Human Gene GRIK4 (uc001pxn.2)
  Description: Homo sapiens glutamate receptor, ionotropic, kainate 4 (GRIK4), mRNA.
RefSeq Summary (NM_014619): This gene encodes a protein that belongs to the glutamate-gated ionic channel family. Glutamate functions as the major excitatory neurotransmitter in the central nervous system through activation of ligand-gated ion channels and G protein-coupled membrane receptors. The protein encoded by this gene forms functional heteromeric kainate-preferring ionic channels with the subunits encoded by related gene family members. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013].
Transcript (Including UTRs)
   Position: hg19 chr11:120,382,468-120,856,969 Size: 474,502 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr11:120,531,028-120,856,969 Size: 325,942 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:120,382,468-120,856,969)mRNA (may differ from genome)Protein (956 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDHuman Cortex Gene ExpressionLynxMalacards
MGIneXtProtOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GRIK4_HUMAN
DESCRIPTION: RecName: Full=Glutamate receptor, ionotropic kainate 4; AltName: Full=Excitatory amino acid receptor 1; Short=EAA1; AltName: Full=Glutamate receptor KA-1; Short=KA1; Flags: Precursor;
FUNCTION: Receptor for glutamate. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. The postsynaptic actions of Glu are mediated by a variety of receptors that are named according to their selective agonists.
SUBUNIT: Forms a heteromeric channel with GRIK1 or GRIK3.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein. Cell junction, synapse, postsynaptic cell membrane; Multi-pass membrane protein.
SIMILARITY: Belongs to the glutamate-gated ion channel (TC 1.A.10.1) family. GRIK4 subfamily.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GRIK4
CDC HuGE Published Literature: GRIK4
Positive Disease Associations: Cognitive performance , Hematocrit , Stroke , Waist Circumference
Related Studies:
  1. Cognitive performance
    Cirulli ,et al. Eur J Hum Genet 2010, Common genetic variation and performance on standardized cognitive tests , European journal of human genetics : EJHG 2010 . [PubMed 20125193]
  2. Hematocrit
    Qiong Yang et al. BMC medical genetics 2007, Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903294]
    Using genome-wide association methodology, we have successfully identified a SNP in complete LD with a sequence variant previously shown to be strongly associated with factor VII, providing proof of principle for this approach. Further study of additional strongly associated SNPs and linked regions may identify novel variants that influence the inter-individual variability in hemostatic factors and hematological phenotypes.
  3. Stroke
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: GRIK4
Diseases sorted by gene-association score: grik4-related altered drug metabolism* (100), schizophrenia (2)
* = 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: 3.10 RPKM in Brain - Caudate (basal ganglia)
Total median expression: 37.18 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 -130.70287-0.455 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

ModBase Predicted Comparative 3D Structure on Q16099
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  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:0034220 ion transmembrane transport
GO:0035235 ionotropic glutamate receptor signaling pathway
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:0032983 kainate selective glutamate receptor complex
GO:0042734 presynaptic membrane
GO:0045202 synapse
GO:0045211 postsynaptic membrane


-  Descriptions from all associated GenBank mRNAs
  AK292726 - Homo sapiens cDNA FLJ77953 complete cds, highly similar to Homo sapiens glutamate receptor, ionotropic, kainate 4 (GRIK4), mRNA.
AK314284 - Homo sapiens cDNA, FLJ95040, highly similar to Homo sapiens glutamate receptor, ionotropic, kainate 4 (GRIK4), mRNA.
BC146652 - Homo sapiens glutamate receptor, ionotropic, kainate 4, mRNA (cDNA clone MGC:164809 IMAGE:40147575), complete cds.
BC150173 - Homo sapiens glutamate receptor, ionotropic, kainate 4, mRNA (cDNA clone MGC:164786 IMAGE:40147389), complete cds.
AB384776 - Synthetic construct DNA, clone: pF1KB3287, Homo sapiens GRIK4 gene for glutamate receptor, ionotropic kainate 4 precursor, complete cds, without stop codon, in Flexi system.
S67803 - excitatory amino acid receptor 1=glutamate ionotropic receptor [human, hippocampus, mRNA Partial, 2871 nt].
AB231709 - Homo sapiens mRNA for hypothetical protein, partial cds, clone:Hsa11-digit07-11-15-R.

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

Reactome (by CSHL, EBI, and GO)

Protein Q16099 (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-451308 Activation of Ca-permeable Kainate Receptor
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: A8K9L1, AK292726, GRIK, GRIK4_HUMAN, NM_014619, NP_055434, Q16099
UCSC ID: uc001pxn.2
RefSeq Accession: NM_014619
Protein: Q16099 (aka GRIK4_HUMAN or GLK4_HUMAN)
CCDS: CCDS8433.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK292726.1
exon count: 21CDS single in 3' UTR: no RNA size: 3321
ORF size: 2871CDS single in intron: no Alignment % ID: 99.94
txCdsPredict score: 5805.00frame shift in genome: no % Coverage: 95.09
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.