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    CD1D CD1d molecule [ Homo sapiens (human) ]

    Gene ID: 912, updated on 10-Dec-2024

    Summary

    Official Symbol
    CD1Dprovided by HGNC
    Official Full Name
    CD1d moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:1637
    See related
    Ensembl:ENSG00000158473 IMGT/GENE-DB:CD1D; MIM:188410; AllianceGenome:HGNC:1637
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    R3; CD1A; R3G1
    Summary
    This gene encodes a divergent member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene localizes to late endosomes and lysosomes via a tyrosine-based motif in the cytoplasmic tail. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]
    Expression
    Broad expression in appendix (RPKM 5.0), spleen (RPKM 5.0) and 17 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See CD1D in Genome Data Viewer
    Location:
    1q23.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (158178030..158186427)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (157297517..157323522)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (158147820..158156217)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1897 Neighboring gene elongation factor for RNA polymerase II 2 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:158155479-158155992 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:158162378-158163084 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:158163085-158163790 Neighboring gene ribosomal protein S10 pseudogene 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:158181915-158182465 Neighboring gene CD1a molecule

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env CD1d surface expression on human cell lines is downregulated after infection with M-tropic HIV, T-tropic HIV, or after exposure to HIV gp120 in vitro PubMed
    Nef nef HIV-1 Nef downregulates the expression of the non-classical MHC-I like CD1d molecule by increasing internalization of CD1d molecules from the cell surface and retaining CD1d in the trans-Golgi-network (TGN) PubMed
    nef HIV-1 Vpu and Nef cooperatively inhibit CD1d-mediated lipid antigen presentation in HIV-1-infected DCs PubMed
    nef Nef-induced downregulation of CD1d is observed when cells are co-expressing Nef and CD1d, and six amino acids (300-305) in the cytoplasmic tail of CD1d are required for the downregulation by Nef PubMed
    nef HIV-1 Nef-mediated downregulation of CD1d requires a tyrosine-based motif in the CD1d cytoplasmic tail and four Nef amino acid motifs (EEEE65, PxxP75, DD165, and LL175), which are known to be involved in the downregulation of MHC-I and CD4 PubMed
    Vpr vpr HIV-1 Vpr downregulates the expression of CD1D in human monocyte-derived dendritic cells PubMed
    Vpu vpu The conserved APW motif in the alpha-helix II domain at the C-terminal region of HIV-1 Vpu is involved in CD1d downregulation PubMed
    vpu HIV-1 Vpu proteins from group M, O, and P, and SIV Vpu proteins efficiently downregulate CD1d surface levels PubMed
    vpu HIV-1 Vpu downregulates CD1d from the cell surface by inhibiting CD1d recycling from early endosomal compartments to the cell surface PubMed
    vpu HIV-1 Vpu proteins from Cameroonian group N viruses are largely unable to downregulate CD1D PubMed
    vpu HIV-1 Vpu and Nef cooperatively inhibit CD1d-mediated lipid antigen presentation in HIV-1-infected DCs PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    General gene information

    Clone Names

    • MGC34622

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables beta-2-microglobulin binding PubMed 
    enables cell adhesion molecule binding PubMed 
    enables endogenous lipid antigen binding  
    enables exogenous lipid antigen binding  
    enables exogenous lipid antigen binding PubMed 
    enables lipid antigen binding PubMed 
    enables lipopeptide binding  
    enables protein binding PubMed 
    Component Evidence Code Pubs
    located_in basolateral plasma membrane  
    located_in cell surface PubMed 
    located_in cytoplasm PubMed 
    located_in endoplasmic reticulum  
    located_in endoplasmic reticulum membrane  
    located_in endosome membrane  
    is_active_in external side of plasma membrane  
    is_active_in extracellular space  
    located_in lysosomal membrane  
    located_in lysosome PubMed 
    located_in plasma membrane PubMed 

    General protein information

    Preferred Names
    antigen-presenting glycoprotein CD1d
    Names
    CD1D antigen, d polypeptide
    HMC class I antigen-like glycoprotein CD1D
    T-cell surface glycoprotein CD1d
    differentiation antigen CD1-alpha-3
    thymocyte antigen CD1D

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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)

    1. NM_001319145.2 → NP_001306074.1  antigen-presenting glycoprotein CD1d isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon and has a shorter 3' UTR compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AL138899
      Consensus CDS
      CCDS91074.1
      UniProtKB/TrEMBL
      A0A669KB34
      Related
      ENSP00000501066.1, ENST00000673623.2
      Conserved Domains (1) summary
      pfam16497
      Location:20 → 198
      MHC_I_3; MHC-I family domain
    2. NM_001371761.1 → NP_001358690.1  antigen-presenting glycoprotein CD1d isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL138899
      Consensus CDS
      CCDS91075.1
      UniProtKB/TrEMBL
      A0A669KAZ2
      Related
      ENSP00000501010.1, ENST00000673701.2
      Conserved Domains (2) summary
      cd21029
      Location:99 → 191
      IgC1_CD1; Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains
      cl08246
      Location:1 → 94
      MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    3. NM_001371762.2 → NP_001358691.1  antigen-presenting glycoprotein CD1d isoform 1 precursor

      Status: REVIEWED

      Source sequence(s)
      AL138899
      Consensus CDS
      CCDS1173.1
      UniProtKB/Swiss-Prot
      D3DVD5, P15813, Q5W0J3, Q9UMM3, Q9Y5M4
      Related
      ENSP00000501100.1, ENST00000674085.2
      Conserved Domains (2) summary
      cd07698
      Location:203 → 295
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam16497
      Location:1 → 198
      MHC_I_3; MHC-I family domain
    4. NM_001371763.1 → NP_001358692.1  antigen-presenting glycoprotein CD1d isoform 1 precursor

      Status: REVIEWED

      Source sequence(s)
      AL138899
      Consensus CDS
      CCDS1173.1
      UniProtKB/Swiss-Prot
      D3DVD5, P15813, Q5W0J3, Q9UMM3, Q9Y5M4
      Related
      ENSP00000357153.3, ENST00000368171.5
      Conserved Domains (2) summary
      cd07698
      Location:203 → 295
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam16497
      Location:1 → 198
      MHC_I_3; MHC-I family domain
    5. NM_001766.4 → NP_001757.1  antigen-presenting glycoprotein CD1d isoform 1 precursor

      See identical proteins and their annotated locations for NP_001757.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL138899, BC027926, BX106524
      Consensus CDS
      CCDS1173.1
      UniProtKB/Swiss-Prot
      D3DVD5, P15813, Q5W0J3, Q9UMM3, Q9Y5M4
      Related
      ENSP00000501245.3, ENST00000673723.4
      Conserved Domains (2) summary
      cd07698
      Location:203 → 295
      IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
      pfam16497
      Location:1 → 198
      MHC_I_3; MHC-I family domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      158178030..158186427
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433945.1 → XP_047289901.1  antigen-presenting glycoprotein CD1d isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      157297517..157323522
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339553.1 → XP_054195528.1  antigen-presenting glycoprotein CD1d isoform X3

      UniProtKB/TrEMBL
      A0A669KB34
    2. XM_054339552.1 → XP_054195527.1  antigen-presenting glycoprotein CD1d isoform X2

      UniProtKB/Swiss-Prot
      D3DVD5, P15813, Q5W0J3, Q9UMM3, Q9Y5M4
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