Human Gene GRIN1 (ENST00000371559.8) from GENCODE V44
  Description: Homo sapiens glutamate ionotropic receptor NMDA type subunit 1 (GRIN1), transcript variant GluN1-4a, mRNA. (from RefSeq NM_000832)
RefSeq Summary (NM_000832): The protein encoded by this gene is a critical subunit of N-methyl-D-aspartate receptors, members of the glutamate receptor channel superfamily which are heteromeric protein complexes with multiple subunits arranged to form a ligand-gated ion channel. These subunits play a key role in the plasticity of synapses, which is believed to underlie memory and learning. Cell-specific factors are thought to control expression of different isoforms, possibly contributing to the functional diversity of the subunits. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000371559.8
Gencode Gene: ENSG00000176884.17
Transcript (Including UTRs)
   Position: hg38 chr9:137,139,481-137,168,755 Size: 29,275 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg38 chr9:137,139,487-137,167,842 Size: 28,356 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:137,139,481-137,168,755)mRNA (may differ from genome)Protein (885 aa)
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HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NMDZ1_HUMAN
DESCRIPTION: RecName: Full=Glutamate [NMDA] receptor subunit zeta-1; AltName: Full=N-methyl-D-aspartate receptor subunit NR1; Short=NMD-R1; Flags: Precursor;
FUNCTION: NMDA receptor subtype of glutamate-gated ion channels with high calcium permeability and voltage-dependent sensitivity to magnesium. Mediated by glycine. This protein plays a key role in synaptic plasticity, synaptogenesis, excitotoxicity, memory acquisition and learning. It mediates neuronal functions in glutamate neurotransmission. Is involved in the cell surface targeting of NMDA receptors (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); disulfide-linked. Found in a complex with GRIN2A or GRIN2B, GRIN3A or GRIN3B and PPP2CB. Interacts with DLG4 and MPDZ (By similarity). Interacts with LRFN1 and LRFN2 (By similarity). Interacts with MYZAP.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein (By similarity). Cell junction, synapse, postsynaptic cell membrane (By similarity). Cell junction, synapse, postsynaptic cell membrane, postsynaptic density (By similarity). Note=Enriched in postsynaptic plasma membrane and postsynaptic densities (By similarity).
PTM: NMDA is probably regulated by C-terminal phosphorylation of an isoform of NR1 by PKC. Dephosphorylated on Ser-897 probably by protein phosphatase 2A (PPP2CB). Its phosphorylated state is influenced by the formation of the NMDAR-PPP2CB complex and the NMDAR channel activity (By similarity).
DISEASE: Defects in GRIN1 are the cause of mental retardation autosomal dominant type 8 (MRD8) [MIM:614254]. Mental retardation is characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period.
SIMILARITY: Belongs to the glutamate-gated ion channel (TC 1.A.10.1) family. NR1/GRIN1 subfamily.
WEB RESOURCE: Name=Wikipedia; Note=NMDA receptor entry; URL="http://en.wikipedia.org/wiki/NMDA_receptor";

-  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: GRIN1
Diseases sorted by gene-association score: mental retardation, autosomal dominant 8* (1329), autosomal dominant non-syndromic intellectual disability* (111), intellectual disability* (102), alacrima, achalasia, and mental retardation syndrome* (73), amblyopia (17), high pressure neurological syndrome (11), spinal cord injury (8), suppression amblyopia (8), temporal lobe epilepsy (7), dysembryoplastic neuroepithelial tumor (7), morphine dependence (6), conduct disorder (6), occlusion precerebral artery (5), huntington disease (5), sudden infant death syndrome (3), rett syndrome (3), schizophrenia (3), alzheimer disease (3), alcohol dependence (2)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 121.07 RPKM in Brain - Cortex
Total median expression: 765.81 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
3' UTR -439.60913-0.481 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
IPR018882 - CaM-bd_C0_NMDA_rcpt_NR1
IPR019594 - Glu_rcpt_Glu/Gly-bd
IPR001320 - Iontro_glu_rcpt
IPR001508 - NMDA_rcpt
IPR001638 - SBP_bac_3

Pfam Domains:
PF01094 - Receptor family ligand binding region
PF10562 - Calmodulin-binding domain C0 of NMDA receptor NR1 subunit
PF00060 - Ligand-gated ion channel
PF00497 - Bacterial extracellular solute-binding proteins, family 3

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2NR1 - NMR MuPIT 3BYA - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q05586
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-  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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  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:0005102 receptor binding
GO:0005216 ion channel activity
GO:0005234 extracellular-glutamate-gated ion channel activity
GO:0005261 cation channel activity
GO:0005262 calcium channel activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0016594 glycine binding
GO:0016595 glutamate binding
GO:0022849 glutamate-gated calcium ion channel activity
GO:0038023 signaling receptor activity
GO:0042165 neurotransmitter binding
GO:0044877 macromolecular complex binding
GO:1904315 transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential

Biological Process:
GO:0000165 MAPK cascade
GO:0001661 conditioned taste aversion
GO:0001964 startle response
GO:0001967 suckling behavior
GO:0001975 response to amphetamine
GO:0006811 ion transport
GO:0006812 cation transport
GO:0006816 calcium ion transport
GO:0006874 cellular calcium ion homeostasis
GO:0007420 brain development
GO:0007585 respiratory gaseous exchange
GO:0007611 learning or memory
GO:0007612 learning
GO:0007613 memory
GO:0007616 long-term memory
GO:0008306 associative learning
GO:0008344 adult locomotory behavior
GO:0008355 olfactory learning
GO:0008542 visual learning
GO:0010524 positive regulation of calcium ion transport into cytosol
GO:0010646 regulation of cell communication
GO:0018964 propylene metabolic process
GO:0019233 sensory perception of pain
GO:0019722 calcium-mediated signaling
GO:0021586 pons maturation
GO:0021987 cerebral cortex development
GO:0035176 social behavior
GO:0035235 ionotropic glutamate receptor signaling pathway
GO:0035249 synaptic transmission, glutamatergic
GO:0042391 regulation of membrane potential
GO:0043065 positive regulation of apoptotic process
GO:0043278 response to morphine
GO:0043523 regulation of neuron apoptotic process
GO:0043524 negative regulation of neuron apoptotic process
GO:0043576 regulation of respiratory gaseous exchange
GO:0045471 response to ethanol
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048013 ephrin receptor signaling pathway
GO:0048167 regulation of synaptic plasticity
GO:0048168 regulation of neuronal synaptic plasticity
GO:0048169 regulation of long-term neuronal synaptic plasticity
GO:0048814 regulation of dendrite morphogenesis
GO:0050770 regulation of axonogenesis
GO:0050905 neuromuscular process
GO:0051290 protein heterotetramerization
GO:0051963 regulation of synapse assembly
GO:0055074 calcium ion homeostasis
GO:0060079 excitatory postsynaptic potential
GO:0060134 prepulse inhibition
GO:0060179 male mating behavior
GO:0097553 calcium ion transmembrane import into cytosol
GO:0098976 excitatory chemical synaptic transmission
GO:1903428 positive regulation of reactive oxygen species biosynthetic process
GO:1903539 protein localization to postsynaptic membrane
GO:1905429 response to glycine
GO:2000463 positive regulation of excitatory postsynaptic potential
GO:2001056 positive regulation of cysteine-type endopeptidase activity
GO:1904646 cellular response to beta-amyloid

Cellular Component:
GO:0005622 intracellular
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0008021 synaptic vesicle
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:0030425 dendrite
GO:0043005 neuron projection
GO:0043083 synaptic cleft
GO:0043195 terminal bouton
GO:0043197 dendritic spine
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0060076 excitatory synapse
GO:0097060 synaptic membrane
GO:0098839 postsynaptic density membrane


-  Descriptions from all associated GenBank mRNAs
  BC156097 - Synthetic construct Homo sapiens clone IMAGE:100062312, MGC:190458 glutamate receptor, ionotropic, N-methyl D-aspartate 1 (GRIN1) mRNA, encodes complete protein.
BC156961 - Synthetic construct Homo sapiens clone IMAGE:100063609, MGC:190823 glutamate receptor, ionotropic, N-methyl D-aspartate 1 (GRIN1) mRNA, encodes complete protein.
L13266 - Homo sapiens N-methyl-d-aspartate receptor (NR1-1) mRNA, complete cds.
AB208999 - Homo sapiens mRNA for NMDA receptor 1 isoform NR1-2 precursor variant protein.
D13515 - Homo sapiens mRNA for key subunit of N-methyl-D-aspartate receptor, complete cds.
AB208918 - Homo sapiens mRNA for NMDA receptor 1 isoform NR1-2 precursor variant protein.
AF015731 - Homo sapiens NMDAR1 subunit isoform 4b (hNMDAR1-4b) mRNA, complete cds.
AF015730 - Homo sapiens NMDAR1 subunit isoform 3b (hNMDAR1-3b) mRNA, complete cds.
L05666 - Homo sapiens NMDA receptor subunit (NR1) mRNA, complete cds.
AB590080 - Synthetic construct DNA, clone: pFN21AB3278, Homo sapiens GRIN1 gene for glutamate receptor, ionotropic, N-methyl D-aspartate 1, without stop codon, in Flexi system.
L13268 - Homo sapiens N-methyl-d-aspartate receptor (NR1-3) mRNA, 3' end.
U08107 - Human N-methyl-D-aspartate receptor subunit splice variant hNR1N (GRIN1) mRNA, partial cds.
L13267 - Homo sapiens N-methyl-d-aspartate receptor (NR1-2) mRNA, 3' end.
U08106 - Human N-methyl-D-aspartate receptor subunit splice variant hNR1-4 (GRIN1) mRNA, partial cds.
S57708 - N-methyl-D-aspartate glutamate receptor channel [human, teratocarcinoma line NT2, mRNA Partial, 304 nt].
JD109448 - Sequence 90472 from Patent EP1572962.
JD487746 - Sequence 468770 from Patent EP1572962.
LF211795 - JP 2014500723-A/19298: Polycomb-Associated Non-Coding RNAs.
MA447372 - JP 2018138019-A/19298: Polycomb-Associated Non-Coding RNAs.
JD054761 - Sequence 35785 from Patent EP1572962.
JD462765 - Sequence 443789 from Patent EP1572962.
JD080028 - Sequence 61052 from Patent EP1572962.
JD394814 - Sequence 375838 from Patent EP1572962.
JD426422 - Sequence 407446 from Patent EP1572962.
JD163697 - Sequence 144721 from Patent EP1572962.
JD140018 - Sequence 121042 from Patent EP1572962.
JD498712 - Sequence 479736 from Patent EP1572962.
JD187303 - Sequence 168327 from Patent EP1572962.
JD134190 - Sequence 115214 from Patent EP1572962.
JD431761 - Sequence 412785 from Patent EP1572962.
JD051324 - Sequence 32348 from Patent EP1572962.
JD174235 - Sequence 155259 from Patent EP1572962.
JD215451 - Sequence 196475 from Patent EP1572962.
JD189581 - Sequence 170605 from Patent EP1572962.
JD383006 - Sequence 364030 from Patent EP1572962.
JD461070 - Sequence 442094 from Patent EP1572962.
JD396330 - Sequence 377354 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04020 - Calcium signaling pathway
hsa04080 - Neuroactive ligand-receptor interaction
hsa04720 - Long-term potentiation
hsa05010 - Alzheimer's disease
hsa05014 - Amyotrophic lateral sclerosis (ALS)
hsa05016 - Huntington's disease

Reactome (by CSHL, EBI, and GO)

Protein Q05586 (Reactome details) participates in the following event(s):

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-442760 Activation of RasGRF
R-HSA-3928623 EPHBs bind NMDARs
R-HSA-3928645 EPHB:NMDAR binds TIAM1
R-HSA-3928583 FYN phosphorylates NMDAR2B
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-432164 Ca2+ influx into the post-synaptic cell
R-HSA-445367 CaMKII enters cytoplasm
R-HSA-3928627 EPHB phosphorylates TIAM1
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-442732 Ras activation
R-HSA-4093336 p-TIAM1 exchanges GTP for GDP on RAC1, activating it
R-HSA-5672965 RAS GEFs promote RAS nucleotide exchange
R-HSA-438066 Unblocking of NMDA receptor, glutamate binding and activation
R-HSA-6794361 Neurexins and neuroligins
R-HSA-442982 Ras activation upon Ca2+ influx through NMDA receptor
R-HSA-442755 Activation of NMDA receptor and postsynaptic events
R-HSA-3928662 EPHB-mediated forward signaling
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-8849932 Synaptic adhesion-like molecules
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-2682334 EPH-Ephrin signaling
R-HSA-112316 Neuronal System
R-HSA-438064 Post NMDA receptor activation events
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-422475 Axon guidance
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-1266738 Developmental Biology
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-5683057 MAPK family signaling cascades
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: A6NLK7, A6NLR1, C9K0X1, ENST00000371559.1, ENST00000371559.2, ENST00000371559.3, ENST00000371559.4, ENST00000371559.5, ENST00000371559.6, ENST00000371559.7, NMDAR1, NMDZ1_HUMAN, NM_000832, P35437, Q05586, Q12867, Q12868, Q5VSF3, Q5VSF6, Q5VSF7, Q5VSF8, uc004clm.1, uc004clm.2, uc004clm.3, uc004clm.4
UCSC ID: ENST00000371559.8
RefSeq Accession: NM_000832
Protein: Q05586 (aka NMDZ1_HUMAN)
CCDS: CCDS7032.1, CCDS43910.1, CCDS55355.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene GRIN1:
grin1-ndd (GRIN1-Related Neurodevelopmental Disorder)

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