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HOMER1 homer scaffold protein 1 [ Homo sapiens (human) ]

Gene ID: 9456, updated on 6-Jan-2019

Summary

Official Symbol
HOMER1provided by HGNC
Official Full Name
homer scaffold protein 1provided by HGNC
Primary source
HGNC:HGNC:17512
See related
Ensembl:ENSG00000152413 MIM:604798
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HOMER; SYN47; Ves-1; HOMER1A; HOMER1B; HOMER1C
Summary
This gene encodes a member of the homer family of dendritic proteins. Members of this family regulate group 1 metabotrophic glutamate receptor function. [provided by RefSeq, Jul 2008]
Expression
Broad expression in brain (RPKM 8.6), thyroid (RPKM 5.8) and 14 other tissues See more
Orthologs

Genomic context

See HOMER1 in Genome Data Viewer
Location:
5q14.1
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (79373824..79513836, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (78669647..78809659, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene junction mediating and regulatory protein, p53 cofactor Neighboring gene uncharacterized LOC102724530 Neighboring gene uncharacterized LOC101929201 Neighboring gene uncharacterized LOC107986426 Neighboring gene ribosomal protein L29 pseudogene 15 Neighboring gene uncharacterized LOC105379047 Neighboring gene ribosomal protein L7a pseudogene 32

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
Common variants in the GDF5-UQCC region are associated with variation in human height.
NHGRI GWA Catalog
Genome-wide association study of selenium concentrations.
NHGRI GWA Catalog
Genome-wide association-, replication-, and neuroimaging study implicates HOMER1 in the etiology of major depression.
NHGRI GWA Catalog

Pathways from BioSystems

  • BDNF-TrkB Signaling, organism-specific biosystem (from WikiPathways)
    BDNF-TrkB Signaling, organism-specific biosystemBrain-derived neurotrophic factor (BDNF) is an important neurotrophin for the regulation of synaptic activity. BDNF-TrkB signaling, TrkB being the receptor of BDNF, is involved in transcription, tran...
  • Circadian rythm related genes, organism-specific biosystem (from WikiPathways)
    Circadian rythm related genes, organism-specific biosystemThis is currently not a pathway but a list of circadian rhythm related genes and proteins. The source for this information is the gene ontology. The genes and proteins were filtered for "circadian rh...
  • FoxO signaling pathway, organism-specific biosystem (from KEGG)
    FoxO signaling pathway, organism-specific biosystemThe forkhead box O (FOXO) family of transcription factors regulates the expression of genes in cellular physiological events including apoptosis, cell-cycle control, glucose metabolism, oxidative str...
  • Glutamatergic synapse, organism-specific biosystem (from KEGG)
    Glutamatergic synapse, organism-specific biosystemGlutamate is the major excitatory neurotransmitter in the mammalian central nervous system(CNS). Glutamate is packaged into synaptic vesicles in the presynaptic terminal. Once released into the synap...
  • Glutamatergic synapse, conserved biosystem (from KEGG)
    Glutamatergic synapse, conserved biosystemGlutamate is the major excitatory neurotransmitter in the mammalian central nervous system(CNS). Glutamate is packaged into synaptic vesicles in the presynaptic terminal. Once released into the synap...
  • Interactions of neurexins and neuroligins at synapses, organism-specific biosystem (from REACTOME)
    Interactions of neurexins and neuroligins at synapses, organism-specific biosystemNeurexins (NRXNs) and neuroligins (NLGNs) are best characterized synaptic cell-adhesion molecules. They are part of excitatory glutamatergic and inhibitory GABAergic synapses in mammalian brain, medi...
  • Neuronal System, organism-specific biosystem (from REACTOME)
    Neuronal System, organism-specific biosystemThe human brain contains at least 100 billion neurons, each with the ability to influence many other cells. Clearly, highly sophisticated and efficient mechanisms are needed to enable communication a...
  • Protein-protein interactions at synapses, organism-specific biosystem (from REACTOME)
    Protein-protein interactions at synapses, organism-specific biosystemSynapses constitute highly specialized sites of asymmetric cell-cell adhesion and intercellular communication. Its formation involves the recruitment of presynaptic and postsynaptic molecules at newl...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
G protein-coupled glutamate receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ion channel binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling adaptor activity IC
Inferred by Curator
more info
PubMed 
Process Evidence Code Pubs
G protein-coupled glutamate receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
behavioral response to cocaine IEA
Inferred from Electronic Annotation
more info
 
chemical homeostasis within a tissue IEA
Inferred from Electronic Annotation
more info
 
chemical synaptic transmission TAS
Traceable Author Statement
more info
PubMed 
phospholipase C-activating G protein-coupled glutamate receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
positive regulation of calcium ion transport IEA
Inferred from Electronic Annotation
more info
 
positive regulation of signal transduction IC
Inferred by Curator
more info
PubMed 
protein tetramerization ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of calcium ion import IEA
Inferred from Electronic Annotation
more info
 
regulation of cation channel activity TAS
Traceable Author Statement
more info
PubMed 
regulation of dendritic spine maintenance ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of postsynaptic neurotransmitter receptor activity IEA
Inferred from Electronic Annotation
more info
 
regulation of store-operated calcium entry IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of store-operated calcium entry TAS
Traceable Author Statement
more info
PubMed 
regulation of synaptic transmission, glutamatergic ISS
Inferred from Sequence or Structural Similarity
more info
 
response to calcium ion IDA
Inferred from Direct Assay
more info
PubMed 
skeletal muscle contraction IEA
Inferred from Electronic Annotation
more info
 
skeletal muscle fiber development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Z disc IEA
Inferred from Electronic Annotation
more info
 
apical part of cell IEA
Inferred from Electronic Annotation
more info
 
axon IEA
Inferred from Electronic Annotation
more info
 
cell junction IEA
Inferred from Electronic Annotation
more info
 
costamere IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
dendrite IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendritic spine IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron spine ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
postsynaptic cytosol IEA
Inferred from Electronic Annotation
more info
 
postsynaptic density IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
homer protein homolog 1
Names
homer homolog 1
homer scaffolding protein 1
homer, neuronal immediate early gene, 1
homer-1

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_001277077.1NP_001264006.1  homer protein homolog 1 isoform 2

    See identical proteins and their annotated locations for NP_001264006.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2, also known as HOMER1E) lacks three consecutive coding exons compared to variant 1. The missing segment is in-frame, so the resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC020898, AC093270, AY189939
    Consensus CDS
    CCDS64188.1
    UniProtKB/Swiss-Prot
    Q86YM7
    Related
    ENSP00000282260.6, ENST00000282260.10
    Conserved Domains (2) summary
    cd01206
    Location:3101
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
    cl25602
    Location:137222
    DUF3552; Domain of unknown function (DUF3552)
  2. NM_001277078.1NP_001264007.1  homer protein homolog 1 isoform 3

    See identical proteins and their annotated locations for NP_001264007.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3, also known as HOMER1H) lacks three consecutive coding exons compared to variant 1, that causes a frameshift. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC020898, AC093270, AY189941
    Consensus CDS
    CCDS64189.1
    UniProtKB/Swiss-Prot
    Q86YM7
    Related
    ENSP00000426651.1, ENST00000508576.5
    Conserved Domains (1) summary
    cd01206
    Location:3111
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
  3. NM_004272.4NP_004263.1  homer protein homolog 1 isoform 1

    See identical proteins and their annotated locations for NP_004263.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC020898, AC093270, AK312481, BC047438
    Consensus CDS
    CCDS43335.1
    UniProtKB/Swiss-Prot
    Q86YM7
    UniProtKB/TrEMBL
    Q5U5K4
    Related
    ENSP00000334382.6, ENST00000334082.10
    Conserved Domains (2) summary
    cd01206
    Location:3111
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
    cl25732
    Location:157352
    SMC_N; RecF/RecN/SMC N terminal domain

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_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    79373824..79513836 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010059.2XP_016865548.1  homer protein homolog 1 isoform X1

    Conserved Domains (1) summary
    cd01206
    Location:3111
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
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