Grin2d glutamate ionotropic receptor NMDA type subunit 2D [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Grin2dprovided by RGD
Official Full Name: glutamate ionotropic receptor NMDA type subunit 2Dprovided by RGD
Primary source: RGD:2740
See related: EnsemblRapid:ENSRNOG00000021063 AllianceGenome:RGD:2740
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: GluN2D
Summary: Enables glutamate binding activity and monoatomic ion channel activity. Involved in several processes, including cellular response to L-glutamate; glutamatergic synaptic transmission; and modulation of chemical synaptic transmission. Located in plasma membrane. Part of NMDA selective glutamate receptor complex. Is active in glutamatergic synapse; hippocampal mossy fiber to CA3 synapse; and synaptic membrane. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 46. Orthologous to human GRIN2D (glutamate ionotropic receptor NMDA type subunit 2D). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Testes (RPKM 11.9), Lung (RPKM 7.2) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q22

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (105443317..105483400, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (96306871..96346994, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (101819068..101859146, complement)

Chromosome 1 - NC_086019.1 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?

Inhibition of GluN2D-Containing NMDA Receptors Protects Dopaminergic Neurons against 6-OHDA-Induced Neurotoxicity via Activating ERK/NRF2/HO-1 Signaling.
Title: Inhibition of GluN2D-Containing NMDA Receptors Protects Dopaminergic Neurons against 6-OHDA-Induced Neurotoxicity via Activating ERK/NRF2/HO-1 Signaling.
UBP791 ((2S*,3R*)-1-(7-(2-carboxyethyl)phenanthrene-2-carbonyl)piperazine-2,3-dicarboxylic acid) inhibits GluN2C/2D with 40-fold selectivity over GluN2A-containing receptors, and that a methionine and a lysine residue in the ligand binding pocket are the critical molecular elements for the subtype-specific binding.
Title: Structural basis of subtype-selective competitive antagonism for GluN2C/2D-containing NMDA receptors.
Study supports a role for GluN2D-NMDARs in L-DOPA-induced dyskinesia (LID), and they confirm that cell-type and subunit specific modifications of NMDARs underlie the pathophysiology of LID.
Title: NMDA receptor GluN2D subunit participates to levodopa-induced dyskinesia pathophysiology.
Data indicate that tetrahydroisoquinolines showed subunit-selective potentiation of NMDA receptors containing the GluN2C or GluN2D subunits.
Title: Synthesis and structure activity relationship of tetrahydroisoquinoline-based potentiators of GluN2C and GluN2D containing N-methyl-D-aspartate receptors.
Data from molecular modeling suggest that GluN2D-containing NMDA receptors can enter a conformation or mode that allows the pore to gate with high probability of burst of activity.
Title: Modal gating of GluN1/GluN2D NMDA receptors.
NR2D expression falls significantly from postnatal day P2 to P3, then levels off until P12, and declines again until P21.
Title: Postnatal development of N-methyl-D-aspartate receptor subunits 2A, 2B, 2C, 2D, and 3B immunoreactivity in brain stem respiratory nuclei of the rat.
NR1, NR2B, and NR2D were robustly expressed in the supraoptic nucleus of adult rats.
Title: NMDA receptor subunit expression in the supraoptic nucleus of adult rats: dominance of NR2B and NR2D.
The deactivation time of GluN1/GluN2D receptors is influenced by the conformational variability of the ligand-binding domain and the structure of the ligand.
Title: Ligand-specific deactivation time course of GluN1/GluN2D NMDA receptors.
Expression of NR2D mRNAs in the thalamus was increased by mustard oil application to molar tooth pulp. This was prevented by lidocaine & reversed by MK-801. Naloxone antagonized this reversal.
Title: The role of N-methyl-D-aspartate receptor subunits in the rat thalamic mediodorsal nucleus during central sensitization.
At 24 hours after pulp exposure, the expression levels of NR2D mRNA were up-regulated in the contralateral thalamus.
Title: Artificial dental pulp exposure injury up-regulates antigen-presenting cell-related molecules in rat central nervous system.

Submit: New GeneRIF Correction See all GeneRIFs (22)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Grin2d (e-PCR), detects polymorphism
- UniSTS:531451

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables NMDA glutamate receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables NMDA glutamate receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables NMDA glutamate receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables NMDA glutamate receptor activity	ISO Inferred from Sequence Orthology more info
enables glutamate binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables glutamate-gated calcium ion channel activity	ISO Inferred from Sequence Orthology more info
enables glutamate-gated calcium ion channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables glutamate-gated receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables glutamate-gated receptor activity	ISO Inferred from Sequence Orthology more info
enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IDA Inferred from Direct Assay more info	PubMed
enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IMP Inferred from Mutant Phenotype more info	PubMed
enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	NAS Non-traceable Author Statement more info	PubMed
enables monoatomic cation channel activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
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	IBA Inferred from Biological aspect of Ancestor more info
enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated monoatomic cation channel activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within adult locomotory behavior	ISO Inferred from Sequence Orthology more info
involved_in calcium ion transmembrane import into cytosol	ISO Inferred from Sequence Orthology more info
involved_in calcium ion transmembrane import into cytosol	ISS Inferred from Sequence or Structural Similarity more info
involved_in calcium-mediated signaling	IEA Inferred from Electronic Annotation more info
involved_in cellular response to L-glutamate	IMP Inferred from Mutant Phenotype more info	PubMed
NOT acts_upstream_of_or_within detection of mechanical stimulus involved in sensory perception of pain	ISO Inferred from Sequence Orthology more info
involved_in excitatory postsynaptic potential	IBA Inferred from Biological aspect of Ancestor more info
NOT acts_upstream_of_or_within excitatory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in ionotropic glutamate receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in long-term synaptic potentiation	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 cation transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of excitatory postsynaptic potential	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of synaptic transmission, glutamatergic	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of monoatomic cation transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of neuronal synaptic plasticity	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of presynaptic membrane potential	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of sensory perception of pain	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within startle response	ISO Inferred from Sequence Orthology more info
involved_in synaptic transmission, glutamatergic	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic transmission, glutamatergic	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of NMDA selective glutamate receptor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NMDA selective glutamate receptor complex	IDA Inferred from Direct Assay more info	PubMed
part_of NMDA selective glutamate receptor complex	ISO Inferred from Sequence Orthology more info
part_of NMDA selective glutamate receptor complex	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
is_active_in glutamatergic synapse	EXP Inferred from Experiment more info	PubMed
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in hippocampal mossy fiber to CA3 synapse	IDA Inferred from Direct Assay more info	PubMed
part_of ionotropic glutamate receptor complex	TAS Traceable Author Statement more info	PubMed
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
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement 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
located_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in postsynaptic membrane	NAS Non-traceable Author Statement more info	PubMed
is_active_in presynaptic active zone membrane	IDA Inferred from Direct Assay more info	PubMed
located_in presynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: glutamate receptor ionotropic, NMDA 2D

Names: N-methyl D-aspartate receptor subtype 2D; NMDAR2D; NR2D; glutamate [NMDA] receptor subunit epsilon-4; glutamate receptor, ionotropic, N-methyl D-aspartate 2D; glutamate receptor, ionotropic, NMDA2D

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_022797.2 → NP_073634.2 glutamate receptor ionotropic, NMDA 2D

Status: PROVISIONAL

Source sequence(s)

JACYVU010000033

UniProtKB/Swiss-Prot

Q62645, Q63381, Q63382, Q63729, Q63730

UniProtKB/TrEMBL

A6JB94

Related

ENSRNOP00000028615.5, ENSRNOT00000028615.6

Conserved Domains (3) summary

PHA03307
Location:1114 → 1301

PHA03307; transcriptional regulator ICP4; Provisional

cd13718
Location:427 → 827

PBP2_iGluR_NMDA_Nr2; The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily

cd06378
Location:46 → 410

PBP1_iGluR_NMDA_NR2; N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family

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_086019.1 Reference GRCr8

Range

105443317..105483400 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063280701.1 → XP_063136771.1 glutamate receptor ionotropic, NMDA 2D isoform X1
XM_039095535.2 → XP_038951463.1 glutamate receptor ionotropic, NMDA 2D isoform X1

UniProtKB/TrEMBL

A6JB94

Conserved Domains (3) summary

PHA03307
Location:1114 → 1301

PHA03307; transcriptional regulator ICP4; Provisional

cd13718
Location:427 → 827

PBP2_iGluR_NMDA_Nr2; The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily

cd06378
Location:46 → 410

PBP1_iGluR_NMDA_NR2; N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family
XM_063280703.1 → XP_063136773.1 glutamate receptor ionotropic, NMDA 2D isoform X2
XM_063280711.1 → XP_063136781.1 glutamate receptor ionotropic, NMDA 2D isoform X3