Slc6a12 solute carrier family 6 member 12 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Slc6a12provided by RGD
Official Full Name: solute carrier family 6 member 12provided by RGD
Primary source: RGD:620255
See related: Ensembl:ENSRNOG00000013547 AllianceGenome:RGD:620255
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: BGT1; Gat1; VGAT; RNU28927
Summary: Predicted to enable gamma-aminobutyric acid:sodium symporter activity. Involved in cellular hyperosmotic response; cellular water homeostasis; and response to organic substance. Is integral component of membrane. Orthologous to human SLC6A12 (solute carrier family 6 member 12). [provided by Alliance of Genome Resources, Apr 2022]
Annotation information: Annotation category: suggests misassembly
Expression: Biased expression in Liver (RPKM 124.6), Kidney (RPKM 42.7) and 2 other tissues See more
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Genomic context

Location:: 4q42

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (156257518..156275870)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (154585386..154603750)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (153921199..153941333)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Changes in vesicular glutamate transporter 2 (Vglut2) and vesicular GABA transporter 1 (Vgat1) in the orofacial pain and temperature perception pathway under low estrogen conditions.
Title: Changes in vesicular glutamate transporter 2 (Vglut2) and vesicular GABA transporter 1 (Vgat1) in the orofacial pain and temperature perception pathway under low estrogen conditions.
GAT-1, which is predominantly presynaptically located, is the major GABA transporter in the hippocampus under baseline, quiescent conditions.
Title: A functional role for both -aminobutyric acid (GABA) transporter-1 and GABA transporter-3 in the modulation of extracellular GABA and GABAergic tonic conductances in the rat hippocampus.
we report the identification of a unique amino acid motif in the vesicular GABA transporter (VGAT) that controls its synaptic localization and activity-dependent recycling
Title: Sorting of the vesicular GABA transporter to functional vesicle pools by an atypical dileucine-like motif.
The results demonstrate a malfunction of GAT-1 in thalamic astrocytes of a well-established genetic model of absence epilepsy, and indicate that this abnormality is not a reflection of a general pathology affecting all astrocytic functions.
Title: Astrocytic GABA transporter GAT-1 dysfunction in experimental absence seizures.
This study provides evidence that the GAT-1-mediated regulation of extracellular GABA can modulate glutamatergic transmission at the subthalamopallidal synapse in the rat globus pallidus.
Title: GABA transporter subtype 1 and GABA transporter subtype 3 modulate glutamatergic transmission via activation of presynaptic GABA(B) receptors in the rat globus pallidus.
BDNF enhances the time span of GAT-1 molecules at the plasma membrane of astrocytes.
Title: Brain-derived neurotrophic factor (BDNF) enhances GABA transport by modulating the trafficking of GABA transporter-1 (GAT-1) from the plasma membrane of rat cortical astrocytes.
These experiments confirmed that, when a high concentration of GABA is present in the cytoplasm, GAT1 can operate in reverse mode. The reverse transport was affected by the the internal concentrations of Na+ and Cl-.
Title: GABA reverse transport by the neuronal cotransporter GAT1: influence of internal chloride depletion.
Data indicate that GAT-1 and GAT-3 represent different target sites through which GABA reuptake may subserve complementary regulation of GABAergic transmission in the rat globus pallidus.
Title: Differential localization and function of GABA transporters, GAT-1 and GAT-3, in the rat globus pallidus.
Excessive expression of GAT-1 as well as GAT-3 and GABA receptor alpha1 subunits in hippocampal tremor may provide potential therapeutic targets for genetic epilepsy.
Title: Up-regulation of GABA transporters and GABA(A) receptor α1 subunit in tremor rat hippocampus.
The GABA transporter GAT-1 is upregulated with no change in GAT-3 or glutamate transporters.
Title: Upregulation of the GABA transporter GAT-1 in the gracile nucleus in the spared nerve injury model of neuropathic pain.

Submit: New GeneRIF Correction See all GeneRIFs (26)

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables gamma-aminobutyric acid:sodium:chloride symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables gamma-aminobutyric acid:sodium:chloride symporter activity	IEA Inferred from Electronic Annotation more info
enables gamma-aminobutyric acid:sodium:chloride symporter activity	ISO Inferred from Sequence Orthology more info
enables gamma-aminobutyric acid:sodium:chloride symporter activity	ISS Inferred from Sequence or Structural Similarity more info
enables gamma-aminobutyric acid:sodium:chloride symporter activity	TAS Traceable Author Statement more info	PubMed
enables monocarboxylic acid transmembrane transporter activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in amino acid transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular hyperosmotic response	IEP Inferred from Expression Pattern more info	PubMed
involved_in gamma-aminobutyric acid transport	IEA Inferred from Electronic Annotation more info
involved_in gamma-aminobutyric acid transport	ISO Inferred from Sequence Orthology more info
involved_in gamma-aminobutyric acid transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycine betaine transport	ISO Inferred from Sequence Orthology more info
involved_in glycine betaine transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular water homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in monocarboxylic acid transport	ISO Inferred from Sequence Orthology more info
involved_in neurotransmitter transport	IEA Inferred from Electronic Annotation more info
involved_in neurotransmitter transport	TAS Traceable Author Statement more info	PubMed
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in basolateral plasma membrane	ISO Inferred from Sequence Orthology more info
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 lateral plasma 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	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: sodium- and chloride-dependent betaine transporter

Names: Betaine/GABA transporter 1; GABA transporter 1; Na(+)/Cl(-) betaine/GABA transporter; solute carrier family 6 (neurotransmitter transporter), member 12; solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12; vesicular GABA transporter

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)

NM_017335.1 → NP_059031.1 sodium- and chloride-dependent betaine transporter

See identical proteins and their annotated locations for NP_059031.1

Status: PROVISIONAL

Source sequence(s)

U28927

UniProtKB/Swiss-Prot

P48056

UniProtKB/TrEMBL

A6ILC6

Related

ENSRNOP00000018821.3, ENSRNOT00000018821.5

Conserved Domains (1) summary

cl00456
Location:49 → 589

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain