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HOMER3 homer scaffold protein 3 [ Homo sapiens (human) ]

Gene ID: 9454, updated on 21-Apr-2019

Summary

Official Symbol
HOMER3provided by HGNC
Official Full Name
homer scaffold protein 3provided by HGNC
Primary source
HGNC:HGNC:17514
See related
Ensembl:ENSG00000051128 MIM:604800
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
VESL3; HOMER-3
Summary
This gene encodes a member of the HOMER family of postsynaptic density scaffolding proteins that share a similar domain structure consisting of an N-terminal Enabled/vasodilator-stimulated phosphoprotein homology 1 domain which mediates protein-protein interactions, and a carboxy-terminal coiled-coil domain and two leucine zipper motifs that are involved in self-oligomerization. The encoded protein binds numerous other proteins including group I metabotropic glutamate receptors, inositol 1,4,5-trisphosphate receptors and amyloid precursor proteins and has been implicated in diverse biological functions such as neuronal signaling, T-cell activation and trafficking of amyloid beta peptides. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]
Expression
Broad expression in spleen (RPKM 29.6), kidney (RPKM 6.7) and 19 other tissues See more
Orthologs

Genomic context

See HOMER3 in Genome Data Viewer
Location:
19p13.11
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 19 NC_000019.10 (18929201..18941258, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19040010..19052041, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene coatomer protein complex subunit epsilon Neighboring gene DEAD-box helicase 49 Neighboring gene HOMER3 antisense RNA 1 Neighboring gene uncharacterized LOC107985268 Neighboring gene RNA, 7SL, cytoplasmic 70, pseudogene

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?

Pathways from BioSystems

  • 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
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
negative regulation of calcineurin-NFAT signaling cascade IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of interleukin-2 production IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein targeting TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cell junction IEA
Inferred from Electronic Annotation
more info
 
cellular_component ND
No biological Data available
more info
 
cytosol TAS
Traceable Author Statement
more info
 
postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
homer protein homolog 3
Names
Homer, neuronal immediate early gene, 3
homer homolog 3
homer scaffolding protein 3

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.

Genomic

  1. NG_033947.1 RefSeqGene

    Range
    5001..17032
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145721.1NP_001139193.1  homer protein homolog 3 isoform 2

    See identical proteins and their annotated locations for NP_001139193.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), termed Homer-3A00, differs in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC002985, AF093265, AW606967, CN284196
    Consensus CDS
    CCDS46023.1
    UniProtKB/Swiss-Prot
    Q9NSC5
    Related
    ENSP00000396154.2, ENST00000433218.6
    Conserved Domains (1) summary
    cd01206
    Location:6114
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
  2. NM_001145722.1NP_001139194.1  homer protein homolog 3 isoform 1

    See identical proteins and their annotated locations for NP_001139194.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), termed Homer-3A01, encodes the longest isoform (1). Both variants 1 and 2 encode the same protein (isoform 1).
    Source sequence(s)
    AC002985, AK313995, CN284196
    Consensus CDS
    CCDS12391.1
    UniProtKB/Swiss-Prot
    Q9NSC5
    Related
    ENSP00000446026.1, ENST00000542541.6
    Conserved Domains (1) summary
    cd01206
    Location:6114
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
  3. NM_001145724.1NP_001139196.1  homer protein homolog 3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), termed Homer-3B00, differs in the 5' UTR and lacks an exon in the coding region, compared to variant 1, but maintains the reading frame. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC002985, AK313995, CN284196, Y18894
    Consensus CDS
    CCDS46022.1
    UniProtKB/Swiss-Prot
    Q9NSC5
    Related
    ENSP00000471835.1, ENST00000594439.5
    Conserved Domains (1) summary
    cd01206
    Location:6102
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
  4. NM_004838.4NP_004829.3  homer protein homolog 3 isoform 1

    See identical proteins and their annotated locations for NP_004829.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), termed Homer-3A01, differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein (isoform 1).
    Source sequence(s)
    AC002985, BC012113, CN284196
    Consensus CDS
    CCDS12391.1
    UniProtKB/Swiss-Prot
    Q9NSC5
    Related
    ENSP00000376162.2, ENST00000392351.8
    Conserved Domains (1) summary
    cd01206
    Location:6114
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain

RNA

  1. NR_027297.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has an alternate 5' exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC002985, AK124450, CN284196

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_000019.10 Reference GRCh38.p12 Primary Assembly

    Range
    18929201..18941258 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006722943.1XP_006723006.1  homer protein homolog 3 isoform X1

    See identical proteins and their annotated locations for XP_006723006.1

    UniProtKB/Swiss-Prot
    Q9NSC5
    Related
    ENSP00000439937.1, ENST00000539827.5
    Conserved Domains (1) summary
    cd01206
    Location:6114
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
  2. XM_006722944.2XP_006723007.1  homer protein homolog 3 isoform X1

    See identical proteins and their annotated locations for XP_006723007.1

    UniProtKB/Swiss-Prot
    Q9NSC5
    Conserved Domains (1) summary
    cd01206
    Location:6114
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
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