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... See more...

Aliases for HOMER3 Gene

Aliases for HOMER3 Gene

  • Homer Scaffold Protein 3 2 3 5
  • Homer Scaffolding Protein 3 2 3
  • Homer Protein Homolog 3 3 4
  • Homer, Neuronal Immediate Early Gene, 3 3
  • Homer Homolog 3 (Drosophila) 2
  • Homer Homolog 3 3
  • HOMER-3 3
  • Homer-3 4
  • VESL3 3

External Ids for HOMER3 Gene

Previous GeneCards Identifiers for HOMER3 Gene

  • GC19M019431
  • GC19M018885
  • GC19M018901
  • GC19M019040
  • GC19M018604

Summaries for HOMER3 Gene

Entrez Gene Summary for HOMER3 Gene

  • 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]

GeneCards Summary for HOMER3 Gene

HOMER3 (Homer Scaffold Protein 3) is a Protein Coding gene. Diseases associated with HOMER3 include Spinocerebellar Ataxia, Autosomal Recessive 13 and Schizophrenia 6. Among its related pathways are Circadian entrainment and Protein-protein interactions at synapses. Gene Ontology (GO) annotations related to this gene include protein domain specific binding and G protein-coupled glutamate receptor binding. An important paralog of this gene is HOMER1.

UniProtKB/Swiss-Prot Summary for HOMER3 Gene

  • Postsynaptic density scaffolding protein. Binds and cross-links cytoplasmic regions of GRM1, GRM5, ITPR1, DNM3, RYR1, RYR2, SHANK1 and SHANK3. By physically linking GRM1 and GRM5 with ER-associated ITPR1 receptors, it aids the coupling of surface receptors to intracellular calcium release. Isoforms can be differently regulated and may play an important role in maintaining the plasticity at glutamatergic synapses. Negatively regulates T cell activation by inhibiting the calcineurin-NFAT pathway. Acts by competing with calcineurin/PPP3CA for NFAT protein binding, hence preventing NFAT activation by PPP3CA (PubMed:18218901).

Gene Wiki entry for HOMER3 Gene

Additional gene information for HOMER3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HOMER3 Gene

Genomics for HOMER3 Gene

GeneHancer (GH) Regulatory Elements for HOMER3 Gene

Promoters and enhancers for HOMER3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J018939 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.6 560 3 CTCF NRF1 USF1 ZNF10 GABPA ZBTB26 HES1 ZBTB7A PRPF4 EZH2 HOMER3-AS1 HOMER3 lnc-COPE-2 MAU2
GH19J018929 Promoter 0.6 EPDnew 500.4 +11.7 11695 0.1 POLR2G POU2F2 AGO2 AGO1 POLR2A RBFOX2 HOMER3 ENSG00000268193 NONHSAG025155.2
GH19J018931 Promoter 0.4 EPDnew 500.4 +9.9 9918 0.1 AGO1 HOMER3 ENSG00000268193 NONHSAG025155.2
GH19J018893 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 5.3 +46.3 46264 3.6 CTCF MYC ZFX GABPA ZBTB26 REST RFX1 TGIF2 ZBTB7A EZH2 GDF1 CERS1 IQCN TMEM59L CRTC1 HAPLN4 HOMER3 NCAN SUGP2 KLHL26
GH19J018918 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 5.6 +22.1 22060 3.6 FOXK2 ZBTB40 ZNF217 CTCF SIN3A TCF12 POLR2G USF1 SP1 GTF2E2 DDX49 COPE lnc-COPE-1 GDF1 HOMER3 LPAR2 piR-47505 ENSG00000268193
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOMER3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HOMER3

Top Transcription factor binding sites by QIAGEN in the HOMER3 gene promoter:
  • AhR
  • Bach2
  • ER-alpha
  • HEN1

Genomic Locations for HOMER3 Gene

Genomic Locations for HOMER3 Gene
chr19:18,929,201-18,941,261
(GRCh38/hg38)
Size:
12,061 bases
Orientation:
Minus strand
chr19:19,040,010-19,052,070
(GRCh37/hg19)
Size:
12,061 bases
Orientation:
Minus strand

Genomic View for HOMER3 Gene

Genes around HOMER3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOMER3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOMER3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOMER3 Gene

Proteins for HOMER3 Gene

  • Protein details for HOMER3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NSC5-HOME3_HUMAN
    Recommended name:
    Homer protein homolog 3
    Protein Accession:
    Q9NSC5
    Secondary Accessions:
    • B2RA10
    • E9PCW9
    • O14580
    • O95350
    • Q9NSB9
    • Q9NSC0
    • Q9NSC1

    Protein attributes for HOMER3 Gene

    Size:
    361 amino acids
    Molecular mass:
    39836 Da
    Quaternary structure:
    • Tetramer (PubMed:19345194). Isoform 1 and isoform 2 encode coiled-coil structures that mediate homo- and heteromultimerization. Interacts with NFATC2; interaction is calcium independent; interaction competes with PPP3CA for NFATC2 binding; interaction is reduced by AKT activation (PubMed:18218901). Interacts with NFATC1 and NFATC4 (PubMed:18218901). Interacts with SHANK1; forms a high-order complex at least composed of SHANK1 and HOMER3; the complex formation is regulated by CAMK2A-mediated phosphorylation (PubMed:19345194).
    SequenceCaution:
    • Sequence=AAB81545.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for HOMER3 Gene

    Alternative splice isoforms for HOMER3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HOMER3 Gene

Post-translational modifications for HOMER3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for HOMER3
  • Boster Bio Antibodies for HOMER3

No data available for DME Specific Peptides for HOMER3 Gene

Domains & Families for HOMER3 Gene

Gene Families for HOMER3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for HOMER3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HOMER3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ94648, Homo sapiens homer homolog 3 (Drosophila) (HOMER3), mRNA (B2RA10_HUMAN)
  • Homer protein homolog 3 (HOME3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NSC5

UniProtKB/Swiss-Prot:

HOME3_HUMAN :
  • The WH1 domain interacts with the PPXXF motif in GRM1, GRM5, RYR1, RYR2, ITPR1, SHANK 1 and SHANK3.
  • Belongs to the Homer family.
Domain:
  • The WH1 domain interacts with the PPXXF motif in GRM1, GRM5, RYR1, RYR2, ITPR1, SHANK 1 and SHANK3.
Family:
  • Belongs to the Homer family.
genes like me logo Genes that share domains with HOMER3: view

Function for HOMER3 Gene

Molecular function for HOMER3 Gene

UniProtKB/Swiss-Prot Function:
Postsynaptic density scaffolding protein. Binds and cross-links cytoplasmic regions of GRM1, GRM5, ITPR1, DNM3, RYR1, RYR2, SHANK1 and SHANK3. By physically linking GRM1 and GRM5 with ER-associated ITPR1 receptors, it aids the coupling of surface receptors to intracellular calcium release. Isoforms can be differently regulated and may play an important role in maintaining the plasticity at glutamatergic synapses. Negatively regulates T cell activation by inhibiting the calcineurin-NFAT pathway. Acts by competing with calcineurin/PPP3CA for NFAT protein binding, hence preventing NFAT activation by PPP3CA (PubMed:18218901).
GENATLAS Biochemistry:
homer,neuronal immediate early gene 3,constitutively expressed at excitating synapses,binding,clustering and linking metabotropic glutamate receptors group I with the inositol triphosphate receptors regulator of GRMs signaling

Phenotypes From GWAS Catalog for HOMER3 Gene

Gene Ontology (GO) - Molecular Function for HOMER3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16098226
GO:0035256 G protein-coupled glutamate receptor binding IBA 21873635
GO:0042802 identical protein binding IPI 25416956
genes like me logo Genes that share ontologies with HOMER3: view
genes like me logo Genes that share phenotypes with HOMER3: view

Animal Models for HOMER3 Gene

MGI Knock Outs for HOMER3:

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for HOMER3 Gene

Localization for HOMER3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOMER3 Gene

Cytoplasm. Cell junction, synapse, postsynaptic density. Cell junction, synapse. Note=Postsynaptic density of neuronal cells. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HOMER3 gene
Compartment Confidence
cytosol 5
plasma membrane 4
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
extracellular 1
cytoskeleton 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (3)
  • Cytoplasmic bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HOMER3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane IBA 21873635
GO:0014069 postsynaptic density IBA 21873635
genes like me logo Genes that share ontologies with HOMER3: view

Pathways & Interactions for HOMER3 Gene

genes like me logo Genes that share pathways with HOMER3: view

Pathways by source for HOMER3 Gene

Gene Ontology (GO) - Biological Process for HOMER3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006605 protein targeting TAS 10653696
GO:0007216 G protein-coupled glutamate receptor signaling pathway IBA,TAS 21873635
GO:0032703 negative regulation of interleukin-2 production IMP 18218901
GO:0070885 negative regulation of calcineurin-NFAT signaling cascade IMP 18218901
GO:2001256 regulation of store-operated calcium entry IBA 21873635
genes like me logo Genes that share ontologies with HOMER3: view

No data available for SIGNOR curated interactions for HOMER3 Gene

Drugs & Compounds for HOMER3 Gene

(1) Drugs for HOMER3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
genes like me logo Genes that share compounds with HOMER3: view

Transcripts for HOMER3 Gene

mRNA/cDNA for HOMER3 Gene

4 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOMER3 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b · 13c ·
SP1: - - - - -
SP2: -
SP3: - -
SP4: - - -
SP5: - - - - - -
SP6: - - -
SP7: - - - - - - - - - - - - - -
SP8: - - - - - - -
SP9: -
SP10:
SP11: - -
SP12:

ExUns: 13d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for HOMER3 Gene

GeneLoc Exon Structure for
HOMER3

Expression for HOMER3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HOMER3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOMER3 Gene

This gene is overexpressed in Spleen (x4.5).

Protein differential expression in normal tissues from HIPED for HOMER3 Gene

This gene is overexpressed in Spleen (41.5) and Monocytes (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HOMER3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HOMER3

SOURCE GeneReport for Unigene cluster for HOMER3 Gene:

Hs.720208

Evidence on tissue expression from TISSUES for HOMER3 Gene

  • Nervous system(4.8)
  • Muscle(2.6)
genes like me logo Genes that share expression patterns with HOMER3: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOMER3 Gene

Orthologs for HOMER3 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOMER3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HOMER3 31 30
  • 99.17 (n)
OneToOne
dog
(Canis familiaris)
Mammalia HOMER3 31 30
  • 88.49 (n)
OneToOne
cow
(Bos Taurus)
Mammalia HOMER3 31 30
  • 87.71 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Homer3 30
  • 83.71 (n)
mouse
(Mus musculus)
Mammalia Homer3 17 31 30
  • 82.77 (n)
oppossum
(Monodelphis domestica)
Mammalia HOMER3 31
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 72 (a)
ManyToMany
chicken
(Gallus gallus)
Aves HOMER3 31 30
  • 70.18 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia homer3 30
  • 64.21 (n)
African clawed frog
(Xenopus laevis)
Amphibia homer3-prov 30
zebrafish
(Danio rerio)
Actinopterygii homer3 31 30
  • 61.56 (n)
OneToOne
zgc55557 30
fruit fly
(Drosophila melanogaster)
Insecta homer 31
  • 34 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 35 (a)
OneToMany
Species where no ortholog for HOMER3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HOMER3 Gene

ENSEMBL:
Gene Tree for HOMER3 (if available)
TreeFam:
Gene Tree for HOMER3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HOMER3: view image

Paralogs for HOMER3 Gene

Paralogs for HOMER3 Gene

(3) SIMAP similar genes for HOMER3 Gene using alignment to 6 proteins:

  • HOME3_HUMAN
  • B2RA10_HUMAN
  • M0QYF9_HUMAN
  • M0QZN1_HUMAN
  • M0R2T8_HUMAN
  • M0R2U7_HUMAN
genes like me logo Genes that share paralogs with HOMER3: view

Variants for HOMER3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HOMER3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
710762 Benign: not provided 18,931,539(-) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
780553 Benign: not provided 18,933,049(-) G/T INTRON_VARIANT
781464 Benign: not provided 18,931,578(-) A/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
rs1059240 - p.Ser342Arg

Additional dbSNP identifiers (rs#s) for HOMER3 Gene

Structural Variations from Database of Genomic Variants (DGV) for HOMER3 Gene

Variant ID Type Subtype PubMed ID
esv2665463 CNV deletion 23128226
esv2667412 CNV deletion 23128226
esv3556142 CNV deletion 23714750
nsv1151217 CNV deletion 26484159
nsv470132 CNV loss 18288195
nsv833778 CNV loss 17160897
nsv952423 CNV deletion 24416366
nsv956592 CNV deletion 24416366

Variation tolerance for HOMER3 Gene

Residual Variation Intolerance Score: 51.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.62; 45.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOMER3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HOMER3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOMER3 Gene

Disorders for HOMER3 Gene

MalaCards: The human disease database

(5) MalaCards diseases for HOMER3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
spinocerebellar ataxia, autosomal recessive 13
  • scar13
schizophrenia 6
  • sczd6
spinocerebellar ataxia 1
  • sca1
hyperekplexia
  • startle disease, familial
aceruloplasminemia
  • hypoceruloplasminemia, hereditary
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HOMER3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HOMER3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HOMER3 Gene

Publications for HOMER3 Gene

  1. Molecular characterisation of two structurally distinct groups of human homers, generated by extensive alternative splicing. (PMID: 10653696) Soloviev MM … McIlhinney RA (Journal of molecular biology 2000) 2 3 4 23 54
  2. The postsynaptic density proteins Homer and Shank form a polymeric network structure. (PMID: 19345194) Hayashi MK … Hayashi Y (Cell 2009) 3 4 54
  3. NFAT binding and regulation of T cell activation by the cytoplasmic scaffolding Homer proteins. (PMID: 18218901) Huang GN … Worley PF (Science (New York, N.Y.) 2008) 3 4 54
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  5. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4 54

Products for HOMER3 Gene

Sources for HOMER3 Gene