Slc6a1 solute carrier family 6 member 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Slc6a1provided by RGD
Official Full Name: solute carrier family 6 member 1provided by RGD
Primary source: RGD:620533
See related: EnsemblRapid:ENSRNOG00000006527 AllianceGenome:RGD:620533
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: Gat1; Gabt1
Summary: Enables gamma-aminobutyric acid:sodium:chloride symporter activity and identical protein binding activity. Involved in several processes, including gamma-aminobutyric acid import; negative regulation of GABAergic synaptic transmission; and positive regulation of gamma-aminobutyric acid secretion. Located in cell surface. Is active in GABA-ergic synapse; postsynaptic membrane; and presynaptic membrane. Used to study brain ischemia. Biomarker of cerebral infarction; epilepsy; temporal lobe epilepsy; and withdrawal disorder. Human ortholog(s) of this gene implicated in alcohol dependence and myoclonic-atonic epilepsy. Orthologous to human SLC6A1 (solute carrier family 6 member 1). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Restricted expression toward (RPKM 302.1) See more
Orthologs: human mouse all
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Genomic context

Location:: 4q42

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (149004447..149037840)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (147448961..147482295)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (146258842..146292176)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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 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?

perturbation of the internal gate of GAT1 selectively impairs the gating mechanism of the empty transporter
Title: Internal gate mutants of the GABA transporter GAT1 are capable of substrate exchange.
Study demonstrated that GAT1 and GAT3 were expressed in glial cells but not at detectable levels in suprachiasmatic hypothalamic nucleus neurons
Title: Localization and expression of GABA transporters in the suprachiasmatic nucleus.
Epileptiform activity is associated with increased synaptic GABA release and is not accompanied by GAT-1 reversal. Sustained efflux of GABA through GAT-1 is unlikely to occur during physiological or pathological network activity.
Title: Synaptic GABA release prevents GABA transporter type-1 reversal during excessive network activity.
Study provides a quantitative analysis of the subcellular distribution of GAT-1 and GAT-3 in cerebral cortex, and a detailed description of their ultrastructural localization at GABAergic synapses.
Title: A quantitative analysis of cellular and synaptic localization of GAT-1 and GAT-3 in rat neocortex.
An inverse relationship links temperature and substrate apparent affinity in the ion-coupled cotransporters rGAT1 and KAAT1.
Title: An inverse relationship links temperature and substrate apparent affinity in the ion-coupled cotransporters rGAT1 and KAAT1.
Both Gat-1 and Gat-3 act synergisticaly to regulate excitability in the immature hippocampus.
Title: Inhibition of different GABA transporter systems is required to attenuate epileptiform activity in the CA3 region of the immature rat hippocampus.
GABA Transporter Mutagenesis Database (GATMD), a web-accessible, relational database of manually annotated biochemical, functional and pharmacological data reported on GAT1.
Title: GATMD: γ-aminobutyric acid transporter mutagenesis database.
the microdomain situated at the external end of transmembrane I is involved in different conformational changes taking place either during the binding and release of sodium or during the initiation of the Li+-induced leak current
Title: Elucidating conformational changes in the gamma-aminobutyric acid transporter-1.
data suggest that the extracellular end of transmembrane domain 7 of GABA transporter 1 not only undergoes conformational changes critical for the translocation process but also plays a role in regulating the conformational equilibrium
Title: Residues in the extracellular loop 4 are critical for maintaining the conformational equilibrium of the gamma-aminobutyric acid transporter-1.
investigated the relation between presteady-state and transport-associated currents in the rat GABA transporter expressed in Xenopus oocytes and have obtained consistent results that can be accounted for by a minimal three-state kinetic scheme
Title: The relation between charge movement and transport-associated currents in the rat GABA cotransporter rGAT1.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Gabt1 (e-PCR), detects polymorphism
- UniSTS:143155

Slc6a1 (e-PCR), detects polymorphism
- UniSTS:525658

Slc6a1 (e-PCR), detects polymorphism
- UniSTS:531382

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables amino acid:sodium symporter activity	ISO Inferred from Sequence Orthology more info
enables gamma-aminobutyric acid transmembrane transporter activity	ISO Inferred from Sequence Orthology more info
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	IDA Inferred from Direct Assay more info	PubMed
enables gamma-aminobutyric acid:sodium:chloride symporter activity	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sodium:chloride symporter activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in amino acid transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in amino acid transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of associative learning	ISO Inferred from Sequence Orthology more info
involved_in chloride transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in gamma-aminobutyric acid import	IDA Inferred from Direct Assay more info	PubMed
involved_in gamma-aminobutyric acid import	ISO Inferred from Sequence Orthology more info
involved_in inorganic anion import across plasma membrane	ISO Inferred from Sequence Orthology more info
involved_in learning	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of memory	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of synaptic transmission, GABAergic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neurotransmitter reuptake	IDA Inferred from Direct Assay more info	PubMed
involved_in neurotransmitter reuptake	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neurotransmitter reuptake	ISO Inferred from Sequence Orthology more info
involved_in neurotransmitter reuptake	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of gamma-aminobutyric acid secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to calcium ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to cocaine	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to lead ion	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to methamphetamine hydrochloride	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to organic cyclic compound	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to purine-containing compound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to sucrose	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to toxic substance	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to toxic substance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sodium ion import across plasma membrane	ISO Inferred from Sequence Orthology more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of synapse organization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in GABA-ergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in GABA-ergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	ISO Inferred from Sequence Orthology more info
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in presynapse	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sodium- and chloride-dependent GABA transporter 1

Names: GABA transporter protein; GAT-1; solute carrier family 6 (neurotransmitter transporter), member 1; solute carrier family 6 (neurotransmitter transporter, GABA), member 1

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_024371.3 → NP_077347.1 sodium- and chloride-dependent GABA transporter 1

See identical proteins and their annotated locations for NP_077347.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

P23978

UniProtKB/TrEMBL

A6IBU6

Conserved Domains (1) summary

cd11506
Location:2 → 599

SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

149004447..149037840

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006237059.4 → XP_006237121.1 sodium- and chloride-dependent GABA transporter 1 isoform X1

See identical proteins and their annotated locations for XP_006237121.1

UniProtKB/Swiss-Prot

P23978

UniProtKB/TrEMBL

A6IBU6

Related

ENSRNOP00000099708.1, ENSRNOT00000153307.1

Conserved Domains (1) summary

cd11506
Location:2 → 599

SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain