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    Grik1 glutamate ionotropic receptor kainate type subunit 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 29559, updated on 9-Dec-2024

    Summary

    Official Symbol
    Grik1provided by RGD
    Official Full Name
    glutamate ionotropic receptor kainate type subunit 1provided by RGD
    Primary source
    RGD:2732
    See related
    EnsemblRapid:ENSRNOG00000001575 AllianceGenome:RGD:2732
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    GluK1; GluR5
    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 Brain (RPKM 56.8) and Testes (RPKM 12.9) See more
    Orthologs
    NEW
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    Genomic context

    See Grik1 in Genome Data Viewer
    Location:
    11q11
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (40655974..41056966, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (27169739..27571131, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (27811954..28213940, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase subunit A7, pseudogene 1 Neighboring gene small nucleolar RNA SNORA17 Neighboring gene BTB domain and CNC homolog 1 Neighboring gene sorting nexin-1-like Neighboring gene uncharacterized LOC108352301 Neighboring gene KAT8 regulatory NSL complex subunit 2, pseudogene 1 Neighboring gene claudin 17

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables L-glutamate transmembrane transporter activity  
    enables SNARE binding PubMed 
    enables extracellularly glutamate-gated ion channel activity PubMed 
    enables glutamate binding PubMed 
    enables glutamate-gated calcium ion channel activity PubMed 
    enables glutamate-gated receptor activity PubMed 
    enables glutamate-gated receptor activity  
    contributes_to heterocyclic compound binding PubMed 
    enables identical protein binding PubMed 
    enables kainate selective glutamate receptor activity  
    enables kainate selective glutamate receptor activity PubMed 
    enables kainate selective glutamate receptor activity  
    enables ligand-gated monoatomic ion channel activity  
    enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential PubMed 
    enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential PubMed 
    enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential PubMed 
    enables protein binding PubMed 
    enables scaffold protein binding PubMed 
    enables signaling receptor activity  
    enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential  
    Items 1 - 25 of 29
    Process Evidence Code Pubs
    involved_in L-glutamate transmembrane transport  
    acts_upstream_of_or_within adult behavior  
    acts_upstream_of_or_within behavioral response to pain  
    involved_in calcium-mediated signaling  
    involved_in chemical synaptic transmission PubMed 
    acts_upstream_of establishment of localization in cell  
    acts_upstream_of_or_within excitatory postsynaptic potential  
    acts_upstream_of gamma-aminobutyric acid secretion  
    acts_upstream_of_or_within inhibitory postsynaptic potential  
    involved_in ionotropic glutamate receptor signaling pathway PubMed 
    acts_upstream_of_or_within membrane depolarization  
    involved_in modulation of chemical synaptic transmission  
    involved_in modulation of excitatory postsynaptic potential PubMed 
    involved_in monoatomic ion transmembrane transport  
    involved_in negative regulation of synaptic transmission, GABAergic PubMed 
    involved_in negative regulation of synaptic transmission, glutamatergic PubMed 
    acts_upstream_of_or_within negative regulation of synaptic transmission, glutamatergic  
    involved_in nervous system development PubMed 
    acts_upstream_of_or_within positive regulation of gamma-aminobutyric acid secretion  
    involved_in positive regulation of synaptic transmission, GABAergic PubMed 
    acts_upstream_of_or_within positive regulation of synaptic transmission, GABAergic  
    acts_upstream_of_or_within presynaptic modulation of chemical synaptic transmission  
    acts_upstream_of_or_within regulation of membrane potential  
    involved_in regulation of presynaptic membrane potential  
    involved_in regulation of short-term neuronal synaptic plasticity PubMed 
    involved_in regulation of synaptic plasticity PubMed 
    acts_upstream_of synaptic transmission, GABAergic  
    involved_in synaptic transmission, glutamatergic  
    acts_upstream_of_or_within synaptic transmission, glutamatergic  
    Items 1 - 25 of 29
    Items 1 - 20 of 22
    Component Evidence Code Pubs
    located_in dendrite PubMed 
    located_in dendrite  
    is_active_in glutamatergic synapse PubMed 
    located_in intracellular membrane-bounded organelle  
    located_in intracellular membrane-bounded organelle  
    part_of ionotropic glutamate receptor complex PubMed 
    part_of kainate selective glutamate receptor complex  
    part_of kainate selective glutamate receptor complex  
    located_in membrane  
    located_in neuronal cell body PubMed 
    is_active_in plasma membrane  
    located_in plasma membrane  
    located_in postsynaptic density  
    is_active_in postsynaptic density membrane  
    located_in postsynaptic membrane  
    located_in postsynaptic membrane PubMed 
    is_active_in presynaptic membrane  
    is_active_in presynaptic membrane PubMed 
    located_in presynaptic membrane  
    part_of receptor complex PubMed 
    located_in synapse  
    located_in terminal bouton PubMed 
    Items 1 - 20 of 22

    General protein information

    Preferred Names
    glutamate receptor ionotropic, kainate 1
    Names
    glutamate receptor 5

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001111114.1NP_001104584.1  glutamate receptor ionotropic, kainate 1 isoform 3

      See identical proteins and their annotated locations for NP_001104584.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) is missing two in-frame coding exons compared to transcript variant 1, resulting in a shorter isoform (3) lacking two protein segments of 15 aa and 29 aa, compared to isoform 1. RNA editing (CAG->CGG) changes Gln621Arg.
      Source sequence(s)
      AI145540, JAXUCZ010000011, M83561
      UniProtKB/Swiss-Prot
      P22756
      UniProtKB/TrEMBL
      A6JL83
      Related
      ENSRNOP00000078137.2, ENSRNOT00000100916.2
      Conserved Domains (4) summary
      pfam00060
      Location:562831
      Lig_chan; Ligand-gated ion channel
      pfam01094
      Location:53396
      ANF_receptor; Receptor family ligand binding region
      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
    2. NM_001111117.1NP_001104587.1  glutamate receptor ionotropic, kainate 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001104587.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). RNA editing (CAG->CGG) changes Gln636Arg.
      Source sequence(s)
      AI145540, JAXUCZ010000011, M83560, Z11714
      UniProtKB/Swiss-Prot
      P22756
      UniProtKB/TrEMBL
      A6JL86, F1M7M9
      Related
      ENSRNOP00000045594.5, ENSRNOT00000050073.7
      Conserved Domains (4) summary
      pfam00060
      Location:577846
      Lig_chan; Ligand-gated ion channel
      pfam01094
      Location:53396
      ANF_receptor; Receptor family ligand binding region
      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_017241.2NP_058937.1  glutamate receptor ionotropic, kainate 1 isoform 2

      See identical proteins and their annotated locations for NP_058937.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is missing an in-frame coding exon at the 3' end compared to transcript variant 1, resulting in a shorter isoform (2) lacking a 29 aa segment, compared to isoform 1. RNA editing (CAG->CGG) changes Gln636Arg.
      Source sequence(s)
      AI145540, JAXUCZ010000011, M83560
      UniProtKB/Swiss-Prot
      P22756
      UniProtKB/TrEMBL
      A0A140TAF9, A6JL85
      Related
      ENSRNOP00000046164.5, ENSRNOT00000051060.7
      Conserved Domains (4) summary
      pfam00060
      Location:577846
      Lig_chan; Ligand-gated ion channel
      pfam01094
      Location:53396
      ANF_receptor; Receptor family ligand binding region
      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

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086029.1 Reference GRCr8

      Range
      40655974..41056966 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006248053.5XP_006248115.1  glutamate receptor ionotropic, kainate 1 isoform X1

      See identical proteins and their annotated locations for XP_006248115.1

      UniProtKB/Swiss-Prot
      P22756
      UniProtKB/TrEMBL
      A0A140TAG6, A6JL84
      Conserved Domains (4) summary
      pfam00060
      Location:562831
      Lig_chan; Ligand-gated ion channel
      pfam01094
      Location:53396
      ANF_receptor; Receptor family ligand binding region
      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
    2. XM_063270448.1XP_063126518.1  glutamate receptor ionotropic, kainate 1 isoform X5

      UniProtKB/TrEMBL
      A0A0G2JVC0
    3. XM_017597947.3XP_017453436.1  glutamate receptor ionotropic, kainate 1 isoform X4

      UniProtKB/TrEMBL
      A0A0G2JVC0
      Related
      ENSRNOP00000069424.2, ENSRNOT00000085629.3
    4. XM_063270451.1XP_063126521.1  glutamate receptor ionotropic, kainate 1 isoform X8

      UniProtKB/TrEMBL
      A0A0G2K830, A6JL87
    5. XM_039088252.2XP_038944180.1  glutamate receptor ionotropic, kainate 1 isoform X3

      UniProtKB/TrEMBL
      A0A0G2K830, A0A8I5Y1Z7, A6JL87, A6JL88
      Related
      ENSRNOP00000105903.1, ENSRNOT00000147508.1
      Conserved Domains (2) summary
      cd06382
      Location:38416
      PBP1_iGluR_Kainate; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate receptors
      cl21456
      Location:431800
      Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily
    6. XM_006248054.5XP_006248116.1  glutamate receptor ionotropic, kainate 1 isoform X2

      UniProtKB/TrEMBL
      A0A0G2K830, A6JL87
      Conserved Domains (4) summary
      pfam00060
      Location:577846
      Lig_chan; Ligand-gated ion channel
      pfam01094
      Location:53396
      ANF_receptor; Receptor family ligand binding region
      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
    7. XM_063270449.1XP_063126519.1  glutamate receptor ionotropic, kainate 1 isoform X6

      UniProtKB/TrEMBL
      A0A0G2K830, A6JL87
      Related
      ENSRNOP00000050263.7, ENSRNOT00000042581.7
    8. XM_039088253.2XP_038944181.1  glutamate receptor ionotropic, kainate 1 isoform X7

      UniProtKB/TrEMBL
      A6JL92
      Conserved Domains (2) summary
      cd06382
      Location:38431
      PBP1_iGluR_Kainate; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate receptors
      cl21456
      Location:446598
      Periplasmic_Binding_Protein_Type_2; Type 2 periplasmic binding fold superfamily

    RNA

    1. XR_005491017.2 RNA Sequence

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