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    GLRA1 glycine receptor alpha 1 [ Homo sapiens (human) ]

    Gene ID: 2741, updated on 11-Apr-2024

    Summary

    Official Symbol
    GLRA1provided by HGNC
    Official Full Name
    glycine receptor alpha 1provided by HGNC
    Primary source
    HGNC:HGNC:4326
    See related
    Ensembl:ENSG00000145888 MIM:138491; AllianceGenome:HGNC:4326
    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
    STHE; HKPX1
    Summary
    The protein encoded by this gene is a subunit of a pentameric inhibitory glycine receptor, which mediates postsynaptic inhibition in the central nervous system. Defects in this gene are a cause of startle disease (STHE), also known as hereditary hyperekplexia or congenital stiff-person syndrome. Multiple transcript variants encoding different isoforms have been found. [provided by RefSeq, Dec 2015]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See GLRA1 in Genome Data Viewer
    Location:
    5q33.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (151822513..151924851, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (152361497..152463867, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (151202074..151304412, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100652758 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:151149602-151150323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23468 Neighboring gene Sharpr-MPRA regulatory region 5918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16529 Neighboring gene ribosomal protein lateral stalk subunit P1 pseudogene 6 Neighboring gene Sharpr-MPRA regulatory region 2380 Neighboring gene G3BP stress granule assembly factor 1 Neighboring gene tRNA-Gln (anticodon CTG) 13-1 Neighboring gene glutamate-ammonia ligase pseudogene 1 Neighboring gene RNA, 5S ribosomal pseudogene 198 Neighboring gene Sharpr-MPRA regulatory region 1877 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:151297277-151297997 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:151304692-151304904 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:151326719-151327918 Neighboring gene long intergenic non-protein coding RNA 1933 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:151431291-151431938 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:151431939-151432585 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:151450292-151450532 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:151456754-151457342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:151503900-151504459 Neighboring gene MPRA-validated peak5547 silencer Neighboring gene uncharacterized LOC105378236

    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 Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC138878, MGC138879

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to chloride channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables excitatory extracellular ligand-gated monoatomic ion channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables extracellularly glycine-gated chloride channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables extracellularly glycine-gated chloride channel activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables glycine binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables neurotransmitter receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables taurine binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transmembrane signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential IEA
    Inferred from Electronic Annotation
    more info
     
    enables zinc ion binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in acrosome reaction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in adult walking behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to amino acid stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to ethanol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to zinc ion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chemical synaptic transmission IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in chloride transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in chloride transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chloride transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in excitatory postsynaptic potential IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inhibitory postsynaptic potential ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in monoatomic ion transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in muscle contraction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transmission of nerve impulse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in neuromuscular process controlling posture IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuronal action potential IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuropeptide signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of acrosome reaction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of membrane potential IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within regulation of membrane potential IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of presynaptic membrane potential IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of respiratory gaseous exchange by nervous system process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to alcohol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in righting reflex IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within startle response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in startle response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in synaptic transmission, glycinergic ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of chloride channel complex IEA
    Inferred from Electronic Annotation
    more info
     
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    located_in external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in glycinergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in inhibitory synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in neuron projection IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in neuron projection ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of transmembrane transporter complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    glycine receptor subunit alpha-1
    Names
    glycine receptor 48 kDa subunit
    glycine receptor strychnine-binding subunit

    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.

    Genomic

    1. NG_011764.1 RefSeqGene

      Range
      4986..107324
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000171.4NP_000162.2  glycine receptor subunit alpha-1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_000162.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site at the 5' end of the last exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC010312, AK226046, AK312702, BC074980, X52009
      Consensus CDS
      CCDS4320.1
      UniProtKB/Swiss-Prot
      P23415
      Related
      ENSP00000274576.5, ENST00000274576.9
      Conserved Domains (1) summary
      TIGR00860
      Location:7438
      LIC; Cation transporter family protein
    2. NM_001146040.2NP_001139512.1  glycine receptor subunit alpha-1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001139512.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC010312, AK226046, BC114947, X52009
      Consensus CDS
      CCDS54942.1
      UniProtKB/Swiss-Prot
      B2R6T3, P23415, Q14C77, Q6DJV9
      Related
      ENSP00000411593.2, ENST00000455880.2
      Conserved Domains (1) summary
      TIGR00860
      Location:7446
      LIC; Cation transporter family protein
    3. NM_001292000.2NP_001278929.1  glycine receptor subunit alpha-1 isoform 3

      See identical proteins and their annotated locations for NP_001278929.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an internal exon in the 5' region, which results in translation initiation at a downstream AUG start codon, and contains an alternate splice site at the 5' end of the last exon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus and lacks an internal segment in the C-terminal region, compared to isoform 1.
      Source sequence(s)
      AC010312, AK226046, AK308539, BC114967
      UniProtKB/TrEMBL
      Q14C71
      Conserved Domains (1) summary
      TIGR00860
      Location:1355
      LIC; Cation transporter family protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      151822513..151924851 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417105.1XP_047273061.1  glycine receptor subunit alpha-1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      152361497..152463867 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352392.1XP_054208367.1  glycine receptor subunit alpha-1 isoform X1