Grid2 glutamate ionotropic receptor delta type subunit 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Grid2provided by RGD
Official Full Name: glutamate ionotropic receptor delta type subunit 2provided by RGD
Primary source: RGD:68368
See related: EnsemblRapid:ENSRNOG00000006174 AllianceGenome:RGD:68368
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: GluD2
Summary: Enables PDZ domain binding activity and identical protein binding activity. Involved in regulation of presynapse assembly. Located in postsynaptic membrane. Is active in glutamatergic synapse; parallel fiber to Purkinje cell synapse; and postsynaptic density membrane. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 18. Orthologous to human GRID2 (glutamate ionotropic receptor delta type subunit 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 124.3), Uterus (RPKM 34.3) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 4q31

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (93745165..95222354)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (92415019..93892472)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (94068112..95476864)

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?

The architecture of GluD2 ionotropic delta glutamate receptor elucidated by cryo-EM.
Title: The architecture of GluD2 ionotropic delta glutamate receptor elucidated by cryo-EM.
the hinge region connecting the two subdomains of the GluD2 ligand-binding domain is responsible for the low affinity of D-serine.
Title: The low binding affinity of D-serine at the ionotropic glutamate receptor GluD2 can be attributed to the hinge region.
Results determined the crystal structures of the trimeric C1q-like domain of cerebellin-1, and the first complete ectodomain of GluD2. Cerebellin binds to the LNS6 domain of alpha- and beta-neurexin-1 through a high-affinity interaction that involves its highly flexible N-terminal domain.
Title: Conformational Plasticity in the Transsynaptic Neurexin-Cerebellin-Glutamate Receptor Adhesion Complex.
study supports the hypothesis that developmental hypothyroxinemia and hypothyroidism reduce PF-PC synapses, which may be attributed to the downregulation of Neurexin1/Cbln1/GluD2 tripartite complex.
Title: Developmental Hypothyroxinemia and Hypothyroidism Reduce Parallel Fiber-Purkinje Cell Synapses in Rat Offspring by Downregulation of Neurexin1/Cbln1/GluD2 Tripartite Complex.
study found that Cbln1 binds directly to the N-terminal domain of glutamate receptor delta2 (GluD2); results indicate that the Cbln1-GluD2 complex is a unique synapse organizer that acts bidirectionally on both pre- and postsynaptic components
Title: Cbln1 is a ligand for an orphan glutamate receptor delta2, a bidirectional synapse organizer.
These results suggest that the C-terminal T site of GluR2 is essential for LTD induction and the regulation of CF territory but is dispensable for PF-PC synapse formation and the elimination of surplus CFs at proximal dendrites during development.
Title: Regulation of long-term depression and climbing fiber territory by glutamate receptor delta2 at parallel fiber synapses through its C-terminal domain in cerebellar Purkinje cells.
the interaction between delta2 receptor and S-SCAM/MAGI-2 may be important for intracellular trafficking of the receptor
Title: PKC regulates the delta2 glutamate receptor interaction with S-SCAM/MAGI-2 protein.
The performance of Grid2(ho/ho) mutant mice was poorer than that of controls on stationary beam, coat hanger, unsteady platform, and rotorod tests. Grid2(ho/Lc) did not differ from Grid2(Lc/+) mice.
Title: Motor coordination in mice with hotfoot, Lurcher, and double mutations of the Grid2 gene encoding the delta-2 excitatory amino acid receptor.
findings show that glutamate receptor delta2 interacted directly with AP-4; results suggest a potential involvement of AP-4 in the trafficking of delta2 in the brain
Title: Adaptor protein complex-4 (AP-4) is expressed in the central nervous system neurons and interacts with glutamate receptor delta2.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU049225 (e-PCR)
- UniSTS:145673

D4Got75 (e-PCR)
- UniSTS:113929

D4Got74 (e-PCR)
- UniSTS:113962

D4Rat37 (e-PCR), detects polymorphism
- UniSTS:118835

D4Got70 (e-PCR)
- UniSTS:111971

AU026439 (e-PCR)
- UniSTS:114280

D4Rat173 (e-PCR), detects polymorphism
- UniSTS:227733

Grid2 (e-PCR), detects polymorphism
- UniSTS:143255

Grid2 (e-PCR), detects polymorphism
- UniSTS:143256

D4Got77 (e-PCR)
- UniSTS:113567

BF416501 (e-PCR)
- UniSTS:249307

BF390815 (e-PCR)
- UniSTS:249581

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables PDZ domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables PDZ domain binding	ISO Inferred from Sequence Orthology more info
enables glutamate receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ligand-gated monoatomic ion channel activity	IEA Inferred from Electronic Annotation more info
enables scaffold protein binding	ISO Inferred from Sequence Orthology more info
enables signaling receptor activity	IEA Inferred from Electronic Annotation more info
enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in cerebellar granule cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in cerebellar granule cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within excitatory postsynaptic potential	ISO Inferred from Sequence Orthology more info
involved_in excitatory synapse assembly	ISO Inferred from Sequence Orthology more info
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	ISO Inferred from Sequence Orthology more info
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	ISS Inferred from Sequence or Structural Similarity more info
involved_in modulation of chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of long-term synaptic depression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synapse assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within prepulse inhibition	ISO Inferred from Sequence Orthology more info
involved_in protein localization	ISO Inferred from Sequence Orthology more info
involved_in protein localization	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in regulation of postsynaptic density assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels	ISO Inferred from Sequence Orthology more info
involved_in regulation of presynapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of presynapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptic transmission, glutamatergic	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within synaptic transmission, glutamatergic	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in dendritic spine	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
part_of ionotropic glutamate receptor complex	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info
is_active_in parallel fiber to Purkinje cell synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in parallel fiber to Purkinje cell synapse	ISO Inferred from Sequence Orthology 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
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	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 somatodendritic compartment	ISO Inferred from Sequence Orthology more info
located_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: glutamate receptor ionotropic, delta-2

Names: gluR delta-2 subunit; glutamate receptor delta-2 subunit

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_024379.2 → NP_077355.2 glutamate receptor ionotropic, delta-2 precursor

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

Q62641, Q63226

UniProtKB/TrEMBL

A6KF16, F1LXB6

Related

ENSRNOP00000084985.1, ENSRNOT00000116787.2

Conserved Domains (2) summary

cd13731
Location:440 → 806

PBP2_iGluR_delta_2; The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the type 2 periplasmic-binding fold protein superfamily

cl10011
Location:28 → 429

Periplasmic_Binding_Protein_type1; Type 1 periplasmic binding fold superfamily

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

93745165..95222354

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017592903.3 → XP_017448392.1 glutamate receptor ionotropic, delta-2 isoform X1

UniProtKB/TrEMBL

A0A8I6AR77, F1LXB6

Related

ENSRNOP00000096742.1, ENSRNOT00000111210.2
XM_039108399.2 → XP_038964327.1 glutamate receptor ionotropic, delta-2 isoform X2

UniProtKB/TrEMBL

F1LXB6

Conserved Domains (2) summary

cd13731
Location:440 → 806

PBP2_iGluR_delta_2; The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the type 2 periplasmic-binding fold protein superfamily

cl10011
Location:28 → 429

Periplasmic_Binding_Protein_type1; Type 1 periplasmic binding fold superfamily