Cd40 (CD40 molecule) - Rat Genome Database

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Gene: Cd40 (CD40 molecule) Rattus norvegicus
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Symbol: Cd40
Name: CD40 molecule
RGD ID: 619830
Description: Enables antigen binding activity and protein domain specific binding activity. Involved in several processes, including cellular response to cytokine stimulus; response to cobalamin; and response to interferon-gamma. Located in several cellular components, including cell surface; neuronal cell body; and varicosity. Used to study several diseases, including Ehrlich tumor carcinoma; artery disease (multiple); colitis; membranous glomerulonephritis; and obesity. Biomarker of asthma; atherosclerosis; and perinatal necrotizing enterocolitis. Human ortholog(s) of this gene implicated in several diseases, including Kawasaki disease; autoimmune disease (multiple); end stage renal disease; hyperimmunoglobulin syndrome (multiple); and non-Hodgkin lymphoma (multiple). Orthologous to human CD40 (CD40 molecule); PARTICIPATES IN allograft rejection pathway; asthma pathway; autoimmune thyroiditis pathway; INTERACTS WITH (+)-pilocarpine; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1,2-dimethylhydrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CD40 antigen; CD40 antigen, TNF receptor superfamily member 5; CD40 molecule, TNF receptor superfamily member 5; LOC311635; Tnfrsf5; tumor necrosis factor receptor superfamily member 5; tumor necrosis factor receptor superfamily, member 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cd40em1Uthal  
Genetic Models: SS-Cd40em1Uthal-/-
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23153,790,372 - 153,805,279 (+)NCBI
Rnor_6.0 Ensembl3161,519,743 - 161,534,704 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03161,519,789 - 161,534,943 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03167,704,285 - 167,719,416 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43156,092,602 - 156,107,427 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13155,998,622 - 156,006,374 (+)NCBI
Celera3152,395,702 - 152,410,527 (+)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Coronary Syndrome  (ISO)
acute myocarditis  (ISO)
allergic rhinitis  (ISO)
Alzheimer's disease  (ISO)
Animal Helminthiasis  (ISO)
Animal Mammary Neoplasms  (ISO)
Animal Viral Hepatitis  (ISO)
anti-basement membrane glomerulonephritis  (ISO)
arthritis  (ISO)
asthma  (IDA,IEP,ISO)
atherosclerosis  (IDA,IEP,ISO)
atopic dermatitis  (ISO)
atrial fibrillation  (ISO)
autoimmune thrombocytopenic purpura  (ISO)
B-Cell Chronic Lymphocytic Leukemia  (ISO)
B-cell lymphoma  (ISO)
bacterial pneumonia  (ISO)
Brain Injuries  (IDA)
Breast Neoplasms  (ISO)
bronchiolitis  (ISO)
Burkitt lymphoma  (ISO)
chlamydia  (ISO)
Chronic Allograft Dysfunction  (IDA)
chronic myeloid leukemia  (ISO)
chronic obstructive pulmonary disease  (ISO)
colitis  (IMP)
crescentic glomerulonephritis  (ISO)
Crohn's disease  (ISO)
cryptococcosis  (ISO)
cutaneous lupus erythematosus  (ISO)
Delayed Hypersensitivity  (ISO)
dermatomyositis  (ISO)
diffuse large B-cell lymphoma  (ISO)
dilated cardiomyopathy  (ISO)
Discoid Lupus Erythematosus  (ISO)
Ehrlich tumor carcinoma  (IDA)
end stage renal disease  (ISO)
Endotoxemia  (ISO)
erythema multiforme  (ISO)
Experimental Arthritis  (ISO)
Experimental Autoimmune Myocarditis  (IMP)
Experimental Autoimmune Neuritis  (IEP)
follicular lymphoma  (ISO)
Graft vs Host Disease  (ISO)
Graves' disease  (ISO)
Hashimoto Disease  (ISO)
high grade glioma  (ISO)
Hodgkin's lymphoma  (ISO)
human immunodeficiency virus infectious disease  (ISO)
Human Influenza  (ISO)
hyper IgM syndrome  (ISO)
Hypercholesterolemia  (IDA,IEP)
hyperglycemia  (ISO)
hyperimmunoglobulin syndrome  (ISO)
hyperinsulinism  (ISO)
hyperthyroidism  (ISO)
immunodeficiency with hyper IgM type 3  (ISO)
Inflammation  (ISO)
Insulin Resistance  (ISO)
insulinoma  (ISO)
Kawasaki disease  (ISO)
Kidney Reperfusion Injury  (IMP)
lichen planus  (ISO)
Liver Reperfusion Injury  (IMP)
lupus nephritis  (ISO)
Lyme Neuroborreliosis  (ISO)
Lymphatic Metastasis  (ISO)
malaria  (ISO)
malignant mesothelioma  (ISO)
Mammary Neoplasms, Experimental  (ISO)
melanoma  (ISO)
membranous glomerulonephritis  (IMP,ISO)
multiple myeloma  (ISO)
multiple sclerosis  (ISO)
Murine Acquired Immunodeficiency Syndrome  (ISO)
myelodysplastic syndrome  (ISO)
Myocardial Ischemia  (IDA)
Neisseriaceae Infections  (ISO)
non-Hodgkin lymphoma  (ISO)
obesity  (IDA,ISO)
pancreatic ductal carcinoma  (ISO)
pemphigus  (ISO)
Perennial Allergic Rhinitis  (ISO)
perinatal necrotizing enterocolitis  (IEP)
peritonitis  (ISO)
plasma cell leukemia  (ISO)
pneumocystosis  (ISO)
pre-eclampsia  (ISO)
psoriasis  (ISO)
pulmonary hypertension  (IMP)
renal artery obstruction  (ISO)
renal cell carcinoma  (ISO)
Reperfusion Injury  (IMP)
rheumatoid arthritis  (ISO)
Schistosomiasis Mansoni  (ISO)
Sepsis  (ISO)
skin melanoma  (ISO)
status epilepticus  (ISO)
Stroke  (ISO)
Subacute Combined Degeneration  (IDA,IMP)
systemic lupus erythematosus  (ISO)
thrombosis  (ISO)
tick-borne encephalitis  (ISO)
transient cerebral ischemia  (ISO)
Transplant Rejection  (IMP,ISO)
type 1 diabetes mellitus  (ISO)
ulcerative colitis  (ISO)
Vascular Calcification  (ISO)
Viral Myocarditis  (ISO)
visceral leishmaniasis  (ISO)
visual epilepsy  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-demecolcine  (ISO)
(R)-mevalonic acid  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,2-dimethylhydrazine  (EXP,ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-trans,6-trans,10-trans-geranylgeranyl diphosphate  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-mercaptopropanoic acid  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (EXP)
4-aminopyridine  (EXP)
4-DAMP(1+)  (ISO)
4-hydroxycyclophosphamide  (EXP)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
afimoxifene  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
aluminium hydroxide  (ISO)
ammonium chloride  (EXP)
ampicillin  (ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
arachidonic acid  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
atorvastatin calcium  (ISO)
atropine  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucan  (ISO)
betamethasone valerate  (ISO)
bicalutamide  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
Calcimycin  (ISO)
calcitriol  (ISO)
carbachol  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
cortisol  (ISO)
curcumin  (ISO)
cyanocob(III)alamin  (ISO)
cyclophosphamide  (ISO)
daidzein  (ISO)
delta-tocotrienol  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
entinostat  (ISO)
ethanol  (EXP)
fenofibrate  (ISO)
fisetin  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
furosemide  (EXP)
gemcitabine  (ISO)
Genipin  (ISO)
glyphosate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
helenalin  (ISO)
histamine  (ISO)
hydroxysafflor yellow A  (EXP)
imiquimod  (ISO)
immunological adjuvant  (ISO)
indirubin-3'-monoxime  (ISO)
indole-3-methanol  (ISO)
indometacin  (ISO)
isoflurane  (EXP)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (EXP,ISO)
lithium chloride  (EXP)
lovastatin  (ISO)
luteolin  (ISO)
mercury atom  (ISO)
mercury dibromide  (ISO)
mercury(0)  (ISO)
metam  (ISO)
mevastatin  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
Monobutylphthalate  (ISO)
muramyl dipeptide  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
niclosamide  (ISO)
nicotinamide  (ISO)
nystatin  (ISO)
o-anisidine  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
pentanal  (ISO)
pevonedistat  (ISO)
phenethyl isothiocyanate  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirenzepine  (ISO)
poly(I:C)  (ISO)
pravastatin  (EXP,ISO)
propanal  (ISO)
protein kinase inhibitor  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
simvastatin  (ISO)
sirtinol  (ISO)
sodium aurothiosulfate  (ISO)
sodium dodecyl sulfate  (ISO)
Soman  (EXP)
succimer  (ISO)
tetrathiomolybdate(2-)  (ISO)
thimerosal  (ISO)
toluene 2,4-diisocyanate  (ISO)
trimellitic anhydride  (EXP)
triprolidine  (ISO)
triptonide  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (ISO)
U-73122  (ISO)
valproic acid  (ISO)
vemurafenib  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zaragozic acid A  (EXP,ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
B cell activation  (IBA,IMP,ISO)
B cell mediated immunity  (ISO)
CD40 signaling pathway  (IBA,ISO)
cellular calcium ion homeostasis  (ISO)
cellular response to erythropoietin  (IEP)
cellular response to interleukin-1  (IBA,IEP)
cellular response to lipopolysaccharide  (IEP)
cellular response to mechanical stimulus  (ISO)
cellular response to tumor necrosis factor  (IBA,IEP)
defense response to protozoan  (IBA,ISO)
defense response to virus  (IBA,ISO)
immune response-regulating cell surface receptor signaling pathway  (IBA,ISO)
inflammatory response  (IBA,IEP,IMP)
positive regulation of angiogenesis  (IBA,ISO)
positive regulation of B cell proliferation  (IBA,ISO)
positive regulation of blood vessel endothelial cell migration  (IBA,ISO)
positive regulation of endothelial cell apoptotic process  (IBA,ISO)
positive regulation of GTPase activity  (ISO)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (IBA,ISO)
positive regulation of interleukin-12 production  (IBA,ISO)
positive regulation of isotype switching to IgG isotypes  (IBA,ISO)
positive regulation of MAP kinase activity  (ISO)
positive regulation of NF-kappaB transcription factor activity  (IBA,ISO)
positive regulation of protein kinase C signaling  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,ISO)
positive regulation of tyrosine phosphorylation of STAT protein  (IBA,ISO)
protein kinase B signaling  (ISO)
regulation of immune response  (ISO)
regulation of immunoglobulin production  (ISO)
response to bacterium  (IEP)
response to cobalamin  (IEP)
response to interferon-gamma  (IBA,IEP)
response to nutrient levels  (IEP)
response to peptide  (IEP)
TRIF-dependent toll-like receptor signaling pathway  (IBA)

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
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Additional References at PubMed
PMID:8566034   PMID:8666928   PMID:8920854   PMID:10979977   PMID:11279055   PMID:11847112   PMID:11886848   PMID:11894097   PMID:12223522   PMID:12477932   PMID:12761501   PMID:12882831  
PMID:12885753   PMID:12958312   PMID:14560001   PMID:14594818   PMID:14607964   PMID:15240714   PMID:15963492   PMID:16546095   PMID:16708399   PMID:17277142   PMID:18684012   PMID:19047410  
PMID:19211155   PMID:19593445   PMID:20458337   PMID:20614026   PMID:20685650   PMID:21410936   PMID:22017688   PMID:23981064   PMID:26432892   PMID:27916733   PMID:28566713   PMID:29843579  
PMID:31331973   PMID:31777165   PMID:32200719  


Genomics

Comparative Map Data
Cd40
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23153,790,372 - 153,805,279 (+)NCBI
Rnor_6.0 Ensembl3161,519,743 - 161,534,704 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03161,519,789 - 161,534,943 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03167,704,285 - 167,719,416 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43156,092,602 - 156,107,427 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13155,998,622 - 156,006,374 (+)NCBI
Celera3152,395,702 - 152,410,527 (+)NCBICelera
Cytogenetic Map3q42NCBI
CD40
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2046,118,278 - 46,129,863 (+)EnsemblGRCh38hg38GRCh38
GRCh382046,118,242 - 46,129,858 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372044,746,953 - 44,758,497 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362044,180,313 - 44,191,791 (+)NCBINCBI36hg18NCBI36
Celera2041,458,363 - 41,469,842 (+)NCBI
Cytogenetic Map20q13.12NCBI
HuRef2041,488,189 - 41,499,674 (+)NCBIHuRef
CHM1_12044,649,540 - 44,661,003 (+)NCBICHM1_1
Cd40
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392164,897,535 - 164,913,574 (+)NCBIGRCm39mm39
GRCm39 Ensembl2164,897,547 - 164,914,868 (+)Ensembl
GRCm382165,055,614 - 165,071,654 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2165,055,627 - 165,072,948 (+)EnsemblGRCm38mm10GRCm38
MGSCv372164,881,136 - 164,897,154 (+)NCBIGRCm37mm9NCBIm37
MGSCv362164,746,841 - 164,762,859 (+)NCBImm8
Celera2170,992,951 - 171,008,953 (+)NCBICelera
Cytogenetic Map2H3NCBI
cM Map285.38NCBI
Cd40
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544511,190,603 - 11,202,093 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544511,191,817 - 11,202,156 (-)NCBIChiLan1.0ChiLan1.0
CD40
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12043,541,619 - 43,552,994 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2043,541,619 - 43,552,994 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02042,455,711 - 42,467,139 (+)NCBIMhudiblu_PPA_v0panPan3
CD40
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12433,352,992 - 33,383,488 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2433,372,930 - 33,383,301 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2432,899,232 - 32,909,488 (+)NCBI
ROS_Cfam_1.02434,062,814 - 34,092,886 (+)NCBI
UMICH_Zoey_3.12433,340,743 - 33,351,000 (+)NCBI
UNSW_CanFamBas_1.02433,456,512 - 33,466,773 (+)NCBI
UU_Cfam_GSD_1.02433,995,494 - 34,005,757 (+)NCBI
Cd40
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640191,483,088 - 191,493,621 (-)NCBI
SpeTri2.0NW_0049365146,936,915 - 6,947,246 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD40
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1748,286,029 - 48,298,528 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11748,286,116 - 48,298,188 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21753,932,001 - 53,943,003 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CD40
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1217,753,713 - 17,765,134 (-)NCBI
ChlSab1.1 Ensembl217,753,394 - 17,764,566 (-)Ensembl
Vero_WHO_p1.0NW_02366605066,388,299 - 66,399,227 (-)NCBI
Cd40
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247908,475,640 - 8,485,927 (-)NCBI

Position Markers
BF403631  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23153,796,507 - 153,796,669 (+)MAPPER
Rnor_6.03161,525,910 - 161,526,071NCBIRnor6.0
Rnor_5.03167,710,383 - 167,710,544UniSTSRnor5.0
RGSC_v3.43156,098,661 - 156,098,822UniSTSRGSC3.4
Celera3152,401,761 - 152,401,922UniSTS
RH 3.4 Map31431.0UniSTS
Cytogenetic Map3q42UniSTS
AW433947  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23153,804,841 - 153,805,013 (+)MAPPER
Rnor_6.03161,534,244 - 161,534,415NCBIRnor6.0
Rnor_5.03167,718,717 - 167,718,888UniSTSRnor5.0
RGSC_v3.43156,106,995 - 156,107,166UniSTSRGSC3.4
Celera3152,410,095 - 152,410,266UniSTS
RH 3.4 Map31432.6UniSTS
Cytogenetic Map3q42UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3148348517171467264Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3150368003177699992Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3136876155170935007Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3153918022177699992Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)3153412455170534769Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3153381237174632112Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3125848628170848628Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3156381661176418101Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3153412455165355668Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3126575595165355668Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3148348739163640325Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3153412455177699992Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3148034701177699992Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3153381237174632112Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3153381237174632112Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3153381237174632112Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3153381237174632112Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3153381237174632112Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3153381237174632112Rat


Genetic Models
This gene Cd40 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:94
Count of miRNA genes:76
Interacting mature miRNAs:89
Transcripts:ENSRNOT00000055148
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 2 8 19 8
Low 1 43 46 38 38 7 10 74 35 40 3 7
Below cutoff 3 3 3 1 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_134360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762463 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762465 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104202 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_591833 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_591835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF241231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC097949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231420 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000055148   ⟹   ENSRNOP00000052022
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3161,519,743 - 161,534,704 (+)Ensembl
RefSeq Acc Id: NM_134360   ⟹   NP_599187
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,452 - 153,805,274 (+)NCBI
Rnor_6.03161,519,851 - 161,534,676 (+)NCBI
Rnor_5.03167,704,285 - 167,719,416 (+)NCBI
RGSC_v3.43156,092,602 - 156,107,427 (+)RGD
Celera3152,395,702 - 152,410,527 (+)RGD
Sequence:
RefSeq Acc Id: XM_006235511   ⟹   XP_006235573
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,373 - 153,805,279 (+)NCBI
Rnor_6.03161,519,789 - 161,534,943 (+)NCBI
Rnor_5.03167,704,285 - 167,719,416 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762463   ⟹   XP_008760685
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,372 - 153,805,279 (+)NCBI
Rnor_6.03161,519,789 - 161,534,681 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762464   ⟹   XP_008760686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,373 - 153,805,279 (+)NCBI
Rnor_6.03161,519,790 - 161,534,681 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008762465   ⟹   XP_008760687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,373 - 153,805,279 (+)NCBI
Rnor_6.03161,519,789 - 161,534,681 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039104199   ⟹   XP_038960127
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,373 - 153,805,279 (+)NCBI
RefSeq Acc Id: XM_039104200   ⟹   XP_038960128
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,373 - 153,805,279 (+)NCBI
RefSeq Acc Id: XM_039104201   ⟹   XP_038960129
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,373 - 153,805,279 (+)NCBI
RefSeq Acc Id: XM_039104202   ⟹   XP_038960130
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,630 - 153,805,279 (+)NCBI
RefSeq Acc Id: XR_591833
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,373 - 153,805,279 (+)NCBI
Rnor_6.03161,519,790 - 161,534,681 (+)NCBI
Sequence:
RefSeq Acc Id: XR_591835
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23153,790,373 - 153,804,816 (+)NCBI
Rnor_6.03161,519,789 - 161,534,155 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_599187   ⟸   NM_134360
- Peptide Label: precursor
- UniProtKB: Q4QQW2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235573   ⟸   XM_006235511
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008760685   ⟸   XM_008762463
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008760687   ⟸   XM_008762465
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_008760686   ⟸   XM_008762464
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000052022   ⟸   ENSRNOT00000055148
RefSeq Acc Id: XP_038960127   ⟸   XM_039104199
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038960128   ⟸   XM_039104200
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038960129   ⟸   XM_039104201
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038960130   ⟸   XM_039104202
- Peptide Label: isoform X8
Protein Domains
TNFR-Cys

Transcriptome

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


Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619830 AgrOrtholog
Ensembl Genes ENSRNOG00000018488 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000052022 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055148 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7387440 IMAGE-MGC_LOAD
InterPro TNFR_5 UniProtKB/TrEMBL
  TNFR_Cys_rich_reg UniProtKB/TrEMBL
  TNFRSF5_N UniProtKB/TrEMBL
KEGG Report rno:171369 UniProtKB/TrEMBL
MGC_CLONE MGC:116072 IMAGE-MGC_LOAD
NCBI Gene 171369 ENTREZGENE
Pfam TNFR_c6 UniProtKB/TrEMBL
PhenoGen Cd40 PhenoGen
PRINTS TNFACTORR5 UniProtKB/TrEMBL
PROSITE TNFR_NGFR_1 UniProtKB/TrEMBL
  TNFR_NGFR_2 UniProtKB/TrEMBL
SMART TNFR UniProtKB/TrEMBL
UniProt Q4QQW2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-20 Cd40  CD40 molecule  Cd40  CD40 molecule, TNF receptor superfamily member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-06-27 Cd40  CD40 molecule, TNF receptor superfamily member 5  Cd40  CD40 antigen, TNF receptor superfamily member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-10 Cd40  CD40 antigen, TNF receptor superfamily member 5  Cd40  CD40 molecule, TNF receptor superfamily member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-22 Cd40  CD40 molecule, TNF receptor superfamily member 5  Tnfrsf5  tumor necrosis factor receptor superfamily, member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-04-28 Tnfrsf5  tumor necrosis factor receptor superfamily, member 5  Tnfrsf5_predicted  tumor necrosis factor receptor superfamily, member 5 (predicted)  Data Merged 737654 APPROVED
2005-01-12 Tnfrsf5_predicted  tumor necrosis factor receptor superfamily, member 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED
2002-08-07 Tnfrsf5  tumor necrosis factor receptor superfamily, member 5      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation induced by various pro-inflammatory cytokines 634252