Cd1d2 CD1d2 antigen [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cd1d2provided by MGI
Official Full Name: CD1d2 antigenprovided by MGI
Primary source: MGI:MGI:107675
See related: Ensembl:ENSMUSG00000041750 AllianceGenome:MGI:107675
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Cd1b; CD1.2; Ly-38
Summary: This gene encodes a MHC class I-like molecule involved in the presentation of lipid antigens to T cells, and is involved in the activation of Natural Killer T (NKT) cells. The gene is highly similar to the CD1d1 antigen gene, which is located adjacent to this gene in a tail-to-tail fashion. This gene contains a frameshift and does not produce a functional product in the C57BL/6 strain. Alternatively splice transcript variants encoding different isoforms have been found in non-C57BL/6 strains. [provided by RefSeq, Jan 2014]
Annotation information: Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Expression: Biased expression in liver adult (RPKM 33.3), subcutaneous fat pad adult (RPKM 32.4) and 12 other tissues See more
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Genomic context

Location:: 3 F1; 3 37.88 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (86893875..86896843)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (86986586..86989533)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

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.
These data demonstrate that both the developmental requirements and functions of Cd1b-autoreactive T cells resemble those of Invariant Natural Killer T-Cells cells and could in turn be manipulated for use in anti-microbial therapies.
Title: Autoreactive CD1b-restricted T cells: a new innate-like T-cell population that contributes to immunity against infection.
Crystal structures of mouse CD1d-iGb3 complex and its cognate Valpha14 T cell receptor.
Title: Crystal structures of mouse CD1d-iGb3 complex and its cognate Valpha14 T cell receptor suggest a model for dual recognition of foreign and self glycolipids.
a new allele for Cd1d2 is characterized by a point mutation, resulting in a replacement of alanine at position 176 by a valine
Title: Identification of a new mouse Cd1d2 allele.
CD1a and CD1b surface expression is independent from de novo synthesized glycosphingolipids.
Title: CD1a and CD1b surface expression is independent from de novo synthesized glycosphingolipids.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Endonuclease-mediated (7)
Targeted (1)

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
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 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

Process	Evidence Code	Pubs
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
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
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

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 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 lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: antigen-presenting glycoprotein CD1d2

Names: T-cell surface glycoprotein CD1d2

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_001289449.1 → NP_001276378.1 antigen-presenting glycoprotein CD1d2 isoform 2 precursor

See identical proteins and their annotated locations for NP_001276378.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an alternate splice site, compared to variant 1. The reading frame is not affected and the resulting isoform (2) lacks an internal segment, compared to isoform 1.

Source sequence(s)

BC057149

UniProtKB/Swiss-Prot

P11610

UniProtKB/TrEMBL

Q6PG97

Conserved Domains (2) summary

cd07698
Location:167 → 260

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

cl08246
Location:19 → 162

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
NM_007640.2 → NP_031666.2 antigen-presenting glycoprotein CD1d2 isoform 1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes a functional protein in 129, NMRI, AKR/J, and other strains, but not in C57BL/6.

Source sequence(s)

M63697, X15036

UniProtKB/Swiss-Prot

P11610

Conserved Domains (2) summary

cd07698
Location:205 → 298

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

cl08246
Location:19 → 200

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

RNA

NR_038188.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks a single internal nt, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC132346

Related

ENSMUST00000194208.6
NR_172885.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) has an alternate splice site, and lacks a single internal nt, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC132346

Related

ENSMUST00000192481.2