Cd1d1 (CD1d1 molecule) - Rat Genome Database

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Gene: Cd1d1 (CD1d1 molecule) Rattus norvegicus
Analyze
Symbol: Cd1d1
Name: CD1d1 molecule
RGD ID: 2296
Description: Predicted to enable several functions, including T cell receptor binding activity; histone binding activity; and lipid antigen binding activity. Predicted to be involved in NK T cell differentiation; antigen processing and presentation, endogenous lipid antigen via MHC class Ib; and regulation of T cell proliferation. Predicted to act 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. Predicted to be located in several cellular components, including endosome; external side of plasma membrane; and lysosome. Human ortholog(s) of this gene implicated in pulmonary tuberculosis. Orthologous to human CD1D (CD1d molecule); PARTICIPATES IN Entamoebiasis pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: antigen-presenting glycoprotein CD1d; Cd1; Cd1d; CD1D antigen; CD1D antigen also localized to RNO7q32 but is presumably on chromosome 2; CD1d1 antigen; T-cell surface glycoprotein CD1d
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
RGSC_v3.12178,961,270 - 178,964,778 (-)NCBI
Celera2166,382,474 - 166,385,981 (-)NCBICelera
Cytogenetic Map2q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,4-dinitrotoluene  (EXP)
2-nitrofluorene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
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  (ISO)
6-propyl-2-thiouracil  (EXP)
actinomycin D  (ISO)
adapalene  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
amphotericin B  (ISO)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
diallyl disulfide  (ISO)
Diallyl sulfide  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (ISO)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
endosulfan  (EXP)
fucoxanthin  (ISO)
gentamycin  (EXP)
glucose  (ISO)
inulin  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
lipopolysaccharide  (ISO)
menadione  (ISO)
methotrexate  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nickel atom  (ISO)
ozone  (EXP)
paracetamol  (EXP,ISO)
PCB138  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
pirinixic acid  (EXP)
Ro 41-5253  (ISO)
rotenone  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
Triptolide  (ISO)
valdecoxib  (EXP)
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
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. 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.
7. 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.
8. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. Structural analysis of the rat homologue of CD1. Evidence for evolutionary conservation of the CD1D class and widespread transcription by rat cells. Ichimiya S, etal., J Immunol 1994 Aug 1;153(3):1112-23.
19. 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.
20. Structural organization of rat CD1 typifies evolutionarily conserved CD1D class genes. Katabami S, etal., Immunogenetics 1998 Jun;48(1):22-31.
21. 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.
22. Improved radiation hybrid map of rat chromosome 2: colocalization of the genes encoding corticotropin-releasing hormone and IL6-receptor with quantitative trait loci regulating the inflammatory response. Laes JF, etal., Cytogenet Cell Genet 2001;92(1-2):130-3.
23. 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.
24. 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.
25. 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.
26. Assignment of the evolutionarily conserved CD1D class gene (Cd1d) to rat chromosome 7q32. Matsuura A, etal., Cytogenet Cell Genet 1997;79(3-4):235-6.
27. Correction and confirmation of the assignment of Cd1d the evolutionarily conserved CD1D class gene to rat chromosome 2q34 and its relationship to human and mouse loci. Matsuura A, etal., Cytogenet Cell Genet 1999;86(3-4):323-4.
28. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
29. 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.
30. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
31. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
32. 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.
33. 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.
34. 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.
35. GOA pipeline RGD automated data pipeline
36. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
37. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
38. 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.
39. 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.
40. 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.
41. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
42. 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.
43. 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.
44. 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:7538697   PMID:9133426   PMID:10201995   PMID:10523605   PMID:11550008   PMID:11754812   PMID:14557411   PMID:14722359   PMID:17082577   PMID:19124746   PMID:20363964   PMID:20927351  
PMID:21460847   PMID:22065767  


Genomics

Comparative Map Data
Cd1d1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
RGSC_v3.12178,961,270 - 178,964,778 (-)NCBI
Celera2166,382,474 - 166,385,981 (-)NCBICelera
Cytogenetic Map2q34NCBI
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
(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
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
28 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:177
Count of miRNA genes:127
Interacting mature miRNAs:141
Transcripts:ENSRNOT00000022150
Prediction methods:Microtar, Miranda, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
6907363Bp357Blood pressure QTL 3574.10.002arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2129540907174540907Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2136916935189599348Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2143657411190602963Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2143657411190602963Rat
6903312Bw112Body weight QTL 1123.20.0013body mass (VT:0001259)body weight (CMO:0000012)2143657569184114274Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2144599348189599348Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147798556192798556Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150341585189039377Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat
12879845Cm89Cardiac mass QTL 890.008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2152413072175950118Rat
12879846Cm90Cardiac mass QTL 900.011heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)2152413072175950118Rat
12879847Am4Aortic mass QTL 40.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2152413072175950118Rat
11565180Kidm56Kidney mass QTL 560.003kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2152413072175950118Rat
11565181Bw176Body weight QTL 1760.002body mass (VT:0001259)body weight (CMO:0000012)2152413072175950118Rat
2301415Cm67Cardiac mass QTL 670.003heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2152413072175950118Rat
12879836Kidm61Kidney mass QTL 610.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2152413072185122374Rat
12879837Am2Aortic mass QTL 20.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2152413072185122374Rat
12879838Cm86Cardiac mass QTL 860.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2152413072185122374Rat
12879839Cm85Cardiac mass QTL 850.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2152413072185122374Rat
12879840Bw179Body weight QTL 1790.005body mass (VT:0001259)body weight (CMO:0000012)2152413072185122374Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2157142078192625452Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2157142209202446871Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168354880185122374Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat

Markers in Region
D2Wox42  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22172,423,734 - 172,424,074 (+)MAPPERmRatBN7.2
Rnor_6.02186,330,451 - 186,330,790NCBIRnor6.0
Rnor_5.02205,728,878 - 205,729,217UniSTSRnor5.0
RGSC_v3.42179,011,318 - 179,011,657UniSTSRGSC3.4
Celera2166,382,627 - 166,382,966UniSTS
Cytogenetic Map2q34UniSTS
RH133461  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22172,423,703 - 172,423,884 (+)MAPPERmRatBN7.2
mRatBN7.22172,423,703 - 172,423,991 (+)MAPPERmRatBN7.2
Rnor_6.02186,330,420 - 186,330,707NCBIRnor6.0
Rnor_6.02186,330,420 - 186,330,600NCBIRnor6.0
Rnor_5.02205,728,847 - 205,729,134UniSTSRnor5.0
Rnor_5.02205,728,847 - 205,729,027UniSTSRnor5.0
RGSC_v3.42179,011,287 - 179,011,467UniSTSRGSC3.4
RGSC_v3.42179,011,287 - 179,011,574UniSTSRGSC3.4
Celera2166,382,596 - 166,382,883UniSTS
Celera2166,382,596 - 166,382,776UniSTS
RH 3.4 Map21129.1UniSTS
Cytogenetic Map2q34UniSTS


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 23 53 37 19 37 6 9 28 21 11 6
Low 3 20 4 4 4 2 2 74 7 18 2
Below cutoff 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022150   ⟹   ENSRNOP00000022150
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2172,423,582 - 172,427,089 (-)Ensembl
Rnor_6.0 Ensembl2186,330,298 - 186,333,805 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117073   ⟹   ENSRNOP00000080498
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2172,423,582 - 172,427,089 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118010   ⟹   ENSRNOP00000087051
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2172,423,582 - 172,427,067 (-)Ensembl
RefSeq Acc Id: NM_017079   ⟹   NP_058775
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22172,423,582 - 172,427,089 (-)NCBI
Rnor_6.02186,330,298 - 186,333,805 (-)NCBI
Rnor_5.02205,728,725 - 205,732,232 (-)NCBI
RGSC_v3.42179,011,165 - 179,014,672 (-)RGD
Celera2166,382,474 - 166,385,981 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_058775 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA05455 (Get FASTA)   NCBI Sequence Viewer  
  BAA82323 (Get FASTA)   NCBI Sequence Viewer  
  EDM00791 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022150
  ENSRNOP00000022150.2
  ENSRNOP00000080498.1
  ENSRNOP00000087051.1
GenBank Protein Q63493 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_058775   ⟸   NM_017079
- Peptide Label: precursor
- UniProtKB: Q63493 (UniProtKB/Swiss-Prot),   Q9R1S6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022150   ⟸   ENSRNOT00000022150
RefSeq Acc Id: ENSRNOP00000080498   ⟸   ENSRNOT00000117073
RefSeq Acc Id: ENSRNOP00000087051   ⟸   ENSRNOT00000118010
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63493-F1-model_v2 AlphaFold Q63493 1-336 view protein structure

Transcriptome

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

Promoters
RGD ID:13691413
Promoter ID:EPDNEW_R1937
Type:initiation region
Name:Cd1d1_1
Description:CD1d1 molecule
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02186,333,748 - 186,333,808EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2296 AgrOrtholog
BioCyc Gene G2FUF-52564 BioCyc
Ensembl Genes ENSRNOG00000016451 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022150 ENTREZGENE
  ENSRNOT00000022150.3 UniProtKB/TrEMBL
  ENSRNOT00000117073.1 UniProtKB/TrEMBL
  ENSRNOT00000118010.1 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 rno:25109 UniProtKB/Swiss-Prot
NCBI Gene 25109 ENTREZGENE
PANTHER ANTIGEN-PRESENTING GLYCOPROTEIN CD1D UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MHC CLASS I-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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
RatGTEx ENSRNOG00000016451 RatGTEx
SMART IGc1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54452 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC233314
UniProt A0A8I5ZPR1_RAT UniProtKB/TrEMBL
  A0A8I6A3N2_RAT UniProtKB/TrEMBL
  A6J5Z8_RAT UniProtKB/TrEMBL
  CD1D_RAT UniProtKB/Swiss-Prot
  G3V837_RAT UniProtKB/TrEMBL
  Q63493 ENTREZGENE
  Q9R1S6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-06-27 Cd1d1  Cd1d1 molecule  Cd1d1  CD1d1 antigen  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-06-27 Cd1d1  CD1d1 molecule  Cd1d1  Cd1d1 molecule  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Cd1d1  CD1d1 antigen  Cd1d  CD1D antigen  Symbol and Name updated 625702 APPROVED
2002-06-10 Cd1d  CD1D antigen      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains binding motifs for two cytokine-inducible transcription factors, NF-IL2-A and NF-IL6 632366