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

Gene ID: 2741, updated on 10-Dec-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
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (151822513..151924851, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (152361497..152463867, complement)
RS_2024_09 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 identical protein binding IPI
Inferred from Physical Interaction
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 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 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 
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 
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
 
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
 
located_in synapse ISS
Inferred from Sequence or Structural Similarity
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_2024_08

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