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 functio... See more...

Aliases for ZHX3 Gene

Aliases for ZHX3 Gene

  • Zinc Fingers And Homeoboxes 3 2 3 5
  • Zinc Fingers And Homeoboxes Protein 3 3 4
  • Zinc Finger And Homeodomain Protein 3 3 4
  • Triple Homeobox Protein 1 3 4
  • Triple Homeobox 1 2 3
  • KIAA0395 2 4
  • TIX1 3 4
  • ZHX3 5

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 Summary 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

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ZHX3 Gene

Genomics for ZHX3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ZHX3 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
GH20J041313 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +0.8 768 5.9 CREB1 GATAD2A HNRNPL PRDM10 ZNF629 IKZF1 ZNF692 BACH1 TARDBP FOXA1 ZHX3 lnc-ZHX3-4 PLCG1 CHD6 PLCG1-AS1 TOP1 LPIN3 L13714-284
GH20J041300 Promoter/Enhancer 0.9 EPDnew Ensembl ENCODE 600.4 +16.8 16771 1.8 ZIC2 GATA3 SPI1 L13714-284 ZHX3 LPIN3 TOP1 RN7SL615P RF00017-3590 lnc-EMILIN3-1 lnc-ZHX3-4 PLCG1
GH20J041145 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.6 +164.6 164581 15.3 SP1 GATAD2A ATF7 YBX1 ZNF629 LEF1 IKZF1 NFKBIZ RCOR2 JUND LPIN3 EMILIN3 ZHX3 PLCG1 CHD6 MIR6871 PLCG1-AS1
GH20J041231 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 10.8 +84.5 84545 4.3 CEBPG CREB1 GATAD2A TFE3 RFX1 NFKBIZ CTCF RCOR2 TARDBP RXRB LPIN3 ZHX3 piR-61101-412 FJ601684-273 lnc-ZHX3-4 PLCG1
GH20J041171 Enhancer 1.1 Ensembl ENCODE dbSUPER 10.9 +142.0 142026 8 CTCF ZNF143 ZIC2 REST RAD21 TRIM22 SCRT2 ZNF512B SP1 JUND LPIN3 PLCG1 PLCG1-AS1 EMILIN3 ZHX3 piR-38209 piR-47271 MIR6871
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZHX3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ZHX3

Top Transcription factor binding sites by QIAGEN in the ZHX3 gene promoter:
  • AML1a
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • C/EBPalpha
  • E2F
  • E2F-1
  • p300

Genomic Locations for ZHX3 Gene

Genomic Locations for ZHX3 Gene
chr20:41,178,448-41,317,672
(GRCh38/hg38)
Size:
139,225 bases
Orientation:
Minus strand
chr20:39,807,088-39,946,312
(GRCh37/hg19)
Size:
139,225 bases
Orientation:
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:
    Q9H4I2-ZHX3_HUMAN
    Recommended name:
    Zinc fingers and homeoboxes protein 3
    Protein Accession:
    Q9H4I2
    Secondary Accessions:
    • E1P5W5
    • F5H820
    • O43145
    • Q6NUJ7

    Protein attributes for ZHX3 Gene

    Size:
    956 amino acids
    Molecular mass:
    104658 Da
    Quaternary structure:
    • Homodimer (via homeobox domain 1) (PubMed:12659632, PubMed:14659886). Heterodimer with ZHX1 (via homeobox domain 1) (PubMed:12659632). Heterodimer with ZHX2 (via homeobox domain 1) (PubMed:14659886). Heterodimerization with ZHX1 is a prerequisite for repressor activity (PubMed:12659632). Interacts with NFYA (PubMed:12659632).
    SequenceCaution:
    • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for ZHX3 Gene

Post-translational modifications for ZHX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for ZHX3
  • Boster Bio Antibodies for ZHX3
  • Santa Cruz Biotechnology (SCBT) Antibodies for ZHX3

No data available for DME Specific Peptides for ZHX3 Gene

Domains & Families for ZHX3 Gene

Gene Families for ZHX3 Gene

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

Suggested Antigen Peptide Sequences for ZHX3 Gene

GenScript: Design optimal peptide antigens:
  • Zinc fingers and homeoboxes 3 (Q5JZ64_HUMAN)
  • Zinc fingers and homeoboxes 3 (Q5JZ65_HUMAN)
  • Zinc fingers and homeoboxes 3 (Q5JZ66_HUMAN)
  • Zinc fingers and homeoboxes 3 (Q5JZ67_HUMAN)
  • Zinc fingers and homeoboxes 3 (Q5JZ68_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H4I2

UniProtKB/Swiss-Prot:

ZHX3_HUMAN :
  • Belongs to the ZHX family.
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:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IBA,IDA 12659632
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 Zhx3<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZHX3

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

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 ZHX3 gene
Compartment Confidence
nucleus 5
extracellular 1
cytoskeleton 1
mitochondrion 1
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:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA,IDA 12659632
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with ZHX3: view

Pathways & Interactions for ZHX3 Gene

PathCards logo

SuperPathways for ZHX3 Gene

No Data Available

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:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0030154 cell differentiation IEA --
GO:0045669 positive regulation of osteoblast differentiation IMP 21174497
GO:0045892 negative regulation of transcription, DNA-templated IDA 12659632
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

mRNA/cDNA for ZHX3 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ZHX3

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

ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b
SP1:
SP2: - -
SP3:
SP4: - - -
SP5:
SP6: -

Relevant External Links for ZHX3 Gene

GeneLoc Exon Structure for
ZHX3

Expression for ZHX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ZHX3

SOURCE GeneReport for Unigene cluster for ZHX3 Gene:

Hs.380133

mRNA Expression by UniProt/SwissProt for ZHX3 Gene:

Q9H4I2-ZHX3_HUMAN
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(4.5)
  • Kidney(2.3)
genes like me logo Genes that share expression patterns with ZHX3: view

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
Chimpanzee
(Pan troglodytes)
Mammalia ZHX3 30 31
  • 99.69 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Zhx3 30 17 31
  • 84.93 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Zhx3 30
  • 84.33 (n)
Dog
(Canis familiaris)
Mammalia ZHX3 30 31
  • 82.35 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ZHX3 30 31
  • 82.34 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia ZHX3 31
  • 78 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia ZHX3 31
  • 69 (a)
OneToOne
Chicken
(Gallus gallus)
Aves ZHX3 30 31
  • 68.1 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia ZHX3 31
  • 61 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia zhx3 30
  • 58.3 (n)
Str.577 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.3322 30
Zebrafish
(Danio rerio)
Actinopterygii zhx3 31
  • 36 (a)
OneToOne
tix1 30
Species where no ortholog for ZHX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for ZHX3 (if available)
TreeFam:
Gene Tree for ZHX3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ZHX3: view image

Paralogs for ZHX3 Gene

Paralogs for ZHX3 Gene

(2) SIMAP similar genes for ZHX3 Gene using alignment to 12 proteins:

  • ZHX3_HUMAN
  • F5H820_HUMAN
  • F6S7L4_HUMAN
  • F6UBH9_HUMAN
  • F6UQN6_HUMAN
  • F6XGA7_HUMAN
  • F6YD28_HUMAN
  • H0Y6F5_HUMAN
  • H0YLR4_HUMAN
  • H0YMK8_HUMAN
  • H0YNY7_HUMAN
  • Q6NUJ7_HUMAN
genes like me logo Genes that share paralogs with ZHX3: view

Variants for ZHX3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ZHX3 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
rs386352383 Uncertain Significance: not provided 41,204,421(-) C/A MISSENSE_VARIANT
rs17265513 - p.Asn310Ser

Additional dbSNP identifiers (rs#s) for ZHX3 Gene

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

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

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)
ZHX3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZHX3

SNP Genotyping and Copy Number Assay Products

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. The mouse zinc-fingers and homeoboxes (ZHX) family; ZHX2 forms a heterodimer with ZHX3. (PMID: 14659886) Kawata H … Miyamoto K (Gene 2003) 3 4 23
  2. 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
  3. 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
  4. 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 23
  5. 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

Products for ZHX3 Gene

Sources for ZHX3 Gene