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GRIN3B glutamate ionotropic receptor NMDA type subunit 3B [ Homo sapiens (human) ]

Gene ID: 116444, updated on 27-Nov-2024

Summary

Official Symbol
GRIN3Bprovided by HGNC
Official Full Name
glutamate ionotropic receptor NMDA type subunit 3Bprovided by HGNC
Primary source
HGNC:HGNC:16768
See related
Ensembl:ENSG00000116032 MIM:606651; AllianceGenome:HGNC:16768
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
NR3B; GluN3B
Summary
The protein encoded by this gene is a subunit of an N-methyl-D-aspartate (NMDA) receptor. The encoded protein is found primarily in motor neurons, where it forms a heterotetramer with GRIN1 to create an excitatory glycine receptor. Variations in this gene have been proposed to be linked to schizophrenia. [provided by RefSeq, Nov 2015]
Expression
Ubiquitous expression in spleen (RPKM 1.5), fat (RPKM 1.0) and 21 other tissues See more
Orthologs
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Genomic context

See GRIN3B in Genome Data Viewer
Location:
19p13.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (1000419..1009732)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (963087..972401)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1000418..1009731)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9636 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:926209-926969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:932426-932957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:932958-933488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:934552-935082 Neighboring gene AT-rich interaction domain 3A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:947299-947798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13576 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:952365-953066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:953067-953768 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:953750-953958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:955173-955874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:956577-957278 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:957654-957846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:962809-963327 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:965021-965198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:980065-980655 Neighboring gene HNF4 motif-containing MPRA enhancer 174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9644 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:983939-984880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:990841-991786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:993929-994462 Neighboring gene WD repeat domain 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:994463-994995 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:996475-997094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9648 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1009528-1009718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1014734-1015267 Neighboring gene transmembrane protein 259 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1018406-1018625 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1019009-1019608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9649 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9651 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:1025533-1026264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9652 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1028384-1028559 Neighboring gene RNA, U6 small nuclear 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1038259-1038760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1038761-1039260 Neighboring gene calponin 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?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2021-02-02)

ClinGen Genome Curation Page
Haploinsufficency

Dosage sensitivity unlikely (Last evaluated 2021-02-02)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans.
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 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 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 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-mediated human cell death involves the NMDA receptor complex; antagonists of the NMDA receptor reverse the gp120-mediated effects 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

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in calcium ion transmembrane transport 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 ionotropic glutamate receptor signaling pathway 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 protein insertion into membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in regulation of calcium ion transport ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in regulation of postsynaptic membrane potential IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of presynaptic membrane potential 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 ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
part_of NMDA selective glutamate receptor complex NAS
Non-traceable Author Statement
more info
PubMed 
located_in neuronal cell body ISS
Inferred from Sequence or Structural Similarity
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
 

General protein information

Preferred Names
glutamate receptor ionotropic, NMDA 3B
Names
N-methyl-D-aspartate receptor subtype 3B
NMDA receptor subunit 3B
NMDA type glutamate receptor subunit NR3B
NMDAR3B
glutamate [NMDA] receptor subunit 3B
glutamate receptor, ionotropic, N-methyl-D-aspartate 3B

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)

  1. NM_138690.3NP_619635.1  glutamate receptor ionotropic, NMDA 3B precursor

    See identical proteins and their annotated locations for NP_619635.1

    Status: REVIEWED

    Source sequence(s)
    AY507106, BK004079, BM977634
    Consensus CDS
    CCDS32861.1
    UniProtKB/Swiss-Prot
    O60391, Q5EAK7, Q7RTW9
    UniProtKB/TrEMBL
    Q5F0I5
    Related
    ENSP00000234389.3, ENST00000234389.3
    Conserved Domains (3) summary
    cd06377
    Location:19405
    PBP1_iGluR_NMDA_NR3; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family
    cd13720
    Location:415808
    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:576842
    Lig_chan; Ligand-gated ion channel

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
    1000419..1009732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    963087..972401
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)