Human Gene GRIN3A (ENST00000361820.6_8) from GENCODE V47lift37
  Description: glutamate ionotropic receptor NMDA type subunit 3A (from RefSeq NM_133445.3)
Gencode Transcript: ENST00000361820.6_8
Gencode Gene: ENSG00000198785.7_11
Transcript (Including UTRs)
   Position: hg19 chr9:104,331,634-104,500,929 Size: 169,296 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr9:104,335,456-104,500,261 Size: 164,806 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:104,331,634-104,500,929)mRNA (may differ from genome)Protein (1115 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NMD3A_HUMAN
DESCRIPTION: RecName: Full=Glutamate [NMDA] receptor subunit 3A; AltName: Full=N-methyl-D-aspartate receptor subtype 3A; Short=NMDAR3A; Short=NR3A; AltName: Full=NMDAR-L; Flags: Precursor;
FUNCTION: NMDA receptor subtype of glutamate-gated ion channels with reduced single-channel conductance, low calcium permeability and low voltage-dependent sensitivity to magnesium. Mediated by glycine. May play a role in the development of dendritic spines. May play a role in PPP2CB-NMDAR mediated signaling mechanism (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). Does not form functional homomeric channels. Found in a complex with GRIN1, GRIN2A or GRIN2B and PPP2CB. Probably interacts with PPP2CB. No complex with PPP2CB is detected when NMDARs are stimulated by NMDA (By similarity).
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. Requires the presence of GRIN1 to be targeted at the plasma membrane (By similarity).
DEVELOPMENTAL STAGE: Expressed in fetal brain.
PTM: N-glycosylated (By similarity).
SIMILARITY: Belongs to the glutamate-gated ion channel (TC 1.A.10.1) family. NR3A/GRIN3A subfamily.
SEQUENCE CAUTION: Sequence=BAB85559.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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: GRIN3A
Diseases sorted by gene-association score: lingual-facial-buccal dyskinesia (6)

-  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: 1.73 RPKM in Brain - Anterior cingulate cortex (BA24)
Total median expression: 12.93 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 -327.80668-0.491 Picture PostScript Text
3' UTR -1086.403822-0.284 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
IPR019594 - Glu_rcpt_Glu/Gly-bd
IPR001320 - Iontro_glu_rcpt
IPR001508 - NMDA_rcpt
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
PF10613 - Ligated ion channel L-glutamate- and glycine-binding site

SCOP Domains:
53822 - Periplasmic binding protein-like I
53850 - Periplasmic binding protein-like II
81324 - Voltage-gated potassium channels

ModBase Predicted Comparative 3D Structure on Q8TCU5
FrontTopSide
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    
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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:0005216 ion channel activity
GO:0005234 extracellular-glutamate-gated ion channel activity
GO:0005262 calcium channel activity
GO:0005515 protein binding
GO:0016594 glycine binding
GO:0038023 signaling receptor activity
GO:0042802 identical protein binding
GO:0051721 protein phosphatase 2A binding

Biological Process:
GO:0006811 ion transport
GO:0006816 calcium ion transport
GO:0007165 signal transduction
GO:0016358 dendrite development
GO:0034220 ion transmembrane transport
GO:0035235 ionotropic glutamate receptor signaling pathway
GO:0045471 response to ethanol
GO:0060079 excitatory postsynaptic potential
GO:0060134 prepulse inhibition
GO:0070588 calcium ion transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
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:0043025 neuronal cell body
GO:0045202 synapse
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  KJ904966 - Synthetic construct Homo sapiens clone ccsbBroadEn_14360 GRIN3A-like gene, encodes complete protein.
BC029757 - Homo sapiens glutamate receptor, ionotropic, N-methyl-D-aspartate 3A, mRNA (cDNA clone IMAGE:4344092), with apparent retained intron.
BC167432 - Homo sapiens glutamate receptor, ionotropic, N-methyl-D-aspartate 3A, mRNA (cDNA clone MGC:166907 IMAGE:8860109), complete cds.
AB075853 - Homo sapiens mRNA for KIAA1973 protein.
BC132866 - Homo sapiens glutamate receptor, ionotropic, N-methyl-D-aspartate 3A, mRNA (cDNA clone MGC:164497 IMAGE:40146888), complete cds.
BC132868 - Homo sapiens glutamate receptor, ionotropic, N-methyl-D-aspartate 3A, mRNA (cDNA clone MGC:164499 IMAGE:40146890), complete cds.
AF416558 - Homo sapiens N-methyl-D-aspartate receptor 3A (GRIN3A) mRNA, complete cds.
AJ416950 - Homo sapiens mRNA for N-methyl D-aspartate subunit 3A (GRIN3A gene).
AB385519 - Synthetic construct DNA, clone: pF1KA1973, Homo sapiens GRIN3A gene for glutamate [NMDA] receptor subunit 3A precursor, complete cds, without stop codon, in Flexi system.
AK127342 - Homo sapiens cDNA FLJ45414 fis, clone BRHIP3033557, highly similar to Rattus norvegicus N-methyl-D-aspartate receptor.
AL137422 - Homo sapiens mRNA; cDNA DKFZp761A1623 (from clone DKFZp761A1623).
JD297500 - Sequence 278524 from Patent EP1572962.
JD408668 - Sequence 389692 from Patent EP1572962.
JD307547 - Sequence 288571 from Patent EP1572962.
JD561742 - Sequence 542766 from Patent EP1572962.
JD296226 - Sequence 277250 from Patent EP1572962.
JD284791 - Sequence 265815 from Patent EP1572962.
JD047372 - Sequence 28396 from Patent EP1572962.
JD552521 - Sequence 533545 from Patent EP1572962.
JD450417 - Sequence 431441 from Patent EP1572962.
JD491034 - Sequence 472058 from Patent EP1572962.
JD259550 - Sequence 240574 from Patent EP1572962.
JD174304 - Sequence 155328 from Patent EP1572962.
JD282190 - Sequence 263214 from Patent EP1572962.
JD494646 - Sequence 475670 from Patent EP1572962.
JD343889 - Sequence 324913 from Patent EP1572962.
JD237917 - Sequence 218941 from Patent EP1572962.
JD274624 - Sequence 255648 from Patent EP1572962.
JD358525 - Sequence 339549 from Patent EP1572962.
JD133338 - Sequence 114362 from Patent EP1572962.
JD068684 - Sequence 49708 from Patent EP1572962.
JD540734 - Sequence 521758 from Patent EP1572962.
JD311044 - Sequence 292068 from Patent EP1572962.
JD409358 - Sequence 390382 from Patent EP1572962.
JD295284 - Sequence 276308 from Patent EP1572962.
JD284756 - Sequence 265780 from Patent EP1572962.
JD153451 - Sequence 134475 from Patent EP1572962.
JD051020 - Sequence 32044 from Patent EP1572962.
JD315981 - Sequence 297005 from Patent EP1572962.
JD392373 - Sequence 373397 from Patent EP1572962.
JD206305 - Sequence 187329 from Patent EP1572962.
JD433817 - Sequence 414841 from Patent EP1572962.
JD199204 - Sequence 180228 from Patent EP1572962.
JD563094 - Sequence 544118 from Patent EP1572962.
JD339308 - Sequence 320332 from Patent EP1572962.
JD475020 - Sequence 456044 from Patent EP1572962.
JD115099 - Sequence 96123 from Patent EP1572962.
JD157115 - Sequence 138139 from Patent EP1572962.
JD433217 - Sequence 414241 from Patent EP1572962.
JD501933 - Sequence 482957 from Patent EP1572962.
JD362680 - Sequence 343704 from Patent EP1572962.
JD444169 - Sequence 425193 from Patent EP1572962.
JD221109 - Sequence 202133 from Patent EP1572962.
JD219094 - Sequence 200118 from Patent EP1572962.
JD544684 - Sequence 525708 from Patent EP1572962.
JD532900 - Sequence 513924 from Patent EP1572962.
JD389184 - Sequence 370208 from Patent EP1572962.
JD320473 - Sequence 301497 from Patent EP1572962.
JD241845 - Sequence 222869 from Patent EP1572962.
JD548877 - Sequence 529901 from Patent EP1572962.
JD146644 - Sequence 127668 from Patent EP1572962.
JD082362 - Sequence 63386 from Patent EP1572962.
JD494794 - Sequence 475818 from Patent EP1572962.
JD365883 - Sequence 346907 from Patent EP1572962.
JD043647 - Sequence 24671 from Patent EP1572962.
JD260127 - Sequence 241151 from Patent EP1572962.
JD273130 - Sequence 254154 from Patent EP1572962.
AL359651 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 2190570.
JD167078 - Sequence 148102 from Patent EP1572962.
JD418120 - Sequence 399144 from Patent EP1572962.
JD370553 - Sequence 351577 from Patent EP1572962.
JD151818 - Sequence 132842 from Patent EP1572962.
JD416642 - Sequence 397666 from Patent EP1572962.
JD264208 - Sequence 245232 from Patent EP1572962.
JD166026 - Sequence 147050 from Patent EP1572962.
JD217523 - Sequence 198547 from Patent EP1572962.
JD474835 - Sequence 455859 from Patent EP1572962.
JD474834 - Sequence 455858 from Patent EP1572962.
JD240371 - Sequence 221395 from Patent EP1572962.
JD172759 - Sequence 153783 from Patent EP1572962.
JD461642 - Sequence 442666 from Patent EP1572962.
JD478175 - Sequence 459199 from Patent EP1572962.
JD484012 - Sequence 465036 from Patent EP1572962.
JD225223 - Sequence 206247 from Patent EP1572962.
JD046371 - Sequence 27395 from Patent EP1572962.
JD065482 - Sequence 46506 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B3DLF9, ENST00000361820.1, ENST00000361820.2, ENST00000361820.3, ENST00000361820.4, ENST00000361820.5, KIAA1973, NMD3A_HUMAN, NM_133445, Q5VTR3, Q8TCU5, Q8TF29, Q8WXI6, uc318cja.1, uc318cja.2
UCSC ID: ENST00000361820.6_8
RefSeq Accession: NM_133445.3
Protein: Q8TCU5 (aka NMD3A_HUMAN or NM3A_HUMAN)

-  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.