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CD47 CD47 molecule [ Homo sapiens (human) ]

Gene ID: 961, updated on 11-Apr-2024

Summary

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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
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Genomic context

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Location:
3q13.12
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (108043091..108091031, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (110762913..110810821, complement)
105.20220307 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. [Latest Findings on the Role of CD47 in Tumor Immune Evasion and Related Targeted Therapies]. Jie XL, et al. Sichuan Da Xue Xue Bao Yi Xue Ban, 2023 May. PMID 37248568, Free PMC Article
  2. CD47 expression is critical for CAR T-cell survival in vivo. Beckett AN, et al. J Immunother Cancer, 2023 Mar. PMID 36918226, Free PMC Article
  3. Reprograming immune microenvironment modulates CD47 cancer stem cells in hepatocellular carcinoma. Abd El-Fattah EE, et al. Int Immunopharmacol, 2022 Dec. PMID 36435064
  4. Significance of CD47 expression in endometrial carcinoma. Sahin N, et al. Indian J Pathol Microbiol, 2022 Oct-Dec. PMID 36308193
  5. The expression profiles of CD47 in the tumor microenvironment of salivary gland cancers: a next step in histology-driven immunotherapy. Votava M, et al. BMC Cancer, 2022 Sep 28. PMID 36171566, Free PMC Article

See all (282) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Co-targeting CD47 and VEGF elicited potent anti-tumor effects in gastric cancer.
    Title: Co-targeting CD47 and VEGF elicited potent anti-tumor effects in gastric cancer.
  2. Restoration of miR-299-3p promotes macrophage phagocytosis and suppresses malignant phenotypes in breast cancer carcinogenesis via dual-targeting CD47 and ABCE1.
    Title: Restoration of miR-299-3p promotes macrophage phagocytosis and suppresses malignant phenotypes in breast cancer carcinogenesis via dual-targeting CD47 and ABCE1.
  3. Expression of a mutant CD47 protects against phagocytosis without inducing cell death or inhibiting angiogenesis.
    Title: Expression of a mutant CD47 protects against phagocytosis without inducing cell death or inhibiting angiogenesis.
  4. CD47-a novel prognostic predicator in epithelial ovarian cancer and correlations with clinicopathological and gene mutation features.
    Title: CD47-a novel prognostic predicator in epithelial ovarian cancer and correlations with clinicopathological and gene mutation features.
  5. m6A-methylated KCTD21-AS1 regulates macrophage phagocytosis through CD47 and cell autophagy through TIPR.
    Title: m6A-methylated KCTD21-AS1 regulates macrophage phagocytosis through CD47 and cell autophagy through TIPR.
  6. CD133, CD47, and PD-L1 Expression in Ovarian High-grade Serous Carcinoma and Its Association with Metastatic Disease: A Cross-sectional Study.
    Title: CD133, CD47, and PD-L1 Expression in Ovarian High-grade Serous Carcinoma and Its Association with Metastatic Disease: A Cross-sectional Study.
  7. Anti-tumor effect of PTEN and its effect on inhibition of the bone tumor through the CD47-SIRPalpha signaling pathway.
    Title: Anti-tumor effect of PTEN and its effect on inhibition of the bone tumor through the CD47-SIRPα signaling pathway.
  8. CD47 expression in urothelial carcinoma and its correlation with histopathological findings.
    Title: CD47 expression in urothelial carcinoma and its correlation with histopathological findings.
  9. Moesin affects the plasma membrane expression and the immune checkpoint function of CD47 in human ovarian clear cell carcinoma.
    Title: Moesin affects the plasma membrane expression and the immune checkpoint function of CD47 in human ovarian clear cell carcinoma.
  10. alpha5-nAChR/STAT3/CD47 axis contributed to nicotine-related lung adenocarcinoma progression and immune escape.
    Title: α5-nAChR/STAT3/CD47 axis contributed to nicotine-related lung adenocarcinoma progression and immune escape.
Submit: New GeneRIF Correction See all GeneRIFs (248)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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
  
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

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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_001382306.1 → NP_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:144 → 292
    CD47; CD47 transmembrane region
    cd16090
    Location:20 → 133
    IgV_CD47; Immunoglobulin variable region (IgV) in Cluster of Differentiation (CD) 47

  2. NM_001777.4 → NP_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
    A8K198, D3DN59, Q08722, Q53Y71, Q96A60
    Related
    ENSP00000355361.5, ENST00000361309.6
    Conserved Domains (2) summary
    pfam04549
    Location:144 → 292
    CD47; CD47 transmembrane region
    pfam08204
    Location:20 → 131
    V-set_CD47; CD47 immunoglobulin-like domain

  3. NM_198793.3 → NP_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:144 → 292
    CD47; CD47 transmembrane region
    pfam08204
    Location:20 → 131
    V-set_CD47; CD47 immunoglobulin-like domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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_005247909.3 → XP_005247966.1  leukocyte surface antigen CD47 isoform X1

    See identical proteins and their annotated locations for XP_005247966.1

    UniProtKB/TrEMBL
    A0A0A1TSG4
    Conserved Domains (2) summary
    pfam04549
    Location:144 → 292
    CD47; CD47 transmembrane region
    pfam08204
    Location:20 → 131
    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_054348478.1 → XP_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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q08722.1 GenPept UniProtKB/Swiss-Prot:Q08722

Gene LinkOut

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Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous