Cd1d1 (CD1d1 antigen) - Rat Genome Database

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Gene: Cd1d1 (CD1d1 antigen) Mus musculus
Analyze
Symbol: Cd1d1
Name: CD1d1 antigen
RGD ID: 1552895
MGI Page MGI
Description: Enables T cell receptor binding activity and endogenous lipid antigen binding activity. Involved in NK T cell differentiation and regulation of immature T cell proliferation in thymus. Acts upstream of or within several processes, including antigen processing and presentation, exogenous lipid antigen via MHC class Ib; positive regulation of cytokine production; and positive regulation of leukocyte activation. Located in endosome; external side of plasma membrane; and lysosome. Is expressed in forebrain; intestine; jaw bone; and liver. Human ortholog(s) of this gene implicated in pulmonary tuberculosis. Orthologous to human CD1D (CD1d molecule).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AI747460; antigen-presenting glycoprotein CD1d1; Cd1; CD1.1; Cd1a; Cd1d; Ly-3; Ly-38; T-cell surface glycoprotein CD1d1
RGD Orthologs
Human
Rat
Bonobo
Dog
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39386,903,141 - 86,919,665 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl386,903,141 - 86,906,748 (-)EnsemblGRCm39 Ensembl
GRCm38386,995,834 - 87,012,358 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl386,995,834 - 86,999,441 (-)EnsemblGRCm38mm10GRCm38
MGSCv37386,799,756 - 86,803,262 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36387,081,765 - 87,085,267 (-)NCBIMGSCv36mm8
Celera387,021,305 - 87,024,811 (-)NCBICelera
Cytogenetic Map3F1NCBI
cM Map337.91NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (EXP)
1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene  (EXP)
1,2-dimethylhydrazine  (EXP)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,4'-trichlorobiphenyl  (EXP)
2,4-dinitrotoluene  (ISO)
2-nitrofluorene  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3-chloropropane-1,2-diol  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-hydroxyphenyl retinamide  (EXP)
6-propyl-2-thiouracil  (ISO)
actinomycin D  (ISO)
adapalene  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (ISO)
amphotericin B  (ISO)
antirheumatic drug  (ISO)
arsenite(3-)  (EXP)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (EXP)
bisphenol A  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (EXP)
CGP 52608  (ISO)
cyclosporin A  (EXP,ISO)
D-glucose  (EXP)
diallyl disulfide  (ISO)
Diallyl sulfide  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (EXP)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (EXP)
dioxygen  (EXP)
endosulfan  (ISO)
fucoxanthin  (EXP)
gentamycin  (ISO)
glucose  (EXP)
inulin  (EXP)
iron atom  (ISO)
iron(0)  (ISO)
lipopolysaccharide  (ISO)
menadione  (EXP)
methotrexate  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (EXP)
nickel atom  (ISO)
nitrates  (EXP)
okadaic acid  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
PCB138  (EXP)
pentachlorophenol  (EXP)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (ISO)
pirinixic acid  (ISO)
Ro 41-5253  (ISO)
rotenone  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP,ISO)
Tartrolon D  (EXP)
tetrachloromethane  (EXP,ISO)
thioacetamide  (ISO)
titanium dioxide  (EXP)
trichostatin A  (ISO)
Triptolide  (EXP)
valdecoxib  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal antigen presentation  (IAGP)
abnormal CD4-positive T cell differentiation  (IAGP)
abnormal dendritic cell antigen presentation  (IAGP)
abnormal interleukin-4 secretion  (IAGP)
abnormal liver morphology  (IAGP)
abnormal NK T cell morphology  (IAGP)
abnormal NK T cell physiology  (IAGP)
abnormal T cell activation  (IAGP)
arrested T cell differentiation  (IAGP)
atherosclerotic lesions  (IAGP)
autoimmune response  (IAGP)
decreased acute inflammation  (IAGP)
decreased circulating VLDL cholesterol level  (IAGP)
decreased IgG level  (IAGP)
decreased interferon-gamma secretion  (IAGP)
decreased interleukin-2 secretion  (IAGP)
decreased interleukin-4 secretion  (IAGP)
decreased NK cell number  (IAGP)
decreased NK T cell number  (IAGP)
decreased physiological sensitivity to xenobiotic  (IAGP)
decreased red blood cell distribution width  (IEA)
decreased regulatory T cell number  (IAGP)
decreased susceptibility to induced arthritis  (IAGP)
decreased tumor necrosis factor secretion  (IAGP)
glomerular crescent  (IAGP)
glomerulonephritis  (IAGP)
glomerulosclerosis  (IAGP)
increased anti-double stranded DNA antibody level  (IAGP)
increased anti-nuclear antigen antibody level  (IAGP)
increased basophil cell number  (IEA)
increased blood urea nitrogen level  (IAGP)
increased circulating amylase level  (IEA)
increased IgG3 level  (IAGP)
increased susceptibility to atherosclerosis  (IAGP)
increased susceptibility to bacterial infection  (IAGP)
increased susceptibility to bacterial infection induced morbidity/mortality  (IAGP)
increased susceptibility to experimental autoimmune encephalomyelitis  (IAGP)
increased susceptibility to ischemic brain injury  (IAGP)
increased urine protein level  (IAGP)
kidney inflammation  (IAGP)
lung inflammation  (IAGP)
paralysis  (IAGP)
premature death  (IAGP)
renal interstitial fibrosis  (IAGP)
renal tubule atrophy  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Regulatory B cells prevent and reverse allergic airway inflammation via FoxP3-positive T regulatory cells in a murine model. Amu S, etal., J Allergy Clin Immunol. 2010 May;125(5):1114-1124.e8. Epub 2010 Mar 20.
2. Natural killer T cells mediate alveolar bone resorption and a systemic inflammatory response in response to oral infection of mice with Porphyromonas gingivalis. Aoki-Nonaka Y, etal., J Periodontal Res. 2014 Feb;49(1):69-76. doi: 10.1111/jre.12080. Epub 2013 Apr 16.
3. Pathogenic mouse hepatitis virus or poly(I:C) induce IL-33 in hepatocytes in murine models of hepatitis. Arshad MI, etal., PLoS One. 2013 Sep 13;8(9):e74278. doi: 10.1371/journal.pone.0074278. eCollection 2013.
4. CD1d-restricted peripheral T cell lymphoma in mice and humans. Bachy E, etal., J Exp Med. 2016 May 2;213(5):841-57. doi: 10.1084/jem.20150794. Epub 2016 Apr 11.
5. Activation of a nonclassical NKT cell subset in a transgenic mouse model of hepatitis B virus infection. Baron JL, etal., Immunity. 2002 Apr;16(4):583-94. doi: 10.1016/s1074-7613(02)00305-9.
6. Molecular cloning, characterization, and genetic mapping of the cDNA coding for a novel secretory protein of mouse. Demonstration of alternative splicing in skin and cartilage. Bhalerao J, etal., J Biol Chem 1995 Jul 7;270(27):16385-94.
7. A role for natural killer T cells and CD1d molecules in counteracting suppression of hematopoiesis in mice induced by infection with murine cytomegalovirus. Broxmeyer HE, etal., Exp Hematol. 2007 Apr;35(4 Suppl 1):87-93. doi: 10.1016/j.exphem.2007.01.015.
8. Both CD1d antigen presentation and interleukin-12 are required to activate natural killer T cells during Trypanosoma cruzi infection. Duthie MS, etal., Infect Immun. 2005 Mar;73(3):1890-4. doi: 10.1128/IAI.73.3.1890-1894.2005.
9. Importance of NKT cells in resistance to herpes simplex virus, fate of virus-infected neurons, and level of latency in mice. Grubor-Bauk B, etal., J Virol. 2008 Nov;82(22):11073-83. doi: 10.1128/JVI.00205-08. Epub 2008 Jul 9.
10. CD1d-restricted NKT cells modulate placental and uterine leukocyte populations during chlamydial infection in mice. Habbeddine M, etal., Microbes Infect. 2013 Nov;15(13):928-38. doi: 10.1016/j.micinf.2013.08.006. Epub 2013 Aug 31.
11. Increased Expression of Two Alternative Spliced Variants of CD1d Molecule in Human Gastric Cancer. Hafezi N, etal., Iran J Immunol. 2015 Jun;12(2):129-40. doi: IJIv12i2A5.
12. CD1d-restricted NKT cells contribute to malarial splenomegaly and enhance parasite-specific antibody responses. Hansen DS, etal., Eur J Immunol. 2003 Sep;33(9):2588-98. doi: 10.1002/eji.200323666.
13. Role of CD1d in coxsackievirus B3-induced myocarditis. Huber S, etal., J Immunol. 2003 Mar 15;170(6):3147-53. doi: 10.4049/jimmunol.170.6.3147.
14. Decay-accelerating factor (CD55) promotes CD1d expression and Vgamma4+ T-cell activation in coxsackievirus B3-induced myocarditis. Huber S, etal., Viral Immunol. 2006 Summer;19(2):156-66. doi: 10.1089/vim.2006.19.156.
15. Tumor necrosis factor-alpha promotes myocarditis in female mice infected with coxsackievirus B3 through upregulation of CD1d on hematopoietic cells. Huber S, Viral Immunol. 2010 Feb;23(1):79-86. doi: 10.1089/vim.2009.0063.
16. gammadelta T lymphocytes kill T regulatory cells through CD1d. Huber SA Immunology. 2010 Oct;131(2):202-9. doi: 10.1111/j.1365-2567.2010.03292.x. Epub 2010 Aug 16.
17. CD1d mediates T-cell-dependent resistance to secondary infection with encephalomyocarditis virus (EMCV) in vitro and immune response to EMCV infection in vivo. Ilyinskii PO, etal., J Virol. 2006 Jul;80(14):7146-58. doi: 10.1128/JVI.02745-05.
18. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
19. Post-sepsis immunosuppression depends on NKT cell regulation of mTOR/IFN-γ in NK cells. Kim EY, etal., J Clin Invest. 2020 Jun 1;130(6):3238-3252. doi: 10.1172/JCI128075.
20. Hepatocyte CD1d protects against liver immunopathology in mice with schistosomiasis japonica. Lei Z, etal., Immunology. 2021 Mar;162(3):328-338. doi: 10.1111/imm.13288. Epub 2020 Dec 22.
21. The mucosal adjuvant effect of alpha-galactosylceramide for induction of protective immunity to sexually transmitted viral infection. Lindqvist M, etal., J Immunol. 2009 May 15;182(10):6435-43. doi: 10.4049/jimmunol.0900136.
22. Invariant NKT cell response to dengue virus infection in human. Matangkasombut P, etal., PLoS Negl Trop Dis. 2014 Jun 19;8(6):e2955. doi: 10.1371/journal.pntd.0002955. eCollection 2014 Jun.
23. MGDs mouse GO annotations MGD data from the GO Consortium
24. MGD IEA MGD IEA
25. Interferon-mediated innate immune responses against malaria parasite liver stages. Miller JL, etal., Cell Rep. 2014 Apr 24;7(2):436-447. doi: 10.1016/j.celrep.2014.03.018. Epub 2014 Apr 3.
26. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
27. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
28. Herpes Simplex Virus 1 Specifically Targets Human CD1d Antigen Presentation To Enhance Its Pathogenicity. Rao P, etal., J Virol. 2018 Oct 29;92(22). pii: JVI.01490-18. doi: 10.1128/JVI.01490-18. Print 2018 Nov 15.
29. The Variable Genomic NK Cell Receptor Locus Is a Key Determinant of CD4+ T Cell Responses During Viral Infection. Raynor J, etal., Front Immunol. 2020 Feb 20;11:197. doi: 10.3389/fimmu.2020.00197. eCollection 2020.
30. Contribution of NKT cells to the immune response and pathogenesis triggered by respiratory viruses. Rey-Jurado E, etal., Virulence. 2020 Dec;11(1):580-593. doi: 10.1080/21505594.2020.1770492.
31. Mouse MP Annotation Import Pipeline RGD automated import pipeline
32. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
33. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
34. Inhibition of CD1d activation suppresses septic mortality: a role for NK-T cells in septic immune dysfunction. Rhee RJ, etal., J Surg Res. 2003 Nov;115(1):74-81. doi: 10.1016/s0022-4804(03)00220-8.
35. Association between genetic variants in CD1A and CD1D genes and pulmonary tuberculosis in an Iranian population. Taheri M, etal., Biomed Rep. 2019 Apr;10(4):259-265. doi: 10.3892/br.2019.1201. Epub 2019 Mar 15.
36. Elevated Hepatic CD1d Levels Coincide with Invariant NKT Cell Defects in Chronic Hepatitis B Virus Infection. Tan X, etal., J Immunol. 2018 May 15;200(10):3530-3538. doi: 10.4049/jimmunol.1701801. Epub 2018 Apr 11.
37. Schistosomes induce regulatory features in human and mouse CD1d(hi) B cells: inhibition of allergic inflammation by IL-10 and regulatory T cells. van der Vlugt LE, etal., PLoS One. 2012;7(2):e30883. doi: 10.1371/journal.pone.0030883. Epub 2012 Feb 8.
38. Direct CD1d-mediated stimulation of APC IL-12 production and protective immune response to virus infection in vivo. Yue SC, etal., J Immunol. 2010 Jan 1;184(1):268-76. doi: 10.4049/jimmunol.0800924. Epub 2009 Nov 30.
39. Activation of natural killer T cells in NZB/W mice induces Th1-type immune responses exacerbating lupus. Zeng D, etal., J Clin Invest. 2003 Oct;112(8):1211-22. doi: 10.1172/JCI17165.
Additional References at PubMed
PMID:376318   PMID:1347284   PMID:1374101   PMID:1382091   PMID:1431091   PMID:1531670   PMID:1617222   PMID:1702817   PMID:1705364   PMID:2460336   PMID:2478463   PMID:7538697  
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PMID:10201995   PMID:10349636   PMID:10377193   PMID:10499927   PMID:10544194   PMID:10575233   PMID:10623818   PMID:10706669   PMID:10836253   PMID:10889161   PMID:10919985   PMID:10973283  
PMID:11034371   PMID:11042159   PMID:11046002   PMID:11076861   PMID:11123275   PMID:11226281   PMID:11238600   PMID:11304550   PMID:11342617   PMID:11358978   PMID:11390496   PMID:11390999  
PMID:11489950   PMID:11489982   PMID:11550008   PMID:11602646   PMID:11683957   PMID:11698470   PMID:11731798   PMID:11745354   PMID:11748161   PMID:11751982   PMID:11754812   PMID:11777966  
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PMID:15810882   PMID:15843569   PMID:15878981   PMID:15944296   PMID:15958069   PMID:15963482   PMID:16002688   PMID:16002697   PMID:16007091   PMID:16027237   PMID:16087715   PMID:16141072  
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PMID:24166975   PMID:24231354   PMID:24344267   PMID:24442431   PMID:24510964   PMID:24550295   PMID:24634489   PMID:24717441   PMID:24756110   PMID:24966328   PMID:24990409   PMID:25070854  
PMID:25244096   PMID:25263549   PMID:25618030   PMID:25654212   PMID:25807531   PMID:25929465   PMID:25968334   PMID:26078271   PMID:26121177   PMID:26447219   PMID:26453755   PMID:26496152  
PMID:26564814   PMID:26571395   PMID:26604037   PMID:26639063   PMID:26752157   PMID:26767500   PMID:26806130   PMID:27006394   PMID:27050305   PMID:27063801   PMID:27329323   PMID:27385215  
PMID:27653688   PMID:27739478   PMID:27799287   PMID:27869820   PMID:28082459   PMID:28095507   PMID:28296542   PMID:28338767   PMID:28392574   PMID:28436935   PMID:28694386   PMID:28893990  
PMID:28986544   PMID:29045904   PMID:29152605   PMID:29249358   PMID:29345057   PMID:29378774   PMID:29576533   PMID:29581354   PMID:30467836   PMID:30508304   PMID:30513408   PMID:30514903  
PMID:30557354   PMID:30745361   PMID:30822302   PMID:30864713   PMID:31085832   PMID:31371502   PMID:31653827   PMID:31690657   PMID:31727774   PMID:32366944   PMID:32516575   PMID:32647184  
PMID:33087357   PMID:33407995   PMID:33483371   PMID:34181769   PMID:34691073   PMID:34740961   PMID:34880299   PMID:35021099   PMID:35137411   PMID:35392825   PMID:35997680   PMID:37077920  
PMID:37354904   PMID:37382154   PMID:37735500   PMID:38040679   PMID:38355793   PMID:38438948   PMID:38586879   PMID:38984869  


Genomics

Comparative Map Data
Cd1d1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39386,903,141 - 86,919,665 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl386,903,141 - 86,906,748 (-)EnsemblGRCm39 Ensembl
GRCm38386,995,834 - 87,012,358 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl386,995,834 - 86,999,441 (-)EnsemblGRCm38mm10GRCm38
MGSCv37386,799,756 - 86,803,262 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36387,081,765 - 87,085,267 (-)NCBIMGSCv36mm8
Celera387,021,305 - 87,024,811 (-)NCBICelera
Cytogenetic Map3F1NCBI
cM Map337.91NCBI
CD1D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381158,178,030 - 158,186,427 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1158,178,030 - 158,186,427 (+)EnsemblGRCh38hg38GRCh38
GRCh371158,147,820 - 158,156,217 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361156,416,361 - 156,422,841 (+)NCBINCBI36Build 36hg18NCBI36
Build 341154,962,809 - 154,967,758NCBI
Celera1131,220,809 - 131,227,289 (+)NCBICelera
Cytogenetic Map1q23.1NCBI
HuRef1129,508,011 - 129,514,491 (+)NCBIHuRef
CHM1_11159,546,145 - 159,552,625 (+)NCBICHM1_1
T2T-CHM13v2.01157,297,517 - 157,323,522 (+)NCBIT2T-CHM13v2.0
Cd1d1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82174,721,522 - 174,725,029 (-)NCBIGRCr8
GRCr8 Ensembl2174,721,522 - 174,725,029 (-)EnsemblGRCr8 Ensembl
mRatBN7.22172,423,582 - 172,427,089 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2172,423,582 - 172,427,089 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2179,568,188 - 179,571,726 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02177,590,509 - 177,594,047 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02172,190,847 - 172,194,381 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02186,330,298 - 186,333,805 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2186,330,298 - 186,333,805 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02205,728,725 - 205,732,232 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42179,011,165 - 179,014,672 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2166,382,474 - 166,385,981 (-)NCBICelera
RGSC_v3.12178,961,270 - 178,964,778 (-)NCBI
Cytogenetic Map2q34NCBI
CD1D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2191,650,464 - 91,694,649 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1191,394,387 - 91,438,560 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01133,549,258 - 133,557,752 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11137,339,774 - 137,348,173 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1137,341,690 - 137,348,173 (+)Ensemblpanpan1.1panPan2
CD1D
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13823,489,169 - 23,491,712 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3823,516,058 - 23,520,487 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03823,658,417 - 23,662,742 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.13823,402,320 - 23,406,627 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03823,956,328 - 23,960,599 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03824,357,336 - 24,361,653 (-)NCBIUU_Cfam_GSD_1.0
PCD1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl492,031,712 - 92,040,742 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1492,035,122 - 92,040,724 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24100,378,316 - 100,383,517 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CD1D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1205,726,307 - 5,733,355 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl205,727,049 - 5,730,061 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660384,918,748 - 4,925,895 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Cd1d1
1156 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:1414
Count of miRNA genes:521
Interacting mature miRNAs:632
Transcripts:ENSMUST00000029717, ENSMUST00000063869, ENSMUST00000107620, ENSMUST00000132131, ENSMUST00000142793
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142399Aec1_mautoimmune exocrinopathy 1 (mouse)Not determined7586174102690034Mouse
26884378Skwq6_mskull length QTL 6, 10 week (mouse)351907421102307316Mouse
1301971Cia5_mcollagen induced arthritis QTL 5 (mouse)Not determined366046658100046795Mouse
1301392Eae3_msusceptibility to experimental allergic encephalomyelitis 3 (mouse)Not determined379548730113548837Mouse
1301904Iba2_minduction of brown adipocytes 2 (mouse)Not determined382147043116147184Mouse
26884382Bzwq1_mbi-zygomatic width QTL 1, 5 week (mouse)352207421137205761Mouse
11041900Lmr11a_mleishmaniasis resistance 11a (mouse)383463991117464137Mouse
26884380Skwq1_mskull length QTL 1, 5 week (mouse)343954435101607316Mouse
13464139Nhdlq17_mnon-HDL QTL 17 (mouse)35292318386923183Mouse
14746984Manh54_mmandible shape 54 (mouse)385289152119289152Mouse
25314313Syncl1_msynaptonemal complex length 1 (mouse)367907333128393649Mouse
1301272Cfsw1_mcystic fibrosis survival to weaning 1 (mouse)Not determined383882912117883044Mouse
1301791Char4_mP. chabaudi malaria resistance QTL 4 (mouse)Not determined369625509100655290Mouse
11049572Lmr11c_mleishmaniasis resistance 11c (mouse)372139967106140094Mouse
26884436Zlq3_mzygomatic length QTL 3, 10 week (mouse)33265060142405761Mouse
26884427Cvht4_mcranial vault height 4, 10 week (mouse)316054164109707316Mouse
4141294Bmd24_mbone mineral density 24 (mouse)Not determined36174006195740241Mouse
1301705Sles3_msystemic lupus erythmatosus suppressor 3 (mouse)Not determined337174862143353183Mouse
13207570Tcq12_mtotal cholesterol QTL 12 (mouse)316504164130163649Mouse
26884422Cvht7_mcranial vault height 7, 16 week (mouse)328954149118893649Mouse
1300595Tmevd2_mTheiler's murine encephalomyelitis virus induced demyelinating disease susceptibility 2 (mouse)Not determined375463302109463549Mouse
11251721Ewc3_methanol withdrawal and consumption 3 (mouse)369568554103568554Mouse
1300982Lmr11_mleishmaniasis resistance 11 (mouse)Not determined372139967106140094Mouse
12880419V125Dq4_mvitamin D active form serum level QTL 4 (mouse)35890730792907307Mouse
1301947Pcfm3_mperiosteal circumference and femur length 3 (mouse)Not determined381084652115084797Mouse
4142099Cq3_mcholesterol QTL 3 (mouse)Not determined384888918118889067Mouse
11039512Ltpr3b_mLeishmania tropica response 3b (mouse)383463991117464137Mouse
11039519Ltpr3_mLeishmania tropica response 3 (mouse)356704102100464137Mouse
1302056Orgwq4_morgan weight QTL 4 (mouse)Not determined330067588147304689Mouse
11039507Ltpr3g_mLeishmania tropica response 3g (mouse)383463991117464137Mouse
11039508Ltpr3f_mLeishmania tropica response 3f (mouse)383463991117464137Mouse
1301422Sle11_msystematic lupus erythematosus susceptibility 11 (mouse)Not determined370208904104209042Mouse
11039509Ltpr3e_mLeishmania tropica response 3e (mouse)383463991117464137Mouse
11039510Ltpr3d_mLeishmania tropica response 3d (mouse)383463991117464137Mouse
13208566Bmiq5_mbody mass index QTL 5 (mouse)340954435115793649Mouse
11039511Ltpr3c_mLeishmania tropica response 3c (mouse)383463991117464137Mouse

Markers in Region
AI747460  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38386,996,237 - 86,996,353UniSTSGRCm38
MGSCv37386,800,159 - 86,800,275UniSTSGRCm37
Celera387,021,708 - 87,021,824UniSTS
Cytogenetic Map3F1UniSTS
cM Map348.0UniSTS
Whitehead/MRC_RH3876.8UniSTS
Whitehead/MRC_RH3877.48UniSTS
Cd1d1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38386,995,966 - 86,996,521UniSTSGRCm38
MGSCv37386,799,888 - 86,800,443UniSTSGRCm37
Celera387,021,437 - 87,021,992UniSTS
Cytogenetic Map3F1UniSTS
cM Map348.0UniSTS
cM Map348.0UniSTS
Cd1d1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map3F1UniSTS
Cd1d1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map3F1UniSTS
cM Map348.0UniSTS


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001379501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001379502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001379503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001409614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001409615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001409616 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001409617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001409618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001409619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001409620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001409621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001409622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_007639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_166722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_030252404 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC132346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI550455 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI553409 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK002582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC055902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ594117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M63695 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X13170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSMUST00000029717   ⟹   ENSMUSP00000029717
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl386,903,141 - 86,906,748 (-)Ensembl
GRCm38.p6 Ensembl386,995,834 - 86,999,441 (-)Ensembl
Ensembl Acc Id: ENSMUST00000063869   ⟹   ENSMUSP00000070616
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl386,903,141 - 86,906,616 (-)Ensembl
GRCm38.p6 Ensembl386,995,834 - 86,999,309 (-)Ensembl
Ensembl Acc Id: ENSMUST00000107620
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl386,903,141 - 86,905,254 (-)Ensembl
GRCm38.p6 Ensembl386,995,834 - 86,997,947 (-)Ensembl
Ensembl Acc Id: ENSMUST00000132131
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl386,905,425 - 86,906,261 (-)Ensembl
GRCm38.p6 Ensembl386,998,118 - 86,998,954 (-)Ensembl
Ensembl Acc Id: ENSMUST00000142793
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl386,905,696 - 86,906,648 (-)Ensembl
GRCm38.p6 Ensembl386,998,389 - 86,999,341 (-)Ensembl
RefSeq Acc Id: NM_001379501   ⟹   NP_001366430
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
GRCm38386,995,834 - 86,999,329 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001379502   ⟹   NP_001366431
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
GRCm38386,995,834 - 86,999,329 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001379503   ⟹   NP_001366432
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,333 (-)NCBI
GRCm38386,995,834 - 86,999,026 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001409614   ⟹   NP_001396543
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
RefSeq Acc Id: NM_001409615   ⟹   NP_001396544
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,919,559 (-)NCBI
RefSeq Acc Id: NM_001409616   ⟹   NP_001396545
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
RefSeq Acc Id: NM_001409617   ⟹   NP_001396546
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
RefSeq Acc Id: NM_001409618   ⟹   NP_001396547
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
RefSeq Acc Id: NM_001409619   ⟹   NP_001396548
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
RefSeq Acc Id: NM_001409620   ⟹   NP_001396549
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
RefSeq Acc Id: NM_001409621   ⟹   NP_001396550
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
RefSeq Acc Id: NM_001409622   ⟹   NP_001396551
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
RefSeq Acc Id: NM_007639   ⟹   NP_031665
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
GRCm38386,995,834 - 86,999,329 (-)NCBI
MGSCv37386,799,756 - 86,803,262 (-)RGD
Celera387,021,305 - 87,024,811 (-)RGD
cM Map3 ENTREZGENE
Sequence:
RefSeq Acc Id: NR_166722
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,141 - 86,906,636 (-)NCBI
GRCm38386,995,834 - 86,999,329 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030252404   ⟹   XP_030108264
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,154 - 86,919,665 (-)NCBI
GRCm38386,995,847 - 87,012,358 (-)NCBI
Sequence:
RefSeq Acc Id: NP_031665   ⟸   NM_007639
- Peptide Label: isoform 1 precursor
- UniProtKB: Q91XK9 (UniProtKB/Swiss-Prot),   P11609 (UniProtKB/Swiss-Prot),   A0A0R4J090 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_030108264   ⟸   XM_030252404
- Peptide Label: isoform X1
- UniProtKB: Q91XK9 (UniProtKB/Swiss-Prot),   P11609 (UniProtKB/Swiss-Prot),   A0A0R4J090 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001366431   ⟸   NM_001379502
- Peptide Label: isoform 3 precursor
- UniProtKB: E9Q395 (UniProtKB/TrEMBL),   Q7TMK5 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001366430   ⟸   NM_001379501
- Peptide Label: isoform 2 precursor
- UniProtKB: Q91XK9 (UniProtKB/Swiss-Prot),   P11609 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: NP_001366432   ⟸   NM_001379503
- Peptide Label: isoform 4
- UniProtKB: Q91XK9 (UniProtKB/Swiss-Prot),   P11609 (UniProtKB/Swiss-Prot)
Ensembl Acc Id: ENSMUSP00000029717   ⟸   ENSMUST00000029717
Ensembl Acc Id: ENSMUSP00000070616   ⟸   ENSMUST00000063869
RefSeq Acc Id: NP_001396544   ⟸   NM_001409615
- Peptide Label: isoform 1 precursor
- UniProtKB: Q91XK9 (UniProtKB/Swiss-Prot),   P11609 (UniProtKB/Swiss-Prot),   A0A0R4J090 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001396548   ⟸   NM_001409619
- Peptide Label: isoform 6
- UniProtKB: B9VQY2 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001396546   ⟸   NM_001409617
- Peptide Label: isoform 4
- UniProtKB: Q91XK9 (UniProtKB/Swiss-Prot),   P11609 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: NP_001396550   ⟸   NM_001409621
- Peptide Label: isoform 9 precursor
RefSeq Acc Id: NP_001396551   ⟸   NM_001409622
- Peptide Label: isoform 7 precursor
- UniProtKB: Q91XK9 (UniProtKB/Swiss-Prot),   P11609 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: NP_001396543   ⟸   NM_001409614
- Peptide Label: isoform 5 precursor
- UniProtKB: Q91XK9 (UniProtKB/Swiss-Prot),   P11609 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: NP_001396549   ⟸   NM_001409620
- Peptide Label: isoform 8
RefSeq Acc Id: NP_001396547   ⟸   NM_001409618
- Peptide Label: isoform 4
- UniProtKB: Q91XK9 (UniProtKB/Swiss-Prot),   P11609 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: NP_001396545   ⟸   NM_001409616
- Peptide Label: isoform 4
- UniProtKB: Q91XK9 (UniProtKB/Swiss-Prot),   P11609 (UniProtKB/Swiss-Prot)
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P11609-F1-model_v2 AlphaFold P11609 1-336 view protein structure

Promoters
RGD ID:6833555
Promoter ID:MM_KWN:34774
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   ES_Cell,   Liver,   Lung,   MEF_B6,   Spleen
Transcripts:ENSMUST00000107620,   OTTMUST00000059801,   OTTMUST00000059803,   OTTMUST00000059804,   OTTMUST00000059805,   UC008PRT.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36386,802,789 - 86,803,289 (-)MPROMDB
RGD ID:6881080
Promoter ID:EPDNEW_M3970
Type:initiation region
Name:Cd1d1_1
Description:Mus musculus CD1d1 antigen , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38386,999,329 - 86,999,389EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:107674 AgrOrtholog
Ensembl Genes ENSMUSG00000028076 Ensembl, ENTREZGENE
Ensembl Transcript ENSMUST00000029717 ENTREZGENE
  ENSMUST00000063869 ENTREZGENE
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
  3.30.500.10 UniProtKB/Swiss-Prot
InterPro Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_C1-set UniProtKB/Swiss-Prot
  MHC_class-I_related UniProtKB/Swiss-Prot
  MHC_I-like_Ag-recog UniProtKB/Swiss-Prot
  MHC_I-like_Ag-recog_sf UniProtKB/Swiss-Prot
  MHC_I/II-like_Ag-recog UniProtKB/Swiss-Prot
KEGG Report mmu:12479 UniProtKB/Swiss-Prot
MGD MGI:107674 ENTREZGENE
NCBI Gene 12479 ENTREZGENE
PANTHER ANTIGEN-PRESENTING GLYCOPROTEIN CD1D UniProtKB/Swiss-Prot
  MHC CLASS I-RELATED UniProtKB/Swiss-Prot
Pfam C1-set UniProtKB/Swiss-Prot
  MHC_I_3 UniProtKB/Swiss-Prot
PhenoGen Cd1d1 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot
SMART IGc1 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
  SSF54452 UniProtKB/Swiss-Prot
UniProt A0A0R4J090 ENTREZGENE, UniProtKB/TrEMBL
  B9VQY2 ENTREZGENE
  CD1D1_MOUSE UniProtKB/Swiss-Prot
  E9Q395 ENTREZGENE, UniProtKB/TrEMBL
  P11609 ENTREZGENE
  Q7TMK5 ENTREZGENE, UniProtKB/TrEMBL
  Q91XK9 ENTREZGENE
UniProt Secondary Q91XK9 UniProtKB/Swiss-Prot