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); PARTICIPATES IN Entamoebiasis pathway; INTERACTS WITH 1,2-dimethylhydrazine; 2,2',4,4',5,5'-hexachlorobiphenyl; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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 Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39386,903,141 - 86,919,665 (-)NCBIGRCm39mm39
GRCm39 Ensembl386,903,141 - 86,906,748 (-)Ensembl
GRCm38386,995,834 - 87,012,358 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl386,995,834 - 86,999,441 (-)EnsemblGRCm38mm10GRCm38
MGSCv37386,799,756 - 86,803,262 (-)NCBIGRCm37mm9NCBIm37
MGSCv36387,081,765 - 87,085,267 (-)NCBImm8
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
1,2-dimethylhydrazine  (EXP)
17beta-estradiol  (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-dinitrotoluene  (ISO)
2-nitrofluorene  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
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)
antirheumatic drug  (ISO)
arsenite(3-)  (EXP)
arsenous acid  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (EXP)
bisphenol A  (ISO)
carbamazepine  (ISO)
carbon nanotube  (EXP)
cyclosporin A  (EXP,ISO)
D-glucose  (EXP)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (EXP)
dibutyl phthalate  (EXP)
diethylstilbestrol  (EXP)
dioxygen  (EXP)
endosulfan  (ISO)
fucoxanthin  (EXP)
glucose  (EXP)
iron atom  (ISO)
iron(0)  (ISO)
menadione  (EXP)
methotrexate  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (EXP)
nickel atom  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
PCB138  (EXP)
pentachlorophenol  (EXP)
perfluorooctanoic acid  (ISO)
pirinixic acid  (ISO)
Ro 41-5253  (ISO)
rotenone  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (EXP)
trichostatin A  (ISO)
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 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 blood urea nitrogen level  (IAGP)
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
1. Amu S, etal., J Allergy Clin Immunol. 2010 May;125(5):1114-1124.e8. Epub 2010 Mar 20.
2. Aoki-Nonaka Y, etal., J Periodontal Res. 2014 Feb;49(1):69-76. doi: 10.1111/jre.12080. Epub 2013 Apr 16.
3. Arshad MI, etal., PLoS One. 2013 Sep 13;8(9):e74278. doi: 10.1371/journal.pone.0074278. eCollection 2013.
4. Bachy E, etal., J Exp Med. 2016 May 2;213(5):841-57. doi: 10.1084/jem.20150794. Epub 2016 Apr 11.
5. Baron JL, etal., Immunity. 2002 Apr;16(4):583-94. doi: 10.1016/s1074-7613(02)00305-9.
6. Bhalerao J, etal., J Biol Chem 1995 Jul 7;270(27):16385-94.
7. Broxmeyer HE, etal., Exp Hematol. 2007 Apr;35(4 Suppl 1):87-93. doi: 10.1016/j.exphem.2007.01.015.
8. Duthie MS, etal., Infect Immun. 2005 Mar;73(3):1890-4. doi: 10.1128/IAI.73.3.1890-1894.2005.
9. Grubor-Bauk B, etal., J Virol. 2008 Nov;82(22):11073-83. doi: 10.1128/JVI.00205-08. Epub 2008 Jul 9.
10. Habbeddine M, etal., Microbes Infect. 2013 Nov;15(13):928-38. doi: 10.1016/j.micinf.2013.08.006. Epub 2013 Aug 31.
11. Hafezi N, etal., Iran J Immunol. 2015 Jun;12(2):129-40. doi: IJIv12i2A5.
12. Hansen DS, etal., Eur J Immunol. 2003 Sep;33(9):2588-98. doi: 10.1002/eji.200323666.
13. Huber S, etal., J Immunol. 2003 Mar 15;170(6):3147-53. doi: 10.4049/jimmunol.170.6.3147.
14. Huber S, etal., Viral Immunol. 2006 Summer;19(2):156-66. doi: 10.1089/vim.2006.19.156.
15. Huber S, Viral Immunol. 2010 Feb;23(1):79-86. doi: 10.1089/vim.2009.0063.
16. Huber SA Immunology. 2010 Oct;131(2):202-9. doi: 10.1111/j.1365-2567.2010.03292.x. Epub 2010 Aug 16.
17. Ilyinskii PO, etal., J Virol. 2006 Jul;80(14):7146-58. doi: 10.1128/JVI.02745-05.
18. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
19. Kim EY, etal., J Clin Invest. 2020 Jun 1;130(6):3238-3252. doi: 10.1172/JCI128075.
20. Lei Z, etal., Immunology. 2021 Mar;162(3):328-338. doi: 10.1111/imm.13288. Epub 2020 Dec 22.
21. Lindqvist M, etal., J Immunol. 2009 May 15;182(10):6435-43. doi: 10.4049/jimmunol.0900136.
22. Matangkasombut P, etal., PLoS Negl Trop Dis. 2014 Jun 19;8(6):e2955. doi: 10.1371/journal.pntd.0002955. eCollection 2014 Jun.
23. MGD data from the GO Consortium
24. MGD IEA
25. 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. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
27. Pipeline to import KEGG annotations from KEGG into RGD
28. 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. Raynor J, etal., Front Immunol. 2020 Feb 20;11:197. doi: 10.3389/fimmu.2020.00197. eCollection 2020.
30. Rey-Jurado E, etal., Virulence. 2020 Dec;11(1):580-593. doi: 10.1080/21505594.2020.1770492.
31. RGD automated import pipeline
32. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
33. RGD automated import pipeline for gene-chemical interactions
34. Rhee RJ, etal., J Surg Res. 2003 Nov;115(1):74-81. doi: 10.1016/s0022-4804(03)00220-8.
35. Taheri M, etal., Biomed Rep. 2019 Apr;10(4):259-265. doi: 10.3892/br.2019.1201. Epub 2019 Mar 15.
36. Tan X, etal., J Immunol. 2018 May 15;200(10):3530-3538. doi: 10.4049/jimmunol.1701801. Epub 2018 Apr 11.
37. van der Vlugt LE, etal., PLoS One. 2012;7(2):e30883. doi: 10.1371/journal.pone.0030883. Epub 2012 Feb 8.
38. Yue SC, etal., J Immunol. 2010 Jan 1;184(1):268-76. doi: 10.4049/jimmunol.0800924. Epub 2009 Nov 30.
39. 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  
PMID:7542403   PMID:7915557   PMID:8398132   PMID:9020080   PMID:9133425   PMID:9133426   PMID:9219685   PMID:9457670   PMID:9551949   PMID:9927517   PMID:10047540   PMID:10190903  
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: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   PMID:11870629  
PMID:11920590   PMID:12042809   PMID:12097395   PMID:12244192   PMID:12244311   PMID:12421960   PMID:12444173   PMID:12477932   PMID:12538704   PMID:12576547   PMID:12594829   PMID:12648456  
PMID:12682110   PMID:12695491   PMID:12730881   PMID:12759418   PMID:12773507   PMID:12794761   PMID:12847222   PMID:12902521   PMID:14530332   PMID:14530337   PMID:14557411   PMID:14632651  
PMID:14684827   PMID:14722359   PMID:14744994   PMID:14764672   PMID:14764695   PMID:14768037   PMID:15004145   PMID:15051763   PMID:15067039   PMID:15100269   PMID:15107843   PMID:15113755  
PMID:15135293   PMID:15162443   PMID:15212710   PMID:15243159   PMID:15325792   PMID:15331412   PMID:15356115   PMID:15368448   PMID:15385796   PMID:15485631   PMID:15500624   PMID:15521020  
PMID:15539565   PMID:15548574   PMID:15591216   PMID:15652515   PMID:15699104   PMID:15728477   PMID:15738056   PMID:15749847   PMID:15778340   PMID:15780994   PMID:15792999   PMID:15810882  
PMID:15843569   PMID:15878981   PMID:15944296   PMID:15958069   PMID:15963482   PMID:16002688   PMID:16002697   PMID:16007091   PMID:16027237   PMID:16087715   PMID:16141072   PMID:16141073  
PMID:16148102   PMID:16148122   PMID:16236129   PMID:16251408   PMID:16277640   PMID:16301636   PMID:16314439   PMID:16339525   PMID:16357187   PMID:16424169   PMID:16456008   PMID:16478801  
PMID:16517731   PMID:16557300   PMID:16585555   PMID:16621990   PMID:16651387   PMID:16675847   PMID:16707424   PMID:16730774   PMID:16754716   PMID:16785493   PMID:16785503   PMID:16864660  
PMID:16878136   PMID:16914507   PMID:16949316   PMID:16982810   PMID:16982895   PMID:17015711   PMID:17082577   PMID:17088433   PMID:17182540   PMID:17237379   PMID:17239632   PMID:17312118  
PMID:17353286   PMID:17403933   PMID:17404272   PMID:17442924   PMID:17476670   PMID:17540734   PMID:17607300   PMID:17641782   PMID:17656680   PMID:17675483   PMID:17705133   PMID:17785781  
PMID:17785826   PMID:17804806   PMID:17885216   PMID:17911598   PMID:17947447   PMID:17950005   PMID:17954569   PMID:18077787   PMID:18097001   PMID:18154620   PMID:18161753   PMID:18172081  
PMID:18212072   PMID:18250191   PMID:18250411   PMID:18295796   PMID:18350547   PMID:18354186   PMID:18417738   PMID:18445005   PMID:18451996   PMID:18490727   PMID:18541714   PMID:18549881  
PMID:18550809   PMID:18566372   PMID:18606153   PMID:18624295   PMID:18684818   PMID:18684921   PMID:18684967   PMID:18760855   PMID:18802047   PMID:18802058   PMID:18815300   PMID:18974295  
PMID:18982019   PMID:19018000   PMID:19033672   PMID:19179286   PMID:19217323   PMID:19234223   PMID:19246642   PMID:19265113   PMID:19325124   PMID:19338001   PMID:19342651   PMID:19349688  
PMID:19401453   PMID:19451264   PMID:19454494   PMID:19477915   PMID:19535622   PMID:19538930   PMID:19582739   PMID:19587017   PMID:19587020   PMID:19732779   PMID:19734232   PMID:19737532  
PMID:19783672   PMID:19830742   PMID:19833737   PMID:19903740   PMID:19923446   PMID:19949076   PMID:20028654   PMID:20067532   PMID:20080535   PMID:20194602   PMID:20215643   PMID:20220086  
PMID:20228797   PMID:20375305   PMID:20383148   PMID:20404101   PMID:20439539   PMID:20504886   PMID:20520738   PMID:20525883   PMID:20534460   PMID:20581146   PMID:20601599   PMID:20660713  
PMID:20844203   PMID:20861015   PMID:20890286   PMID:21089371   PMID:21145835   PMID:21191069   PMID:21191075   PMID:21209282   PMID:21267068   PMID:21297009   PMID:21376640   PMID:21389252  
PMID:21398691   PMID:21460847   PMID:21469102   PMID:21478404   PMID:21490153   PMID:21552205   PMID:21555485   PMID:21624939   PMID:21666690   PMID:21677750   PMID:21695190   PMID:21809338  
PMID:21810611   PMID:21844383   PMID:21873635   PMID:21921158   PMID:21964024   PMID:21987790   PMID:21996456   PMID:22021367   PMID:22037601   PMID:22041925   PMID:22046304   PMID:22057113  
PMID:22058413   PMID:22065098   PMID:22065767   PMID:22066016   PMID:22084435   PMID:22101430   PMID:22130674   PMID:22135456   PMID:22253596   PMID:22268994   PMID:22291186   PMID:22331103  
PMID:22346732   PMID:22383967   PMID:22393151   PMID:22396530   PMID:22493234   PMID:22504642   PMID:22535665   PMID:22645141   PMID:22798686   PMID:22814339   PMID:22820602   PMID:22820603  
PMID:22854104   PMID:22875802   PMID:22880059   PMID:22906987   PMID:22933629   PMID:22941735   PMID:22980983   PMID:22981538   PMID:22995911   PMID:23027937   PMID:23028952   PMID:23071286  
PMID:23086918   PMID:23121668   PMID:23190881   PMID:23255360   PMID:23280365   PMID:23296703   PMID:23307809   PMID:23340309   PMID:23345328   PMID:23382238   PMID:23426944   PMID:23427253  
PMID:23523122   PMID:23527709   PMID:23531237   PMID:23545566   PMID:23615906   PMID:23652797   PMID:23658368   PMID:23867896   PMID:23943651   PMID:24043771   PMID:24097110   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: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:31371502   PMID:31653827   PMID:31727774   PMID:32366944   PMID:32516575   PMID:32647184   PMID:33407995   PMID:34181769  


Genomics

Comparative Map Data
Cd1d1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39386,903,141 - 86,919,665 (-)NCBIGRCm39mm39
GRCm39 Ensembl386,903,141 - 86,906,748 (-)Ensembl
GRCm38386,995,834 - 87,012,358 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl386,995,834 - 86,999,441 (-)EnsemblGRCm38mm10GRCm38
MGSCv37386,799,756 - 86,803,262 (-)NCBIGRCm37mm9NCBIm37
MGSCv36387,081,765 - 87,085,267 (-)NCBImm8
Celera387,021,305 - 87,024,811 (-)NCBICelera
Cytogenetic Map3F1NCBI
cM Map337.91NCBI
CD1D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1158,178,030 - 158,186,427 (+)EnsemblGRCh38hg38GRCh38
GRCh381158,178,030 - 158,186,427 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371158,147,820 - 158,156,217 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361156,416,361 - 156,422,841 (+)NCBINCBI36hg18NCBI36
Build 341154,962,809 - 154,967,758NCBI
Celera1131,220,809 - 131,227,289 (+)NCBI
Cytogenetic Map1q23.1NCBI
HuRef1129,508,011 - 129,514,491 (+)NCBIHuRef
CHM1_11159,546,145 - 159,552,625 (+)NCBICHM1_1
Cd1d1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22172,423,582 - 172,427,089 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl2172,423,582 - 172,427,089 (-)Ensembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12178,961,270 - 178,964,778 (-)NCBI
Celera2166,382,474 - 166,385,981 (-)NCBICelera
Cytogenetic Map2q34NCBI
CD1D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11137,339,774 - 137,348,173 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1137,341,690 - 137,348,173 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01133,549,258 - 133,557,752 (+)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.03823,658,417 - 23,662,742 (-)NCBI
UMICH_Zoey_3.13823,402,320 - 23,406,627 (-)NCBI
UNSW_CanFamBas_1.03823,956,328 - 23,960,599 (-)NCBI
UU_Cfam_GSD_1.03824,357,336 - 24,361,653 (-)NCBI
PCD1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl205,727,049 - 5,730,061 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660384,918,748 - 4,925,895 (-)NCBIVero_WHO_p1.0

Position Markers
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


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
26884436Zlq3_mzygomatic length QTL 3, 10 week (mouse)33200000142700000Mouse
4142399Aec1_mautoimmune exocrinopathy 1 (mouse)Not determined7521114102782718Mouse
26884427Cvht4_mcranial vault height 4, 10 week (mouse)316000000109800000Mouse
13207570Tcq12_mtotal cholesterol QTL 12 (mouse)316450000130370000Mouse
26884422Cvht7_mcranial vault height 7, 16 week (mouse)328900000119100000Mouse
1302056Orgwq4_morgan weight QTL 4 (mouse)Not determined330013439147599053Mouse
1301705Sles3_msystemic lupus erythmatosus suppressor 3 (mouse)Not determined337120713143647422Mouse
13208566Bmiq5_mbody mass index QTL 5 (mouse)341000000116000000Mouse
26884380Skwq1_mskull length QTL 1, 5 week (mouse)344000000101700000Mouse
26884378Skwq6_mskull length QTL 6, 10 week (mouse)352000000102400000Mouse
26884382Bzwq1_mbi-zygomatic width QTL 1, 5 week (mouse)352300000137500000Mouse
13464139Nhdlq17_mnon-HDL QTL 17 (mouse)35301585087015850Mouse
11039519Ltpr3_mLeishmania tropica response 3 (mouse)356796681100556821Mouse
12880419V125Dq4_mvitamin D active form serum level QTL 4 (mouse)35900000093000000Mouse
4141294Bmd24_mbone mineral density 24 (mouse)Not determined36183275495832934Mouse
1301971Cia5_mcollagen induced arthritis QTL 5 (mouse)Not determined366139351100139488Mouse
25314313Syncl1_msynaptonemal complex length 1 (mouse)368000000128600000Mouse
11251721Ewc3_methanol withdrawal and consumption 3 (mouse)369661247103661247Mouse
1301791Char4_mP. chabaudi malaria resistance QTL 4 (mouse)Not determined369718176100747974Mouse
1301422Sle11_msystematic lupus erythematosus susceptibility 11 (mouse)Not determined370301597104301735Mouse
1300982Lmr11_mleishmaniasis resistance 11 (mouse)Not determined372232660106232787Mouse
11049572Lmr11c_mleishmaniasis resistance 11c (mouse)372232660106232787Mouse
1300595Tmevd2_mTheiler's murine encephalomyelitis virus induced demyelinating disease susceptibility 2 (mouse)Not determined375555995109556242Mouse
1301392Eae3_msusceptibility to experimental allergic encephalomyelitis 3 (mouse)Not determined379641414113641521Mouse
1301947Pcfm3_mperiosteal circumference and femur length 3 (mouse)Not determined381177336115177481Mouse
1301904Iba2_minduction of brown adipocytes 2 (mouse)Not determined382239727116239868Mouse
11039507Ltpr3g_mLeishmania tropica response 3g (mouse)383556675117556821Mouse
11039508Ltpr3f_mLeishmania tropica response 3f (mouse)383556675117556821Mouse
11039509Ltpr3e_mLeishmania tropica response 3e (mouse)383556675117556821Mouse
11039510Ltpr3d_mLeishmania tropica response 3d (mouse)383556675117556821Mouse
11039511Ltpr3c_mLeishmania tropica response 3c (mouse)383556675117556821Mouse
11039512Ltpr3b_mLeishmania tropica response 3b (mouse)383556675117556821Mouse
11041900Lmr11a_mleishmaniasis resistance 11a (mouse)383556675117556821Mouse
1301272Cfsw1_mcystic fibrosis survival to weaning 1 (mouse)Not determined383975596117975728Mouse
4142099Cq3_mcholesterol QTL 3 (mouse)Not determined384981602118981751Mouse
14746984Manh54_mmandible shape 54 (mouse)385381836119381836Mouse

miRNA Target Status

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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000029717   ⟹   ENSMUSP00000029717
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl386,903,141 - 86,906,748 (-)Ensembl
GRCm38.p6 Ensembl386,995,834 - 86,999,441 (-)Ensembl
RefSeq Acc Id: ENSMUST00000063869   ⟹   ENSMUSP00000070616
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl386,903,141 - 86,906,616 (-)Ensembl
GRCm38.p6 Ensembl386,995,834 - 86,999,309 (-)Ensembl
RefSeq Acc Id: ENSMUST00000107620
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl386,903,141 - 86,905,254 (-)Ensembl
GRCm38.p6 Ensembl386,995,834 - 86,997,947 (-)Ensembl
RefSeq Acc Id: ENSMUST00000132131
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl386,905,425 - 86,906,261 (-)Ensembl
GRCm38.p6 Ensembl386,998,118 - 86,998,954 (-)Ensembl
RefSeq Acc Id: ENSMUST00000142793
RefSeq Status:
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
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
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
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
RefSeq Acc Id: XM_030252403   ⟹   XP_030108263
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,154 - 86,919,546 (-)NCBI
GRCm38386,995,847 - 87,012,239 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030252404   ⟹   XP_030108264
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39386,903,154 - 86,919,665 (-)NCBI
GRCm38386,995,847 - 87,012,358 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_031665   ⟸   NM_007639
- Peptide Label: isoform 1 precursor
- UniProtKB: P11609 (UniProtKB/Swiss-Prot),   A0A0R4J090 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_030108264   ⟸   XM_030252404
- Peptide Label: isoform X1
RefSeq Acc Id: XP_030108263   ⟸   XM_030252403
- Peptide Label: isoform X1
RefSeq Acc Id: NP_001366431   ⟸   NM_001379502
- Peptide Label: isoform 3 precursor
RefSeq Acc Id: NP_001366430   ⟸   NM_001379501
- Peptide Label: isoform 2 precursor
RefSeq Acc Id: NP_001366432   ⟸   NM_001379503
- Peptide Label: isoform 4
RefSeq Acc Id: ENSMUSP00000029717   ⟸   ENSMUST00000029717
RefSeq Acc Id: ENSMUSP00000070616   ⟸   ENSMUST00000063869
Protein Domains
Ig-like

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, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000029717 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUSP00000070616 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000029717 ENTREZGENE, UniProtKB/TrEMBL
  ENSMUST00000063869 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.500.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro 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_C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I-like_Ag-recog UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I-like_Ag-recog_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I/II-like_Ag-recog UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:12479 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:107674 ENTREZGENE
NCBI Gene 12479 ENTREZGENE
Pfam C1-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC_I_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cd1d1 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART IGc1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54452 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0R4J090 ENTREZGENE, UniProtKB/TrEMBL
  CD1D1_MOUSE UniProtKB/Swiss-Prot
  E9Q395_MOUSE UniProtKB/TrEMBL
  P11609 ENTREZGENE
  Q7TMK5_MOUSE UniProtKB/TrEMBL
UniProt Secondary Q91XK9 UniProtKB/Swiss-Prot