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    CD47 CD47 molecule [ Homo sapiens (human) ]

    Gene ID: 961, updated on 9-Dec-2024

    Summary

    Official Symbol
    CD47provided by HGNC
    Official Full Name
    CD47 moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:1682
    See related
    Ensembl:ENSG00000196776 MIM:601028; AllianceGenome:HGNC:1682
    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
    IAP; OA3; MER6
    Summary
    This gene encodes a membrane protein, which is involved in the increase in intracellular calcium concentration that occurs upon cell adhesion to extracellular matrix. The encoded protein is also a receptor for the C-terminal cell binding domain of thrombospondin, and it may play a role in membrane transport and signal transduction. This gene has broad tissue distribution, and is reduced in expression on Rh erythrocytes. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2010]
    Expression
    Ubiquitous expression in lung (RPKM 24.2), brain (RPKM 20.9) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CD47 in Genome Data Viewer
    Location:
    3q13.12
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (108043091..108091031, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (110762913..110810821, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (107761938..107809878, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906266 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:107744361-107744884 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:107745409-107745930 Neighboring gene uncharacterized LOC124906265 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14591 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14592 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14593 Neighboring gene uncharacterized LOC105374031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20208 Neighboring gene CRISPRi-validated cis-regulatory element chr3.3177 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:107843148-107843648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20214 Neighboring gene long intergenic non-protein coding RNA 1215 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:107849902-107851101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14595 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20215

    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

    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CD3/CD28-activated primary CD4+ T cells downregulates plasma membrane expression of CD47 (IAP) PubMed
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of CD47 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cell-cell adhesion mediator activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables fibrinogen binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding involved in heterotypic cell-cell adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables thrombospondin receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables thrombospondin receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables thrombospondin receptor activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within ATP export IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to interleukin-1 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to interleukin-12 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to type II interferon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in heterotypic cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in integrin-mediated signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of phagocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of T cell activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of cell-cell adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of inflammatory response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of monocyte extravasation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of phagocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of stress fiber assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of Fc receptor mediated stimulatory signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of interleukin-10 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of interleukin-12 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of interleukin-6 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of nitric oxide biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of tumor necrosis factor production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of type II interferon production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell surface ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell surface NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in extracellular exosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in specific granule membrane TAS
    Traceable Author Statement
    more info
     
    located_in tertiary granule membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    leukocyte surface antigen CD47
    Names
    CD47 antigen (Rh-related antigen, integrin-associated signal transducer)
    CD47 glycoprotein
    Rh-related antigen
    antigen identified by monoclonal antibody 1D8
    antigenic surface determinant protein OA3
    integrin associated protein
    integrin-associated signal transducer

    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_001382306.1NP_001369235.1  leukocyte surface antigen CD47 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame alternate coding exon compared to variant t. The encoded isoform (2) has a shorter C-terminus compared to isoform 1.
      Source sequence(s)
      AC012020
      Conserved Domains (2) summary
      pfam04549
      Location:144292
      CD47; CD47 transmembrane region
      cd16090
      Location:20133
      IgV_CD47; Immunoglobulin variable region (IgV) in Cluster of Differentiation (CD) 47
    2. NM_001777.4NP_001768.1  leukocyte surface antigen CD47 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC012020, CB995865, X69398
      Consensus CDS
      CCDS43126.1
      UniProtKB/Swiss-Prot
      A8K198, D3DN59, Q08722, Q53Y71, Q96A60
      Related
      ENSP00000355361.5, ENST00000361309.6
      Conserved Domains (2) summary
      pfam04549
      Location:144292
      CD47; CD47 transmembrane region
      pfam08204
      Location:20131
      V-set_CD47; CD47 immunoglobulin-like domain
    3. NM_198793.3NP_942088.1  leukocyte surface antigen CD47 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two alternate coding exons compared to variant 1, resulting in a frameshift. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC012020, BC037306, CB995865
      Consensus CDS
      CCDS43125.1
      UniProtKB/Swiss-Prot
      Q08722
      Related
      ENSP00000347512.7, ENST00000355354.13
      Conserved Domains (2) summary
      pfam04549
      Location:144292
      CD47; CD47 transmembrane region
      pfam08204
      Location:20131
      V-set_CD47; CD47 immunoglobulin-like 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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      108043091..108091031 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005247909.3XP_005247966.1  leukocyte surface antigen CD47 isoform X1

      UniProtKB/TrEMBL
      A0A0A1TSG4
      Conserved Domains (2) summary
      pfam04549
      Location:144292
      CD47; CD47 transmembrane region
      pfam08204
      Location:20131
      V-set_CD47; CD47 immunoglobulin-like domain

    RNA

    1. XR_241522.3 RNA Sequence

    2. XR_924218.3 RNA Sequence

    3. XR_007095769.1 RNA Sequence

    4. XR_007095768.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      110762913..110810821 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348478.1XP_054204453.1  leukocyte surface antigen CD47 isoform X1

      UniProtKB/TrEMBL
      A0A0A1TSG4

    RNA

    1. XR_008486856.1 RNA Sequence

    2. XR_008486855.1 RNA Sequence

    3. XR_008486858.1 RNA Sequence

    4. XR_008486857.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001025079.1: Suppressed sequence

      Description
      NM_001025079.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    2. NM_001025080.1: Suppressed sequence

      Description
      NM_001025080.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate and lacks homolog support.