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    GRIN3A glutamate ionotropic receptor NMDA type subunit 3A [ Homo sapiens (human) ]

    Gene ID: 116443, updated on 6-Jun-2024

    Summary

    Official Symbol
    GRIN3Aprovided by HGNC
    Official Full Name
    glutamate ionotropic receptor NMDA type subunit 3Aprovided by HGNC
    Primary source
    HGNC:HGNC:16767
    See related
    Ensembl:ENSG00000198785 MIM:606650; AllianceGenome:HGNC:16767
    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
    NR3A; GluN3A; NMDAR-L; NMDAR3A
    Summary
    This gene encodes a subunit of the N-methyl-D-aspartate (NMDA) receptors, which belong to the superfamily of glutamate-regulated ion channels, and function in physiological and pathological processes in the central nervous system. This subunit shows greater than 90% identity to the corresponding subunit in rat. Studies in the knockout mouse deficient in this subunit suggest that this gene may be involved in the development of synaptic elements by modulating NMDA receptor activity. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 4.0), prostate (RPKM 0.5) and 3 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See GRIN3A in Genome Data Viewer
    Location:
    9q31.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (101569352..101738647, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (113744124..113912649, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (104331634..104500929, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene TMEM246 antisense RNA 1 Neighboring gene post-GPI attachment to proteins GalNAc transferase 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:104275376-104275886 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:104275887-104276395 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:104276396-104276905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:104286647-104287146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28726 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:104316489-104316706 Neighboring gene ring finger protein 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28727 Neighboring gene uncharacterized LOC105376186 Neighboring gene protein phosphatase 3 regulatory subunit B, beta Neighboring gene Sharpr-MPRA regulatory region 1857 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:104500238-104500762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:104500763-104501286 Neighboring gene MT-ND3 pseudogene 4 Neighboring gene uncharacterized LOC105376187

    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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genetics of coronary artery calcification among African Americans, a meta-analysis.
    EBI GWAS Catalog
    Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    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 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 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
    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 causes an activation of phospholipase A2, resulting in the increased release of arachidonic acid, which may sensitize the NMDA receptor PubMed
    Tat 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 interacts with NMDA receptors in primary neuronal-glial cultures and in hippocampal slice cultures 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 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

    Clone Names

    • FLJ45414

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables NMDA glutamate receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    contributes_to NMDA glutamate receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables calcium channel activity IEA
    Inferred from Electronic Annotation
    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 identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein phosphatase 2A binding ISS
    Inferred from Sequence or Structural Similarity
    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 calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in calcium ion transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in dendrite development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ionotropic glutamate receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in modulation of chemical synaptic transmission IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of dendritic spine development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in prepulse inhibition IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in presynaptic modulation of chemical synaptic transmission IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of postsynaptic membrane potential IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to ethanol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in rhythmic process 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 IDA
    Inferred from Direct Assay
    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 membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in neuron projection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in neuronal cell body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in postsynaptic density membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    glutamate receptor ionotropic, NMDA 3A
    Names
    N-methyl-D-aspartate receptor subtype 3A
    glutamate [NMDA] receptor subunit 3A
    glutamate receptor, ionotropic, N-methyl-D-aspartate 3A

    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.

    mRNA and Protein(s)

    1. NM_133445.3NP_597702.2  glutamate receptor ionotropic, NMDA 3A precursor

      See identical proteins and their annotated locations for NP_597702.2

      Status: REVIEWED

      Source sequence(s)
      AF416558, AL356516, AL591377, BC167432
      Consensus CDS
      CCDS6758.1
      UniProtKB/Swiss-Prot
      B3DLF9, Q5VTR3, Q8TCU5, Q8TF29, Q8WXI6
      UniProtKB/TrEMBL
      A2RUE7
      Related
      ENSP00000355155.3, ENST00000361820.6
      Conserved Domains (4) summary
      cd06377
      Location:30497
      PBP1_iGluR_NMDA_NR3; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family
      cd13720
      Location:512908
      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:676942
      Lig_chan; Ligand-gated ion channel
      pfam01094
      Location:127469
      ANF_receptor; Receptor family ligand binding region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      101569352..101738647 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011518211.3XP_011516513.1  glutamate receptor ionotropic, NMDA 3A isoform X1

      UniProtKB/TrEMBL
      A2RUE7
      Conserved Domains (4) summary
      cd06377
      Location:30497
      PBP1_iGluR_NMDA_NR3; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family
      cd13720
      Location:512908
      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:676922
      Lig_chan; Ligand-gated ion channel
      pfam01094
      Location:127469
      ANF_receptor; Receptor family ligand binding region

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      113744124..113912649 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361948.1XP_054217923.1  glutamate receptor ionotropic, NMDA 3A isoform X1

      UniProtKB/TrEMBL
      A2RUE7