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CD47 CD47 molecule [ Homo sapiens (human) ]

Gene ID: 961, updated on 6-May-2021

Summary

Official Symbol
CD47provided by HGNC
Official Full Name
CD47 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1682
See related
Ensembl:ENSG00000196776 MIM:601028
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
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Genomic context

See CD47 in Genome Data Viewer
Location:
3q13.12
Exon count:
14
Annotation release Status Assembly Chr Location
109.20210226 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (108043091..108094200, complement)
105.20201022 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 long intergenic non-protein coding RNA 635 Neighboring gene long intergenic non-protein coding RNA 636 Neighboring gene uncharacterized LOC105374031 Neighboring gene CRISPRi-validated cis-regulatory element chr3.3177 Neighboring gene long intergenic non-protein coding RNA 1215

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cell-cell adhesion mediator activity IPI
Inferred from Physical Interaction
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
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 cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cellular response to interferon-gamma 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 extracellular matrix organization TAS
Traceable Author Statement
more info
 
involved_in heterotypic cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
 
involved_in integrin-mediated signaling pathway TAS
Traceable Author Statement
more info
PubMed 
involved_in leukocyte migration TAS
Traceable Author Statement
more info
 
involved_in monocyte extravasation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of Fc-gamma receptor signaling pathway involved in phagocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in neutrophil degranulation TAS
Traceable Author Statement
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
PubMed 
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
PubMed 
involved_in positive regulation of phagocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of stress fiber assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of interferon-gamma production IMP
Inferred from Mutant Phenotype
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 
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
PubMed 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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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)

  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

    See identical proteins and their annotated locations for NP_001768.1

    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
    Q08722
    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

    See identical proteins and their annotated locations for NP_942088.1

    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: Homo sapiens Updated Annotation Release 109.20210226

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    108043091..108094200 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005247909.2XP_005247966.1  leukocyte surface antigen CD47 isoform X2

    See identical proteins and their annotated locations for XP_005247966.1

    UniProtKB/TrEMBL
    A0A0A1TSG4
    Conserved Domains (2) summary
    pfam04549
    Location:144292
    CD47; CD47 transmembrane region
    pfam08204
    Location:20131
    V-set_CD47; CD47 immunoglobulin-like domain
  2. XM_017007536.1XP_016863025.1  leukocyte surface antigen CD47 isoform X3

RNA

  1. XR_001740374.2 RNA Sequence

  2. XR_924220.2 RNA Sequence

  3. XR_001740375.2 RNA Sequence

  4. XR_241522.2 RNA Sequence

  5. XR_924218.2 RNA Sequence

  6. XR_241521.2 RNA Sequence

  7. XR_924219.2 RNA Sequence

  8. XR_002959611.1 RNA Sequence

  9. XR_002959610.1 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.
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