Human Gene GRIN2B (ENST00000609686.4_6) from GENCODE V47lift37
  Description: glutamate ionotropic receptor NMDA type subunit 2B (from RefSeq NM_000834.5)
Gencode Transcript: ENST00000609686.4_6
Gencode Gene: ENSG00000273079.7_13
Transcript (Including UTRs)
   Position: hg19 chr12:13,690,271-14,134,536 Size: 444,266 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr12:13,715,717-14,019,142 Size: 303,426 Coding Exon Count: 12 

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Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:13,690,271-14,134,536)mRNA (may differ from genome)Protein (1484 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
ReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NMDE2_HUMAN
DESCRIPTION: RecName: Full=Glutamate [NMDA] receptor subunit epsilon-2; AltName: Full=N-methyl D-aspartate receptor subtype 2B; Short=NMDAR2B; Short=NR2B; AltName: Full=N-methyl-D-aspartate receptor subunit 3; Short=NR3; Short=hNR3; Flags: Precursor;
FUNCTION: NMDA receptor subtype of glutamate-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Mediated by glycine. In concert with DAPK1 at extrasynaptic sites, acts as a central mediator for stroke damage. Its phosphorylation at Ser-1303 by DAPK1 enhances synaptic NMDA receptor channel activity inducing injurious Ca2+ influx through them, resulting in an irreversible neuronal death (By similarity).
SUBUNIT: Forms heteromeric channel of a zeta subunit (GRIN1), a epsilon subunit (GRIN2A, GRIN2B, GRIN2C or GRIN2D) and a third subunit (GRIN3A or GRIN3B). Found in a complex with GRIN1 and GRIN3B. Found in a complex with GRIN1, GRIN3A and PPP2CB. Interacts with PDZ domains of INADL and DLG4. Interacts with HIP1 and NETO1 (By similarity). Interacts with MAGI3. Interacts with DAPK1 (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein. Cell junction, synapse, postsynaptic cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Primarily found in the fronto-parieto-temporal cortex and hippocampus pyramidal cells, lower expression in the basal ganglia.
PTM: Phosphorylation at Ser-1303 by DAPK1 enhances synaptic NMDA receptor channel activity (By similarity).
DISEASE: Defects in GRIN2B are the cause of mental retardation autosomal dominant type 6 (MRD6) [MIM:613970]. Mental retardation is characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. Note=Chromosomal aberrations involving GRIN2B have been found in patients with mental retardation. Translocations t(9;12)(p23;p13.1) and t(10;12)(q21.1;p13.1) with a common breakpoint in 12p13.1.
SIMILARITY: Belongs to the glutamate-gated ion channel (TC 1.A.10.1) family. NR2B/GRIN2B subfamily.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: GRIN2B
Diseases sorted by gene-association score: epileptic encephalopathy, early infantile, 27* (1330), mental retardation, autosomal dominant 6* (1330), autosomal dominant non-syndromic intellectual disability* (97), west syndrome* (90), huntington disease (13), myoclonic astatic epilepsy (11), von economo's disease (10), limbic encephalitis (7), fetal alcohol spectrum disorder (7), attention deficit-hyperactivity disorder (7), schizophrenia (7), focal epilepsy (6), status epilepticus (6), phencyclidine abuse (6), fetal alcohol syndrome (5), toxic encephalopathy (4), valproate embryopathy, susceptibility to (4), d-2-hydroxyglutaric aciduria (4), alcohol dependence (4), temporal lobe epilepsy (4), alzheimer disease (3), obsessive-compulsive disorder (3), autism spectrum disorder (3), disease of mental health (1), parkinson disease, late-onset (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.24 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 27.35 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -186.70708-0.264 Picture PostScript Text
3' UTR -7471.3725446-0.294 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001828 - ANF_lig-bd_rcpt
IPR019594 - Glu_rcpt_Glu/Gly-bd
IPR001320 - Iontro_glu_rcpt
IPR001508 - NMDA_rcpt
IPR018884 - NMDAR2_C
IPR001638 - SBP_bac_3

Pfam Domains:
PF00060 - Ligand-gated ion channel
PF00497 - Bacterial extracellular solute-binding proteins, family 3
PF01094 - Receptor family ligand binding region
PF10565 - N-methyl D-aspartate receptor 2B3 C-terminus
PF10613 - Ligated ion channel L-glutamate- and glycine-binding site

SCOP Domains:
47353 - Retrovirus capsid dimerization domain-like
53822 - Periplasmic binding protein-like I
53850 - Periplasmic binding protein-like II
81324 - Voltage-gated potassium channels

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1S11 - Model 1S2S - Model 2IPV - Model


ModBase Predicted Comparative 3D Structure on Q13224
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004970 ionotropic glutamate receptor activity
GO:0004972 NMDA glutamate receptor activity
GO:0005088 Ras guanyl-nucleotide exchange factor activity
GO:0005216 ion channel activity
GO:0005234 extracellular-glutamate-gated ion channel activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016594 glycine binding
GO:0016595 glutamate binding
GO:0022849 glutamate-gated calcium ion channel activity
GO:0038023 signaling receptor activity
GO:0046872 metal ion binding

Biological Process:
GO:0000165 MAPK cascade
GO:0006811 ion transport
GO:0007215 glutamate receptor signaling pathway
GO:0007268 chemical synaptic transmission
GO:0007275 multicellular organism development
GO:0007420 brain development
GO:0007611 learning or memory
GO:0019722 calcium-mediated signaling
GO:0035235 ionotropic glutamate receptor signaling pathway
GO:0045471 response to ethanol
GO:0048013 ephrin receptor signaling pathway
GO:0048167 regulation of synaptic plasticity
GO:0051290 protein heterotetramerization
GO:0060079 excitatory postsynaptic potential
GO:0097553 calcium ion transmembrane import into cytosol
GO:0098976 excitatory chemical synaptic transmission
GO:1901216 positive regulation of neuron death
GO:1902951 negative regulation of dendritic spine maintenance
GO:2001056 positive regulation of cysteine-type endopeptidase activity

Cellular Component:
GO:0005622 intracellular
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009986 cell surface
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0017146 NMDA selective glutamate receptor complex
GO:0030054 cell junction
GO:0043005 neuron projection
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0097060 synaptic membrane


-  Descriptions from all associated GenBank mRNAs
  AB208850 - Homo sapiens mRNA for Glutamate [NMDA] receptor subunit epsilon 2 precursor variant protein.
U88963 - Human N-methyl-D-aspartate receptor subunit 2B (GRIN2B) mRNA, complete cds.
U11287 - Human N-methyl-D-aspartate receptor subunit NR3 (hNR3) mRNA, complete cds.
U90278 - Human N-methyl-D-aspartate receptor 2B subunit precursor mRNA, complete cds.
BC113618 - Homo sapiens glutamate receptor, ionotropic, N-methyl D-aspartate 2B, mRNA (cDNA clone MGC:142178 IMAGE:8322670), complete cds.
BC113620 - Homo sapiens glutamate receptor, ionotropic, N-methyl D-aspartate 2B, mRNA (cDNA clone MGC:142180 IMAGE:8322672), complete cds.
BX648060 - Homo sapiens mRNA; cDNA DKFZp686G08203 (from clone DKFZp686G08203).
AK125440 - Homo sapiens cDNA FLJ43451 fis, clone OCBBF2033413.
AK091524 - Homo sapiens cDNA FLJ34205 fis, clone FCBBF3020138.
JD281745 - Sequence 262769 from Patent EP1572962.
JD101704 - Sequence 82728 from Patent EP1572962.
JD094694 - Sequence 75718 from Patent EP1572962.
JD509259 - Sequence 490283 from Patent EP1572962.
JD528740 - Sequence 509764 from Patent EP1572962.
JD434878 - Sequence 415902 from Patent EP1572962.
JD323354 - Sequence 304378 from Patent EP1572962.
JD268285 - Sequence 249309 from Patent EP1572962.
JD126645 - Sequence 107669 from Patent EP1572962.
JD061722 - Sequence 42746 from Patent EP1572962.
JD341131 - Sequence 322155 from Patent EP1572962.
JD544676 - Sequence 525700 from Patent EP1572962.
JD350436 - Sequence 331460 from Patent EP1572962.
JD509844 - Sequence 490868 from Patent EP1572962.
JD161158 - Sequence 142182 from Patent EP1572962.
JD563301 - Sequence 544325 from Patent EP1572962.
JD327965 - Sequence 308989 from Patent EP1572962.
JD113073 - Sequence 94097 from Patent EP1572962.
JD440439 - Sequence 421463 from Patent EP1572962.
JD504377 - Sequence 485401 from Patent EP1572962.
JD083369 - Sequence 64393 from Patent EP1572962.
JD067872 - Sequence 48896 from Patent EP1572962.
JD188401 - Sequence 169425 from Patent EP1572962.
JD183161 - Sequence 164185 from Patent EP1572962.
JD556901 - Sequence 537925 from Patent EP1572962.
JD473322 - Sequence 454346 from Patent EP1572962.
JD247238 - Sequence 228262 from Patent EP1572962.
JD226231 - Sequence 207255 from Patent EP1572962.
JD052416 - Sequence 33440 from Patent EP1572962.
JD305057 - Sequence 286081 from Patent EP1572962.
JD267898 - Sequence 248922 from Patent EP1572962.
JD274504 - Sequence 255528 from Patent EP1572962.
JD266939 - Sequence 247963 from Patent EP1572962.
JD045203 - Sequence 26227 from Patent EP1572962.
JD301946 - Sequence 282970 from Patent EP1572962.
JD433865 - Sequence 414889 from Patent EP1572962.
JD250183 - Sequence 231207 from Patent EP1572962.
JD059990 - Sequence 41014 from Patent EP1572962.
JD286225 - Sequence 267249 from Patent EP1572962.
JD565152 - Sequence 546176 from Patent EP1572962.
JD176707 - Sequence 157731 from Patent EP1572962.
JD124149 - Sequence 105173 from Patent EP1572962.
JD462037 - Sequence 443061 from Patent EP1572962.
JD091260 - Sequence 72284 from Patent EP1572962.
JD495713 - Sequence 476737 from Patent EP1572962.
JD355227 - Sequence 336251 from Patent EP1572962.
JD288109 - Sequence 269133 from Patent EP1572962.
JD297166 - Sequence 278190 from Patent EP1572962.
JD086884 - Sequence 67908 from Patent EP1572962.
JD324613 - Sequence 305637 from Patent EP1572962.
JD215330 - Sequence 196354 from Patent EP1572962.
JD343686 - Sequence 324710 from Patent EP1572962.
JD512973 - Sequence 493997 from Patent EP1572962.
JD356178 - Sequence 337202 from Patent EP1572962.
JD498131 - Sequence 479155 from Patent EP1572962.
JD342962 - Sequence 323986 from Patent EP1572962.
JD187596 - Sequence 168620 from Patent EP1572962.
JD186131 - Sequence 167155 from Patent EP1572962.
JD538586 - Sequence 519610 from Patent EP1572962.
JD206155 - Sequence 187179 from Patent EP1572962.
JD296830 - Sequence 277854 from Patent EP1572962.
JD176700 - Sequence 157724 from Patent EP1572962.
JD112645 - Sequence 93669 from Patent EP1572962.
JD374188 - Sequence 355212 from Patent EP1572962.
JD188150 - Sequence 169174 from Patent EP1572962.
JD124180 - Sequence 105204 from Patent EP1572962.
JD281908 - Sequence 262932 from Patent EP1572962.
JD244166 - Sequence 225190 from Patent EP1572962.
JD067001 - Sequence 48025 from Patent EP1572962.
JD530388 - Sequence 511412 from Patent EP1572962.
JD378333 - Sequence 359357 from Patent EP1572962.
JD204398 - Sequence 185422 from Patent EP1572962.
JD278095 - Sequence 259119 from Patent EP1572962.
JD356001 - Sequence 337025 from Patent EP1572962.
JD467018 - Sequence 448042 from Patent EP1572962.
JD141751 - Sequence 122775 from Patent EP1572962.
U28862 - Human NMDA receptor subtype 2B subunit (GRIN2B) mRNA, clone D, partial cds.
U28758 - Human NMDA receptor subtype 2B subunit (GRIN2B) mRNA, partial cds.
U28861 - Human NMDA receptor subtype 2B subunit (GRIN2B) mRNA, clone 52, partial cds.
JD042759 - Sequence 23783 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_nos1Pathway - Nitric Oxide Signaling Pathway

Reactome (by CSHL, EBI, and GO)

Protein Q13224 (Reactome details) participates in the following event(s):

R-HSA-3928623 EPHBs bind NMDARs
R-HSA-432172 Activation of NMDA receptor
R-HSA-432162 Unblocking of NMDA receptor
R-HSA-6794336 NMDAR binds PSD-95 subfamily members
R-HSA-3928645 EPHB:NMDAR binds TIAM1
R-HSA-3928583 FYN phosphorylates NMDAR2B
R-HSA-442760 Activation of RasGRF
R-HSA-6794349 NMDA receptor complex:DLG2,DLG3,DLG4 binds SPAR
R-HSA-6794356 BEGAIN binds DLG2,DLG3,DLG4
R-HSA-8849878 PSD-95 binds NMDA receptor
R-HSA-3928627 EPHB phosphorylates TIAM1
R-HSA-432164 Ca2+ influx into the post-synaptic cell
R-HSA-445367 CaMKII enters cytoplasm
R-HSA-6794354 NMDA receptor complex:DLG2,DLG3,DLG4:SPAR binds PDLIM5
R-HSA-8849906 SALM1 binds NMDA receptor
R-HSA-8849881 SALM2 associate with AMPA and NMDA receptors
R-HSA-4093336 p-TIAM1 exchanges GTP for GDP on RAC1, activating it
R-HSA-442732 Ras activation
R-HSA-5672965 RAS GEFs promote RAS nucleotide exchange
R-HSA-9032500 Activated NTRK2 signals through FYN
R-HSA-9006115 Signaling by NTRK2 (TRKB)
R-HSA-3928662 EPHB-mediated forward signaling
R-HSA-438066 Unblocking of NMDA receptor, glutamate binding and activation
R-HSA-6794361 Neurexins and neuroligins
R-HSA-166520 Signaling by NTRKs
R-HSA-2682334 EPH-Ephrin signaling
R-HSA-442982 Ras activation upon Ca2+ influx through NMDA receptor
R-HSA-442755 Activation of NMDA receptor and postsynaptic events
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-8849932 Synaptic adhesion-like molecules
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-422475 Axon guidance
R-HSA-442742 CREB phosphorylation through the activation of Ras
R-HSA-442729 CREB phosphorylation through the activation of CaMKII
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission
R-HSA-112316 Neuronal System
R-HSA-162582 Signal Transduction
R-HSA-1266738 Developmental Biology
R-HSA-438064 Post NMDA receptor activation events
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-5683057 MAPK family signaling cascades

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000609686.1, ENST00000609686.2, ENST00000609686.3, NMDAR2B, NMDE2_HUMAN, NM_000834, Q12919, Q13220, Q13224, Q13225, Q14CU4, Q9UM56, uc327mfb.1, uc327mfb.2
UCSC ID: ENST00000609686.4_6
RefSeq Accession: NM_000834.5
Protein: Q13224 (aka NMDE2_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene GRIN2B:
grin2b (GRIN2B-Related Neurodevelopmental Disorder)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.