Grin3a glutamate ionotropic receptor NMDA type subunit 3A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Grin3aprovided by RGD
Official Full Name: glutamate ionotropic receptor NMDA type subunit 3Aprovided by RGD
Primary source: RGD:621704
See related: Ensembl:ENSRNOG00000005723 AllianceGenome:RGD:621704
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: NR3; chi-1; GluN3A
Summary: Enables carboxylic acid binding activity; glutamate-gated receptor activity; and protein phosphatase 2A binding activity. Contributes to NMDA glutamate receptor activity. Involved in several processes, including ionotropic glutamate receptor signaling pathway; monoatomic cation transport; and negative regulation of dendritic spine development. Located in cytoplasm and postsynaptic membrane. Part of NMDA selective glutamate receptor complex. Is active in glutamatergic synapse and postsynaptic density membrane. Orthologous to human GRIN3A (glutamate ionotropic receptor NMDA type subunit 3A). [provided by Alliance of Genome Resources, Jul 2025]
Expression: Biased expression in Brain (RPKM 52.7), Muscle (RPKM 4.6) and 1 other tissue See more
Orthologs: all
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Genomic context

Location:: 5q22

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (68802333..69001880, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (64006847..64206408, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

GluN3 subunit expression correlates with increased vulnerability of hippocampus and entorhinal cortex to neurodegeneration in a model of temporal lobe epilepsy.
Title: GluN3 subunit expression correlates with increased vulnerability of hippocampus and entorhinal cortex to neurodegeneration in a model of temporal lobe epilepsy.
The NMDA receptor subunit GluN3A regulates synaptic activity-induced and myocyte enhancer factor 2C (MEF2C)-dependent transcription.
Title: The NMDA receptor subunit GluN3A regulates synaptic activity-induced and myocyte enhancer factor 2C (MEF2C)-dependent transcription.
Structural features in the glycine-binding sites of the GluN1 and GluN3A subunits regulate the surface delivery of NMDA receptors.
Title: Structural features in the glycine-binding sites of the GluN1 and GluN3A subunits regulate the surface delivery of NMDA receptors.
N-methyl-D-aspartate receptor-mediated synaptic responses are induced by glycine in hippocampal CA1 neurons
Title: Glycine induces bidirectional modifications in N-methyl-D-aspartate receptor-mediated synaptic responses in hippocampal CA1 neurons.
The hippocampus of fetuses gestated under light:dark photoperiod (12:12 LD) displayed daily oscillatory expression of the clock genes Bmal1 and Per2, clock-controlled genes Mtnr1b, Slc2a4, Nr3c1 and NMDA receptor subunits 1B-3A-3B
Title: Gestational chronodisruption impairs hippocampal expression of NMDA receptor subunits Grin1b/Grin3a and spatial memory in the adult offspring.
GluN3A protein expression in rat hippocampus and the prefrontal cortex was increased quickly after brain ischemia and remained at a high level for at least 24 h. After OGD, neurons with GluN3A subunit overexpression were more viable than wild-type neurons
Title: The GluN3A subunit exerts a neuroprotective effect in brain ischemia and the hypoxia process.
Crystallization and structural analysis of the GluN1 and GluN3A ligand binding domains of the rat NMDA receptor subunits Grin1 and Grin3a.
Title: Conformational analysis of NMDA receptor GluN1, GluN2, and GluN3 ligand-binding domains reveals subtype-specific characteristics.
binding of GluN3A to GIT1 is regulated by synaptic activity, a response that might restrict the negative regulatory effects of GluN3A on actin signaling to inactive synapses.
Title: GluN3A expression restricts spine maturation via inhibition of GIT1/Rac1 signaling.
denitrosylation of nNOS induced by calcium ion influx is a NMDAR-dependent process during the early stage of ischemia/reperfusion, which is majorly mediated by thioredoxin-1 (Trx1) system.
Title: N-methyl-D-aspartate receptor-dependent denitrosylation of neuronal nitric oxide synthase increase the enzyme activity.
a model whereby NR3A negatively regulates the developmental stabilization of glutamate receptors involved in excitatory neurotransmission, synaptogenesis, and spine growth.
Title: Genetic deletion of NR3A accelerates glutamatergic synapse maturation.

Submit: New GeneRIF Correction See all GeneRIFs (18)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D5Rat140 (e-PCR), detects polymorphism
- UniSTS:227865

AW530893 (e-PCR)
- UniSTS:244571

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
contributes_to NMDA glutamate receptor activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to NMDA glutamate receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables NMDA glutamate receptor activity	IEA Inferred from Electronic Annotation more info
enables NMDA glutamate receptor activity	ISO Inferred from Sequence Orthology more info
enables calcium channel activity	IEA Inferred from Electronic Annotation more info
enables calcium channel activity	ISO Inferred from Sequence Orthology more info
enables glutamate receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables glycine binding	IDA Inferred from Direct Assay more info	PubMed
enables glycine binding	IEA Inferred from Electronic Annotation more info
enables glycine binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables ligand-gated monoatomic ion channel activity	IEA Inferred from Electronic Annotation more info
enables monoatomic ion channel activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein phosphatase 2A binding	IDA Inferred from Direct Assay more info	PubMed
enables serine binding	IDA Inferred from Direct Assay more info	PubMed
enables signaling receptor activity	IEA Inferred from Electronic Annotation more info
enables transmitter-gated monoatomic ion channel activity	IDA Inferred from Direct Assay more info	PubMed
enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	IBA Inferred from Biological aspect of Ancestor more info
enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	IEA Inferred from Electronic Annotation more info
enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in brain development	IEP Inferred from Expression Pattern more info	PubMed
involved_in calcium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in calcium ion transport	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within calcium ion transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dendrite development	ISO Inferred from Sequence Orthology more info
involved_in hippocampus development	IEP Inferred from Expression Pattern more info	PubMed
involved_in hypothalamus development	IEP Inferred from Expression Pattern more info	PubMed
involved_in ionotropic glutamate receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in mesencephalic trigeminal nucleus development	IEP Inferred from Expression Pattern more info	PubMed
involved_in modulation of chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic cation transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in monoatomic ion transport	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of dendritic spine development	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of dendritic spine maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within prepulse inhibition	ISO Inferred from Sequence Orthology more info
involved_in presynaptic modulation of chemical synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in presynaptic modulation of chemical synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in regulation of postsynaptic membrane potential	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic plasticity	IDA Inferred from Direct Assay more info	PubMed
involved_in response to ethanol	IEA Inferred from Electronic Annotation more info
involved_in response to ethanol	ISO Inferred from Sequence Orthology more info
involved_in synaptic transmission, glutamatergic	IBA Inferred from Biological aspect of Ancestor more info
involved_in trigeminal motor nucleus development	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
part_of NMDA selective glutamate receptor complex	IDA Inferred from Direct Assay more info	PubMed
part_of NMDA selective glutamate receptor complex	IEA Inferred from Electronic Annotation more info
part_of NMDA selective glutamate receptor complex	ISO Inferred from Sequence Orthology more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in neuron projection	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection	IEA Inferred from Electronic Annotation more info
located_in neuron projection	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
part_of neurotransmitter receptor complex	IEA Inferred from Electronic Annotation more info
part_of neurotransmitter receptor complex	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	EXP Inferred from Experiment more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic density	EXP Inferred from Experiment more info	PubMed
located_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
is_active_in postsynaptic density membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in postsynaptic density membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic density membrane	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density membrane	IEA Inferred from Electronic Annotation more info
is_active_in postsynaptic density membrane	ISO Inferred from Sequence Orthology more info
located_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in postsynaptic membrane	ISO Inferred from Sequence Orthology more info
located_in presynapse	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info
located_in synapse	ISO Inferred from Sequence Orthology more info
located_in synaptic membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: glutamate receptor ionotropic, NMDA 3A

Names: N-methyl-D-aspartate receptor subtype 3A; NMDAR-L; NMDAR-L1; NMDAR3A; NR3 chi-1; NR3A; glutamate [NMDA] receptor subunit 3A; glutamate receptor chi-1; glutamate receptor, ionotropic, N-methyl-D-aspartate 3A

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_001198583.2 → NP_001185512.1 glutamate receptor ionotropic, NMDA 3A isoform 2 precursor

See identical proteins and their annotated locations for NP_001185512.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.

Source sequence(s)

BI294379, U29873

Conserved Domains (4) summary

cd06377
Location:30 → 497

PBP1_iGluR_NMDA_NR3; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family

cd13720
Location:512 → 908

PBP2_iGluR_NMDA_Nr3; The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily

pfam00060
Location:676 → 942

Lig_chan; Ligand-gated ion channel

pfam01094
Location:127 → 469

ANF_receptor; Receptor family ligand binding region
NM_138546.2 → NP_612555.1 glutamate receptor ionotropic, NMDA 3A isoform 1 precursor

See identical proteins and their annotated locations for NP_612555.1

Status: VALIDATED

Description

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

Source sequence(s)

AF073379, BI294379

UniProtKB/Swiss-Prot

O09098, O09155, Q62800, Q63268, Q9R1M7, Q9Z2H0

Conserved Domains (4) summary

cd06377
Location:30 → 497

PBP1_iGluR_NMDA_NR3; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family

cd13720
Location:512 → 908

PBP2_iGluR_NMDA_Nr3; The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily

pfam00060
Location:676 → 942

Lig_chan; Ligand-gated ion channel

pfam01094
Location:127 → 469

ANF_receptor; Receptor family ligand binding region

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_086023.1 Reference GRCr8

Range

68802333..69001880 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039109241.2 → XP_038965169.1 glutamate receptor ionotropic, NMDA 3A isoform X1

UniProtKB/TrEMBL

A0A096MIS4

Related

ENSRNOP00000007957.7, ENSRNOT00000007957.8

Conserved Domains (3) summary

cd13720
Location:512 → 908

PBP2_iGluR_NMDA_Nr3; The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily

cd06377
Location:40 → 496

PBP1_iGluR_NMDA_NR3; N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family

pfam00060
Location:676 → 942

Lig_chan; Ligand-gated ion channel