Human Gene CD63 (ENST00000257857.9_6) from GENCODE V47lift37
  Description: CD63 molecule, transcript variant 1 (from RefSeq NM_001780.6)
Gencode Transcript: ENST00000257857.9_6
Gencode Gene: ENSG00000135404.12_16
Transcript (Including UTRs)
   Position: hg19 chr12:56,119,107-56,122,793 Size: 3,687 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr12:56,119,345-56,122,125 Size: 2,781 Coding Exon Count: 7 

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 (chr12:56,119,107-56,122,793)mRNA (may differ from genome)Protein (238 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CD63_HUMAN
DESCRIPTION: RecName: Full=CD63 antigen; AltName: Full=Granulophysin; AltName: Full=Lysosomal-associated membrane protein 3; Short=LAMP-3; AltName: Full=Melanoma-associated antigen ME491; AltName: Full=OMA81H; AltName: Full=Ocular melanoma-associated antigen; AltName: Full=Tetraspanin-30; Short=Tspan-30; AltName: CD_antigen=CD63;
FUNCTION: This antigen is associated with early stages of melanoma tumor progression. May play a role in growth regulation.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein. Lysosome membrane; Multi-pass membrane protein. Late endosome membrane; Multi-pass membrane protein. Note=Also found in Weibel- Palade bodies of endothelial cells. Located in platelet dense granules.
TISSUE SPECIFICITY: Dysplastic nevi, radial growth phase primary melanomas, hematopoietic cells, tissue macrophages.
MISCELLANEOUS: Lack of expression of CD63 in platelets has been observed in a patient with Hermansky-Pudlak syndrome (HPS). Hermansky-Pudlak syndrome (HPS) is a genetically heterogeneous, rare, autosomal recessive disorder characterized by oculocutaneous albinism, bleeding due to platelet storage pool deficiency, and lysosomal storage defects. This syndrome results from defects of diverse cytoplasmic organelles including melanosomes, platelet dense granules and lysosomes. Ceroid storage in the lungs is associated with pulmonary fibrosis, a common cause of premature death in individuals with HPS.
SIMILARITY: Belongs to the tetraspanin (TM4SF) family.

-  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: CD63
Diseases sorted by gene-association score: hermansky-pudlak syndrome (15), melanoma (8), hermansky-pudlak syndrome 9 (3), quebec platelet disorder (2), essential thrombocythemia (2), shwartzman phenomenon (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 316.96 RPKM in Cells - Cultured fibroblasts
Total median expression: 7722.42 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 -24.7068-0.363 Picture PostScript Text
3' UTR -68.60238-0.288 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
IPR000301 - Tetraspanin
IPR018499 - Tetraspanin/Peripherin
IPR018503 - Tetraspanin_CS
IPR008952 - Tetraspanin_EC2

Pfam Domains:
PF00335 - Tetraspanin family

SCOP Domains:
48652 - Tetraspanin

ModBase Predicted Comparative 3D Structure on P08962
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    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0002092 positive regulation of receptor internalization
GO:0002576 platelet degranulation
GO:0007160 cell-matrix adhesion
GO:0015031 protein transport
GO:0016477 cell migration
GO:0034613 cellular protein localization
GO:0035646 endosome to melanosome transport
GO:0043312 neutrophil degranulation
GO:0043473 pigmentation
GO:0048757 pigment granule maturation
GO:0050931 pigment cell differentiation
GO:1900746 regulation of vascular endothelial growth factor signaling pathway
GO:1901379 regulation of potassium ion transmembrane transport
GO:2001046 positive regulation of integrin-mediated signaling pathway

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005770 late endosome
GO:0005771 multivesicular body
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009986 cell surface
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031088 platelet dense granule membrane
GO:0031226 intrinsic component of plasma membrane
GO:0031902 late endosome membrane
GO:0031904 endosome lumen
GO:0032585 multivesicular body membrane
GO:0035577 azurophil granule membrane
GO:0042470 melanosome
GO:0070062 extracellular exosome
GO:0097487 multivesicular body, internal vesicle


-  Descriptions from all associated GenBank mRNAs
  LF384699 - JP 2014500723-A/192202: Polycomb-Associated Non-Coding RNAs.
BC013017 - Homo sapiens CD63 molecule, mRNA (cDNA clone MGC:4528 IMAGE:3010594), complete cds.
BC071882 - Homo sapiens CD63 molecule, mRNA (cDNA clone IMAGE:6261964), **** WARNING: chimeric clone ****.
BC098441 - Homo sapiens CD63 molecule, mRNA (cDNA clone IMAGE:6089206), **** WARNING: chimeric clone ****.
BC001424 - Homo sapiens CD63 molecule, mRNA (cDNA clone IMAGE:3139551), **** WARNING: chimeric clone ****.
M58485 - Human lysosomal membrane glycoprotein CD63 mRNA.
LF343494 - JP 2014500723-A/150997: Polycomb-Associated Non-Coding RNAs.
M59907 - Homo sapiens melanoma-associated antigen (ME491) mRNA, complete cds.
X07982 - Human mRNA for melanoma-associated antigen ME491.
BC002349 - Homo sapiens CD63 molecule, mRNA (cDNA clone MGC:8339 IMAGE:2819554), complete cds.
S93788 - ocular melanoma-associated antigen [human, uveal melanoma, mRNA, 818 nt].
LF324522 - JP 2014500723-A/132025: Polycomb-Associated Non-Coding RNAs.
JD527270 - Sequence 508294 from Patent EP1572962.
AF508304 - Homo sapiens lysosome-associated membrane protein-3 variant mRNA, complete cds.
LF324521 - JP 2014500723-A/132024: Polycomb-Associated Non-Coding RNAs.
KJ896570 - Synthetic construct Homo sapiens clone ccsbBroadEn_05964 CD63 gene, encodes complete protein.
DQ891248 - Synthetic construct clone IMAGE:100003878; FLH176524.01X; RZPDo839E04122D CD63 molecule (CD63) gene, encodes complete protein.
BT007073 - Homo sapiens CD63 antigen (melanoma 1 antigen) mRNA, complete cds.
BT020137 - Homo sapiens CD63 antigen (melanoma 1 antigen) mRNA, complete cds.
BT020138 - Homo sapiens CD63 antigen (melanoma 1 antigen) mRNA, complete cds.
AK311893 - Homo sapiens cDNA, FLJ92159, Homo sapiens CD63 antigen (melanoma 1 antigen) (CD63), mRNA.
DQ894433 - Synthetic construct Homo sapiens clone IMAGE:100008893; FLH176520.01L; RZPDo839E04121D CD63 molecule (CD63) gene, encodes complete protein.
CR542096 - Homo sapiens full open reading frame cDNA clone RZPDo834C0837D for gene CD63, CD63 antigen (melanoma 1 antigen); complete cds, without stopcodon.
KF998086 - Homo sapiens CD63 (CD63) mRNA, partial cds.
AB529147 - Synthetic construct DNA, clone: pF1KB5195, Homo sapiens CD63 gene for CD63 molecule, without stop codon, in Flexi system.
LF343493 - JP 2014500723-A/150996: Polycomb-Associated Non-Coding RNAs.
LF343492 - JP 2014500723-A/150995: Polycomb-Associated Non-Coding RNAs.
LF324520 - JP 2014500723-A/132023: Polycomb-Associated Non-Coding RNAs.
LF343491 - JP 2014500723-A/150994: Polycomb-Associated Non-Coding RNAs.
LF324519 - JP 2014500723-A/132022: Polycomb-Associated Non-Coding RNAs.
LF343490 - JP 2014500723-A/150993: Polycomb-Associated Non-Coding RNAs.
LF324518 - JP 2014500723-A/132021: Polycomb-Associated Non-Coding RNAs.
LF324517 - JP 2014500723-A/132020: Polycomb-Associated Non-Coding RNAs.
LF324516 - JP 2014500723-A/132019: Polycomb-Associated Non-Coding RNAs.
LF343489 - JP 2014500723-A/150992: Polycomb-Associated Non-Coding RNAs.
LF324514 - JP 2014500723-A/132017: Polycomb-Associated Non-Coding RNAs.
LF343488 - JP 2014500723-A/150991: Polycomb-Associated Non-Coding RNAs.
JD468201 - Sequence 449225 from Patent EP1572962.
JD191285 - Sequence 172309 from Patent EP1572962.
MA620276 - JP 2018138019-A/192202: Polycomb-Associated Non-Coding RNAs.
MA579071 - JP 2018138019-A/150997: Polycomb-Associated Non-Coding RNAs.
MA560099 - JP 2018138019-A/132025: Polycomb-Associated Non-Coding RNAs.
MA560098 - JP 2018138019-A/132024: Polycomb-Associated Non-Coding RNAs.
MA579070 - JP 2018138019-A/150996: Polycomb-Associated Non-Coding RNAs.
MA579069 - JP 2018138019-A/150995: Polycomb-Associated Non-Coding RNAs.
MA560097 - JP 2018138019-A/132023: Polycomb-Associated Non-Coding RNAs.
MA579068 - JP 2018138019-A/150994: Polycomb-Associated Non-Coding RNAs.
MA560096 - JP 2018138019-A/132022: Polycomb-Associated Non-Coding RNAs.
MA579067 - JP 2018138019-A/150993: Polycomb-Associated Non-Coding RNAs.
MA560095 - JP 2018138019-A/132021: Polycomb-Associated Non-Coding RNAs.
MA560094 - JP 2018138019-A/132020: Polycomb-Associated Non-Coding RNAs.
MA560093 - JP 2018138019-A/132019: Polycomb-Associated Non-Coding RNAs.
MA579066 - JP 2018138019-A/150992: Polycomb-Associated Non-Coding RNAs.
MA560091 - JP 2018138019-A/132017: Polycomb-Associated Non-Coding RNAs.
MA579065 - JP 2018138019-A/150991: Polycomb-Associated Non-Coding RNAs.

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

Protein P08962 (Reactome details) participates in the following event(s):

R-HSA-481010 Surface deployment of platelet dense granule membrane components
R-HSA-6798739 Exocytosis of azurophil granule membrane proteins
R-HSA-114608 Platelet degranulation
R-HSA-6798695 Neutrophil degranulation
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-168249 Innate Immune System
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-168256 Immune System
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: CD63_HUMAN, ENST00000257857.1, ENST00000257857.2, ENST00000257857.3, ENST00000257857.4, ENST00000257857.5, ENST00000257857.6, ENST00000257857.7, ENST00000257857.8, F8VZE2, MLA1, NM_001780, P08962, Q5TZP3, Q8N6Z9, Q9UCG6, TSPAN30, uc317fzs.1, uc317fzs.2
UCSC ID: ENST00000257857.9_6
RefSeq Accession: NM_001780.6
Protein: P08962 (aka CD63_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.