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    grin1b glutamate receptor, ionotropic, N-methyl D-aspartate 1b [ Danio rerio (zebrafish) ]

    Gene ID: 100005675, updated on 9-Dec-2024

    Summary

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    Official Symbol
    grin1bprovided by ZNC
    Official Full Name
    glutamate receptor, ionotropic, N-methyl D-aspartate 1bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-051202-2
    See related
    Ensembl:ENSDARG00000025728 AllianceGenome:ZFIN:ZDB-GENE-051202-2
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    NMDAR1.2; si:rp71-1o1.1
    Summary
    Enables ligand-gated channel activity. Involved in calcium ion transmembrane transport. Predicted to be located in postsynaptic membrane. Predicted to be part of NMDA selective glutamate receptor complex. Predicted to be active in neuron projection; plasma membrane; and synapse. Is expressed in brain and retina. Used to study epilepsy. Human ortholog(s) of this gene implicated in alcohol use disorder; autosomal dominant intellectual developmental disorder 8; cerebral infarction; and developmental and epileptic encephalopathy 101. Orthologous to human GRIN1 (glutamate ionotropic receptor NMDA type subunit 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See grin1b in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 5 NC_007116.7 (29597950..29643829, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 5 NC_007116.6 (28997791..29043676, complement)

    Chromosome 5 - NC_007116.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137495597 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 2a, tandem duplicate 2 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 2a, tandem duplicate 1 Neighboring gene TSC complex subunit 1a Neighboring gene sperm acrosome associated 9

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Identification and characterization of two novel RNA editing sites in grin1b transcripts of embryonic Danio rerio. Pozo P, et al. Neural Plast, 2012. PMID 22530154, Free PMC Article
    2. Developmental loss of NMDA receptors results in supernumerary forebrain neurons through delayed maturation of transit-amplifying neuroblasts. Napoli AJ, et al. Sci Rep, 2024 Feb 9. PMID 38336823, Free PMC Article
    3. Molecular and functional studies of tilapia (Oreochromis mossambicus) NMDA receptor NR1 subunits. Tzeng DW, et al. Comp Biochem Physiol B Biochem Mol Biol, 2007 Mar. PMID 17258920
    4. A Model to Study NMDA Receptors in Early Nervous System Development. Zoodsma JD, et al. J Neurosci, 2020 Apr 29. PMID 32245827, Free PMC Article
    5. The Midline Axon Crossing Decision Is Regulated through an Activity-Dependent Mechanism by the NMDA Receptor. Gao J, et al. eNeuro, 2018 Mar-Apr. PMID 29766040, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Using a comparative sequence-based approach and sequence analysis, two novel RNA editing sites were located in grin1b transcripts of embryonic Danio rerio.
      Title: Identification and characterization of two novel RNA editing sites in grin1b transcripts of embryonic Danio rerio.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    contributes_to NMDA glutamate receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ligand-gated channel activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ligand-gated monoatomic ion channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ligand-gated monoatomic ion channel activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables monoatomic ion channel activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables signaling receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chemical synaptic transmission IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ionotropic glutamate receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within monoatomic ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within monoatomic ion transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of membrane potential IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of NMDA selective glutamate receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in neuron projection IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    glutamate receptor ionotropic, NMDA 1b

    NCBI Reference Sequences (RefSeq)

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    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_001144131.1 → NP_001137603.1  glutamate receptor ionotropic, NMDA 1b precursor

      Status: VALIDATED

      Source sequence(s)
      AL831768, BX276128
      UniProtKB/TrEMBL
      A0A8M1NPN1, A0A8M9PCT9, Q6ZM67
      Related
      ENSDARP00000038151.8, ENSDART00000034849.9
      Conserved Domains (5) summary
      cd06379
      Location:5 → 401
      PBP1_iGluR_NMDA_NR1; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor
      cd13719
      Location:413 → 815
      PBP2_iGluR_NMDA_Nr1; The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily
      pfam00060
      Location:577 → 840
      Lig_chan; Ligand-gated ion channel
      pfam01094
      Location:36 → 372
      ANF_receptor; Receptor family ligand binding region
      pfam10562
      Location:851 → 879
      CaM_bdg_C0; Calmodulin-binding domain C0 of NMDA receptor NR1 subunit

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007116.7 Reference GRCz11 Primary Assembly

      Range
      29597950..29643829 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068221045.1 → XP_068077146.1  glutamate receptor ionotropic, NMDA 1b isoform X3

      UniProtKB/TrEMBL
      A0A8M2B7Z7
      Related
      ENSDARP00000133472.2, ENSDART00000161250.2

    2. XM_005171776.3 → XP_005171833.1  glutamate receptor ionotropic, NMDA 1b isoform X1

      UniProtKB/TrEMBL
      A0A8M2BJ41, A0A8M9PIG4
      Conserved Domains (5) summary
      cd06379
      Location:5 → 380
      PBP1_iGluR_NMDA_NR1; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor
      cd13719
      Location:392 → 794
      PBP2_iGluR_NMDA_Nr1; The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily
      pfam00060
      Location:556 → 819
      Lig_chan; Ligand-gated ion channel
      pfam01094
      Location:36 → 351
      ANF_receptor; Receptor family ligand binding region
      pfam10562
      Location:830 → 858
      CaM_bdg_C0; Calmodulin-binding domain C0 of NMDA receptor NR1 subunit

    3. XM_005171777.3 → XP_005171834.1  glutamate receptor ionotropic, NMDA 1b isoform X2

      UniProtKB/TrEMBL
      A0A8M2B7Z7, A0A8M2BJ28
      Conserved Domains (5) summary
      cd06379
      Location:5 → 401
      PBP1_iGluR_NMDA_NR1; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor
      cd13719
      Location:413 → 815
      PBP2_iGluR_NMDA_Nr1; The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily
      pfam00060
      Location:577 → 840
      Lig_chan; Ligand-gated ion channel
      pfam01094
      Location:36 → 372
      ANF_receptor; Receptor family ligand binding region
      pfam10562
      Location:851 → 879
      CaM_bdg_C0; Calmodulin-binding domain C0 of NMDA receptor NR1 subunit

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394581.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      2562..3412 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCz11 ALT_DRER_TU_2

    Genomic

    1. NW_018395239.1 Reference GRCz11 ALT_DRER_TU_2

      Range
      2518..3368 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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