Free for academic non-profit institutions. Other users need a Commercial license

Aliases for TET3 Gene

Aliases for TET3 Gene

  • Tet Methylcytosine Dioxygenase 3 2 3 5
  • Tet Oncogene Family Member 3 2 3
  • EC 1.14.11.n2 4 56
  • Probable Methylcytosine Dioxygenase TET3 3
  • Putative Methylcytosine Dioxygenase 3
  • Methylcytosine Dioxygenase TET3 3
  • HCG_40738 3
  • KIAA0401 4

External Ids for TET3 Gene

Previous GeneCards Identifiers for TET3 Gene

  • GC02P074127
  • GC02P074213
  • GC02P074009
  • GC02P074229

Summaries for TET3 Gene

Entrez Gene Summary for TET3 Gene

  • Members of the ten-eleven translocation (TET) gene family, including TET3, play a role in the DNA methylation process (Langemeijer et al., 2009 [PubMed 19923888]).[supplied by OMIM, Nov 2010]

GeneCards Summary for TET3 Gene

TET3 (Tet Methylcytosine Dioxygenase 3) is a Protein Coding gene. Among its related pathways are Gene Expression and Cytosine methylation. Gene Ontology (GO) annotations related to this gene include methylcytosine dioxygenase activity. An important paralog of this gene is TET2.

UniProtKB/Swiss-Prot for TET3 Gene

  • Dioxygenase that catalyzes the conversion of the modified genomic base 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) and plays a key role in epigenetic chromatin reprogramming in the zygote following fertilization. Also mediates subsequent conversion of 5hmC into 5-formylcytosine (5fC), and conversion of 5fC to 5-carboxylcytosine (5caC). Conversion of 5mC into 5hmC, 5fC and 5caC probably constitutes the first step in cytosine demethylation (By similarity). Selectively binds to the promoter region of target genes and contributes to regulate the expression of numerous developmental genes (PubMed:23217707). In zygotes, DNA demethylation occurs selectively in the paternal pronucleus before the first cell division, while the adjacent maternal pronucleus and certain paternally-imprinted loci are protected from this process. Participates in DNA demethylation in the paternal pronucleus by mediating conversion of 5mC into 5hmC, 5fC and 5caC. Does not mediate DNA demethylation of maternal pronucleus because of the presence of DPPA3/PGC7 on maternal chromatin that prevents TET3-binding to chromatin (By similarity). In addition to its role in DNA demethylation, also involved in the recruitment of the O-GlcNAc transferase OGT to CpG-rich transcription start sites of active genes, thereby promoting histone H2B GlcNAcylation by OGT (PubMed:23353889).

Additional gene information for TET3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TET3 Gene

Genomics for TET3 Gene

GeneHancer (GH) Regulatory Elements for TET3 Gene

Promoters and enhancers for TET3 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
GH02I073978 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 552.3 -0.4 -364 8.3 HDGF PKNOX1 CLOCK FOXA2 MLX ZFP64 ARID4B NEUROD1 SIN3A FEZF1 DGUOK-AS1 TET3 LOC107985899 MOB1A SLC4A5 ENSG00000235499
GH02I073892 Promoter/Enhancer 1.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.4 -89.6 -89586 3.2 BCOR ZNF664 SRF ZFP36 ZMYM3 MAFK SPI1 ACTG2 STAMBP DGUOK TET3 BOLA3-AS1 BOLA3 TPRKB HTRA2 MOB1A ALMS1
GH02I074035 Enhancer 1.3 Ensembl ENCODE dbSUPER 12.7 +54.2 54185 3.4 PKNOX1 SMAD1 ATF1 ARNT TCF12 GATA2 E2F8 ATF7 RUNX3 NCOA1 TET3 STAMBP BOLA3-AS1 BOLA3 ACTG2 LOC107985899 DGUOK-AS1 ENSG00000279181 FNBP1P1
GH02I074030 Enhancer 1.3 Ensembl ENCODE dbSUPER 12.2 +49.0 49043 3.8 HDGF HDAC1 PKNOX1 ATF1 ARNT ZSCAN4 YBX1 KLF5 TCF12 ZNF766 TET3 FNBP1P1 DGUOK-AS1 ENSG00000279181
GH02I074042 Enhancer 1.2 Ensembl ENCODE dbSUPER 11.8 +60.0 60046 1.4 ELF3 FOXA2 MLX RAD21 RARA TCF12 MIXL1 RXRA SP5 ZEB2 TET3 ACTG2 BOLA3 BOLA3-AS1 LOC107985899 MTHFD2 DGUOK-AS1 ENSG00000279181 FNBP1P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TET3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TET3 gene promoter:

Genomic Locations for TET3 Gene

Genomic Locations for TET3 Gene
chr2:73,983,335-74,108,176
(GRCh38/hg38)
Size:
124,842 bases
Orientation:
Plus strand
chr2:74,229,840-74,335,303
(GRCh37/hg19)

Genomic View for TET3 Gene

Genes around TET3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TET3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TET3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TET3 Gene

Proteins for TET3 Gene

  • Protein details for TET3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43151-TET3_HUMAN
    Recommended name:
    Methylcytosine dioxygenase TET3
    Protein Accession:
    O43151
    Secondary Accessions:
    • A6NEI3
    • K9JJH7
    • Q86Z24
    • Q8TBM9

    Protein attributes for TET3 Gene

    Size:
    1660 amino acids
    Molecular mass:
    179350 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Interacts with HCFC1 and OGT.
    SequenceCaution:
    • Sequence=AAH22243.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAX93057.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=BAA23697.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TET3 Gene

    Alternative splice isoforms for TET3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TET3 Gene

Selected DME Specific Peptides for TET3 Gene

O43151:
  • SLVFYQHK
  • GCPIAKWV
  • EEKLLCLVR

Post-translational modifications for TET3 Gene

No Post-translational modifications

Domains & Families for TET3 Gene

Gene Families for TET3 Gene

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

Protein Domains for TET3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TET3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O43151

UniProtKB/Swiss-Prot:

TET3_HUMAN :
  • Isoform 4 contains an N-terminal CXXC-type zinc-finger domain that binds to DNA.
  • Belongs to the TET family.
Domain:
  • Isoform 4 contains an N-terminal CXXC-type zinc-finger domain that binds to DNA.
Family:
  • Belongs to the TET family.
genes like me logo Genes that share domains with TET3: view

Function for TET3 Gene

Molecular function for TET3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
DNA 5-methylcytosine + 2-oxoglutarate + O(2) = DNA 5-hydroxymethylcytosine + succinate + CO(2).
UniProtKB/Swiss-Prot Function:
Dioxygenase that catalyzes the conversion of the modified genomic base 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) and plays a key role in epigenetic chromatin reprogramming in the zygote following fertilization. Also mediates subsequent conversion of 5hmC into 5-formylcytosine (5fC), and conversion of 5fC to 5-carboxylcytosine (5caC). Conversion of 5mC into 5hmC, 5fC and 5caC probably constitutes the first step in cytosine demethylation (By similarity). Selectively binds to the promoter region of target genes and contributes to regulate the expression of numerous developmental genes (PubMed:23217707). In zygotes, DNA demethylation occurs selectively in the paternal pronucleus before the first cell division, while the adjacent maternal pronucleus and certain paternally-imprinted loci are protected from this process. Participates in DNA demethylation in the paternal pronucleus by mediating conversion of 5mC into 5hmC, 5fC and 5caC. Does not mediate DNA demethylation of maternal pronucleus because of the presence of DPPA3/PGC7 on maternal chromatin that prevents TET3-binding to chromatin (By similarity). In addition to its role in DNA demethylation, also involved in the recruitment of the O-GlcNAc transferase OGT to CpG-rich transcription start sites of active genes, thereby promoting histone H2B GlcNAcylation by OGT (PubMed:23353889).

Enzyme Numbers (IUBMB) for TET3 Gene

Phenotypes From GWAS Catalog for TET3 Gene

Gene Ontology (GO) - Molecular Function for TET3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 23222540
GO:0016491 oxidoreductase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0051213 dioxygenase activity IEA --
genes like me logo Genes that share ontologies with TET3: view

Phenotypes for TET3 Gene

MGI mutant phenotypes for TET3:
inferred from 2 alleles
GenomeRNAi human phenotypes for TET3:
genes like me logo Genes that share phenotypes with TET3: view

Animal Models for TET3 Gene

MGI Knock Outs for TET3:

miRNA for TET3 Gene

miRTarBase miRNAs that target TET3

Clone Products

  • Addgene plasmids for TET3

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TET3 Gene

Localization for TET3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TET3 Gene

Nucleus. Cytoplasm. Chromosome. Note=At the zygotic stage, localizes in the male pronucleus, while it localizes to the cytoplasm at other preimplantation stages. Binds to the promoter of target genes, close to the transcription start site. {ECO:0000250 UniProtKB:Q8BG87}.

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 TET3 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TET3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001940 male pronucleus ISS --
GO:0005634 nucleus IEA --
GO:0005694 chromosome IEA --
GO:0005737 cytoplasm ISS --
genes like me logo Genes that share ontologies with TET3: view

Pathways & Interactions for TET3 Gene

genes like me logo Genes that share pathways with TET3: view

Pathways by source for TET3 Gene

SIGNOR curated interactions for TET3 Gene

Activates:

Gene Ontology (GO) - Biological Process for TET3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006493 protein O-linked glycosylation IMP 23353889
GO:0007275 multicellular organism development IEA --
GO:0016569 covalent chromatin modification IEA --
GO:0044727 DNA demethylation of male pronucleus ISS --
GO:0045944 positive regulation of transcription by RNA polymerase II IMP 23353889
genes like me logo Genes that share ontologies with TET3: view

Drugs & Compounds for TET3 Gene

(2) Drugs for TET3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Oxygen Approved, Vet_approved Pharma 0
Succinic acid Approved Nutra Full agonist, Agonist 0

(1) Additional Compounds for TET3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
328-50-7
genes like me logo Genes that share compounds with TET3: view

Transcripts for TET3 Gene

Unigene Clusters for TET3 Gene

Tet methylcytosine dioxygenase 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for TET3

Alternative Splicing Database (ASD) splice patterns (SP) for TET3 Gene

No ASD Table

Relevant External Links for TET3 Gene

GeneLoc Exon Structure for
TET3
ECgene alternative splicing isoforms for
TET3

Expression for TET3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TET3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TET3 Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x4.2) and Skin - Sun Exposed (Lower leg) (x4.1).

Protein differential expression in normal tissues from HIPED for TET3 Gene

This gene is overexpressed in Tlymphocyte (66.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TET3 Gene



Protein tissue co-expression partners for TET3 Gene

NURSA nuclear receptor signaling pathways regulating expression of TET3 Gene:

TET3

SOURCE GeneReport for Unigene cluster for TET3 Gene:

Hs.516107

mRNA Expression by UniProt/SwissProt for TET3 Gene:

O43151-TET3_HUMAN
Tissue specificity: Expressed in colon, muscle, adrenal gland and peripheral blood lymphocytes.

Evidence on tissue expression from TISSUES for TET3 Gene

  • Nervous system(4.4)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with TET3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for TET3 Gene

Orthologs for TET3 Gene

This gene was present in the common ancestor of animals.

Orthologs for TET3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TET3 33 34
  • 99.56 (n)
dog
(Canis familiaris)
Mammalia TET3 33 34
  • 91.75 (n)
cow
(Bos Taurus)
Mammalia LOC101904937 33
  • 91.62 (n)
TET3 34
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TET3 34
  • 89 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tet3 33
  • 87.95 (n)
mouse
(Mus musculus)
Mammalia Tet3 33 16 34
  • 87.31 (n)
oppossum
(Monodelphis domestica)
Mammalia TET3 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves TET3 33 34
  • 70.88 (n)
lizard
(Anolis carolinensis)
Reptilia TET3 34
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tet3 33
  • 58.21 (n)
Str.17563 33
zebrafish
(Danio rerio)
Actinopterygii LOC794865 33
  • 55.24 (n)
tet3 34
  • 48 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG43444 34
  • 10 (a)
OneToMany
Species where no ortholog for TET3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 TET3 Gene

ENSEMBL:
Gene Tree for TET3 (if available)
TreeFam:
Gene Tree for TET3 (if available)

Paralogs for TET3 Gene

Paralogs for TET3 Gene

(2) SIMAP similar genes for TET3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with TET3: view

Variants for TET3 Gene

Sequence variations from dbSNP and Humsavar for TET3 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000015880 -- 74,032,868(+) T/C intron_variant
rs1000044001 -- 74,066,797(+) TTT/TTTT intron_variant
rs1000069249 -- 73,997,041(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000069980 -- 73,992,519(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000117342 -- 74,014,331(+) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for TET3 Gene

Variant ID Type Subtype PubMed ID
nsv954227 CNV deletion 24416366
nsv818048 CNV gain 17921354
nsv479007 CNV novel sequence insertion 20440878
nsv2782 CNV insertion 18451855
nsv1011177 CNV gain 25217958
esv3892681 CNV gain 25118596
esv3591276 CNV loss 21293372
esv3584956 CNV gain 24956385
esv28348 CNV loss 19812545
esv1346659 CNV insertion 17803354
esv1018075 CNV insertion 17803354
esv1001756 CNV insertion 20482838

Variation tolerance for TET3 Gene

Residual Variation Intolerance Score: 3.79% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.34; 63.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TET3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TET3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TET3 Gene

Disorders for TET3 Gene

Additional Disease Information for TET3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for TET3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TET3 Gene

Publications for TET3 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. TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS. (PMID: 23353889) Deplus R … Fuks F (The EMBO journal 2013) 3 4 58
  3. ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection. (PMID: 23697932) Long HK … Klose RJ (Biochemical Society transactions 2013) 2 3 58
  4. TET2 promotes histone O-GlcNAcylation during gene transcription. (PMID: 23222540) Chen Q … Yu X (Nature 2013) 3 4 58
  5. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development. (PMID: 23217707) Xu Y … Shi YG (Cell 2012) 3 4 58

Products for TET3 Gene

Sources for TET3 Gene

Content
Loading form....