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SLC6A11 solute carrier family 6 member 11 [ Homo sapiens (human) ]

Gene ID: 6538, updated on 15-Jun-2019

Summary

Official Symbol
SLC6A11provided by HGNC
Official Full Name
solute carrier family 6 member 11provided by HGNC
Primary source
HGNC:HGNC:11044
See related
Ensembl:ENSG00000132164 MIM:607952
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
GAT3; GAT4; GAT-3
Summary
The protein encoded by this gene is a sodium-dependent transporter that uptakes gamma-aminobutyric acid (GABA), an inhibitory neurotransmitter, which ends the GABA neurotransmission. Defects in this gene may result in epilepsy, behavioral problems, or intellectual problems. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]
Expression
Biased expression in brain (RPKM 2.2), esophagus (RPKM 0.8) and 3 other tissues See more
Orthologs

Genomic context

See SLC6A11 in Genome Data Viewer
Location:
3p25.3
Exon count:
16
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (10816200..10940733)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (10857917..10980146)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATPase plasma membrane Ca2+ transporting 2 Neighboring gene ATP2B2 intronic transcript 2 Neighboring gene long intergenic non-protein coding RNA 606 Neighboring gene uncharacterized LOC105376950 Neighboring gene SLC6A1 antisense RNA 1 Neighboring gene solute carrier family 6 member 1 Neighboring gene uncharacterized LOC101927467

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis.
NHGRI GWA Catalog
Genome-wide Interrogation of Longitudinal FEV1 in Children with Asthma.
NHGRI GWA Catalog

Pathways from BioSystems

  • Creatine metabolism, organism-specific biosystem (from REACTOME)
    Creatine metabolism, organism-specific biosystemIn humans, creatine is synthesized primarily in the liver and kidney, from glycine, arginine, and S-adenosylmethionine, in a sequence of two reactions. From the liver, creatine is exported to tissues...
  • 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...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of amino acids and derivatives, organism-specific biosystem (from REACTOME)
    Metabolism of amino acids and derivatives, organism-specific biosystemThis group of reactions is responsible for: 1) the breakdown of amino acids; 2) the synthesis of urea from ammonia and amino groups generated by amino acid breakdown; 3) the synthesis of the ten amin...
  • Metabolism of polyamines, organism-specific biosystem (from REACTOME)
    Metabolism of polyamines, organism-specific biosystemPolyamines is a family of molecules (i.e. putrescine, spermine, spermidine) derived from ornithine according to a decarboxylation/condensative process. More recently, it has been demonstrated that ar...
  • 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...

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
gamma-aminobutyric acid:sodium symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neurotransmitter binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
brain development IEA
Inferred from Electronic Annotation
more info
 
gamma-aminobutyric acid transport IEA
Inferred from Electronic Annotation
more info
 
neurotransmitter reuptake IEA
Inferred from Electronic Annotation
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane TAS
Traceable Author Statement
more info
PubMed 
integral component of postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
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 TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
sodium- and chloride-dependent GABA transporter 3
Names
GABA transporter 3
solute carrier family 6 (neurotransmitter transporter), member 11
solute carrier family 6 (neurotransmitter transporter, GABA), member 11

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.

mRNA and Protein(s)

  1. NM_001317406.2NP_001304335.1  sodium- and chloride-dependent GABA transporter 3 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) is shorter at the C-terminus compared to isoform 1.
    Source sequence(s)
    AC018495, BC036083
    Consensus CDS
    CCDS82734.1
    UniProtKB/Swiss-Prot
    P48066
    Related
    ENSP00000404120.1, ENST00000454147.1
    Conserved Domains (1) summary
    cl00456
    Location:49208
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. NM_014229.3NP_055044.1  sodium- and chloride-dependent GABA transporter 3 isoform 1

    See identical proteins and their annotated locations for NP_055044.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC027128, AK312719, S75989
    Consensus CDS
    CCDS2602.1
    UniProtKB/Swiss-Prot
    P48066
    Related
    ENSP00000254488.2, ENST00000254488.7
    Conserved Domains (1) summary
    cd11508
    Location:49590
    SLC6sbd_GAT3; Na(+)- and Cl(-)-dependent GABA transporter 3; solute-binding domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    10816200..10940714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534033.2XP_011532335.1  sodium- and chloride-dependent GABA transporter 3 isoform X2

    Conserved Domains (1) summary
    cl00456
    Location:49374
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. XM_017007073.1XP_016862562.1  sodium- and chloride-dependent GABA transporter 3 isoform X1

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