Human Gene CD47 (ENST00000361309.6_10) from GENCODE V47lift37
  Description: CD47 molecule, transcript variant 1 (from RefSeq NM_001777.4)
Gencode Transcript: ENST00000361309.6_10
Gencode Gene: ENSG00000196776.17_14
Transcript (Including UTRs)
   Position: hg19 chr3:107,761,938-107,809,878 Size: 47,941 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr3:107,766,135-107,809,755 Size: 43,621 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:107,761,938-107,809,878)mRNA (may differ from genome)Protein (323 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CD47_HUMAN
DESCRIPTION: RecName: Full=Leukocyte surface antigen CD47; AltName: Full=Antigenic surface determinant protein OA3; AltName: Full=Integrin-associated protein; Short=IAP; AltName: Full=Protein MER6; AltName: CD_antigen=CD47; Flags: Precursor;
FUNCTION: Has a role in both cell adhesion by acting as an adhesion receptor for THBS1 on platelets, and in the modulation of integrins. Plays an important role in memory formation and synaptic plasticity in the hippocampus (By similarity). Receptor for SIRPA, binding to which prevents maturation of immature dendritic cells and inhibits cytokine production by mature dendritic cells. Interaction with SIRPG mediates cell-cell adhesion, enhances superantigen-dependent T-cell-mediated proliferation and costimulates T-cell activation. May play a role in membrane transport and/or integrin dependent signal transduction. May prevent premature elimination of red blood cells. May be involved in membrane permeability changes induced following virus infection.
SUBUNIT: Interacts with THBS1 and fibrinogen (By similarity). Monomer. Interacts with SIRPA, SIRPG, UBQLN1 and UBQLN2.
INTERACTION: Q9P1W8:SIRPG; NbExp=2; IntAct=EBI-1268321, EBI-1268284;
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Very broadly distributed on normal adult tissues, as well as ovarian tumors, being especially abundant in some epithelia and the brain.
SIMILARITY: Contains 1 Ig-like V-type (immunoglobulin-like) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CD47
Diseases sorted by gene-association score: hereditary spherocytosis (5), neonatal meningitis (4), rh deficiency syndrome (3), chronic laryngitis (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • D001564 Benzo(a)pyrene
  • D004997 Ethinyl Estradiol
  • D010126 Ozone
  • C049325 1,2-dithiol-3-thione
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • C472791 3-(4'-hydroxy-3'-adamantylbiphenyl-4-yl)acrylic acid
  • C027576 4-hydroxy-2-nonenal
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 36.60 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 736.71 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -68.10123-0.554 Picture PostScript Text
3' UTR -1010.204197-0.241 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006704 - CD47
IPR013147 - CD47_TM
IPR013270 - CD47_Vset
IPR007110 - Ig-like
IPR013783 - Ig-like_fold

Pfam Domains:
PF04549 - CD47 transmembrane region
PF08204 - CD47 immunoglobulin-like domain

SCOP Domains:
48726 - Immunoglobulin

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2JJS - X-ray MuPIT 2JJT - X-ray MuPIT 2VSC - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q08722
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0070053 thrombospondin receptor activity

Biological Process:
GO:0007155 cell adhesion
GO:0007229 integrin-mediated signaling pathway
GO:0008228 opsonization
GO:0008284 positive regulation of cell proliferation
GO:0009617 response to bacterium
GO:0022409 positive regulation of cell-cell adhesion
GO:0030198 extracellular matrix organization
GO:0043312 neutrophil degranulation
GO:0050729 positive regulation of inflammatory response
GO:0050766 positive regulation of phagocytosis
GO:0050870 positive regulation of T cell activation
GO:0050900 leukocyte migration

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0035579 specific granule membrane
GO:0070062 extracellular exosome
GO:0070821 tertiary granule membrane


-  Descriptions from all associated GenBank mRNAs
  AL832675 - Homo sapiens mRNA; cDNA DKFZp313F0317 (from clone DKFZp313F0317).
BX640889 - Homo sapiens mRNA; cDNA DKFZp686I08120 (from clone DKFZp686I08120).
BC037306 - Homo sapiens CD47 molecule, mRNA (cDNA clone MGC:33903 IMAGE:5260986), complete cds.
AK096670 - Homo sapiens cDNA FLJ39351 fis, clone PEBLM2001072.
BC045593 - Homo sapiens CD47 molecule, mRNA (cDNA clone IMAGE:5287620).
BC053959 - Homo sapiens CD47 molecule, mRNA (cDNA clone IMAGE:5275016).
AK289813 - Homo sapiens cDNA FLJ75907 complete cds, highly similar to Homo sapiens CD47 antigen (Rh-related antigen, integrin-associatedsignal transducer) (CD47), transcript variant 1, mRNA.
BC010016 - Homo sapiens CD47 molecule, mRNA (cDNA clone MGC:15298 IMAGE:4303534), complete cds.
BC012884 - Homo sapiens CD47 molecule, mRNA (cDNA clone MGC:9240 IMAGE:3857911), complete cds.
BC042889 - Homo sapiens CD47 molecule, mRNA (cDNA clone IMAGE:4822825), with apparent retained intron.
Z25521 - H.sapiens integrin associated protein mRNA, complete CDS.
AK124152 - Homo sapiens cDNA FLJ42158 fis, clone THYMU2004108.
X69398 - H.sapiens mRNA for OA3 antigenic surface determinant.
LN680437 - Homo sapiens mRNA for CD47.
JD205154 - Sequence 186178 from Patent EP1572962.
DQ893920 - Synthetic construct Homo sapiens clone IMAGE:100008380; FLH165697.01L; RZPDo839F08159D CD47 molecule (CD47) gene, encodes complete protein.
AB590342 - Synthetic construct DNA, clone: pFN21AE1472, Homo sapiens CD47 gene for CD47 molecule, without stop codon, in Flexi system.
BT006907 - Homo sapiens CD47 antigen (Rh-related antigen, integrin-associated signal transducer) mRNA, complete cds.
DQ890756 - Synthetic construct clone IMAGE:100003386; FLH165701.01X; RZPDo839F08160D CD47 molecule (CD47) gene, encodes complete protein.
DQ891811 - Synthetic construct clone IMAGE:100004441; FLH180155.01X; RZPDo839G08132D CD47 molecule (CD47) gene, encodes complete protein.
KJ904432 - Synthetic construct Homo sapiens clone ccsbBroadEn_13826 CD47 gene, encodes complete protein.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q08722 (Reactome details) participates in the following event(s):

R-HSA-202703 CD47 binds SIRP
R-HSA-391158 SIRP alpha binds CD47
R-HSA-391168 SIRP gamma binds CD47
R-HSA-391156 Phosphorylation of ITIM motif in SIRP alpha
R-HSA-391150 p-4Y-SIRPA:CD47 binds PTPN6,PTPN11
R-HSA-391152 p-4Y-SIRPA:CD47 binds PTK2B
R-HSA-391153 p-4Y-SIRPA:CD47 binds GRB2-1
R-HSA-391157 p-4Y-SIRPA:CD47 binds SKAP2
R-HSA-2426259 COMP binds Integrin alpha5beta1, Integrin alphaVbeta3, CD47
R-HSA-6799350 Exocytosis of specific granule membrane proteins
R-HSA-6798747 Exocytosis of tertiary granule membrane proteins
R-HSA-391151 p-4Y-SIRPA:CD47:SKAP2 binds FYB
R-HSA-202733 Cell surface interactions at the vascular wall
R-HSA-391160 Signal regulatory protein family interactions
R-HSA-216083 Integrin cell surface interactions
R-HSA-6798695 Neutrophil degranulation
R-HSA-109582 Hemostasis
R-HSA-1500931 Cell-Cell communication
R-HSA-1474244 Extracellular matrix organization
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A8K198, CD47_HUMAN, D3DN59, ENST00000361309.1, ENST00000361309.2, ENST00000361309.3, ENST00000361309.4, ENST00000361309.5, MER6, NM_001777, Q08722, Q53Y71, Q96A60, uc318bzk.1, uc318bzk.2
UCSC ID: ENST00000361309.6_10
RefSeq Accession: NM_001777.4
Protein: Q08722 (aka CD47_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.