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TET3 tet methylcytosine dioxygenase 3 [ Homo sapiens (human) ]

Gene ID: 200424, updated on 22-Aug-2021

Summary

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Official Symbol
TET3provided by HGNC
Official Full Name
tet methylcytosine dioxygenase 3provided by HGNC
Primary source
HGNC:HGNC:28313
See related
Ensembl:ENSG00000187605 MIM:613555
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BEFAHRS; hCG_40738
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 6.8), skin (RPKM 6.6) and 23 other tissues See more
Orthologs
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Genomic context

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See TET3 in Genome Data Viewer
Location:
2p13.1
Exon count:
17
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (73982036..74135394)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (74212037..74335303)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene deoxyguanosine kinase Neighboring gene DGUOK antisense RNA 1 Neighboring gene RNA, 5S ribosomal pseudogene 97 Neighboring gene uncharacterized LOC107985898 Neighboring gene formin binding protein 1 pseudogene 1 Neighboring gene bolA family member 3 Neighboring gene BOLA3 divergent transcript

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Neurodevelopmental Disorder Defined in TET3-Deficient Individuals. . Am J Med Genet A, 2020 Jun. PMID 32453507
  2. Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency. Beck DB, et al. Am J Hum Genet, 2020 Feb 6. PMID 31928709, Free PMC Article
  3. Somatic mutation and loss of expression of a candidate tumor suppressor gene TET3 in gastric and colorectal cancers. Mo HY, et al. Pathol Res Pract, 2020 Mar. PMID 31859118
  4. Increased expression of TET3 predicts unfavorable prognosis in patients with ovarian cancer-a bioinformatics integrative analysis. Cao T, et al. J Ovarian Res, 2019 Oct 27. PMID 31656201, Free PMC Article
  5. Epigenetic downregulation of TET3 reduces genome-wide 5hmC levels and promotes glioblastoma tumorigenesis. Carella A, et al. Int J Cancer, 2020 Jan 15. PMID 31211412

See all (74) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Regulation of DNA methylation signatures on NF-kappaB and STAT3 pathway genes and TET activity in cigarette smoke extract-challenged cells/COPD exacerbation model in vitro.
    Title: Regulation of DNA methylation signatures on NF-κB and STAT3 pathway genes and TET activity in cigarette smoke extract-challenged cells/COPD exacerbation model in vitro.
  2. Redirected nuclear glutamate dehydrogenase supplies Tet3 with alpha-ketoglutarate in neurons.
    Title: Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons.
  3. Epigenetic induction of tumor stemness via the lipopolysaccharide-TET3-HOXB2 signaling axis in esophageal squamous cell carcinoma.
    Title: Epigenetic induction of tumor stemness via the lipopolysaccharide-TET3-HOXB2 signaling axis in esophageal squamous cell carcinoma.
  4. Role of Chromatin Remodeling Genes and TETs in the Development of Human Midbrain Dopaminergic Neurons.
    Title: Role of Chromatin Remodeling Genes and TETs in the Development of Human Midbrain Dopaminergic Neurons.
  5. Glyphosate and AMPA Induce Alterations in Expression of Genes Involved in Chromatin Architecture in Human Peripheral Blood Mononuclear Cells (In Vitro).
    Title: Glyphosate and AMPA Induce Alterations in Expression of Genes Involved in Chromatin Architecture in Human Peripheral Blood Mononuclear Cells (In Vitro).
  6. A Positive Feedback Loop of TET3 and TGF-beta1 Promotes Liver Fibrosis.
    Title: A Positive Feedback Loop of TET3 and TGF-β1 Promotes Liver Fibrosis.
  7. Neurodevelopmental Disorder Defined in TET3-Deficient Individuals.
    Title: Neurodevelopmental Disorder Defined in TET3-Deficient Individuals.
  8. Integrin alpha6 signaling induces STAT3-TET3-mediated hydroxymethylation of genes critical for maintenance of glioma stem cells.
    Title: Integrin α6 signaling induces STAT3-TET3-mediated hydroxymethylation of genes critical for maintenance of glioma stem cells.
  9. Somatic mutation and loss of expression of a candidate tumor suppressor gene TET3 in gastric and colorectal cancers.
    Title: Somatic mutation and loss of expression of a candidate tumor suppressor gene TET3 in gastric and colorectal cancers.
  10. Identification and validation of mRNA 3'untranslated regions of DNMT3B and TET3 as novel competing endogenous RNAs of the tumor suppressor PTEN.
    Title: Identification and validation of mRNA 3'untranslated regions of DNMT3B and TET3 as novel competing endogenous RNAs of the tumor suppressor PTEN.
Submit: New GeneRIF Correction See all GeneRIFs (52)

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

Associated conditions

Description Tests
Beck-Fahrner syndrome
MedGen: C5394097 OMIM: 618798 GeneReviews: Not available
not available
Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
GeneReviews: Not available
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
GeneReviews: Not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0401, MGC22014, AC073046.25

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables methyl-CpG binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables methylcytosine dioxygenase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables methylcytosine dioxygenase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in 5-methylcytosine catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA demethylation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in DNA demethylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in DNA demethylation of male pronucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in histone H3-K4 trimethylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in oxidative demethylation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein O-linked glycosylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in female pronucleus IEA
Inferred from Electronic Annotation
more info
  
located_in male pronucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 

General protein information

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Preferred Names
methylcytosine dioxygenase TET3
Names
probable methylcytosine dioxygenase TET3
putative methylcytosine dioxygenase
ten-eleven translocation 3
tet oncogene family member 3
NP_001274420.1
NP_001352951.1
XP_011530984.1
XP_011530985.1
XP_011530986.1
XP_011530987.1
XP_011530988.1
XP_011530989.1
XP_011530990.1
XP_011530992.1
XP_016859055.1
XP_024308513.1
XP_024308514.1
XP_024308515.1

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.

mRNA and Protein(s)

  1. NM_001287491.2 → NP_001274420.1  methylcytosine dioxygenase TET3 isoform 1

    See identical proteins and their annotated locations for NP_001274420.1

    Status: VALIDATED

    Source sequence(s)
    AC073046, AC073263, AI438961, HQ220209
    Consensus CDS
    CCDS46339.2
    UniProtKB/Swiss-Prot
    O43151
    Related
    ENSP00000386869.3, ENST00000409262.8
    Conserved Domains (4) summary
    PHA03247
    Location:383 → 752
    PHA03247; large tegument protein UL36; Provisional
    pfam02008
    Location:50 → 89
    zf-CXXC; CXXC zinc finger domain
    cd18897
    Location:828 → 1152
    TET3; oxygenase domain of ten-eleven translocation (TET)3 methylcytosine dioxygenase and similar proteins
    cl40427
    Location:1638 → 1766
    Tet_JBP; oxygenase domain of ten-eleven translocation (TET) enzymes, J-binding proteins (JBPs), and similar proteins

  2. NM_001366022.1 → NP_001352951.1  methylcytosine dioxygenase TET3 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC073263, AC110801
    Related
    ENSP00000307803.8, ENST00000305799.8
    Conserved Domains (2) summary
    pfam12851
    Location:892 → 1019
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
    cl26464
    Location:290 → 659
    Atrophin-1; Atrophin-1 family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    73982036..74135394
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017003566.1 → XP_016859055.1  methylcytosine dioxygenase TET3 isoform X1

    Conserved Domains (2) summary
    pfam02008
    Location:50 → 89
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:985 → 1128
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  2. XM_011532684.2 → XP_011530986.1  methylcytosine dioxygenase TET3 isoform X1

    See identical proteins and their annotated locations for XP_011530986.1

    Conserved Domains (2) summary
    pfam02008
    Location:50 → 89
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:985 → 1128
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  3. XM_011532683.2 → XP_011530985.1  methylcytosine dioxygenase TET3 isoform X1

    See identical proteins and their annotated locations for XP_011530985.1

    Conserved Domains (2) summary
    pfam02008
    Location:50 → 89
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:985 → 1128
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  4. XM_024452746.1 → XP_024308514.1  methylcytosine dioxygenase TET3 isoform X8

    Conserved Domains (3) summary
    pfam02008
    Location:50 → 89
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:985 → 1089
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
    cl26464
    Location:383 → 752
    Atrophin-1; Atrophin-1 family

  5. XM_024452745.1 → XP_024308513.1  methylcytosine dioxygenase TET3 isoform X7

    Conserved Domains (3) summary
    pfam02008
    Location:50 → 89
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:985 → 1105
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
    cl26464
    Location:383 → 752
    Atrophin-1; Atrophin-1 family

  6. XM_011532682.2 → XP_011530984.1  methylcytosine dioxygenase TET3 isoform X1

    See identical proteins and their annotated locations for XP_011530984.1

    Conserved Domains (2) summary
    pfam02008
    Location:50 → 89
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:985 → 1128
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  7. XM_011532685.2 → XP_011530987.1  methylcytosine dioxygenase TET3 isoform X3

    Conserved Domains (2) summary
    pfam02008
    Location:50 → 89
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:966 → 1109
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  8. XM_011532686.2 → XP_011530988.1  methylcytosine dioxygenase TET3 isoform X4

    Conserved Domains (2) summary
    pfam02008
    Location:50 → 89
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:966 → 1093
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  9. XM_011532688.2 → XP_011530990.1  methylcytosine dioxygenase TET3 isoform X9

    Conserved Domains (2) summary
    pfam02008
    Location:50 → 89
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:985 → 1045
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  10. XM_011532690.1 → XP_011530992.1  methylcytosine dioxygenase TET3 isoform X10

    See identical proteins and their annotated locations for XP_011530992.1

    Conserved Domains (3) summary
    pfam05956
    Location:520 → 644
    APC_basic; APC basic domain
    pfam12851
    Location:127 → 270
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
    cl00109
    Location:418 → 553
    MADS; MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ ...

  11. XM_011532687.2 → XP_011530989.1  methylcytosine dioxygenase TET3 isoform X5

    Conserved Domains (1) summary
    pfam12851
    Location:892 → 1035
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

  12. XM_024452747.1 → XP_024308515.1  methylcytosine dioxygenase TET3 isoform X10

    Conserved Domains (3) summary
    pfam05956
    Location:520 → 644
    APC_basic; APC basic domain
    pfam12851
    Location:127 → 270
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
    cl00109
    Location:418 → 553
    MADS; MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ ...
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43151.4 GenPept UniProtKB/Swiss-Prot:O43151

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