Cd1d1 CD1d1 antigen [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cd1d1provided by MGI
Official Full Name: CD1d1 antigenprovided by MGI
Primary source: MGI:MGI:107674
See related: Ensembl:ENSMUSG00000028076 AllianceGenome:MGI:107674
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Cd1a; Cd1d; CD1.1; Ly-38
Summary: 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). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in subcutaneous fat pad adult (RPKM 94.7), liver adult (RPKM 78.0) and 12 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 F1; 3 37.91 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (86903141..86919665, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (86995834..87012358, complement)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Cutting Edge: Redundant Roles for MHC Class II-, CD1d-, and MR1-restricted T Cells in Clearing Bartonella Infection.
Title: Cutting Edge: Redundant Roles for MHC Class II-, CD1d-, and MR1-restricted T Cells in Clearing Bartonella Infection.
Ox-LDL-induced CD80[+] macrophages expand pro-atherosclerotic NKT cells via CD1d in atherosclerotic mice and hyperlipidemic patients.
Title: Ox-LDL-induced CD80(+) macrophages expand pro-atherosclerotic NKT cells via CD1d in atherosclerotic mice and hyperlipidemic patients.
CD1d protects against hepatocyte apoptosis in non-alcoholic steatohepatitis.
Title: CD1d protects against hepatocyte apoptosis in non-alcoholic steatohepatitis.
Cancer-associated fibroblasts express CD1d and activate invariant natural killer T cells under cellular stress.
Title: Cancer-associated fibroblasts express CD1d and activate invariant natural killer T cells under cellular stress.
Intrinsic factors and CD1d1 but not CD1d2 expression levels control invariant natural killer T cell subset differentiation.
Title: Intrinsic factors and CD1d1 but not CD1d2 expression levels control invariant natural killer T cell subset differentiation.
Epigenetic control of CD1D expression as a mechanism of resistance to immune checkpoint therapy in poorly immunogenic melanomas.
Title: Epigenetic control of CD1D expression as a mechanism of resistance to immune checkpoint therapy in poorly immunogenic melanomas.
CD1d-Dependent Natural Killer T Cells Mediate Hypertension and Vascular Injury Through Interleukin-17A.
Title: CD1d-Dependent Natural Killer T Cells Mediate Hypertension and Vascular Injury Through Interleukin-17A.
Steroid-mediated liver steatosis is CD1d-dependent, while steroid-induced liver necrosis, inflammation, and metabolic changes are CD1d-independent.
Title: Steroid-mediated liver steatosis is CD1d-dependent, while steroid-induced liver necrosis, inflammation, and metabolic changes are CD1d-independent.
CD1d deficiency limits tolerogenic properties of peritoneal macrophages.
Title: CD1d deficiency limits tolerogenic properties of peritoneal macrophages.
Hepatocyte CD1d protects against liver immunopathology in mice with schistosomiasis japonica.
Title: Hepatocyte CD1d protects against liver immunopathology in mice with schistosomiasis japonica.

Submit: New GeneRIF Correction See all GeneRIFs (139)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (8)
Targeted (11) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Cd1d1 (e-PCR), detects polymorphism
- UniSTS:256656

Cd1d1 (e-PCR), detects polymorphism
- UniSTS:256657

AI747460 (e-PCR)
- UniSTS:178857

Cd1d1 (e-PCR), detects polymorphism
- UniSTS:527277

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables T cell receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables cell adhesion molecule binding	ISO Inferred from Sequence Orthology more info
enables endogenous lipid antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables endogenous lipid antigen binding	IDA Inferred from Direct Assay more info	PubMed
enables exogenous lipid antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables exogenous lipid antigen binding	ISO Inferred from Sequence Orthology more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables lipid antigen binding	ISO Inferred from Sequence Orthology more info
enables lipopeptide binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in NK T cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within antigen processing and presentation	IDA Inferred from Direct Assay more info	PubMed
involved_in antigen processing and presentation, endogenous lipid antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
involved_in antigen processing and presentation, endogenous lipid antigen via MHC class Ib	ISO Inferred from Sequence Orthology more info
involved_in antigen processing and presentation, exogenous lipid antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within antigen processing and presentation, exogenous lipid antigen via MHC class Ib	IDA Inferred from Direct Assay more info	PubMed
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of NK T cell activation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of NK T cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of T cell mediated cytotoxicity	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of T cell mediated cytotoxicity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of T cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of interleukin-2 production	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of interleukin-4 production	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of interleukin-4 production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of macrophage activation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of type II interferon production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive thymic T cell selection	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of immature T cell proliferation in thymus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of immune response	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in external side of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: antigen-presenting glycoprotein CD1d1

Names: T-cell surface glycoprotein CD1d1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001379501.1 → NP_001366430.1 antigen-presenting glycoprotein CD1d1 isoform 2 precursor

Status: VALIDATED

Source sequence(s)

AC132346

UniProtKB/Swiss-Prot

P11609, Q91XK9

Conserved Domains (2) summary

cd21029
Location:167 → 259

IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains

cl08246
Location:19 → 162

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001379502.1 → NP_001366431.1 antigen-presenting glycoprotein CD1d1 isoform 3 precursor

Status: VALIDATED

Source sequence(s)

AC132346

UniProtKB/TrEMBL

E9Q395, Q7TMK5

Related

ENSMUSP00000070616.6, ENSMUST00000063869.11

Conserved Domains (2) summary

cd21029
Location:74 → 166

IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains

cl08246
Location:19 → 73

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001379503.1 → NP_001366432.1 antigen-presenting glycoprotein CD1d1 isoform 4

Status: VALIDATED

Source sequence(s)

AC132346

UniProtKB/Swiss-Prot

P11609, Q91XK9

Conserved Domains (2) summary

cd21029
Location:173 → 265

IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains

cl08246
Location:1 → 168

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001409614.1 → NP_001396543.1 antigen-presenting glycoprotein CD1d1 isoform 5 precursor

Status: VALIDATED

Source sequence(s)

AC132346
NM_001409615.1 → NP_001396544.1 antigen-presenting glycoprotein CD1d1 isoform 1 precursor

Status: VALIDATED

Source sequence(s)

AC132346

UniProtKB/TrEMBL

A0A0R4J090
NM_001409616.1 → NP_001396545.1 antigen-presenting glycoprotein CD1d1 isoform 4

Status: VALIDATED

Source sequence(s)

AC132346

Conserved Domains (2) summary

cd21029
Location:173 → 265

IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains

cl08246
Location:1 → 168

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001409617.1 → NP_001396546.1 antigen-presenting glycoprotein CD1d1 isoform 4

Status: VALIDATED

Source sequence(s)

AC132346

Conserved Domains (2) summary

cd21029
Location:173 → 265

IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains

cl08246
Location:1 → 168

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001409618.1 → NP_001396547.1 antigen-presenting glycoprotein CD1d1 isoform 4

Status: VALIDATED

Source sequence(s)

AC132346

Conserved Domains (2) summary

cd21029
Location:173 → 265

IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains

cl08246
Location:1 → 168

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_001409619.1 → NP_001396548.1 antigen-presenting glycoprotein CD1d1 isoform 6

Status: VALIDATED

Source sequence(s)

AC132346
NM_001409620.1 → NP_001396549.1 antigen-presenting glycoprotein CD1d1 isoform 8

Status: VALIDATED

Source sequence(s)

AC132346
NM_001409621.1 → NP_001396550.1 antigen-presenting glycoprotein CD1d1 isoform 9 precursor

Status: VALIDATED

Source sequence(s)

AC132346
NM_001409622.1 → NP_001396551.1 antigen-presenting glycoprotein CD1d1 isoform 7 precursor

Status: VALIDATED

Source sequence(s)

AC132346
NM_007639.4 → NP_031665.2 antigen-presenting glycoprotein CD1d1 isoform 1 precursor

See identical proteins and their annotated locations for NP_031665.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC132346

Consensus CDS

CCDS17449.1

UniProtKB/Swiss-Prot

P11609, Q91XK9

UniProtKB/TrEMBL

A0A0R4J090

Related

ENSMUSP00000029717.3, ENSMUST00000029717.4

Conserved Domains (2) summary

cd07698
Location:205 → 298

IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain

pfam16497
Location:1 → 200

MHC_I_3; MHC-I family domain

RNA

NR_166722.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC132346

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

86903141..86919665 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030252404.1 → XP_030108264.1 antigen-presenting glycoprotein CD1d1 isoform X1

UniProtKB/Swiss-Prot

P11609, Q91XK9

UniProtKB/TrEMBL

A0A0R4J090

Conserved Domains (2) summary

cd07698
Location:205 → 298

IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain

pfam16497
Location:1 → 200

MHC_I_3; MHC-I family domain