Human Gene CD9 (ENST00000382518.6)
  Description: Involved in platelet activation and aggregation. Regulates paranodal junction formation. Involved in cell adhesion, cell motility and tumor metastasis. Required for sperm-egg fusion. (from UniProt P21926)
RefSeq Summary (NM_001769): This gene encodes a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Tetraspanins are cell surface glycoproteins with four transmembrane domains that form multimeric complexes with other cell surface proteins. The encoded protein functions in many cellular processes including differentiation, adhesion, and signal transduction, and expression of this gene plays a critical role in the suppression of cancer cell motility and metastasis. [provided by RefSeq, Jan 2011].
Gencode Transcript: ENST00000382518.6
Gencode Gene: ENSG00000010278.15
Transcript (Including UTRs)
   Position: hg38 chr12:6,199,715-6,238,271 Size: 38,557 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg38 chr12:6,200,500-6,237,828 Size: 37,329 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2021-01-14 15:32:12

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:6,199,715-6,238,271)mRNA (may differ from genome)Protein (228 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=CD9 antigen; AltName: Full=5H9 antigen; AltName: Full=Cell growth-inhibiting gene 2 protein; AltName: Full=Leukocyte antigen MIC3; AltName: Full=Motility-related protein; Short=MRP-1; AltName: Full=Tetraspanin-29; Short=Tspan-29; AltName: Full=p24; AltName: CD_antigen=CD9;
FUNCTION: Involved in platelet activation and aggregation. Regulates paranodal junction formation. Involved in cell adhesion, cell motility and tumor metastasis. Required for sperm-egg fusion.
SUBUNIT: Forms both disulfide-linked homodimers and higher homooligomers as well as heterooligomers with other members of the tetraspanin family. Associates with CR2/CD21 and with PTGFRN/CD9P1. Interacts directly with IGSF8.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed by a variety of hematopoietic and epithelial cells.
PTM: Protein exists in three forms with molecular masses between 22 and 27 kDa, and is known to carry covalently linked fatty acids.
SIMILARITY: Belongs to the tetraspanin (TM4SF) family.
WEB RESOURCE: Name=SeattleSNPs; URL="";

-  MalaCards Disease Associations
  MalaCards Gene Search: CD9
Diseases sorted by gene-association score: cytomegalovirus retinitis (16), enterocele (15), prolapse of female genital organ (15), diphtheria (14), hemangioma of spleen (11), testicular leukemia (11), pediatric lymphoma (6), hemangioma of intra-abdominal structure (6), glanzmann thrombasthenia (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 205.58 RPKM in Esophagus - Mucosa
Total median expression: 2915.63 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 -142.70436-0.327 Picture PostScript Text
3' UTR -89.90443-0.203 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
IPR023396 - CD81_extracellular
IPR000301 - Tetraspanin
IPR018499 - Tetraspanin/Peripherin
IPR018503 - Tetraspanin_CS
IPR008952 - Tetraspanin_EC2

Pfam Domains:
PF00335 - Tetraspanin family

ModBase Predicted Comparative 3D Structure on P21926
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005178 integrin binding
GO:0005515 protein binding

Biological Process:
GO:0002576 platelet degranulation
GO:0007155 cell adhesion
GO:0007166 cell surface receptor signaling pathway
GO:0007338 single fertilization
GO:0007342 fusion of sperm to egg plasma membrane
GO:0007420 brain development
GO:0008285 negative regulation of cell proliferation
GO:0009414 response to water deprivation
GO:0014003 oligodendrocyte development
GO:0030168 platelet activation
GO:0030913 paranodal junction assembly
GO:0031623 receptor internalization
GO:0051271 negative regulation of cellular component movement
GO:0071404 cellular response to low-density lipoprotein particle stimulus
GO:0090331 negative regulation of platelet aggregation

Cellular Component:
GO:0005615 extracellular space
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005925 focal adhesion
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016324 apical plasma membrane
GO:0030666 endocytic vesicle membrane
GO:0030669 clathrin-coated endocytic vesicle membrane
GO:0031092 platelet alpha granule membrane
GO:0070062 extracellular exosome
GO:1903561 extracellular vesicle

-  Descriptions from all associated GenBank mRNAs
  AK311020 - Homo sapiens cDNA, FLJ18062.
LF207403 - JP 2014500723-A/14906: Polycomb-Associated Non-Coding RNAs.
MA442980 - JP 2018138019-A/14906: Polycomb-Associated Non-Coding RNAs.
AK315219 - Homo sapiens cDNA, FLJ96215.
AK308700 - Homo sapiens cDNA, FLJ98741.
AK296332 - Homo sapiens cDNA FLJ56697 complete cds, highly similar to CD9 antigen.
AK309527 - Homo sapiens cDNA, FLJ99568.
X60111 - H.sapiens mRNA for MRP-1.
AY966455 - Homo sapiens bladder cancer related CD9 variant (BTCC-1) mRNA, complete cds.
AK296894 - Homo sapiens cDNA FLJ60662 complete cds, moderately similar to CD9 antigen.
AK298431 - Homo sapiens cDNA FLJ51032 complete cds, highly similar to CD9 antigen.
LF365970 - JP 2014500723-A/173473: Polycomb-Associated Non-Coding RNAs.
MA601547 - JP 2018138019-A/173473: Polycomb-Associated Non-Coding RNAs.
JD085579 - Sequence 66603 from Patent EP1572962.
AB079244 - Homo sapiens mRNA for 5H9 antigen, complete cds.
M38690 - Human CD9 antigen mRNA, complete cds.
BC011988 - Homo sapiens CD9 molecule, mRNA (cDNA clone MGC:9067 IMAGE:3860667), complete cds.
JD129891 - Sequence 110915 from Patent EP1572962.
AY423720 - Homo sapiens growth-inhibiting gene 2 protein mRNA, complete cds.
DQ894498 - Synthetic construct Homo sapiens clone IMAGE:100008958; FLH171012.01L; RZPDo839E0299D CD9 molecule (CD9) gene, encodes complete protein.
DQ891314 - Synthetic construct clone IMAGE:100003944; FLH171016.01X; RZPDo839E02100D CD9 molecule (CD9) gene, encodes complete protein.
AB590218 - Synthetic construct DNA, clone: pFN21AE1546, Homo sapiens CD9 gene for CD9 molecule, without stop codon, in Flexi system.
CU680148 - Synthetic construct Homo sapiens gateway clone IMAGE:100016823 5' read CD9 mRNA.
KJ896563 - Synthetic construct Homo sapiens clone ccsbBroadEn_05957 CD9 gene, encodes complete protein.
E05732 - cDNA encoding a metastasis related protein.
L34068 - Human antigen (p24/CD9) mRNA, complete cds.
HM245393 - Homo sapiens CDKN1A-CD9 breakpoint junction mRNA sequence.
LF365948 - JP 2014500723-A/173451: Polycomb-Associated Non-Coding RNAs.
MA601525 - JP 2018138019-A/173451: Polycomb-Associated Non-Coding RNAs.
LF365942 - JP 2014500723-A/173445: Polycomb-Associated Non-Coding RNAs.
MA601519 - JP 2018138019-A/173445: Polycomb-Associated Non-Coding RNAs.
LF365940 - JP 2014500723-A/173443: Polycomb-Associated Non-Coding RNAs.
MA601517 - JP 2018138019-A/173443: Polycomb-Associated Non-Coding RNAs.
JD406579 - Sequence 387603 from Patent EP1572962.
LF365939 - JP 2014500723-A/173442: Polycomb-Associated Non-Coding RNAs.
MA601516 - JP 2018138019-A/173442: Polycomb-Associated Non-Coding RNAs.
LF365938 - JP 2014500723-A/173441: Polycomb-Associated Non-Coding RNAs.
MA601515 - JP 2018138019-A/173441: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04640 - Hematopoietic cell lineage

Reactome (by CSHL, EBI, and GO)

Protein P21926 (Reactome details) participates in the following event(s):

R-HSA-1297275 CD9:Izumo Binding
R-HSA-5336417 DT A:B binds HBEGF and CD9 on the target cell surface
R-HSA-481044 Surface deployment of platelet alpha granule membrane components
R-HSA-1300652 Sperm:Oocyte Membrane Binding
R-HSA-5336415 Uptake and function of diphtheria toxin
R-HSA-114608 Platelet degranulation
R-HSA-1187000 Fertilization
R-HSA-5339562 Uptake and actions of bacterial toxins
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-1474165 Reproduction
R-HSA-5663205 Infectious disease
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-1643685 Disease
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: AY966455, CD9_HUMAN, D3DUQ9, ENST00000382518.1, ENST00000382518.2, ENST00000382518.3, ENST00000382518.4, ENST00000382518.5, GIG2, MIC3, P21926, Q5J7W6, Q96ES4, TSPAN29, uc058kcc.1, uc058kcc.2
UCSC ID: ENST00000382518.6
RefSeq Accession: NM_001769
Protein: P21926 (aka CD9_HUMAN)
CCDS: CCDS8540.1

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