Human Gene GRIK1 (uc002yno.1) Description and Page Index
  Description: Homo sapiens glutamate receptor, ionotropic, kainate 1 (GRIK1), transcript variant 1, mRNA.
RefSeq Summary (NM_000830): Glutamate receptors are the predominant excitatory neurotransmitter receptors in the mammalian brain and are activated in a variety of normal neurophysiologic processes. This gene product belongs to the kainate family of glutamate receptors, which are composed of four subunits and function as ligand-activated ion channels. The subunit encoded by this gene is subject to RNA editing (CAG->CGG; Q->R) within the second transmembrane domain, which is thought to alter the properties of ion flow. Alternative splicing, resulting in transcript variants encoding different isoforms, has been noted for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr21:30,925,866-31,312,282 Size: 386,417 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr21:30,925,876-31,311,818 Size: 385,943 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:30,925,866-31,312,282)mRNA (may differ from genome)Protein (918 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: GRIK1_HUMAN
DESCRIPTION: RecName: Full=Glutamate receptor, ionotropic kainate 1; AltName: Full=Excitatory amino acid receptor 3; Short=EAA3; AltName: Full=Glutamate receptor 5; Short=GluR-5; Short=GluR5; Flags: Precursor;
FUNCTION: Ionotropic glutamate receptor. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L- glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. May be involved in the transmission of light information from the retina to the hypothalamus.
SUBUNIT: Homotetramer or heterotetramer of pore-forming glutamate receptor subunits. Tetramers may be formed by the dimerization of dimers (Probable). The unedited version (Q) assembles into a functional kainate-gated homomeric channel, whereas the edited version (R) is unable to produce channel activity when expressed alone. Both edited and unedited versions can form functional channels with GRIK4 and GRIK5. Interacts with KLHL17 (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein. Cell junction, synapse, postsynaptic cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Most abundant in the cerebellum and the suprachiasmatic nuclei (SCN) of the hypothalamus.
RNA EDITING: Modified_positions=636; Note=Partially edited.
MISCELLANEOUS: The postsynaptic actions of Glu are mediated by a variety of receptors that are named according to their selective agonists. This receptor binds domoate > kainate > L-glutamate = quisqualate > CNQX = DNQX > AMPA > dihydrokainate > NMDA.
SIMILARITY: Belongs to the glutamate-gated ion channel (TC 1.A.10.1) family. GRIK1 subfamily.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GRIK1
CDC HuGE Published Literature: GRIK1
Positive Disease Associations: Attention Deficit Disorder with Hyperactivity , Body Mass Index , Body Weight , Breast cancer , epilepsy , Huntington disease , hyperactive-impulsive symptoms , Leukocyte Count , Sleep
Related Studies:
  1. Attention Deficit Disorder with Hyperactivity
    Jessica Lasky-Su et al. American journal of medical genetics. Part B, Neuropsychiatric genetics 2008, Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations., American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetic. [PubMed 18821565]
  2. Body Mass Index
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Body Mass Index
    Ke-Sheng Wang et al. Gene 2012, A novel locus for body mass index on 5p15.2: a meta-analysis of two genome-wide association studies., Gene. [PubMed 22446040]
    We identified a novel locus for BMI. These findings offer the potential for new insights into the pathogenesis of BMI and obesity and will serve as a resource for replication in other populations to elucidate the potential role of these genetic variants in BMI and obesity.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: GRIK1
Diseases sorted by gene-association score: monosomy 21 (18), juvenile absence epilepsy (14), schizophrenia 4 (10), temporal lobe epilepsy (9), autosomal recessive non-syndromic intellectual disability (2), childhood absence epilepsy (2), schizophrenia (1)

-  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: 6.48 RPKM in Brain - Hypothalamus
Total median expression: 43.65 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 -195.80464-0.422 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

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

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2ZNS
- X-ray MuPIT

2ZNT
- X-ray MuPIT

2ZNU
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
3FUZ - X-ray MuPIT 3FV1 - X-ray MuPIT 3FV2 - X-ray MuPIT
3FVG - X-ray MuPIT 3FVK - X-ray MuPIT 3FVN - X-ray MuPIT
3FVO - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P39086
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004970 ionotropic glutamate receptor activity
GO:0005216 ion channel activity
GO:0005234 extracellular-glutamate-gated ion channel activity
GO:0015276 ligand-gated ion channel activity
GO:0015277 kainate selective glutamate receptor activity
GO:0038023 signaling receptor activity

Biological Process:
GO:0006811 ion transport
GO:0007215 glutamate receptor signaling pathway
GO:0007268 chemical synaptic transmission
GO:0007399 nervous system development
GO:0007417 central nervous system development
GO:0034220 ion transmembrane transport
GO:0035235 ionotropic glutamate receptor signaling pathway
GO:0051966 regulation of synaptic transmission, glutamatergic
GO:0060079 excitatory postsynaptic potential

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0045202 synapse
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  AK296404 - Homo sapiens cDNA FLJ61302 complete cds, highly similar to Glutamate receptor, ionotropic kainate 1 precursor.
BC111793 - Homo sapiens cDNA clone IMAGE:40028200, **** WARNING: chimeric clone ****.
AJ249208 - Homo sapiens mRNA for glutamate receptor subunit GluR5 (GRIK1 gene).
U16125 - Human glutamate/kainate receptor subunit (EEA3) mRNA, complete cds.
BC152727 - Synthetic construct Homo sapiens clone IMAGE:100015997, MGC:184110 glutamate receptor, ionotropic, kainate 1 (GRIK1) mRNA, encodes complete protein.
BC156975 - Synthetic construct Homo sapiens clone IMAGE:100062820, MGC:190620 glutamate receptor, ionotropic, kainate 1 (GRIK1) mRNA, encodes complete protein.
AK294353 - Homo sapiens cDNA FLJ50134 partial cds, highly similar to Homo sapiens glutamate receptor, ionotropic, kainate 1 (GRIK1), transcript variant 2, mRNA.
L19058 - Human glutamate receptor (GLUR5) mRNA, complete cds.
BC028238 - Homo sapiens, clone IMAGE:5244103, mRNA.
AK095150 - Homo sapiens cDNA FLJ37831 fis, clone BRSSN2009627.
JD436556 - Sequence 417580 from Patent EP1572962.
JD122765 - Sequence 103789 from Patent EP1572962.
JD142227 - Sequence 123251 from Patent EP1572962.
JD520435 - Sequence 501459 from Patent EP1572962.
JD260167 - Sequence 241191 from Patent EP1572962.
JD376917 - Sequence 357941 from Patent EP1572962.
JD389720 - Sequence 370744 from Patent EP1572962.
JD389678 - Sequence 370702 from Patent EP1572962.
JD253376 - Sequence 234400 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04080 - Neuroactive ligand-receptor interaction

Reactome (by CSHL, EBI, and GO)

Protein P39086 (Reactome details) participates in the following event(s):

R-HSA-451283 kainate receptor binds glutamate
R-HSA-451311 Activation of Ca-permeable Kainate receptors
R-HSA-451309 Edited Kainate Receptor binds glutamate
R-HSA-451310 Activation of Edited Kainate receptors
R-HSA-451308 Activation of Ca-permeable Kainate Receptor
R-HSA-451307 Activation of Na-permeable kainate receptors
R-HSA-451306 Ionotropic activity of kainate receptors
R-HSA-451326 Activation of kainate receptors upon glutamate binding
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: GLUR5, GRIK1_HUMAN, NM_000830, NP_000821, P39086, Q13001, Q86SU9
UCSC ID: uc002yno.1
RefSeq Accession: NM_000830
Protein: P39086 (aka GRIK1_HUMAN or GLK1_HUMAN)
CCDS: CCDS42913.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000830.3
exon count: 17CDS single in 3' UTR: no RNA size: 3231
ORF size: 2757CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5554.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.