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    SLC6A4 solute carrier family 6 member 4 [ Homo sapiens (human) ]

    Gene ID: 6532, updated on 13-Jan-2020

    Summary

    Official Symbol
    SLC6A4provided by HGNC
    Official Full Name
    solute carrier family 6 member 4provided by HGNC
    Primary source
    HGNC:HGNC:11050
    See related
    Ensembl:ENSG00000108576 MIM:182138
    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
    HTT; 5HTT; OCD1; SERT; 5-HTT; SERT1; hSERT; 5-HTTLPR
    Summary
    This gene encodes an integral membrane protein that transports the neurotransmitter serotonin from synaptic spaces into presynaptic neurons. The encoded protein terminates the action of serotonin and recycles it in a sodium-dependent manner. This protein is a target of psychomotor stimulants, such as amphetamines and cocaine, and is a member of the sodium:neurotransmitter symporter family. A repeat length polymorphism in the promoter of this gene has been shown to affect the rate of serotonin uptake. There have been conflicting results in the literature about the possible effect, if any, that this polymorphism may play in behavior and depression. [provided by RefSeq, May 2019]
    Expression
    Biased expression in lung (RPKM 18.0), small intestine (RPKM 13.9) and 3 other tissues See more
    Orthologs

    Genomic context

    See SLC6A4 in Genome Data Viewer
    Location:
    17q11.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    109.20191205 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (30194319..30235697, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (28521337..28562986, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene EF-hand calcium binding domain 5 Neighboring gene syntaxin 18 pseudogene 1 Neighboring gene microRNA 3184 Neighboring gene microRNA 423 Neighboring gene nuclear speckle splicing regulatory protein 1 Neighboring gene uncharacterized LOC107984991 Neighboring gene serotonin transporter intronic VNTR enhancer Neighboring gene solute carrier family 6 member 4 gene promoter Neighboring gene uncharacterized LOC105371720 Neighboring gene bleomycin hydrolase Neighboring gene RNA, U6 small nuclear 1267, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Anxiety
    MedGen: C0003467 OMIM: 607834 GeneReviews: Not available
    Compare labs
    Obsessive-compulsive disorder
    MedGen: C0028768 OMIM: 164230 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated (2012-05-10)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated (2012-05-10)

    ClinGen Genome Curation Page

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 clade B Tat up-regulates IDO and down-regulates 5-HTT gene and protein expressions in immature dendritic cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    Rab GTPase binding IPI
    Inferred from Physical Interaction
    more info
     
    actin filament binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cocaine binding IEA
    Inferred from Electronic Annotation
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    monoamine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nitric-oxide synthase binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    serotonin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    serotonin:sodium symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    serotonin:sodium symporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    serotonin:sodium symporter activity TAS
    Traceable Author Statement
    more info
     
    syntaxin-1 binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    brain morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular response to cGMP IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to retinoic acid IEA
    Inferred from Electronic Annotation
    more info
     
    circadian rhythm IEA
    Inferred from Electronic Annotation
    more info
     
    memory IEA
    Inferred from Electronic Annotation
    more info
     
    monoamine transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of cerebellar granule cell precursor proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of organ growth ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of synaptic transmission, dopaminergic IEA
    Inferred from Electronic Annotation
    more info
     
    neurotransmitter biosynthetic process TAS
    Traceable Author Statement
    more info
     
    positive regulation of cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of serotonin secretion IEA
    Inferred from Electronic Annotation
    more info
     
    protein complex oligomerization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein homooligomerization IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of thalamus size IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to drug IEA
    Inferred from Electronic Annotation
    more info
     
    response to estradiol IEA
    Inferred from Electronic Annotation
    more info
     
    response to hypoxia IEA
    Inferred from Electronic Annotation
    more info
     
    response to nutrient IEA
    Inferred from Electronic Annotation
    more info
     
    response to toxic substance IDA
    Inferred from Direct Assay
    more info
    PubMed 
    serotonin uptake IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    serotonin uptake IDA
    Inferred from Direct Assay
    more info
    PubMed 
    serotonin uptake IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    social behavior ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    sperm ejaculation IEA
    Inferred from Electronic Annotation
    more info
     
    transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    vasoconstriction IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    endomembrane system IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    focal adhesion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    integral component of postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of presynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    neuron projection IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    serotonergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    sodium-dependent serotonin transporter
    Names
    5-hydroxytryptamine (serotonin) transporter
    5HT transporter
    Na+/Cl- dependent serotonin transporter
    serotonin transporter 1
    solute carrier family 6 (neurotransmitter transporter), member 4
    solute carrier family 6 (neurotransmitter transporter, serotonin), member 4

    NCBI Reference Sequences (RefSeq)

    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

    1. NG_011747.2 RefSeqGene

      Range
      5240..46618
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001045.6NP_001036.1  sodium-dependent serotonin transporter

      See identical proteins and their annotated locations for NP_001036.1

      Status: REVIEWED

      Source sequence(s)
      AC104984, AK313166, AY902473, BE645279, DC345903
      Consensus CDS
      CCDS11256.1
      UniProtKB/Swiss-Prot
      P31645
      UniProtKB/TrEMBL
      B2R7Y7
      Related
      ENSP00000498537.1, ENST00000650711.1
      Conserved Domains (2) summary
      cd11513
      Location:79615
      SLC6sbd_SERT; Na(+)- and Cl(-)-dependent serotonin transporter SERT; solute-binding domain
      pfam03491
      Location:2464
      5HT_transport_N; Serotonin (5-HT) neurotransmitter transporter, N-terminus

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

      Range
      30194319..30235697 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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