Gene Page: GRIN2D

Summary ?
GeneID2906
SymbolGRIN2D
SynonymsEB11|GluN2D|NMDAR2D|NR2D
Descriptionglutamate ionotropic receptor NMDA type subunit 2D
ReferenceMIM:602717|HGNC:HGNC:4588|Ensembl:ENSG00000105464|HPRD:04095|Vega:OTTHUMG00000183304
Gene typeprotein-coding
Map location19q13.33
Pascal p-value0.35
Fetal beta-0.967
SupportLIGAND GATED ION SIGNALING
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
G2Cdb.human_TAP-PSD-95-CORE
G2Cdb.humanPSD
G2Cdb.humanPSP
CompositeSet
Potential synaptic genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
AssociationA combined odds ratio method (Sun et al. 2008), association studies1Link to SZGene
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 4 
NetworkShortest path distance of core genes in the Human protein-protein interaction networkContribution to shortest path in PPI network: 0.092 

Section I. Genetics and epigenetics annotation


Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
HSP90B10.870.85
TM9SF20.860.84
COPB20.860.83
SRP540.860.86
RAB5A0.860.83
ATP2C10.850.84
CANX0.850.83
NIPA20.850.79
CALR0.840.79
PSMD10.830.83
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.21-0.69-0.59
MT-CO2-0.69-0.66
FXYD1-0.67-0.62
AF347015.33-0.66-0.64
AF347015.31-0.66-0.64
AF347015.8-0.65-0.63
AF347015.2-0.64-0.65
HIGD1B-0.64-0.60
IFI27-0.63-0.60
MT-CYB-0.62-0.60

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004972N-methyl-D-aspartate selective glutamate receptor activityIEAglutamate (GO term level: 8)-
GO:0005234extracellular-glutamate-gated ion channel activityIEAglutamate (GO term level: 11)-
GO:0000287magnesium ion bindingIEA-
GO:0004872receptor activityIEA-
GO:0005509calcium ion bindingIEA-
GO:0005216ion channel activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0001964startle responseIEA-
GO:0007165signal transductionNAS9480759 
GO:0008344adult locomotory behaviorIEA-
GO:0006811ion transportIEA-
GO:0051930regulation of sensory perception of painIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0019717synaptosomeIEASynap, Brain (GO term level: 7)-
GO:0045211postsynaptic membraneIEASynap, Neurotransmitter (GO term level: 5)-
GO:0045202synapseIEAneuron, Synap, Neurotransmitter, Glial (GO term level: 2)-
GO:0016021integral to membraneIEA-
GO:0005886plasma membraneIEA-
GO:0030054cell junctionIEA-

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
ABL1ABL | JTK7 | bcr/abl | c-ABL | p150 | v-ablc-abl oncogene 1, receptor tyrosine kinase-HPRD10777567 
DLG4FLJ97752 | FLJ98574 | PSD95 | SAP90discs, large homolog 4 (Drosophila)-HPRD,BioGRID7569905 
DLGAP4DAP4 | KIAA0964 | MGC131862 | RP5-977B1.6 | SAPAP4discs, large (Drosophila) homolog-associated protein 4-HPRD10862698 
DNM1DNMdynamin 1-HPRD10862698 
DUSP4HVH2 | MKP-2 | MKP2 | TYPdual specificity phosphatase 4-HPRD10862698 
GRIN1NMDA1 | NMDAR1 | NR1glutamate receptor, ionotropic, N-methyl D-aspartate 1-HPRD12191494 
IL16FLJ16806 | FLJ42735 | FLJ44234 | HsT19289 | IL-16 | LCF | prIL-16interleukin 16 (lymphocyte chemoattractant factor)-HPRD,BioGRID10479680 
INADLCipp | FLJ26982 | InaD-like | PATJInaD-like (Drosophila)-HPRD9647694 
MAP2DKFZp686I2148 | MAP2A | MAP2B | MAP2Cmicrotubule-associated protein 2-HPRD10862698 
NANOS1NOS1nanos homolog 1 (Drosophila)-HPRD10862698 
PPP2R1AMGC786 | PR65Aprotein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform-HPRD10862698 
SYNGAP1DKFZp761G1421 | KIAA1938 | RASA1 | RASA5 | SYNGAPsynaptic Ras GTPase activating protein 1 homolog (rat)-HPRD10862698 
TJP1DKFZp686M05161 | MGC133289 | ZO-1tight junction protein 1 (zona occludens 1)-HPRD10862698 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG CALCIUM SIGNALING PATHWAY 178134All SZGR 2.0 genes in this pathway
KEGG NEUROACTIVE LIGAND RECEPTOR INTERACTION 272195All SZGR 2.0 genes in this pathway
KEGG LONG TERM POTENTIATION 7057All SZGR 2.0 genes in this pathway
KEGG ALZHEIMERS DISEASE 169110All SZGR 2.0 genes in this pathway
KEGG AMYOTROPHIC LATERAL SCLEROSIS ALS 5343All SZGR 2.0 genes in this pathway
BIOCARTA NOS1 PATHWAY 2421All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES 186155All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM 279221All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 137110All SZGR 2.0 genes in this pathway
REACTOME RAS ACTIVATION UOPN CA2 INFUX THROUGH NMDA RECEPTOR 1715All SZGR 2.0 genes in this pathway
REACTOME ACTIVATION OF NMDA RECEPTOR UPON GLUTAMATE BINDING AND POSTSYNAPTIC EVENTS 3732All SZGR 2.0 genes in this pathway
REACTOME CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF RAS 2723All SZGR 2.0 genes in this pathway
REACTOME POST NMDA RECEPTOR ACTIVATION EVENTS 3328All SZGR 2.0 genes in this pathway
REACTOME UNBLOCKING OF NMDA RECEPTOR GLUTAMATE BINDING AND ACTIVATION 1514All SZGR 2.0 genes in this pathway
REACTOME CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII 1514All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038678All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS 882572All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE UP 578341All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491319All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE 1137655All SZGR 2.0 genes in this pathway