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

Gene ID: 6540, updated on 13-Mar-2020

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
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
Expression
Biased expression in kidney (RPKM 28.5) and liver (RPKM 1.5) See more
Orthologs

Genomic context

See SLC6A13 in Genome Data Viewer
Location:
12p13.33
Exon count:
20
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 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 ArfGEF 3 Neighboring gene uncharacterized LOC105369592 Neighboring gene SLC6A12 antisense RNA 1 Neighboring gene solute carrier family 6 member 12 Neighboring gene uncharacterized LOC102723544 Neighboring gene lysine demethylase 5A Neighboring gene Sharpr-MPRA regulatory region 4015 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

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

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
gamma-aminobutyric acid 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
PubMed 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
integral component of plasma 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 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)

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_001243392.2NP_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
    Q9NSD5
    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: Homo sapiens Updated 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_000012.12 Reference GRCh38.p13 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_011521013.1XP_011519315.1  sodium- and chloride-dependent GABA transporter 2 isoform X3

    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
  3. XM_017019842.1XP_016875331.1  sodium- and chloride-dependent GABA transporter 2 isoform X2

  4. XM_006719008.3XP_006719071.1  sodium- and chloride-dependent GABA transporter 2 isoform X5

    Conserved Domains (1) summary
    cl00456
    Location:1332
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  5. XM_017019845.1XP_016875334.1  sodium- and chloride-dependent GABA transporter 2 isoform X5

    Conserved Domains (1) summary
    cl00456
    Location:1332
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  6. XM_017019844.1XP_016875333.1  sodium- and chloride-dependent GABA transporter 2 isoform X4

  7. XM_017019847.1XP_016875336.1  sodium- and chloride-dependent GABA transporter 2 isoform X6

  8. XM_017019846.1XP_016875335.1  sodium- and chloride-dependent GABA transporter 2 isoform X6

RNA

  1. XR_002957372.1 RNA Sequence

  2. XR_001748849.1 RNA Sequence

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