Gabra6 gamma-aminobutyric acid type A receptor subunit alpha 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Gabra6provided by MGI
Official Full Name: gamma-aminobutyric acid type A receptor subunit alpha 6provided by MGI
Primary source: MGI:MGI:95618
See related: Ensembl:ENSMUSG00000020428 AllianceGenome:MGI:95618
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: alpha6; Gabra-6; GABA-ARalpha6
Summary: Enables transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential. Predicted to be involved in several processes, including GABAergic synaptic transmission; chloride transmembrane transport; and gamma-aminobutyric acid signaling pathway. Predicted to act upstream of or within chloride transport. Is active in cerebellar Golgi cell to granule cell synapse. Is expressed in central nervous system and retina. Orthologous to human GABRA6 (gamma-aminobutyric acid type A receptor subunit alpha6). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Restricted expression toward cerebellum adult (RPKM 99.3) See more
Orthologs: human all
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Genomic context

Location:: 11 A5; 11 25.03 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (42197264..42211977, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (42306437..42321072, complement)

Chromosome 11 - NC_000077.7 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The GABRA6 SNP rs3219151 has been significantly associated with alcohol dependence in studies on the Taiwanese Han, Korean, Finnish and South-western Native American populations.
Title: Association of serotonin and GABA pathway gene polymorphisms with alcohol dependence: A preliminary study.
D3R modulates GABAA receptors function in striatum: chronic blockade of D3R increases alpha6 subunit expression and induces insensitivity to the anxiolytic effect of diazepam
Title: Dopamine D3 receptor-dependent changes in alpha6 GABAA subunit expression in striatum modulate anxiety-like behaviour: Responsiveness and tolerance to diazepam.
This study demonstrated that Ectopic Expression of alpha6 GABAA Receptor Subunits in Hilar Somatostatin Neurons Increases Tonic Inhibition and Alters Network Activity in the Dentate Gyrus.
Title: Ectopic Expression of α6 and δ GABAA Receptor Subunits in Hilar Somatostatin Neurons Increases Tonic Inhibition and Alters Network Activity in the Dentate Gyrus.
results indicate that in addition to the central role of homologous gamma-aminobutyric acid (GABA) A receptor subunit alpha 6-100R/Q (alpha1-101H) residue in benzodiazepine(BZ) binding this critical BZ binding site has a major impact on BZ binding kinetics
Title: The cerebellar GABAAR α6-R100Q polymorphism alters ligand binding in outbred Sprague-Dawley rats in a similar manner as in selectively bred AT and ANT rats.
We tested the hypothesis that homocysteine (Hcy) antagonizes the GABA(A) receptor and behaves as an excitotoxic neurotransmitter that causes blood brain barrier (BBB) permeability and vascular dementia.
Title: GABAA receptor agonist mitigates homocysteine-induced cerebrovascular remodeling in knockout mice.
These findings suggest that the higher CNS depressant level achieved by ketamine may be the result of its selective actions on alpha6beta2/3delta receptors.
Title: Ketamine, but not phencyclidine, selectively modulates cerebellar GABA(A) receptors containing alpha6 and delta subunits.
Abnormal cerebellar P/Q-type VGCC activity results in a deficit of CGC-specific subtype(s) of GABA(A) receptors which may contribute to, or may be a consequence of the impaired cerebellar network signaling that occurs in cacna1a(tg) mice.
Title: Aberrant cerebellar granule cell-specific GABAA receptor expression in the epileptic and ataxic mouse mutant, Tottering.
some aspects of assembly, trafficking, targeting, and/or expression of extrasynaptic alpha6-containing GABA(A) receptors in cerebellar granule cells are selectively regulated by AMPA receptor-mediated signaling
Title: GABAA alpha6-containing receptors are selectively compromised in cerebellar granule cells of the ataxic mouse, stargazer.
Differential cell surface expression of GABAA receptor alpha1, alpha6, beta2 and beta3 subunits in cultured mouse cerebellar granule cells influence of cAMP-activated signalling.
Title: Differential cell surface expression of GABAA receptor alpha1, alpha6, beta2 and beta3 subunits in cultured mouse cerebellar granule cells influence of cAMP-activated signalling.
ectopic expression of the GABA(A) receptor alpha6 subunit in hippocampal pyramidal neurons produces extrasynaptic receptors and an increased tonic inhibition
Title: Ectopic expression of the GABA(A) receptor alpha6 subunit in hippocampal pyramidal neurons produces extrasynaptic receptors and an increased tonic inhibition.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (5)
Targeted (3) 1 citation

General gene information

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Markers

Gabra6 (e-PCR), detects polymorphism
- UniSTS:143151

X51986 (e-PCR)
- UniSTS:163497

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
contributes_to GABA-A receptor activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to GABA-A receptor activity	ISO Inferred from Sequence Orthology more info
enables GABA-gated chloride ion channel activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to GABA-gated chloride ion channel activity	ISO Inferred from Sequence Orthology more info
contributes_to benzodiazepine receptor activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to benzodiazepine receptor activity	ISO Inferred from Sequence Orthology more info
contributes_to chloride channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables diazepam binding	ISO Inferred from Sequence Orthology more info
enables extracellular ligand-gated monoatomic ion channel activity	IEA Inferred from Electronic Annotation more info
enables heterocyclic compound binding	ISO Inferred from Sequence Orthology more info
enables inhibitory extracellular ligand-gated monoatomic ion channel activity	ISO Inferred from Sequence Orthology more info
enables monoatomic ion channel activity	IEA Inferred from Electronic Annotation more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables transmembrane signaling receptor activity	IEA Inferred from Electronic Annotation more info
enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	EXP Inferred from Experiment more info	PubMed
enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chloride transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within chloride transport	IEA Inferred from Electronic Annotation more info
involved_in chloride transport	IEA Inferred from Electronic Annotation more info
involved_in gamma-aminobutyric acid signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in inhibitory synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within monoatomic ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in monoatomic ion transmembrane transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within monoatomic ion transport	IEA Inferred from Electronic Annotation more info
involved_in monoatomic ion transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of postsynaptic membrane potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic transmission, GABAergic	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic transmission, GABAergic	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of GABA-A receptor complex	IBA Inferred from Biological aspect of Ancestor more info
is_active_in GABA-ergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in cerebellar Golgi cell to granule cell synapse	EXP Inferred from Experiment more info	PubMed
is_active_in cerebellar Golgi cell to granule cell synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in cerebellar Golgi cell to granule cell synapse	ISO Inferred from Sequence Orthology more info
part_of chloride channel complex	IEA Inferred from Electronic Annotation more info
located_in dendrite	ISO Inferred from Sequence Orthology more info
is_active_in dendrite membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in hippocampal mossy fiber to CA3 synapse	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
located_in neuronal cell body membrane	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in postsynapse	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic specialization membrane	ISO Inferred from Sequence Orthology more info
located_in presynaptic membrane	ISO Inferred from Sequence Orthology more info
part_of receptor complex	ISO Inferred from Sequence Orthology more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
part_of transmembrane transporter complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: gamma-aminobutyric acid receptor subunit alpha-6

Names: GABA(A) receptor subunit alpha-6; GABAA receptor alpha 6 subunit; gamma-aminobutyric acid (GABA) A receptor, subunit alpha 6; subunit alpha 6 gamma-aminobutyric acid (GABA-A) receptor

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_001099641.2 → NP_001093111.1 gamma-aminobutyric acid receptor subunit alpha-6 isoform 1 precursor

See identical proteins and their annotated locations for NP_001093111.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AI841957, AK135145, BF471204

Consensus CDS

CCDS48769.1

UniProtKB/Swiss-Prot

P16305, Q5SUU5, Q9R0V3, Q9R0V4, Q9R0V5

Related

ENSMUSP00000126114.2, ENSMUST00000155218.9

Conserved Domains (3) summary

TIGR00860
Location:1 → 440

LIC; Cation transporter family protein

pfam02931
Location:33 → 240

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

pfam02932
Location:247 → 437

Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region
NM_001359049.1 → NP_001345978.1 gamma-aminobutyric acid receptor subunit alpha-6 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region and uses an alternate start codon, compared to variant 1. It encodes isoform 3, which has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AI841957, AK135145, BF471204

Consensus CDS

CCDS88145.1

Related

ENSMUSP00000104909.4, ENSMUST00000109286.4

Conserved Domains (1) summary

cl27321
Location:33 → 439

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
NM_008068.3 → NP_032094.2 gamma-aminobutyric acid receptor subunit alpha-6 isoform 2 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an alternate splice site in the 5' coding region but maintains the reading frame, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.

Source sequence(s)

AI841957, AK135145, BF471204

Consensus CDS

CCDS24554.1

UniProtKB/Swiss-Prot

P16305

Related

ENSMUSP00000020703.7, ENSMUST00000020703.13

Conserved Domains (3) summary

TIGR00860
Location:1 → 430

LIC; Cation transporter family protein

pfam02931
Location:33 → 230

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

pfam02932
Location:237 → 427

Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region

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

NC_000077.7 Reference GRCm39 C57BL/6J

Range

42197264..42211977 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036156328.1 → XP_036012221.1 gamma-aminobutyric acid receptor subunit alpha-6 isoform X1

Conserved Domains (2) summary

cd19039
Location:42 → 239

LGIC_ECD_GABAAR_A6; extracellular domain of gamma-aminobutyric acid receptor subunit alpha-6 (GABAAR-A6 or GABRA6)

cd19052
Location:242 → 337

LGIC_TM_GABAAR_alpha; transmembrane domain of alpha subunits of type-A gamma-aminobutyric acid receptor (GABAAR)
XM_036156330.1 → XP_036012223.1 gamma-aminobutyric acid receptor subunit alpha-6 isoform X3

Conserved Domains (3) summary

cd03558
Location:146 → 160

LGIC_ECD; Cys-loop [structural motif]

cd19052
Location:232 → 327

LGIC_TM_GABAAR_alpha; transmembrane domain of alpha subunits of type-A gamma-aminobutyric acid receptor (GABAAR)

cl28912
Location:42 → 229

LGIC_ECD; extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC))
XM_036156331.1 → XP_036012224.1 gamma-aminobutyric acid receptor subunit alpha-6 isoform X4

Conserved Domains (3) summary

cd03558
Location:145 → 159

LGIC_ECD; Cys-loop [structural motif]

cd19052
Location:231 → 326

LGIC_TM_GABAAR_alpha; transmembrane domain of alpha subunits of type-A gamma-aminobutyric acid receptor (GABAAR)

cl28912
Location:41 → 228

LGIC_ECD; extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC))
XM_030245559.2 → XP_030101419.1 gamma-aminobutyric acid receptor subunit alpha-6 isoform X5

Conserved Domains (3) summary

TIGR00860
Location:33 → 429

LIC; Cation transporter family protein

cd03558
Location:145 → 159

LGIC_ECD; Cys-loop [structural motif]

cl28912
Location:41 → 228

LGIC_ECD; extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC))
XM_006532198.4 → XP_006532261.1 gamma-aminobutyric acid receptor subunit alpha-6 isoform X7

Conserved Domains (3) summary

TIGR00860
Location:4 → 357

LIC; Cation transporter family protein

cd03558
Location:73 → 87

LGIC_ECD; Cys-loop [structural motif]

cl28912
Location:2 → 156

LGIC_ECD; extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC))
XM_036156329.1 → XP_036012222.1 gamma-aminobutyric acid receptor subunit alpha-6 isoform X2

Conserved Domains (2) summary

cd19039
Location:41 → 238

LGIC_ECD_GABAAR_A6; extracellular domain of gamma-aminobutyric acid receptor subunit alpha-6 (GABAAR-A6 or GABRA6)

cd19052
Location:241 → 336

LGIC_TM_GABAAR_alpha; transmembrane domain of alpha subunits of type-A gamma-aminobutyric acid receptor (GABAAR)
XM_036156332.1 → XP_036012225.1 gamma-aminobutyric acid receptor subunit alpha-6 isoform X6

Conserved Domains (3) summary

cd03558
Location:73 → 87

LGIC_ECD; Cys-loop [structural motif]

cd19052
Location:159 → 254

LGIC_TM_GABAAR_alpha; transmembrane domain of alpha subunits of type-A gamma-aminobutyric acid receptor (GABAAR)

cl28912
Location:2 → 156

LGIC_ECD; extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC))