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

Gene ID: 9454, updated on 11-May-2025
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; AllianceGenome:HGNC:17514
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
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See HOMER3 in Genome Data Viewer
Location:
19p13.11
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18929201..18941217, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19064989..19077095, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19040010..19052026, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene COPI coat complex subunit epsilon Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19028406-19029296 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19042288-19042799 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19042800-19043310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19043997-19044615 Neighboring gene DEAD-box helicase 49 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10426 Neighboring gene HOMER3 antisense RNA 1 Neighboring gene RNA, 7SL, cytoplasmic 70, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19088899-19089543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19100696-19101196 Neighboring gene SURP and G-patch domain containing 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:19136044-19137243 Neighboring gene NANOG hESC enhancer GRCh37_chr19:19143058-19143559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10428 Neighboring gene armadillo repeat containing 6

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
Products Interactant Other Gene Complex Source Pubs Description

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables G protein-coupled glutamate receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables G protein-coupled glutamate receptor binding IEA
Inferred from Electronic Annotation
more info
 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein domain specific binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in basal part of cell IEA
Inferred from Electronic Annotation
more info
 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
is_active_in dendrite IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in postsynaptic density IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in postsynaptic density IEA
Inferred from Electronic Annotation
more info
 
located_in synapse IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
homer protein homolog 3
Names
Homer, neuronal immediate early gene, 3
homer homolog 3
homer scaffolding protein 3

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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.

Genomic

  1. NG_033947.1 RefSeqGene

    Range
    5016..17030
    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/TrEMBL
    Q5U0L9
    Related
    ENSP00000396154.2, ENST00000433218.6
    Conserved Domains (1) summary
    cd01206
    Location:6114
    EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
  2. NM_001145722.2NP_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
    B2RA10, E9PCW9, O14580, O95350, Q9NSB9, Q9NSC0, Q9NSC1, Q9NSC5
    UniProtKB/TrEMBL
    Q5U0L9
    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/TrEMBL
    Q5U0L9
    Related
    ENSP00000471835.1, ENST00000594439.5
    Conserved Domains (2) summary
    COG1196
    Location:115305
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    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
    B2RA10, E9PCW9, O14580, O95350, Q9NSB9, Q9NSC0, Q9NSC1, Q9NSC5
    UniProtKB/TrEMBL
    Q5U0L9
    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: 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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    18929201..18941217 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439733.1XP_047295689.1  homer protein homolog 3 isoform X1

    UniProtKB/Swiss-Prot
    B2RA10, E9PCW9, O14580, O95350, Q9NSB9, Q9NSC0, Q9NSC1, Q9NSC5
    UniProtKB/TrEMBL
    Q5U0L9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    19064989..19077095 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322697.1XP_054178672.1  homer protein homolog 3 isoform X1

    UniProtKB/TrEMBL
    Q5U0L9
  2. XM_054322696.1XP_054178671.1  homer protein homolog 3 isoform X1

    UniProtKB/TrEMBL
    Q5U0L9