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Slc6a12 solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12 [ Mus musculus (house mouse) ]

Gene ID: 14411, updated on 12-May-2024

Summary

Official Symbol
Slc6a12provided by MGI
Official Full Name
solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12provided by MGI
Primary source
MGI:MGI:95628
See related
Ensembl:ENSMUSG00000030109 AllianceGenome:MGI:95628
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
BGT1; GAT2; BGT-1; GAT-2; Gabt2
Summary
Predicted to enable gamma-aminobutyric acid:sodium symporter activity. Predicted to be involved in cellular water homeostasis; monocarboxylic acid transport; and sodium ion transmembrane transport. Predicted to act upstream of or within neurotransmitter transport. Predicted to be integral component of membrane. Predicted to be active in neuron projection. Predicted to be integral component of plasma membrane. Is expressed in several structures, including central nervous system; eye; genitourinary system; gut; and liver and biliary system. Orthologous to human SLC6A12 (solute carrier family 6 member 12). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in liver adult (RPKM 40.1), placenta adult (RPKM 10.5) and 1 other tissue See more
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Genomic context

See Slc6a12 in Genome Data Viewer
Location:
6 F1; 6 57.25 cM
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (121319533..121342732)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (121342574..121365773)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:121222283-121222466 Neighboring gene predicted gene, 44148 Neighboring gene ubiquitin specific peptidase 18 Neighboring gene solute carrier family 6 (neurotransmitter transporter, GABA), member 13 Neighboring gene STARR-positive B cell enhancer ABC_E6482 Neighboring gene IQ motif and Sec7 domain 3 Neighboring gene STARR-seq mESC enhancer starr_17212 Neighboring gene STARR-seq mESC enhancer starr_17213 Neighboring gene voltage-dependent anion-selective channel protein 2 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Targeted (3)  1 citation

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Process Evidence Code Pubs
involved_in amino acid transport IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in gamma-aminobutyric acid transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in gamma-aminobutyric acid transport ISO
Inferred from Sequence Orthology
more info
 
involved_in glycine betaine transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in intracellular water homeostasis ISO
Inferred from Sequence Orthology
more info
 
involved_in monocarboxylic acid transport ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within neurotransmitter transport IEA
Inferred from Electronic Annotation
more info
 
involved_in neurotransmitter transport IEA
Inferred from Electronic Annotation
more info
 
involved_in sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
located_in basolateral plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cell projection IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
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 

General protein information

Preferred Names
sodium- and chloride-dependent betaine transporter
Names
Na(+)/Cl(-) betaine/GABA transporter
gamma-aminobutyric acid (GABA-A) transporter 2
sodium- and chloride-dependent GABA transporter 2
solute carrier family 6 member 12

NCBI Reference Sequences (RefSeq)

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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_001347433.1NP_001334362.1  sodium- and chloride-dependent betaine transporter isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and results in an isoform (2) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC153982
    Consensus CDS
    CCDS90118.1
    UniProtKB/Swiss-Prot
    P31651
    UniProtKB/TrEMBL
    G5E8Z4
    Related
    ENSMUSP00000126937.2, ENSMUST00000166457.8
    Conserved Domains (1) summary
    cl00456
    Location:35575
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. NM_001381903.1NP_001368832.1  sodium- and chloride-dependent betaine transporter isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC153982
    UniProtKB/Swiss-Prot
    P31651
    UniProtKB/TrEMBL
    G5E8Z4
    Conserved Domains (1) summary
    cl00456
    Location:35575
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  3. NM_001381904.1NP_001368833.1  sodium- and chloride-dependent betaine transporter isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC153982
    UniProtKB/Swiss-Prot
    P31651
    UniProtKB/TrEMBL
    G5E8Z4
    Conserved Domains (1) summary
    cl00456
    Location:35575
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  4. NM_001381905.1NP_001368834.1  sodium- and chloride-dependent betaine transporter isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC153982
    UniProtKB/Swiss-Prot
    P31651
    UniProtKB/TrEMBL
    G5E8Z4
    Conserved Domains (1) summary
    cl00456
    Location:35575
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  5. NM_001381906.1NP_001368835.1  sodium- and chloride-dependent betaine transporter isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC153982
    UniProtKB/Swiss-Prot
    P31651
    Conserved Domains (1) summary
    cl00456
    Location:49589
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  6. NM_133661.3NP_598422.2  sodium- and chloride-dependent betaine transporter isoform 1

    See identical proteins and their annotated locations for NP_598422.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC153982
    Consensus CDS
    CCDS39616.1
    UniProtKB/Swiss-Prot
    P31651
    UniProtKB/TrEMBL
    Q8VCS9
    Related
    ENSMUSP00000032200.10, ENSMUST00000032200.16
    Conserved Domains (1) summary
    cl00456
    Location:49589
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    121319533..121342732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006505536.1XP_006505599.1  sodium- and chloride-dependent betaine transporter isoform X1

    See identical proteins and their annotated locations for XP_006505599.1

    UniProtKB/Swiss-Prot
    P31651
    UniProtKB/TrEMBL
    G5E8Z4
    Related
    ENSMUSP00000126708.2, ENSMUST00000171008.8
    Conserved Domains (1) summary
    cl00456
    Location:35575
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain