CD9 CD9 molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CD9provided by HGNC
Official Full Name: CD9 moleculeprovided by HGNC
Primary source: HGNC:HGNC:1709
See related: Ensembl:ENSG00000010278 MIM:143030; AllianceGenome:HGNC:1709
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: MIC3; MRP-1; BTCC-1; DRAP-27; TSPAN29; TSPAN-29
Summary: 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]
Expression: Broad expression in esophagus (RPKM 210.8), prostate (RPKM 168.1) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p13.31

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (6199946..6238266)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (6207556..6245881)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (6309112..6347432)

Chromosome 12 - NC_000012.12 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 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?

CD9 promotes TbetaR2-TbetaR1 association driving the transition of human dermal fibroblasts to myofibroblast under hypoxia.
Title: CD9 promotes TβR2-TβR1 association driving the transition of human dermal fibroblasts to myofibroblast under hypoxia.
Immunohistochemical analysis of CD9, CD29 and epithelial to mesenchymal transition in triple-negative breast cancer.
Title: Immunohistochemical analysis of CD9, CD29 and epithelial to mesenchymal transition in triple-negative breast cancer.
CD9 shapes glucocorticoid sensitivity in pediatric B-cell precursor acute lymphoblastic leukemia.
Title: CD9 shapes glucocorticoid sensitivity in pediatric B-cell precursor acute lymphoblastic leukemia.
High expression of CD9 and Epidermal Growth Factor Receptor promotes the development of tongue cancer.
Title: High expression of CD9 and Epidermal Growth Factor Receptor promotes the development of tongue cancer.
CD9 co-operation with syndecan-1 is required for a major staphylococcal adhesion pathway.
Title: CD9 co-operation with syndecan-1 is required for a major staphylococcal adhesion pathway.
Prognostic implications of CD9 in childhood acute lymphoblastic leukemia: insights from a nationwide multicenter study in China.
Title: Prognostic implications of CD9 in childhood acute lymphoblastic leukemia: insights from a nationwide multicenter study in China.
Differential proteomics argues against a general role for CD9, CD81 or CD63 in the sorting of proteins into extracellular vesicles.
Title: Differential proteomics argues against a general role for CD9, CD81 or CD63 in the sorting of proteins into extracellular vesicles.
Small extracellular vesicles have distinct CD81 and CD9 tetraspanin expression profiles in plasma from rheumatoid arthritis patients.
Title: Small extracellular vesicles have distinct CD81 and CD9 tetraspanin expression profiles in plasma from rheumatoid arthritis patients.
Prognostic significance of tetraspanin CD9 and oncogenic epidermal growth factor receptor in tongue squamous cell carcinoma survival.
Title: Prognostic significance of tetraspanin CD9 and oncogenic epidermal growth factor receptor in tongue squamous cell carcinoma survival.
Lack of involvement of CD63 and CD9 tetraspanins in the extracellular vesicle content delivery process.
Title: Lack of involvement of CD63 and CD9 tetraspanins in the extracellular vesicle content delivery process.

Submit: New GeneRIF Correction See all GeneRIFs (159)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies ephrin type A receptors implicated in paclitaxel induced peripheral sensory neuropathy. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
New gene functions in megakaryopoiesis and platelet formation. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Recruitment of Env to tetraspanin-enriched micro domains (TEMs) is required for cell-cell fusion repression by CD9 and CD63	PubMed
	env	Tetraspanin proteins, such as CD9, CD63, CD81, CD82, and CD231, are incorporated on the membrane of released virions in an HIV-1 envelope protein (Env)-independent manner and have the potential to inhibit HIV-1 Env-mediated infection	PubMed
	env	Overexpression of CD81 and CD9 renders cells less susceptible to HIV-1 gp120/gp41-mediated syncytia formation; antibodies raised against CD9 and CD81 enhance syncytia formation	PubMed
Pr55(Gag)	gag	HIV-1 Gag recruits and traps CD9 to Gag assembly sites at the plasma membrane, which is dependent upon Gag polymerization and the presence of cholesterol	PubMed
	gag	HIV-1 Gag proteins co-localize with tetraspanins CD9, CD81, and CD82 in CD63-enriched micro domains	PubMed
	gag	Env-mediated cell-cell fusion repression by CD9 and CD63 requires the presence of HIV-1 Gag	PubMed
matrix	gag	HIV-1 MA co-localizes with CD9 in monocyte-derived macrophages	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-132041 (e-PCR)
- UniSTS:182539

G10611 (e-PCR)
- UniSTS:39698

A010B11 (e-PCR)
- UniSTS:44068

STS-M38690 (e-PCR)
- UniSTS:72251

D12S1887 (e-PCR)
- UniSTS:32084

RH44617 (e-PCR)
- UniSTS:50043

GDB:384746 (e-PCR)
- UniSTS:13450

G33070 (e-PCR)
- UniSTS:117646

SHGC-34900 (e-PCR)
- UniSTS:65429

D12S1005 (e-PCR)
- UniSTS:149946

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables integrin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to low-density lipoprotein particle stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in fusion of sperm to egg plasma membrane involved in single fertilization	IDA Inferred from Direct Assay more info	PubMed
involved_in glial cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in myoblast fusion involved in skeletal muscle regeneration	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of platelet aggregation	IDA Inferred from Direct Assay more info	PubMed
involved_in paranodal junction assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in platelet activation	NAS Non-traceable Author Statement more info	PubMed
involved_in receptor internalization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of macrophage migration	IEA Inferred from Electronic Annotation more info
involved_in sperm-egg recognition	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in clathrin-coated endocytic vesicle membrane	TAS Traceable Author Statement more info
located_in endocytic vesicle membrane	TAS Traceable Author Statement more info
located_in external side of plasma membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular exosome	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular space	HDA more info	PubMed
located_in extracellular vesicle	HDA more info	PubMed
located_in focal adhesion	HDA more info	PubMed
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info
located_in platelet alpha granule membrane	TAS Traceable Author Statement more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: CD9 antigen

Names: 5H9 antigen; BA-2/p24 antigen; CD9 antigen (p24); antigen CD9; cell growth-inhibiting gene 2 protein; leukocyte antigen MIC3; motility related protein-1; tetraspanin-29

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.

Genomic

NG_055677.1 RefSeqGene

Range

5694..43560

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1189

mRNA and Protein(s)

NM_001330312.2 → NP_001317241.1 CD9 antigen isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1. Variants 2 and 11-14 all encode the same isoform (2).

Source sequence(s)

AI003581, AL523128, X60111

Consensus CDS

CCDS81654.1

UniProtKB/TrEMBL

A6NNI4, B4DPP0

Related

ENSP00000494858.1, ENST00000642746.1

Conserved Domains (1) summary

cd03152
Location:42 → 124

CD9_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), CD9 family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans ...
NM_001413241.1 → NP_001400170.1 CD9 antigen isoform 3

Status: REVIEWED

Source sequence(s)

AC006057

UniProtKB/TrEMBL

A0A087WU13

Related

ENSP00000478288.2, ENST00000610354.5
NM_001413242.1 → NP_001400171.1 CD9 antigen isoform 4

Status: REVIEWED

Source sequence(s)

AC006057

UniProtKB/TrEMBL

G8JLH6

Related

ENSP00000371959.5, ENST00000382519.9
NM_001413243.1 → NP_001400172.1 CD9 antigen isoform 1

Status: REVIEWED

Source sequence(s)

AC006057

UniProtKB/Swiss-Prot

D3DUQ9, P21926, Q5J7W6, Q96ES4

Related

ENSP00000371958.1, ENST00000382518.6
NM_001413244.1 → NP_001400173.1 CD9 antigen isoform 5

Status: REVIEWED

Source sequence(s)

AC006057
NM_001413245.1 → NP_001400174.1 CD9 antigen isoform 6

Status: REVIEWED

Source sequence(s)

AC006057
NM_001413246.1 → NP_001400175.1 CD9 antigen isoform 7

Status: REVIEWED

Source sequence(s)

AC006057
NM_001413247.1 → NP_001400176.1 CD9 antigen isoform 8

Status: REVIEWED

Source sequence(s)

AC006057
NM_001413248.1 → NP_001400177.1 CD9 antigen isoform 9

Status: REVIEWED

Source sequence(s)

AC006057
NM_001413249.1 → NP_001400178.1 CD9 antigen isoform 2

Status: REVIEWED

Source sequence(s)

AC006057

UniProtKB/TrEMBL

A6NNI4

Related

ENST00000676788.1
NM_001413250.1 → NP_001400179.1 CD9 antigen isoform 2

Status: REVIEWED

Source sequence(s)

AC006057

UniProtKB/TrEMBL

A6NNI4
NM_001413251.1 → NP_001400180.1 CD9 antigen isoform 2

Status: REVIEWED

Source sequence(s)

AC006057

UniProtKB/TrEMBL

A6NNI4

Related

ENSP00000371955.2, ENST00000382515.7
NM_001413252.1 → NP_001400181.1 CD9 antigen isoform 2

Status: REVIEWED

Source sequence(s)

AC006057

UniProtKB/TrEMBL

A6NNI4

Related

ENSP00000495090.1, ENST00000646407.1
NM_001769.4 → NP_001760.1 CD9 antigen isoform 1

See identical proteins and their annotated locations for NP_001760.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1. Variants 1 and 5 both encode the same isoform (1).

Source sequence(s)

AI003581, BM763066, X60111

Consensus CDS

CCDS8540.1

UniProtKB/Swiss-Prot

D3DUQ9, P21926, Q5J7W6, Q96ES4

UniProtKB/TrEMBL

A0A7I2V3T7

Related

ENSP00000009180.4, ENST00000009180.10

Conserved Domains (2) summary

cd03152
Location:111 → 193

CD9_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), CD9 family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans ...

pfam00335
Location:10 → 217

Tetraspannin; Tetraspanin family

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_000012.12 Reference GRCh38.p14 Primary Assembly

Range

6199946..6238266

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005253814.5 → XP_005253871.1 CD9 antigen isoform X1

See identical proteins and their annotated locations for XP_005253871.1

UniProtKB/TrEMBL

B4DK09

Conserved Domains (2) summary

cl02781
Location:111 → 149

tetraspanin_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the ...

pfam00335
Location:9 → 147

Tetraspannin; Tetraspanin family