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

    Gene ID: 6540, updated on 27-Nov-2024

    Summary

    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; AllianceGenome:HGNC:11046
    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
    Summary
    Enables gamma-aminobutyric acid:sodium:chloride symporter activity. Involved in amino acid import across plasma membrane and monocarboxylic acid transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in kidney (RPKM 28.5) and liver (RPKM 1.5) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC6A13 in Genome Data Viewer
    Location:
    12p13.33
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (220622..262836, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (217551..259667, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (329788..372002, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene IQ motif and Sec7 domain ArfGEF 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:277504-277977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:282005-282530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:282531-283057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:283058-283583 Neighboring gene IQSEC3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:287986-288528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:291153-291654 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:294419-294609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4100 Neighboring gene SLC6A12 antisense RNA 1 Neighboring gene solute carrier family 6 member 12 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:320888-321660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:322433-323204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:329915-330870 Neighboring gene uncharacterized LOC102723544 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:415875-417074 Neighboring gene lysine demethylase 5A Neighboring gene Sharpr-MPRA regulatory region 4015 Neighboring gene uncharacterized LOC105369594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5778 Neighboring gene coiled-coil domain containing 77

    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

    EBI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Genetic determinants influencing human serum metabolome among African Americans.
    EBI GWAS Catalog
    Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
    EBI GWAS Catalog
    New loci associated with kidney function and chronic kidney disease.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in amino acid import across plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in amino acid transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in creatine transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in gamma-aminobutyric acid import ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in gamma-aminobutyric acid reuptake TAS
    Traceable Author Statement
    more info
     
    involved_in monocarboxylic acid transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of nitrogen compound transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nitrogen compound transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sodium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in taurine transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in basolateral plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in cell projection IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular exosome 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 plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001190997.3NP_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, 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_001243392.2NP_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
      Consensus CDS
      CCDS58198.1
      UniProtKB/Swiss-Prot
      Q9NSD5
      Related
      ENSP00000389316.1, ENST00000436453.1
      Conserved Domains (1) summary
      cl00456
      Location:3268
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    3. NM_016615.5NP_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
      B4DJL1, Q8TCC2, Q8WW56, Q9NSD5
      UniProtKB/TrEMBL
      B4DJS3
      Related
      ENSP00000339260.4, ENST00000343164.9
      Conserved Domains (1) summary
      cd11507
      Location:32575
      SLC6sbd_GAT2; Na(+)- and Cl(-)-dependent GABA transporter 2; solute-binding domain

    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
      220622..262836 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047429420.1XP_047285376.1  sodium- and chloride-dependent GABA transporter 2 isoform X2

    2. XM_017019845.2XP_016875334.1  sodium- and chloride-dependent GABA transporter 2 isoform X3

      Conserved Domains (1) summary
      cl00456
      Location:1332
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    3. XM_006719008.4XP_006719071.1  sodium- and chloride-dependent GABA transporter 2 isoform X3

      Conserved Domains (1) summary
      cl00456
      Location:1332
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    4. XM_017019842.2XP_016875331.1  sodium- and chloride-dependent GABA transporter 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      217551..259667 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373005.1XP_054228980.1  sodium- and chloride-dependent GABA transporter 2 isoform X2

    2. XM_054373004.1XP_054228979.1  sodium- and chloride-dependent GABA transporter 2 isoform X1

    3. XM_054373007.1XP_054228982.1  sodium- and chloride-dependent GABA transporter 2 isoform X3

    4. XM_054373006.1XP_054228981.1  sodium- and chloride-dependent GABA transporter 2 isoform X3