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CD47 CD47 molecule [ Homo sapiens (human) ]

Gene ID: 961, updated on 12-Aug-2018

Summary

Official Symbol
CD47provided by HGNC
Official Full Name
CD47 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1682
See related
Ensembl:ENSG00000196776 MIM:601028; Vega:OTTHUMG00000044216
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

Genomic context

See CD47 in Genome Data Viewer
Location:
3q13.12
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (108043094..108094200, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (107761941..107809935, 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 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat'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 BioSystems

  • Cell surface interactions at the vascular wall, organism-specific biosystem (from REACTOME)
    Cell surface interactions at the vascular wall, organism-specific biosystemLeukocyte extravasation is a rigorously controlled process that guides white cell movement from the vascular lumen to sites of tissue inflammation. The powerful adhesive interactions that are require...
  • Cell-Cell communication, organism-specific biosystem (from REACTOME)
    Cell-Cell communication, organism-specific biosystemCell-to-Cell communication is crucial for multicellular organisms because it allows organisms to coordinate the activity of their cells. Some cell-to-cell communication requires direct cell-cell cont...
  • ECM-receptor interaction, organism-specific biosystem (from KEGG)
    ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • ECM-receptor interaction, conserved biosystem (from KEGG)
    ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Hemostasis, organism-specific biosystem (from REACTOME)
    Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...
  • 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...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
    Integrin cell surface interactions, organism-specific biosystemThe extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength...
  • Integrins in angiogenesis, organism-specific biosystem (from Pathway Interaction Database)
    Integrins in angiogenesis, organism-specific biosystem
    Integrins in angiogenesis
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
  • Signal regulatory protein (SIRP) family interactions, organism-specific biosystem (from REACTOME)
    Signal regulatory protein (SIRP) family interactions, organism-specific biosystemSignal regulatory protein (SIRP)alpha, also known as SHPS-1 or SIRPA or CD172a, is a transmembrane protein expressed mostly on myeloid cells. CD47, a widely expressed transmembrane protein, is a liga...
  • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
    Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multistep process that...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
thrombospondin receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
thrombospondin receptor activity IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
integrin-mediated signaling pathway TAS
Traceable Author Statement
more info
PubMed 
leukocyte migration TAS
Traceable Author Statement
more info
 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
opsonization IEA
Inferred from Electronic Annotation
more info
 
positive regulation of T cell activation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cell-cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of inflammatory response IEA
Inferred from Electronic Annotation
more info
 
positive regulation of phagocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of phagocytosis IEA
Inferred from Electronic Annotation
more info
 
response to bacterium IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
extracellular exosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular exosome IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
specific granule membrane TAS
Traceable Author Statement
more info
 
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)

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_001777.3NP_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, OTTHUMP00000041153, ENST00000361309.5, OTTHUMT00000102793
    Conserved Domains (2) summary
    pfam04549
    Location:144292
    CD47; CD47 transmembrane region
    pfam08204
    Location:20131
    V-set_CD47; CD47 immunoglobulin-like domain
  2. NM_198793.2NP_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 exons compared to variant 1, that causes a frameshift. The resulting 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, OTTHUMP00000041152, ENST00000355354.12, OTTHUMT00000102791
    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 Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    108043094..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_005247908.2XP_005247965.1  leukocyte surface antigen CD47 isoform X1

    See identical proteins and their annotated locations for XP_005247965.1

    Conserved Domains (2) summary
    pfam04549
    Location:144292
    CD47; CD47 transmembrane region
    pfam08204
    Location:20131
    V-set_CD47; CD47 immunoglobulin-like domain
  3. 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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