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Aliases for ZHX3 Gene

Aliases for ZHX3 Gene

  • Zinc Fingers And Homeoboxes 3 2 3 5
  • Zinc Finger And Homeodomain Protein 3 3 4
  • Triple Homeobox Protein 1 3 4
  • Triple Homeobox 1 2 3
  • TIX1 3 4
  • Zinc Fingers And Homeoboxes Protein 3 3
  • KIAA0395 4

External Ids for ZHX3 Gene

Previous HGNC Symbols for ZHX3 Gene

  • TIX1

Previous GeneCards Identifiers for ZHX3 Gene

  • GC20M040492
  • GC20M039240
  • GC20M039807
  • GC20M036545

Summaries for ZHX3 Gene

Entrez Gene Summary for ZHX3 Gene

  • This gene encodes a member of the zinc fingers and homeoboxes (ZHX) gene family. The encoded protein contains two C2H2-type zinc fingers and five homeodomains and forms a dimer with itself or with zinc fingers and homeoboxes family member 1. In the nucleus, the dimerized protein interacts with the A subunit of the ubiquitous transcription factor nuclear factor-Y and may function as a transcriptional repressor. [provided by RefSeq, Jul 2008]

GeneCards Summary for ZHX3 Gene

ZHX3 (Zinc Fingers And Homeoboxes 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and protein heterodimerization activity. An important paralog of this gene is ZHX1.

UniProtKB/Swiss-Prot for ZHX3 Gene

  • Acts as a transcriptional repressor. Involved in the early stages of mesenchymal stem cell (MSC) osteogenic differentiation. Is a regulator of podocyte gene expression during primary glomerula disease. Binds to promoter DNA.

Gene Wiki entry for ZHX3 Gene

Additional gene information for ZHX3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZHX3 Gene

Genomics for ZHX3 Gene

GeneHancer (GH) Regulatory Elements for ZHX3 Gene

Promoters and enhancers for ZHX3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20I041313 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 550.8 +0.8 768 5.9 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZHX3 PLCG1 CHD6 LPIN3 PLCG1-AS1 TOP1 RN7SL615P GC20M041291
GH20I041300 Promoter/Enhancer 0.7 EPDnew ENCODE 550.4 +17.5 17536 0.2 ZHX3 LPIN3 TOP1 GC20M041291 RN7SL615P
GH20I041145 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.6 +164.6 164581 15.3 HDGF PKNOX1 FOXA2 ARID4B YBX1 IRF4 FOS SP5 JUNB REST LPIN3 EMILIN3 ZHX3 PLCG1 CHD6 PLCG1-AS1 MIR6871 GC20P041111
GH20I041231 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.8 +84.4 84384 3.9 ARID4B SIN3A IRF4 ZNF48 YY1 FOS RUNX3 RXRA NFYC JUNB LPIN3 ZHX3 PIR61683 GC20M041291 RN7SL615P
GH20I041171 Enhancer 1.2 Ensembl ENCODE dbSUPER 10.9 +142.1 142094 7.9 HDGF RB1 ARID4B SIN3A ZNF48 RAD21 ELK1 SCRT2 ZNF143 FOS LPIN3 PLCG1 PLCG1-AS1 EMILIN3 ZHX3 PIR61254 MIR6871
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZHX3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZHX3 gene promoter:

Genomic Locations for ZHX3 Gene

Genomic Locations for ZHX3 Gene
139,225 bases
Minus strand

Genomic View for ZHX3 Gene

Genes around ZHX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZHX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZHX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZHX3 Gene

Proteins for ZHX3 Gene

  • Protein details for ZHX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc fingers and homeoboxes protein 3
    Protein Accession:
    Secondary Accessions:
    • E1P5W5
    • F5H820
    • O43145
    • Q6NUJ7

    Protein attributes for ZHX3 Gene

    956 amino acids
    Molecular mass:
    104658 Da
    Quaternary structure:
    • Homodimer (via homeobox domain). Also forms heterodimers with ZHX1 and ZHX2. Heterodimerization with ZHX1 is a prerequisite for repressor activity. Interacts with NFYA.
    • Sequence=BAA23691.3; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ZHX3 Gene

    Alternative splice isoforms for ZHX3 Gene


neXtProt entry for ZHX3 Gene

Post-translational modifications for ZHX3 Gene

No Post-translational modifications

No data available for DME Specific Peptides for ZHX3 Gene

Domains & Families for ZHX3 Gene

Gene Families for ZHX3 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the ZHX family.
  • Belongs to the ZHX family.
genes like me logo Genes that share domains with ZHX3: view

Function for ZHX3 Gene

Molecular function for ZHX3 Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional repressor. Involved in the early stages of mesenchymal stem cell (MSC) osteogenic differentiation. Is a regulator of podocyte gene expression during primary glomerula disease. Binds to promoter DNA.
UniProtKB/Swiss-Prot Induction:
Up-regulated during osteogenic differentiation of mesenchymal stem cells.

Phenotypes From GWAS Catalog for ZHX3 Gene

Gene Ontology (GO) - Molecular Function for ZHX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IDA 12659632
GO:0003714 transcription corepressor activity IBA --
genes like me logo Genes that share ontologies with ZHX3: view
genes like me logo Genes that share phenotypes with ZHX3: view

Animal Models for ZHX3 Gene

MGI Knock Outs for ZHX3:
  • Zhx3 tm1.1(KOMP)Vlcg

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ZHX3 Gene

Localization for ZHX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZHX3 Gene

Subcellular locations from

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 ZHX3 gene
Compartment Confidence
nucleus 5
mitochondrion 2
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ZHX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 12659632
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with ZHX3: view

Pathways & Interactions for ZHX3 Gene

No Data Available

Interacting Proteins for ZHX3 Gene

Gene Ontology (GO) - Biological Process for ZHX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0030154 cell differentiation IEA --
GO:0045669 positive regulation of osteoblast differentiation IMP 21174497
genes like me logo Genes that share ontologies with ZHX3: view

No data available for Pathways by source and SIGNOR curated interactions for ZHX3 Gene

Drugs & Compounds for ZHX3 Gene

No Compound Related Data Available

Transcripts for ZHX3 Gene

Unigene Clusters for ZHX3 Gene

Zinc fingers and homeoboxes 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZHX3 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b
SP2: - -
SP4: - - -
SP6: -

Relevant External Links for ZHX3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZHX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZHX3 Gene

Protein differential expression in normal tissues from HIPED for ZHX3 Gene

This gene is overexpressed in Adrenal (31.4) and Plasma (13.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ZHX3 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZHX3 Gene:


SOURCE GeneReport for Unigene cluster for ZHX3 Gene:


mRNA Expression by UniProt/SwissProt for ZHX3 Gene:

Tissue specificity: Widely expressed. High expression in kidney. Expressed during osteogenic differentiation.

Evidence on tissue expression from TISSUES for ZHX3 Gene

  • Nervous system(4.8)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with ZHX3: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZHX3 Gene

Orthologs for ZHX3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ZHX3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZHX3 33 34
  • 99.69 (n)
(Mus musculus)
Mammalia Zhx3 33 16 34
  • 84.93 (n)
(Rattus norvegicus)
Mammalia Zhx3 33
  • 84.33 (n)
(Canis familiaris)
Mammalia ZHX3 33 34
  • 82.35 (n)
(Bos Taurus)
Mammalia ZHX3 33 34
  • 82.34 (n)
(Monodelphis domestica)
Mammalia ZHX3 34
  • 78 (a)
(Ornithorhynchus anatinus)
Mammalia ZHX3 34
  • 69 (a)
(Gallus gallus)
Aves ZHX3 33 34
  • 68.1 (n)
(Anolis carolinensis)
Reptilia ZHX3 34
  • 61 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia zhx3 33
  • 58.3 (n)
Str.577 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.3322 33
(Danio rerio)
Actinopterygii zhx3 34
  • 36 (a)
tix1 33
Species where no ortholog for ZHX3 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 ZHX3 Gene

Gene Tree for ZHX3 (if available)
Gene Tree for ZHX3 (if available)

Paralogs for ZHX3 Gene

Paralogs for ZHX3 Gene

genes like me logo Genes that share paralogs with ZHX3: view

Variants for ZHX3 Gene

Sequence variations from dbSNP and Humsavar for ZHX3 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs386352383 uncertain-significance, not provided 41,204,421(-) C/A coding_sequence_variant, missense_variant
rs1000000650 -- 41,290,704(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000015065 -- 41,192,844(-) T/G intron_variant
rs1000050729 -- 41,190,505(-) A/C intron_variant
rs1000056477 -- 41,276,774(-) G/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ZHX3 Gene

Variant ID Type Subtype PubMed ID
nsv954038 CNV deletion 24416366
nsv833984 CNV loss 17160897
nsv833983 CNV loss 17160897
nsv821330 CNV deletion 20802225
nsv585991 CNV loss 21841781
nsv585990 CNV loss 21841781
nsv585989 CNV loss 21841781
nsv512615 CNV loss 21212237
nsv498970 CNV loss 21111241
nsv3381 CNV deletion 18451855
nsv3380 CNV deletion 18451855
nsv1071696 CNV deletion 25765185
nsv1064246 CNV loss 25217958
esv990825 CNV gain 20482838
esv3645835 CNV loss 21293372
esv3645834 CNV loss 21293372
esv3567966 CNV loss 25503493
esv3557073 CNV deletion 23714750
esv3557072 CNV deletion 23714750
esv3557071 CNV deletion 23714750
esv3557070 CNV deletion 23714750
esv29587 CNV loss 19812545
esv2722418 CNV deletion 23290073
esv2722416 CNV deletion 23290073
esv27181 CNV gain+loss 19812545
esv2673884 CNV deletion 23128226
esv1745872 CNV insertion 17803354
dgv786e199 CNV deletion 23128226
dgv7571n54 CNV loss 21841781
dgv700n67 CNV loss 20364138

Variation tolerance for ZHX3 Gene

Residual Variation Intolerance Score: 4.91% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.00; 68.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZHX3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZHX3 Gene

Disorders for ZHX3 Gene

Additional Disease Information for ZHX3

No disorders were found for ZHX3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZHX3 Gene

Publications for ZHX3 Gene

  1. Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9455477) Ishikawa K … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4 58
  2. Impact of zinc fingers and homeoboxes 3 on the regulation of mesenchymal stem cell osteogenic differentiation. (PMID: 21174497) Suehiro F … Kato Y (Stem cells and development 2011) 3 4 58
  3. ZHX proteins regulate podocyte gene expression during the development of nephrotic syndrome. (PMID: 17056598) Liu G … Chugh SS (The Journal of biological chemistry 2006) 3 22 58
  4. Analysis of zinc-fingers and homeoboxes (ZHX)-1-interacting proteins: molecular cloning and characterization of a member of the ZHX family, ZHX3. (PMID: 12659632) Yamada K … Miyamoto K (The Biochemical journal 2003) 3 4 58
  5. The mouse zinc-fingers and homeoboxes (ZHX) family; ZHX2 forms a heterodimer with ZHX3. (PMID: 14659886) Kawata H … Miyamoto K (Gene 2003) 3 22 58

Products for ZHX3 Gene

Sources for ZHX3 Gene

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