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    GRIN2D glutamate ionotropic receptor NMDA type subunit 2D [ Homo sapiens (human) ]

    Gene ID: 2906, updated on 27-Nov-2024

    Summary

    Official Symbol
    GRIN2Dprovided by HGNC
    Official Full Name
    glutamate ionotropic receptor NMDA type subunit 2Dprovided by HGNC
    Primary source
    HGNC:HGNC:4588
    See related
    Ensembl:ENSG00000105464 MIM:602717; AllianceGenome:HGNC:4588
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    EB11; NR2D; DEE46; EIEE46; GluN2D; NMDAR2D
    Summary
    N-methyl-D-aspartate (NMDA) receptors are a class of ionotropic glutamate receptors. NMDA channel has been shown to be involved in long-term potentiation, an activity-dependent increase in the efficiency of synaptic transmission thought to underlie certain kinds of memory and learning. NMDA receptor channels are heteromers composed of the key receptor subunit NMDAR1 (GRIN1) and 1 or more of the 4 NMDAR2 subunits: NMDAR2A (GRIN2A), NMDAR2B (GRIN2B), NMDAR2C (GRIN2C), and NMDAR2D (GRIN2D). [provided by RefSeq, Mar 2010]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See GRIN2D in Genome Data Viewer
    Location:
    19q13.33
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (48393668..48444931)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (51387832..51439100)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (48896925..48948188)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48836515-48837250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48842328-48843265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48845414-48845914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48845915-48846415 Neighboring gene transmembrane protein 143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14889 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48876382-48876882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48876883-48877383 Neighboring gene synaptogyrin 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10878 Neighboring gene KDEL endoplasmic reticulum protein retention receptor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:48899313-48899496 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10879 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10880 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48903941-48904482 Neighboring gene Sharpr-MPRA regulatory region 12315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48917645-48918366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48921924-48922690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14894 Neighboring gene Sharpr-MPRA regulatory region 8588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48947127-48947818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14896 Neighboring gene glutamate rich WD repeat containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48964846-48965804 Neighboring gene uncharacterized LOC105372430 Neighboring gene potassium inwardly rectifying channel subfamily J member 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48971727-48972227 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48972285-48973278 Neighboring gene cytohesin 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120-induced dephosphorylation of KV2.1 is dependent on NMDA receptor-mediated activation of protein phosphatase 2B or calcineurin PubMed
    env HIV-1 gp120 activates forward trafficking and surface clustering of NMDA receptors in membrane microdomains by a PKA-dependent phosphorylation of the NR1 C-terminal Ser897, followed by a PKC-dependent phosphorylation of Ser896 PubMed
    env HIV-1 gp120-induced synapse loss requires sequential activation of CXCR4, IL-1beta receptor, and NMDA receptor PubMed
    env HIV-1 clade B gp120 significantly downregulates NMDA receptor gene and protein expression and levels of glutamine compared to clade C gp120 PubMed
    env HIV-1 gp120 activates NMDA receptor directly and phosphorylates JNK through a gp120-mediated apoptotic pathway in human neuroblastoma cells PubMed
    env HIV-1 gp120-mediated human cell death involves the NMDA receptor complex; antagonists of the NMDA receptor reverse the gp120-mediated effects PubMed
    env HIV-1 gp120 causes an activation of phospholipase A2, resulting in the increased release of arachidonic acid, which may sensitize the NMDA receptor PubMed
    env HIV-1 gp120 binds to cells expressing epsilon1/zeta1 or epsilon2/zeta1 combined NMDA receptor subunits, but not to cells expressing a single epsilon1, epsilon2, or zeta1 NMDA receptor subunit PubMed
    Tat tat The gene expression of GRIN2D is significantly upregulated in both clade B and clade C Tat treated SK-N-MC neuroblastoma cells PubMed
    tat Ca(2+) influx through the NMDA receptor is necessary for HIV-1 Tat-induced synapse loss PubMed
    tat HIV-1 Tat upregulates the expression of NMDARs for the apoptosis of retinal pigmen epithelium (RPE) cells. Silencing of NMDARs by siRNA abolishes Tat-induced RPE apoptosis PubMed
    tat HIV-1 Tat-induced activation of spermine oxidase (SMO) activity involves NMDAR stimulation in human neuroblastoma PubMed
    tat HIV-1 Tat and methamphetamine inhibit the normal conjunction of signaling between D1 and NMDA receptors, resulting in neural dysfunction and death PubMed
    tat HIV-1 Tat interacts with NMDA receptors in primary neuronal-glial cultures and in hippocampal slice cultures PubMed
    tat Tat treatment causes activation of neuronal nitric oxide synthase (nNOS) through association with NMDA receptors PubMed
    tat HIV-1 Tat treatment induces the formation of complexes involving the low-density lipoprotein receptor-related protein (LRP), postsynaptic density protein-95 (PSD-95), and N-methyl-d-aspartic acid (NMDA) receptors at the neuron surface PubMed
    tat HIV-1 Tat-induced NMDA receptor activation is clade dependent. The Cys 30-Cys 31 motif in Tat is critical for the NMDA receptor activation PubMed
    tat HIV-1 Tat induces apoptosis of neurons and neurotoxicity through the activation of both NMDA and non-NMDA receptors PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in adult locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in brain development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in calcium ion transmembrane import into cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in calcium-mediated signaling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to L-glutamate IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in excitatory chemical synaptic transmission NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in excitatory postsynaptic potential IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ionotropic glutamate receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of synaptic transmission, glutamatergic ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of monoatomic cation transmembrane transport ISO
    Inferred from Sequence Orthology
    more info
     
    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
     
    involved_in regulation of sensory perception of pain IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of synaptic plasticity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of synaptic plasticity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in startle response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in synaptic transmission, glutamatergic IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of NMDA selective glutamate receptor complex TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in hippocampal mossy fiber to CA3 synapse IEA
    Inferred from Electronic Annotation
    more info
     
    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 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
     
    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 
    located_in presynaptic active zone membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    glutamate receptor ionotropic, NMDA 2D
    Names
    N-methyl D-aspartate receptor subtype 2D
    N-methyl-d-aspartate receptor subunit 2D
    estrogen receptor binding CpG island
    glutamate [NMDA] receptor subunit epsilon-4
    glutamate receptor, ionotropic, N-methyl D-aspartate 2D

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_052829.1 RefSeqGene

      Range
      3794..55057
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000836.4NP_000827.2  glutamate receptor ionotropic, NMDA 2D precursor

      See identical proteins and their annotated locations for NP_000827.2

      Status: REVIEWED

      Source sequence(s)
      AB209292, AC011527, AW139866, U77783
      Consensus CDS
      CCDS12719.1
      UniProtKB/Swiss-Prot
      O15399
      Related
      ENSP00000263269.2, ENST00000263269.4
      Conserved Domains (2) summary
      cd13718
      Location:430830
      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:49413
      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_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      48393668..48444931
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011526872.2XP_011525174.1  glutamate receptor ionotropic, NMDA 2D isoform X1

      See identical proteins and their annotated locations for XP_011525174.1

      UniProtKB/Swiss-Prot
      O15399
      Conserved Domains (2) summary
      cd13718
      Location:430830
      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:49413
      PBP1_iGluR_NMDA_NR2; N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      51387832..51439100
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)