U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

CD1A CD1a molecule [ Homo sapiens (human) ]

Gene ID: 909, updated on 17-Sep-2024

Summary

Official Symbol
CD1Aprovided by HGNC
Official Full Name
CD1a moleculeprovided by HGNC
Primary source
HGNC:HGNC:1634
See related
Ensembl:ENSG00000158477 MIM:188370; AllianceGenome:HGNC:1634
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
R4; T6; CD1; FCB6; HTA1
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 localizes to the plasma membrane and to recycling vesicles of the early endocytic system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
Expression
Biased expression in skin (RPKM 10.0), esophagus (RPKM 4.8) and 4 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See CD1A 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 (158248336..158258269)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (157385427..157395365)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (158218126..158228059)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1897 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 CD1d molecule Neighboring gene ribosomal protein S10 pseudogene 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:158181915-158182465 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1899 Neighboring gene CD1b molecule Neighboring gene CD1c molecule

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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

Related articles in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef impairs the generation of a CD3epsilon(+)CD5(+) CD1a(+) T cell differentiation precursor stage that initiates a D-J rearrangement of the TCRbeta locus PubMed
nef CD1a molecules are downregulated by and co-localized with Nef in CD1a-transfected cells; this co-localization is dependent upon the CD1a cytoplasmic tail from amino acid position 325 to 327 PubMed
Tat tat CD4 and CD1a surface expression are greatly decreased in Tat expression Jurkat cells PubMed
tat Only the wild-type Tat induces CD1A-expressing MDDC maturation and increases the production of cytokines TNF-alpha, IL-12, MIP-1alpha, and MIP-1beta PubMed
tat CD1A-expressing monocyte-derived dendritic cells (MDDC) efficiently uptake wild-type and Cys-22 Tat but not oxidized Tat PubMed
Vpr vpr HIV-1 Vpr upregulates the gene expression of CD1A in human monocyte-derived dendritic cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 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 adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
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, 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 immune response NAS
Non-traceable Author Statement
more info
PubMed 
involved_in positive regulation of T cell mediated cytotoxicity IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
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
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in membrane raft IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane NAS
Non-traceable Author Statement
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
T-cell surface glycoprotein CD1a
Names
CD1A antigen, a polypeptide
T-cell surface antigen T6/Leu-6
cluster of differentiation 1 A
cortical thymocyte antigen CD1A
differentiation antigen CD1-alpha-3
epidermal dendritic cell marker CD1a
hTa1 thymocyte antigen

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_001320652.2NP_001307581.1  T-cell surface glycoprotein CD1a isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK312945, AW949640, CA432941, DA822513
    UniProtKB/TrEMBL
    Q8N5T0
    Conserved Domains (2) summary
    cd07698
    Location:191284
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:12185
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
  2. NM_001763.3NP_001754.2  T-cell surface glycoprotein CD1a isoform 1 precursor

    See identical proteins and their annotated locations for NP_001754.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    CA432941, DB108750, M28825
    Consensus CDS
    CCDS1174.1
    UniProtKB/Swiss-Prot
    D3DVD7, P06126, Q13962, Q5TDJ8, Q9UMM4, Q9Y5M5
    UniProtKB/TrEMBL
    Q8N5T0
    Related
    ENSP00000289429.5, ENST00000289429.6
    Conserved Domains (2) summary
    cd07698
    Location:202295
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:19196
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

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
    158248336..158258269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024450738.2XP_024306506.1  T-cell surface glycoprotein CD1a isoform X1

    Conserved Domains (2) summary
    cd07698
    Location:46139
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:240
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    157385427..157395365
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339535.1XP_054195510.1  T-cell surface glycoprotein CD1a isoform X1