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

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; 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: mouse all
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Genomic context

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_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HOMER3 promotes liver hepatocellular carcinoma cancer progression by -upregulating EZH2 and mediating miR-361/GPNMB axis.
Title: HOMER3 promotes liver hepatocellular carcinoma cancer progression by -upregulating EZH2 and mediating miR-361/GPNMB axis.
Glycoproteomics identifies HOMER3 as a potentially targetable biomarker triggered by hypoxia and glucose deprivation in bladder cancer.
Title: Glycoproteomics identifies HOMER3 as a potentially targetable biomarker triggered by hypoxia and glucose deprivation in bladder cancer.
HOMER3 facilitates growth factor-mediated beta-Catenin tyrosine phosphorylation and activation to promote metastasis in triple negative breast cancer.
Title: HOMER3 facilitates growth factor-mediated β-Catenin tyrosine phosphorylation and activation to promote metastasis in triple negative breast cancer.
Homer3 acts as a scaffold that spatially organizes actin assembly to support neutrophil polarity and motility downstream of GPCR activation.
Title: Homer3 regulates the establishment of neutrophil polarity.
Interaction of the protein with amyloid precursor protein is regulated by calcium homeostasis.
Title: Calcium regulates the interaction of amyloid precursor protein with Homer3 protein.
Loss of Homer3 is associated with acute myeloid leukemia.
Title: Growth and differentiation effects of Homer3 on a leukemia cell line.
Homer3 specifically associates with a novel ubiquitin-like domain in the I kappa B kinase (IKK) beta subunit of the IKK complex.
Title: Cutting edge: association with I kappa B kinase beta regulates the subcellular localization of Homer3.
Observational study of gene-disease association. (HuGE Navigator)
Title: Mutation screening of the Homer gene family and association analysis in schizophrenia.
study found that Homer2 and Homer3 are negative regulators of T cell activation; this is achieved through binding of nuclear factor of activated T cells (NFAT) and by competing with calcineurin
Title: NFAT binding and regulation of T cell activation by the cytoplasmic scaffolding Homer proteins.
Fat1 exhibit co-localisation with Homer-3 in cellular protrusions and at the plasma membrane of HeLa cells
Title: The intracellular domain of the human protocadherin hFat1 interacts with Homer signalling scaffolding proteins.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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 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

Process	Evidence Code	Pubs
involved_in G protein-coupled glutamate receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of calcineurin-NFAT signaling cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of interleukin-2 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting	TAS Traceable Author Statement more info	PubMed
involved_in regulation of store-operated calcium entry	IBA Inferred from Biological aspect of Ancestor 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 cytosol	TAS Traceable Author Statement more info
is_active_in dendrite	IBA Inferred from Biological aspect of Ancestor more info
located_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

General protein information

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Preferred Names: homer protein homolog 3

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

NCBI Reference Sequences (RefSeq)

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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

NG_033947.1 RefSeqGene

Range

5016..17030

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001145721.1 → NP_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:6 → 114

EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
NM_001145722.2 → NP_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:6 → 114

EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
NM_001145724.1 → NP_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:115 → 305

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

cd01206
Location:6 → 102

EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain
NM_004838.4 → NP_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:6 → 114

EVH1_Homer_Vesl; Homer/Vesl family proteins EVH1 domain

RNA

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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

18929201..18941217 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439733.1 → XP_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

NC_060943.1 Alternate T2T-CHM13v2.0

Range

19064989..19077095 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

Q5U0L9
XM_054322696.1 → XP_054178671.1 homer protein homolog 3 isoform X1

UniProtKB/TrEMBL

Q5U0L9