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GRIK1 glutamate ionotropic receptor kainate type subunit 1 [ Homo sapiens (human) ]

Gene ID: 2897, updated on 3-Jan-2019

Summary

Official Symbol
GRIK1provided by HGNC
Official Full Name
glutamate ionotropic receptor kainate type subunit 1provided by HGNC
Primary source
HGNC:HGNC:4579
See related
Ensembl:ENSG00000171189 MIM:138245
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EAA3; EEA3; GLR5; GLUR5; GluK1; gluR-5
Summary
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]
Expression
Biased expression in adrenal (RPKM 3.8), brain (RPKM 1.9) and 2 other tissues See more
Orthologs

Genomic context

See GRIK1 in Genome Data Viewer
Location:
21q21.3
Exon count:
19
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 21 NC_000021.9 (29536933..29940052, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (30909254..31312282, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985486 Neighboring gene uncharacterized LOC105372770 Neighboring gene BACH1 intronic transcript 3 Neighboring gene uncharacterized LOC105372768 Neighboring gene GRIK1 antisense RNA 2 Neighboring gene GRIK1 antisense RNA 1 Neighboring gene long intergenic non-protein coding RNA 307 Neighboring gene claudin 17

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study.
NHGRI GWA Catalog
A novel locus for body mass index on 5p15.2: a meta-analysis of two genome-wide association studies.
NHGRI GWA Catalog
Genome-wide association of lipid-lowering response to statins in combined study populations.
NHGRI GWA Catalog
Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations.
NHGRI GWA Catalog
Genome-wide association study of chronic periodontitis in a general German population.
NHGRI GWA Catalog
GWAS identifies novel susceptibility loci on 6p21.32 and 21q21.3 for hepatocellular carcinoma in chronic hepatitis B virus carriers.
NHGRI GWA Catalog
Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
glutamate receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
kainate selective glutamate receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
kainate selective glutamate receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
central nervous system development TAS
Traceable Author Statement
more info
PubMed 
chemical synaptic transmission TAS
Traceable Author Statement
more info
PubMed 
glutamate receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
ionotropic glutamate receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
modulation of chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
regulation of postsynaptic membrane potential IEA
Inferred from Electronic Annotation
more info
 
regulation of synaptic transmission, glutamatergic TAS
Traceable Author Statement
more info
PubMed 
synaptic transmission, glutamatergic IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cell junction IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
kainate selective glutamate receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
postsynaptic membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
presynaptic membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
glutamate receptor ionotropic, kainate 1
Names
excitatory amino acid receptor 3
glutamate receptor 5

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_000830.4NP_000821.1  glutamate receptor ionotropic, kainate 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_000821.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as GluR5-1D, contains an alternate 3' terminal exon compared to variant 3. It encodes isoform 1, which is shorter than and has a distinct C-terminus compared to isoform 3.
    Source sequence(s)
    AP000239, BC028238, BC039447, DC341703, L19058
    Consensus CDS
    CCDS42913.1
    UniProtKB/Swiss-Prot
    P39086
    Related
    ENSP00000382791.1, ENST00000399907.5
    Conserved Domains (2) summary
    cl10011
    Location:35430
    Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
    cl21456
    Location:446815
    Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily
  2. NM_001320616.1NP_001307545.1  glutamate receptor ionotropic, kainate 1 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) encodes the longest isoform (3).
    Source sequence(s)
    AA404271, AJ249208, AK296404, BC111793, DC341703
    Consensus CDS
    CCDS82658.1
    UniProtKB/Swiss-Prot
    P39086
    UniProtKB/TrEMBL
    B7Z3V7, E9PD61
    Related
    ENSP00000382797.1, ENST00000399913.5
    Conserved Domains (2) summary
    cl10011
    Location:35430
    Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
    cl21456
    Location:446815
    Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily
  3. NM_001320618.1NP_001307547.1  glutamate receptor ionotropic, kainate 1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks several alternate, in-frame exons in the 5' and central coding regions compared to variant 3. It encodes isoform 4, which is shorter than isoform 3.
    Source sequence(s)
    AA404271, AJ249208, AK294353, AK296404, DC341703
    UniProtKB/Swiss-Prot
    P39086
    UniProtKB/TrEMBL
    B7Z256, B7Z3V7
    Conserved Domains (4) summary
    pfam00060
    Location:438707
    Lig_chan; Ligand-gated ion channel
    pfam01094
    Location:40340
    ANF_receptor; Receptor family ligand binding region
    cl10011
    Location:38359
    Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
    cl21456
    Location:385676
    Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily
  4. NM_001320621.1NP_001307550.1  glutamate receptor ionotropic, kainate 1 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks several alternate, in-frame exons in the 5' and central coding regions compared to variant 3. It encodes isoform 5, which is shorter than isoform 3.
    Source sequence(s)
    AA404271, AK296404, BC111793, DC341703
    UniProtKB/TrEMBL
    B7Z3V7
    Conserved Domains (4) summary
    pfam00060
    Location:420689
    Lig_chan; Ligand-gated ion channel
    pfam01094
    Location:38254
    ANF_receptor; Receptor family ligand binding region
    cl10011
    Location:40273
    Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
    cl21456
    Location:289658
    Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily
  5. NM_001320630.1NP_001307559.1  glutamate receptor ionotropic, kainate 1 isoform 6 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 3. This results in a novel 3' coding region and 3' UTR, compared to variant 3. It encodes isoform 6, which is shorter than and has a distinct C-terminus compared to isoform 3
    Source sequence(s)
    BC028238, DC341703
    Conserved Domains (2) summary
    pfam01094
    Location:53396
    ANF_receptor; Receptor family ligand binding region
    cl10011
    Location:35403
    Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
  6. NM_001330993.1NP_001317922.1  glutamate receptor ionotropic, kainate 1 isoform 7 precursor

    Status: REVIEWED

    Source sequence(s)
    AA404271, AP000236, AP000237, AP000238, AP000239
    Consensus CDS
    CCDS82656.1
    UniProtKB/TrEMBL
    E7EPY9
    Related
    ENSP00000382798.1, ENST00000399914.5
    Conserved Domains (2) summary
    cl10011
    Location:35415
    Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
    cl21456
    Location:431800
    Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily
  7. NM_001330994.1NP_001317923.1  glutamate receptor ionotropic, kainate 1 isoform 8 precursor

    Status: REVIEWED

    Source sequence(s)
    AA404271, AP000236, AP000237, AP000238, AP000239
    Consensus CDS
    CCDS82659.1
    UniProtKB/TrEMBL
    E7ENK3
    Related
    ENSP00000327687.4, ENST00000327783.8
    Conserved Domains (2) summary
    cl10011
    Location:35430
    Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
    cl21456
    Location:446815
    Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily
  8. NM_175611.2NP_783300.1  glutamate receptor ionotropic, kainate 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_783300.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as EAA3A, lacks an alternate in-frame exon in the 3' coding region compared to variant 3. It encodes isoform 2, which is shorter than isoform 3.
    Source sequence(s)
    AA404271, AJ249208, BC028238, U16125
    Consensus CDS
    CCDS33530.1
    UniProtKB/Swiss-Prot
    P39086
    Related
    ENSP00000373777.3, ENST00000389125.7
    Conserved Domains (2) summary
    cl10011
    Location:35415
    Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
    cl21456
    Location:431800
    Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p12 Primary Assembly

    Range
    29536933..29940052 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005260944.3XP_005261001.1  glutamate receptor ionotropic, kainate 1 isoform X1

    UniProtKB/TrEMBL
    E7EPZ0
    Related
    ENSP00000382793.1, ENST00000399909.5
    Conserved Domains (2) summary
    cl10011
    Location:35415
    Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
    cl21456
    Location:431800
    Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily

RNA

  1. XR_001754829.2 RNA Sequence

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