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CD1C CD1c molecule [ Homo sapiens (human) ]

Gene ID: 911, updated on 17-Jun-2019

Summary

Official Symbol
CD1Cprovided by HGNC
Official Full Name
CD1c moleculeprovided by HGNC
Primary source
HGNC:HGNC:1636
See related
Ensembl:ENSG00000158481 MIM:188340
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
R7; CD1; CD1A; BDCA1
Summary
This gene encodes a 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 is broadly distributed throughout the endocytic system via a tyrosine-based motif in the cytoplasmic tail. Alternatively spliced transcript variants of this gene have been observed, but their full-length nature is not known. [provided by RefSeq, Jul 2008]
Expression
Broad expression in lymph node (RPKM 8.6), appendix (RPKM 6.9) and 15 other tissues See more
Orthologs

Genomic context

See CD1C in Genome Data Viewer
Location:
1q23.1
Exon count:
6
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (158289887..158294774)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (158259563..158264564)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene CD1a molecule Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 5 Neighboring gene CD1b molecule Neighboring gene CD1e molecule Neighboring gene olfactory receptor family 10 subfamily T member 2

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 FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpu vpu HIV-1 Vpu downregulates CD1c in Jurkat cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Hematopoietic cell lineage, organism-specific biosystem (from KEGG)
    Hematopoietic cell lineage, organism-specific biosystemBlood-cell development progresses from a hematopoietic stem cell (HSC), which can undergo either self-renewal or differentiation into a multilineage committed progenitor cell: a common lymphoid proge...
  • Hematopoietic cell lineage, conserved biosystem (from KEGG)
    Hematopoietic cell lineage, conserved biosystemBlood-cell development progresses from a hematopoietic stem cell (HSC), which can undergo either self-renewal or differentiation into a multilineage committed progenitor cell: a common lymphoid proge...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystem (from REACTOME)
    Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, organism-specific biosystemA number of receptors and cell adhesion molecules play a key role in modifying the response of cells of lymphoid origin (such as B-, T- and NK cells) to self and tumor antigens, as well as to pathoge...
  • Tight junction, organism-specific biosystem (from KEGG)
    Tight junction, organism-specific biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...
  • Tight junction, conserved biosystem (from KEGG)
    Tight junction, conserved biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
endogenous lipid antigen binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endogenous lipid antigen binding IDA
Inferred from Direct Assay
more info
PubMed 
exogenous lipid antigen binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exogenous lipid antigen binding IDA
Inferred from Direct Assay
more info
PubMed 
glycolipid binding IDA
Inferred from Direct Assay
more info
PubMed 
lipopeptide binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lipopeptide binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
T cell activation involved in immune response IDA
Inferred from Direct Assay
more info
PubMed 
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
antigen processing and presentation, endogenous lipid antigen via MHC class Ib IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
antigen processing and presentation, exogenous lipid antigen via MHC class Ib IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of T cell mediated cytotoxicity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of immune response TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
lysosome IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
T-cell surface glycoprotein CD1c
Names
CD1C antigen, c polypeptide
cortical thymocyte antigen CD1C
differentiation antigen CD1-alpha-3

NCBI Reference Sequences (RefSeq)

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_001765.3NP_001756.2  T-cell surface glycoprotein CD1c precursor

    See identical proteins and their annotated locations for NP_001756.2

    Status: REVIEWED

    Source sequence(s)
    AA824381, AL121986, M28827
    Consensus CDS
    CCDS1175.1
    UniProtKB/Swiss-Prot
    P29017
    Related
    ENSP00000357152.3, ENST00000368170.8
    Conserved Domains (2) summary
    cd07698
    Location:204296
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:20197
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    158289887..158294774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005245579.5XP_005245636.1  T-cell surface glycoprotein CD1c isoform X1

    Related
    ENSP00000408755.1, ENST00000443761.1
    Conserved Domains (2) summary
    cd07698
    Location:204297
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:20197
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
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