CD47 CD47 molecule [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CD47 and IFT57 Are Colinear Genes That Are Highly Coexpressed in Most Cancers and Exhibit Parallel Cancer-Specific Correlations with Survival.
Title: CD47 and IFT57 Are Colinear Genes That Are Highly Coexpressed in Most Cancers and Exhibit Parallel Cancer-Specific Correlations with Survival.
CD47-mediated immune evasion in early-stage lung cancer progression.
Title: CD47-mediated immune evasion in early-stage lung cancer progression.
BCMA/CD47-directed universal CAR-T cells exhibit excellent antitumor activity in multiple myeloma.
Title: BCMA/CD47-directed universal CAR-T cells exhibit excellent antitumor activity in multiple myeloma.
Airway epithelial CD47 plays a critical role in inducing influenza virus-mediated bacterial super-infection.
Title: Airway epithelial CD47 plays a critical role in inducing influenza virus-mediated bacterial super-infection.
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.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (252)

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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-12537 (e-PCR)
- UniSTS:16400

SHGC-77177 (e-PCR)
- UniSTS:72729

SHGC-77187 (e-PCR)
- UniSTS:1834

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

RH121206 (e-PCR)
- UniSTS:138316

SHGC-77192 (e-PCR)
- UniSTS:35445

RH94184 (e-PCR)
- UniSTS:92029

RH78668 (e-PCR)
- UniSTS:60057

D3S3910 (e-PCR)
- UniSTS:2204

D3S4195 (e-PCR)
- UniSTS:23455

CD47_2027 (e-PCR)
- UniSTS:280485

STS-Z25521 (e-PCR)
- UniSTS:42422

STS-X69398 (e-PCR)
- UniSTS:42423

D3S4214 (e-PCR)
- UniSTS:73921

SHGC-77188 (e-PCR)
- UniSTS:37058

RH78419 (e-PCR)
- UniSTS:34026

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

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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)

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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

108043091..108091031 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

XR_241522.3 RNA Sequence
XR_924218.3 RNA Sequence
XR_007095769.1 RNA Sequence
XR_007095768.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

110762913..110810821 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0A1TSG4

RNA

XR_008486856.1 RNA Sequence
XR_008486855.1 RNA Sequence
XR_008486858.1 RNA Sequence
XR_008486857.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.
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.