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    SLC6A13 solute carrier family 6 member 13 [ Homo sapiens (human) ]

    Gene ID: 6540, updated on 7-May-2017
    Official Symbol
    SLC6A13provided by HGNC
    Official Full Name
    solute carrier family 6 member 13provided by HGNC
    Primary source
    HGNC:HGNC:11046
    See related
    Ensembl:ENSG00000010379 MIM:615097; Vega:OTTHUMG00000168053
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GAT2; GAT3; GAT-2
    Orthologs
    Location:
    12p13.33
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 12 NC_000012.12 (220621..262930, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (329787..372039, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene IQ motif and Sec7 domain 3 Neighboring gene uncharacterized LOC105369592 Neighboring gene uncharacterized LOC101929384 Neighboring gene solute carrier family 6 member 12 Neighboring gene uncharacterized LOC102723544 Neighboring gene lysine demethylase 5A Neighboring gene uncharacterized LOC105369594 Neighboring gene coiled-coil domain containing 77

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    NHGRI GWA Catalog
    Genetic determinants influencing human serum metabolome among African Americans.
    NHGRI GWA Catalog
    Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
    NHGRI GWA Catalog
    New loci associated with kidney function and chronic kidney disease.
    NHGRI GWA Catalog
    • GABA synthesis, release, reuptake and degradation, organism-specific biosystem (from REACTOME)
      GABA synthesis, release, reuptake and degradation, organism-specific biosystemGABA is a major inhibitory neurotransmitter in the mammalian central nervous system. GABA modulates neuronal excitability throughout the nervous system. Disruption of GABA neurotransmission leads to ...
    • GABAergic synapse, organism-specific biosystem (from KEGG)
      GABAergic synapse, organism-specific biosystemGamma aminobutyric acid (GABA) is the most abundant inhibitory neurotransmitter in the mammalian central nervous system (CNS). When released in the synaptic cleft, GABA binds to three major classes o...
    • GABAergic synapse, conserved biosystem (from KEGG)
      GABAergic synapse, conserved biosystemGamma aminobutyric acid (GABA) is the most abundant inhibitory neurotransmitter in the mammalian central nervous system (CNS). When released in the synaptic cleft, GABA binds to three major classes o...
    • NRF2 pathway, organism-specific biosystem (from WikiPathways)
      NRF2 pathway, organism-specific biosystemNRF2 is part of a group of transcription factors called nuclear receptors. It is activated under oxidative stress conditions and subsequently activates several antioxidative genes and proteins.
    • Na+/Cl- dependent neurotransmitter transporters, organism-specific biosystem (from REACTOME)
      Na+/Cl- dependent neurotransmitter transporters, organism-specific biosystemThe SLC6 gene family encodes proteins that mediate neurotransmitter uptake thus terminating a synaptic signal. The proteins mediate transport of GABA (gamma-aminobutyric acid), norepinephrine, dopami...
    • Neuronal System, organism-specific biosystem (from REACTOME)
      Neuronal System, organism-specific biosystemThe human brain contains at least 100 billion neurons, each with the ability to influence many other cells. Clearly, highly sophisticated and efficient mechanisms are needed to enable communication a...
    • Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
      Neurotransmitter Release Cycle, organism-specific biosystemNeurotransmitter is stored in the synaptic vesicle in the pre-synaptic terminal prior to its release in the synaptic cleft upon depolarization of the pre-synaptic membrane. The release of the neurotr...
    • Reuptake of GABA, organism-specific biosystem (from REACTOME)
      Reuptake of GABA, organism-specific biosystemReuptake of GABA from the synapse terminates the action of GABA thus regulating GABA action. GABA taken up from the synapse into the neurons is reused for synaptic loading. GABA taken up by astrocyte...
    • SLC-mediated transmembrane transport, organism-specific biosystem (from REACTOME)
      SLC-mediated transmembrane transport, organism-specific biosystemProteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the m...
    • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
      Transmembrane transport of small molecules, organism-specific biosystem
      Transmembrane transport of small molecules
    • Transmission across Chemical Synapses, organism-specific biosystem (from REACTOME)
      Transmission across Chemical Synapses, organism-specific biosystemChemical synapses are specialized junctions that are used for communication between neurons, neurons and muscle or gland cells. The synapse involves a pre-synaptic neuron and a post-synaptic neuron,...
    • Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds, organism-specific biosystem (from REACTOME)
      Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds, organism-specific biosystemHexoses like glucose, galactose and fructose serve as basic fuel molecules for eukaryotic cells. Indeed, glucose is the main energy source for mammalian cells. These sugars are unable to diffuse acro...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    gamma-aminobutyric acid:sodium symporter activity TAS
    Traceable Author Statement
    more info
     
    neurotransmitter:sodium symporter activity IEA
    Inferred from Electronic Annotation
    more info
     
    transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    gamma-aminobutyric acid transport IEA
    Inferred from Electronic Annotation
    more info
     
    neurotransmitter transport IEA
    Inferred from Electronic Annotation
    more info
     
    transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    Preferred Names
    sodium- and chloride-dependent GABA transporter 2
    Names
    GABA transport protein
    GABA transporter 2
    solute carrier family 6 (neurotransmitter transporter), member 13
    solute carrier family 6 (neurotransmitter transporter, GABA), member 13

    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_001190997.2NP_001177926.1  sodium- and chloride-dependent GABA transporter 2 isoform 2

      See identical proteins and their annotated locations for NP_001177926.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two consecutive exons in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK296127, DA374290, DB540466
      Consensus CDS
      CCDS53729.1
      UniProtKB/Swiss-Prot
      Q9NSD5
      Related
      ENSP00000407104.2, ENST00000445055.6
      Conserved Domains (1) summary
      cl00456
      Location:32483
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    2. NM_001243392.1NP_001230321.1  sodium- and chloride-dependent GABA transporter 2 isoform 3

      See identical proteins and their annotated locations for NP_001230321.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks a splice site and a large portion of the coding region, compared to variant 1. The encoded isoform (3) is significantly shorter and has a disctinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AI802118, BC020867, DA374290
      Consensus CDS
      CCDS58198.1
      UniProtKB/Swiss-Prot
      Q9NSD5
      Related
      ENSP00000389316.1, OTTHUMP00000237741, ENST00000436453.1, OTTHUMT00000397810
      Conserved Domains (1) summary
      cl00456
      Location:3268
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    3. NM_016615.4NP_057699.2  sodium- and chloride-dependent GABA transporter 2 isoform 1

      See identical proteins and their annotated locations for NP_057699.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK313511, BM662288, DA374290, DB540466
      Consensus CDS
      CCDS8502.1
      UniProtKB/Swiss-Prot
      Q9NSD5
      Related
      ENSP00000339260.4, OTTHUMP00000237738, ENST00000343164.8, OTTHUMT00000397801
      Conserved Domains (1) summary
      cd11507
      Location:32575
      SLC6sbd_GAT2; Na(+)- and Cl(-)-dependent GABA transporter 2; solute-binding domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p7 Primary Assembly

      Range
      220621..262930 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521012.2XP_011519314.1  sodium- and chloride-dependent GABA transporter 2 isoform X1

      Conserved Domains (1) summary
      cl00456
      Location:1456
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    2. XM_017019843.1XP_016875332.1  sodium- and chloride-dependent GABA transporter 2 isoform X3

    3. XM_011521013.1XP_011519315.1  sodium- and chloride-dependent GABA transporter 2 isoform X4

      See identical proteins and their annotated locations for XP_011519315.1

      Conserved Domains (1) summary
      cl00456
      Location:1413
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    4. XM_011521014.1XP_011519316.1  sodium- and chloride-dependent GABA transporter 2 isoform X4

      See identical proteins and their annotated locations for XP_011519316.1

      Conserved Domains (1) summary
      cl00456
      Location:1413
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    5. XM_017019842.1XP_016875331.1  sodium- and chloride-dependent GABA transporter 2 isoform X2

    6. XM_006719008.3XP_006719071.1  sodium- and chloride-dependent GABA transporter 2 isoform X6

      Conserved Domains (1) summary
      cl00456
      Location:1332
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    7. XM_017019845.1XP_016875334.1  sodium- and chloride-dependent GABA transporter 2 isoform X6

      Conserved Domains (1) summary
      cl00456
      Location:1332
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    8. XM_017019844.1XP_016875333.1  sodium- and chloride-dependent GABA transporter 2 isoform X5

    9. XM_017019847.1XP_016875336.1  sodium- and chloride-dependent GABA transporter 2 isoform X7

    10. XM_017019846.1XP_016875335.1  sodium- and chloride-dependent GABA transporter 2 isoform X7

    RNA

    1. XR_001748849.1 RNA Sequence

    2. XR_001748850.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018923.2 Alternate CHM1_1.1

      Range
      328777..371038 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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