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    TSPAN9 tetraspanin 9 [ Homo sapiens (human) ]

    Gene ID: 10867, updated on 27-Nov-2024

    Summary

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    Official Symbol
    TSPAN9provided by HGNC
    Official Full Name
    tetraspanin 9provided by HGNC
    Primary source
    HGNC:HGNC:21640
    See related
    Ensembl:ENSG00000011105 MIM:613137; AllianceGenome:HGNC:21640
    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
    NET5; NET-5; PP1057
    Summary
    The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. Alternatively spliced transcripts encoding the same protein have been identified. [provided by RefSeq, Nov 2009]
    Expression
    Broad expression in heart (RPKM 31.5), placenta (RPKM 20.4) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TSPAN9 in Genome Data Viewer
    Location:
    12p13.33-p13.32
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (3077379..3286559)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (3083510..3293033)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (3186545..3395725)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902859 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:3068733-3069468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3073099-3073924 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:3075837-3076336 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3090196-3090815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3100825-3101326 Neighboring gene Sharpr-MPRA regulatory region 741 Neighboring gene TEA domain transcription factor 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3112529-3113410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3122802-3123643 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3141331-3141892 Neighboring gene Sharpr-MPRA regulatory region 13344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4139 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3192842-3193517 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3193518-3194192 Neighboring gene Sharpr-MPRA regulatory region 10584 Neighboring gene ribosomal protein L13a pseudogene 24 Neighboring gene Sharpr-MPRA regulatory region 6988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3244823-3245324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3245325-3245824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3245886-3246736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3257812-3258357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3260221-3261034 Neighboring gene TSPAN9 intronic transcript 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:3271635-3272136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3277658-3278241 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3278242-3278824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3281002-3281760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3281761-3282518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3297721-3298231 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3306798-3307336 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3307337-3307874 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3323859-3324398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3336210-3336725 Neighboring gene uncharacterized LOC124902861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3340427-3341425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3344565-3345246 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3345247-3345928 Neighboring gene ribosomal protein S27 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3351329-3352214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3352304-3352804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3373683-3374271 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:3373093-3373682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3393392-3393892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3393893-3394393 Neighboring gene uncharacterized LOC100128253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5817 Neighboring gene Sharpr-MPRA regulatory region 1542 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:3421757-3422956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4140 Neighboring gene long intergenic non-protein coding RNA 2827 Neighboring gene tetraspanin 11 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3435715-3436214 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:3443867-3445066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3474236-3474788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:3474789-3475339 Neighboring gene long intergenic non-protein coding RNA 2417

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Genome-wide association study of degenerative bony changes of the temporomandibular joint. Yamaguchi T, et al. Oral Dis, 2014 May. PMID 23746317
    2. Role of TSPAN9 in Alphavirus Entry and Early Endosomes. Stiles KM, et al. J Virol, 2016 May. PMID 26865714, Free PMC Article
    3. Tspan9 inhibits the proliferation, migration and invasion of human gastric cancer SGC7901 cells via the ERK1/2 pathway. Li PY, et al. Oncol Rep, 2016 Jul. PMID 27177197
    4. TSPAN9 and EMILIN1 synergistically inhibit the migration and invasion of gastric cancer cells by increasing TSPAN9 expression. Qi Y, et al. BMC Cancer, 2019 Jun 26. PMID 31242895, Free PMC Article
    5. Functional relevance of tetraspanin CD9 in vascular smooth muscle cell injury phenotypes: a novel target for the prevention of neointimal hyperplasia. Kotha J, et al. Atherosclerosis, 2009 Apr. PMID 18799160

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. expression of the membrane protein TSPAN9 regulates gastric cancer cell migration and invasion by inhibiting the FAK-RAS-ERK1/2 signaling pathway. The extracellular secretory protein EMILIN1 can increase this tumor suppressive effect by promoting the expression of TSPAN9.
      Title: TSPAN9 and EMILIN1 synergistically inhibit the migration and invasion of gastric cancer cells by increasing TSPAN9 expression.
    2. The proliferation, migration and invasion of human gastric cancer SGC7901 cells were significantly inhibited by overexpression of Tspan9.
      Title: Tspan9 inhibits the proliferation, migration and invasion of human gastric cancer SGC7901 cells via the ERK1/2 pathway.
    3. TSPAN9 is an endosomal tetraspanin whose depletion has a pronounced effect on the entry of several viruses that fuse in the early endosome.
      Title: Role of TSPAN9 in Alphavirus Entry and Early Endosomes.
    4. tetraspanin CD9 has a role in determining vascular smooth muscle cell injury phenotypes
      Title: Functional relevance of tetraspanin CD9 in vascular smooth muscle cell injury phenotypes: a novel target for the prevention of neointimal hyperplasia.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    6. Findings suggest a role for Tspan9 in regulating platelet function in concert with other platelet tetraspanins and their associated proteins.
      Title: Identification of Tspan9 as a novel platelet tetraspanin and the collagen receptor GPVI as a component of tetraspanin microdomains.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
    EBI GWAS Catalog
    Genome-wide association study of degenerative bony changes of the temporomandibular joint.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in focal adhesion HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in tetraspanin-enriched microdomain IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    tetraspanin-9
    Names
    new EST tetraspan 5
    tetraspan NET-5
    transmembrane 4 superfamily member tetraspan NET-5
    tspan-9

    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)

    1. NM_001168320.2 → NP_001161792.1  tetraspanin-9

      See identical proteins and their annotated locations for NP_001161792.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC005865, AC005912, AC125807
      Consensus CDS
      CCDS8520.1
      UniProtKB/Swiss-Prot
      D3DUQ7, O75954, Q53FV2, Q6FGJ8
      UniProtKB/TrEMBL
      B5MD23
      Related
      ENSP00000444799.1, ENST00000537971.5
      Conserved Domains (2) summary
      cd03165
      Location:105 → 202
      NET-5_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), NET-5_like 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 ...
      pfam00335
      Location:9 → 226
      Tetraspannin; Tetraspanin family

    2. NM_006675.5 → NP_006666.1  tetraspanin-9

      See identical proteins and their annotated locations for NP_006666.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC005865, AC005912, AC125807, BC071881
      Consensus CDS
      CCDS8520.1
      UniProtKB/Swiss-Prot
      D3DUQ7, O75954, Q53FV2, Q6FGJ8
      UniProtKB/TrEMBL
      B5MD23
      Related
      ENSP00000011898.5, ENST00000011898.10
      Conserved Domains (2) summary
      cd03165
      Location:105 → 202
      NET-5_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), NET-5_like 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 ...
      pfam00335
      Location:9 → 226
      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

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      3077379..3286559
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428125.1 → XP_047284081.1  tetraspanin-9 isoform X2

      UniProtKB/Swiss-Prot
      D3DUQ7, O75954, Q53FV2, Q6FGJ8

    2. XM_047428128.1 → XP_047284084.1  tetraspanin-9 isoform X3

    3. XM_047428127.1 → XP_047284083.1  tetraspanin-9 isoform X3

    4. XM_011520912.4 → XP_011519214.1  tetraspanin-9 isoform X3

      See identical proteins and their annotated locations for XP_011519214.1

      Conserved Domains (2) summary
      cd03165
      Location:41 → 138
      NET-5_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), NET-5_like 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 ...
      pfam00335
      Location:1 → 166
      Tetraspannin; Tetraspanin family

    5. XM_047428126.1 → XP_047284082.1  tetraspanin-9 isoform X2

      UniProtKB/Swiss-Prot
      D3DUQ7, O75954, Q53FV2, Q6FGJ8

    6. XM_047428124.1 → XP_047284080.1  tetraspanin-9 isoform X1

    7. XM_047428130.1 → XP_047284086.1  tetraspanin-9 isoform X3

    8. XM_047428129.1 → XP_047284085.1  tetraspanin-9 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      3083510..3293033
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370833.1 → XP_054226808.1  tetraspanin-9 isoform X2

      UniProtKB/Swiss-Prot
      D3DUQ7, O75954, Q53FV2, Q6FGJ8

    2. XM_054370834.1 → XP_054226809.1  tetraspanin-9 isoform X2

      UniProtKB/Swiss-Prot
      D3DUQ7, O75954, Q53FV2, Q6FGJ8

    3. XM_054370838.1 → XP_054226813.1  tetraspanin-9 isoform X3

    4. XM_054370837.1 → XP_054226812.1  tetraspanin-9 isoform X3

    5. XM_054370836.1 → XP_054226811.1  tetraspanin-9 isoform X3

    6. XM_054370835.1 → XP_054226810.1  tetraspanin-9 isoform X2

      UniProtKB/Swiss-Prot
      D3DUQ7, O75954, Q53FV2, Q6FGJ8

    7. XM_054370839.1 → XP_054226814.1  tetraspanin-9 isoform X4

    RNA

    1. XR_008488508.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75954.1 GenPept UniProtKB/Swiss-Prot:O75954

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    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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