor5.0
RGSC_v3.41857,083,271 - 57,083,353UniSTSRGSC3.4
Celera1852,719,125 - 52,719,207UniSTS
Cytogenetic Map18q12.1UniSTS
CSF1R_1770  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01856,457,651 - 56,458,292NCBIRnor6.0
Rnor_5.01855,688,648 - 55,689,289UniSTSRnor5.0
RGSC_v3.41857,106,646 - 57,107,287UniSTSRGSC3.4
Celera1852,742,087 - 52,742,728UniSTS
Cytogenetic Map18q12.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18440751362570466Rat
2313082Bss85Bone structure and strength QTL 850.80.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)181467885259678852Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181553942761499684Rat
6903359Bp355Blood pressure QTL 3553.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)181553967161985648Rat
2293708Bss46Bone structure and strength QTL 468.80.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)181569587268524999Rat
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181569587287080053Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181569587287080053Rat
1358193Emca2Estrogen-induced mammary cancer QTL 21.6mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)181903103068436105Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)182028575887080053Rat
7387267Uae42Urinary albumin excretion QTL 420.61urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)142163949166639491Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182260373687074531Rat
6903353Bp353Blood pressure QTL 3532.8arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182260476461985648Rat
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182596102681761656Rat
2300157Bmd66Bone mineral density QTL 6613.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)183053361475533614Rat
2300177Bmd65Bone mineral density QTL 6519.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)183053361475533614Rat
2293704Bss35Bone structure and strength QTL 354.590.0002femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)183053361475533614Rat
9590318Scort22Serum corticosterone level QTL 227.640.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)183136134176361341Rat
1331754Bp230Blood pressure QTL 2304.61609arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183136134176361341Rat
9589816Gluco68Glucose level QTL 687.250.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)183136134176361341Rat
8694378Bw157Body weight QTL 1573.590.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)183136134176361341Rat
738005Anxrr11Anxiety related response QTL 113.4exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)183160842476608424Rat
61383Bp47Blood pressure QTL 4717.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)183172837362570429Rat
1331776Bp225Blood pressure QTL 2252.829arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)183267035261985812Rat
1331774Bp226Blood pressure QTL 2264.41065arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183267035261985812Rat
1331742Bp228Blood pressure QTL 2283.88752arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183267035261985812Rat
1331798Bp224Blood pressure QTL 2243.53873arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183267035261985812Rat
1331727Bp237Blood pressure QTL 2373.053arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183267035263897621Rat
61429Cia17Collagen induced arthritis QTL 174.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)183267035273016546Rat
2303120Mamtr8Mammary tumor resistance QTL 80.001mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)183267035287080053Rat
6903347Bp350Blood pressure QTL 3504.4arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183267047361985648Rat
631274Sprol1Serum protein level QTL 15.3blood total protein amount (VT:0005567)serum total protein level (CMO:0000661)183270402280696226Rat
631518Bw11Body weight QTL 112.8body mass (VT:0001259)body weight (CMO:0000012)183822191983221919Rat
61367Iddm4Insulin dependent diabetes mellitus QTL 42.330.0074blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)184037576985375769Rat
6893683Bw110Body weight QTL 1102.70.002body mass (VT:0001259)body weight (CMO:0000012)184500219488201929Rat
1598826Anxrr20Anxiety related response QTL 203.04body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)184631947688201929Rat
1331806Bp229Blood pressure QTL 2294.36484arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184824887759473805Rat
1331736Bp227Blood pressure QTL 2272.791arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)184824887761985812Rat
1331780Bp238Blood pressure QTL 2383.269arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184824887761985812Rat
6903345Bp349Blood pressure QTL 3493.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184824904861985648Rat
6903349Bp351Blood pressure QTL 3513.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184824904861985648Rat
6903351Bp352Blood pressure QTL 3523.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)184824904861985648Rat
61360EaeyExperimental allergic encephalomyelitis QTL y3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)184851929962570427Rat
9589041Epfw12Epididymal fat weight QTL 1217.080.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)184913092088201929Rat
8694432Bw165Body weight QTL 1653.810.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)184913092088201929Rat
8694366Abfw8Abdominal fat weight QTL 86.380.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)184913092088201929Rat
2303571Bw92Body weight QTL 923body mass (VT:0001259)body weight (CMO:0000012)185137581688201929Rat
2303584Gluco55Glucose level QTL 552blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185137581688201929Rat
7411719Strs5Sensitivity to stroke QTL 59.4cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)185160903267502266Rat
2293658Bmd23Bone mineral density QTL 237.30.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)185303349468524999Rat
738008Hcar14Hepatocarcinoma resistance QTL 144.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion number (CMO:0001462)185303349487080053Rat
1331730Scl27Serum cholesterol level QTL 273.826blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)185386125261985812Rat
1331752Bw27Body weight QTL 272.963body mass (VT:0001259)body weight (CMO:0000012)185386125267502266Rat
1359020Ppulsi2Prepulse inhibition QTL 22.71prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)185386125277151443Rat
1600375Mcs22Mammary carcinoma susceptibility QTL 223.3mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)185410837568819562Rat
631509Sald2Serum aldosterone level QTL 22.9blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)185410837571692768Rat
2301417Bp319Blood pressure QTL 3190.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)185410837579575348Rat
12880368Bw187Body weight QTL 1870.045body mass (VT:0001259)body weight (CMO:0000012)185410837579575348Rat
12904067Cm122Cardiac mass QTL 1220.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)185410837579575348Rat
12904069Cm123Cardiac mass QTL 1230.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)185410837579575348Rat
12904070Cm124Cardiac mass QTL 1240.01heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)185410837579575348Rat
12904071Am18Aortic mass QTL 180.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)185410837579575348Rat
12904073Kidm71Kidney mass QTL 710.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)185410837579575348Rat
1300125Rf26Renal function QTL 263.2urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)185410847467502122Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:75
Interacting mature miRNAs:89
Transcripts:ENSRNOT00000049357
Prediction methods: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 3 27 52 37 19 37 7 9 62 28 28 11 7
Low 16 5 4 4 1 2 12 7 13 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000049357   ⟹   ENSRNOP00000040411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1856,431,891 - 56,458,300 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079360   ⟹   ENSRNOP00000075739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1856,431,820 - 56,457,869 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088988   ⟹   ENSRNOP00000072826
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1856,414,488 - 56,446,303 (+)Ensembl
RefSeq Acc Id: NM_001029901   ⟹   NP_001025072
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01856,431,891 - 56,458,300 (+)NCBI
Rnor_5.01855,662,670 - 55,689,297 (+)NCBI
RGSC_v3.41857,080,324 - 57,107,295 (+)RGD
Celera1852,716,221 - 52,742,736 (+)RGD
Sequence:
RefSeq Acc Id: XM_006254813   ⟹   XP_006254875
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01856,431,661 - 56,458,299 (+)NCBI
Rnor_5.01855,662,670 - 55,689,297 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772147   ⟹   XP_008770369
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01856,422,303 - 56,458,299 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772148   ⟹   XP_008770370
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01856,414,493 - 56,458,299 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001025072   ⟸   NM_001029901
- Peptide Label: precursor
- UniProtKB: D4ACA7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006254875   ⟸   XM_006254813
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KBC4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770370   ⟸   XM_008772148
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KBC4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770369   ⟸   XM_008772147
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KBC4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075739   ⟸   ENSRNOT00000079360
RefSeq Acc Id: ENSRNOP00000072826   ⟸   ENSRNOT00000088988
RefSeq Acc Id: ENSRNOP00000040411   ⟸   ENSRNOT00000049357
Protein Domains
Ig-like   Ig-like C2-type   Protein kinase

Transcriptome

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

Promoters
RGD ID:13700816
Promoter ID:EPDNEW_R11337
Type:initiation region
Name:Csf1r_1
Description:colony stimulating factor 1 receptor
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_6.01856,431,809 - 56,431,869EPDNEW

Strain Variation

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


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
18 55682600 55682601 C A snv GH/OmrMcwi (MCW), KFRS3B/Kyo (KyushuU), FHL/EurMcwi (MCW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), GK/Ox (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), F344/NSlc (KyushuU), RCS/Kyo (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), F344/Jcl (KyushuU), FHH/EurMcwi (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
18 56451603 56451604 C A snv GH/OmrMcwi (MCW), WKY/NHsd (RGD), FHL/EurMcwi (MCW), Buf/N (MCW), F344/NRrrc (MCW), WKY/N (MCW), FHL/EurMcwi (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), GK/Ox (RGD), LE/Stm (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/Gcrc (RGD), FHH/EurMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
18 57100220 57100221 C A snv SHR/OlaIpcv (ICL), LCR/2Mco (UMich), SHRSP/Gcrc (MDC), BUF/N (KNAW), F344/NRrrc (KNAW), LE/Stm (KNAW), WKY/N (KNAW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), F344/NCrl (ICL), LE/Stm (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), GK/Ox (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WKY/Gcrc (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), FHH/EurMcwi (MDC)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2425 AgrOrtholog
Ensembl Genes ENSRNOG00000018414 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040411 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072826 UniProtKB/TrEMBL
  ENSRNOP00000075739 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049357 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000079360 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000088988 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CSF-1_receptor UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Immunoglobulin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kinase-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ser-Thr/Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tyr_kinase_rcpt_3_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:307403 UniProtKB/TrEMBL
NCBI Gene 307403 ENTREZGENE
Pfam PF00047 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pkinase_Tyr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB CSF1R RGD
PhenoGen Csf1r PhenoGen
PIRSF CSF-1_receptor UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PROTEIN_KINASE_TYR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RECEPTOR_TYR_KIN_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TyrKc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.72599 ENTREZGENE
UniProt A0A0G2K3Y5_RAT UniProtKB/TrEMBL
  A0A0G2KBC4 ENTREZGENE, UniProtKB/TrEMBL
  CSF1R_RAT UniProtKB/Swiss-Prot
  D4ACA7 ENTREZGENE, UniProtKB/TrEMBL
  Q00495 ENTREZGENE
  Q3B7T5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Csf1r  Colony stimulating factor 1 receptor      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation transcriptionally active only in undifferentiated myoblasts 727559
 



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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.