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    TSPAN16 tetraspanin 16 [ Homo sapiens (human) ]

    Gene ID: 26526, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TSPAN16provided by HGNC
    Official Full Name
    tetraspanin 16provided by HGNC
    Primary source
    HGNC:HGNC:30725
    See related
    Ensembl:ENSG00000130167 MIM:617580; AllianceGenome:HGNC:30725
    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
    TM-8; TM4-B; TM4SF16
    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. This encoded protein might couple to signal transduction pathways and possibly modulate cellular activation and adhesion in haemopoietic and neural tissue. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]
    Expression
    Restricted expression toward testis (RPKM 28.9) See more
    Orthologs
    all
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    Genomic context

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    See TSPAN16 in Genome Data Viewer
    Location:
    19p13.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (11296160..11326996)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (11423134..11453981)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (11406836..11437672)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene DOCK6 antisense RNA 1 Neighboring gene dedicator of cytokinesis 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11347000-11347810 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11347811-11348621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11354157-11354967 Neighboring gene angiopoietin like 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11363424-11364392 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11364393-11365361 Neighboring gene Sharpr-MPRA regulatory region 11176 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:11367378-11367534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10106 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:11408869-11409370 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:11409371-11409870 Neighboring gene uncharacterized HSPC102 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14008 Neighboring gene RAB3D, member RAS oncogene family Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11456465-11457295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11461146-11461646 Neighboring gene transmembrane protein 205 Neighboring gene coiled-coil domain containing 159

    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 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. The molecular characterisation of a novel tetraspanin protein, TM4-B(1). Puls KL, et al. Biochim Biophys Acta, 1999 Oct 6. PMID 10500248
    2. Cysteine Scanning Mutagenesis of TM4b-4c Loop of Glutamate Transporter EAAT1 Reveals Three Conformationally Sensitive Residues. Zhang W, et al. Mol Pharmacol, 2018 Jul. PMID 29654220
    3. Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci. Weissglas-Volkov D, et al. J Med Genet, 2013 May. PMID 23505323, Free PMC Article
    4. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Huttlin EL, et al. Cell, 2021 May 27. PMID 33961781, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. To probe the structural role of the TM4b-4c loop of EAAT1 (Rattus norvegicus), each of the 57 amino acid residues was mutated to cysteine.
      Title: Cysteine Scanning Mutagenesis of TM4b-4c Loop of Glutamate Transporter EAAT1 Reveals Three Conformationally Sensitive Residues.
    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
    Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
    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)

    Genotypes

    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

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    tetraspanin-16
    Names
    tetraspanin TM4-B
    transmembrane 4 superfamily member 16
    tspan-16

    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_001282509.2 → NP_001269438.1  tetraspanin-16 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AI688554, AW169944, BM560276, DB457828
      Consensus CDS
      CCDS62549.1
      UniProtKB/Swiss-Prot
      Q9UKR8
      Related
      ENSP00000467341.1, ENST00000590327.6
      Conserved Domains (2) summary
      cd03156
      Location:120 → 215
      uroplakin_I_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), uroplakin_I_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 ...
      pfam00335
      Location:19 → 240
      Tetraspannin; Tetraspanin family

    2. NM_001282510.2 → NP_001269439.1  tetraspanin-16 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus and lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AI688554, AW169944, BM560276, DB457828
      Consensus CDS
      CCDS62550.1
      UniProtKB/Swiss-Prot
      Q9UKR8
      Related
      ENSP00000466751.1, ENST00000592955.5
      Conserved Domains (2) summary
      cd03156
      Location:95 → 190
      uroplakin_I_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), uroplakin_I_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 ...
      pfam00335
      Location:19 → 215
      Tetraspannin; Tetraspanin family

    3. NM_012466.4 → NP_036598.1  tetraspanin-16 isoform 1

      See identical proteins and their annotated locations for NP_036598.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AF133424, DB457828
      Consensus CDS
      CCDS12256.1
      UniProtKB/Swiss-Prot
      K7EN22, K7EPD8, Q8N6J7, Q9UKR8
      Related
      ENSP00000319486.1, ENST00000316737.5
      Conserved Domains (2) summary
      cd03156
      Location:120 → 215
      uroplakin_I_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), uroplakin_I_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 ...
      pfam00335
      Location:19 → 232
      Tetraspannin; Tetraspanin family

    RNA

    1. NR_104199.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' end and uses an alternate splice junction at the 5' end of an exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI688554, AW169944, BC029908, DB457828
      Related
      ENST00000337994.5

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      11296160..11326996
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011527901.2 → XP_011526203.1  tetraspanin-16 isoform X1

      Conserved Domains (2) summary
      cd03156
      Location:120 → 201
      uroplakin_I_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), uroplakin_I_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 ...
      pfam00335
      Location:19 → 201
      Tetraspannin; Tetraspanin family

    2. XM_011527902.2 → XP_011526204.1  tetraspanin-16 isoform X2

      Conserved Domains (2) summary
      cl02781
      Location:115 → 179
      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:19 → 204
      Tetraspannin; Tetraspanin family

    3. XM_024451450.2 → XP_024307218.1  tetraspanin-16 isoform X3

      Conserved Domains (1) summary
      cd03156
      Location:95 → 176
      uroplakin_I_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), uroplakin_I_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 ...

    4. XM_011527903.4 → XP_011526205.1  tetraspanin-16 isoform X4

      Conserved Domains (2) summary
      cd03156
      Location:57 → 152
      uroplakin_I_like_LEL; Tetraspanin, extracellular domain or large extracellular loop (LEL), uroplakin_I_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 ...
      pfam00335
      Location:1 → 177
      Tetraspannin; Tetraspanin family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      11423134..11453981
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054320499.1 → XP_054176474.1  tetraspanin-16 isoform X1

    2. XM_054320500.1 → XP_054176475.1  tetraspanin-16 isoform X2

    3. XM_054320501.1 → XP_054176476.1  tetraspanin-16 isoform X3

    4. XM_054320502.1 → XP_054176477.1  tetraspanin-16 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UKR8.1 GenPept UniProtKB/Swiss-Prot:Q9UKR8

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