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

Gene ID: 200424, updated on 23-Nov-2023

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; AllianceGenome:HGNC:28313
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
Enables methyl-CpG binding activity and zinc ion binding activity. Involved in histone H3-K4 trimethylation; positive regulation of transcription by RNA polymerase II; and protein O-linked glycosylation. Predicted to be located in cytoplasm and male pronucleus. Predicted to be active in nucleus. Biomarker of esophagus squamous cell carcinoma. [provided by Alliance of Genome Resources, Apr 2022]
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
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (73983631..74135498)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (73991778..74143844)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (74212037..74335303)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74164465-74164964 Neighboring gene deoxyguanosine kinase Neighboring gene DGUOK antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16037 Neighboring gene RNA, 5S ribosomal pseudogene 97 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74210413-74211336 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:74211958-74212156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16041 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11649 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74230812-74231328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74231329-74231844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74235869-74236827 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74248449-74248948 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74252809-74253686 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:74253687-74254564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74257891-74258392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74258393-74258892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16044 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:74259869-74260014 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:74278831-74279332 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:74279333-74279832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74312841-74313340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74326577-74327076 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16045 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:74350700-74351402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:74357269-74357882 Neighboring gene formin binding protein 1 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:74374793-74375452 Neighboring gene bolA family member 3 Neighboring gene BOLA3 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr2:74403666-74403858 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:74405031-74405714 Neighboring gene MOB kinase activator 1A

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. TET3-Related Beck-Fahrner Syndrome. Adam MP, et al. , 1993. PMID 37200470
  2. Two families with TET3-related disorder showing neurodevelopmental delay with craniofacial dysmorphisms. Seyama R, et al. J Hum Genet, 2022 Mar. PMID 34719681
  3. TET3 promotes AML growth and epigenetically regulates glucose metabolism and leukemic stem cell associated pathways. Pulikkottil AJ, et al. Leukemia, 2022 Feb. PMID 34462525
  4. Neurodevelopmental Disorder Defined in TET3-Deficient Individuals. . Am J Med Genet A, 2020 Jun. PMID 32453507
  5. 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

See all (87) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The impact and mechanism of TET3 overexpression on the progression of hepatic fibrosis.
    Title: The impact and mechanism of TET3 overexpression on the progression of hepatic fibrosis.
  2. DNMT3B attenuated the inhibition of TET3 on epithelial-mesenchymal transition in TGF-beta1-induced ovarian cancer by methylating the TET3 promoter.
    Title: DNMT3B attenuated the inhibition of TET3 on epithelial-mesenchymal transition in TGF-β1-induced ovarian cancer by methylating the TET3 promoter.
  3. TET3 epigenetically controls feeding and stress response behaviors via AGRP neurons.
    Title: TET3 epigenetically controls feeding and stress response behaviors via AGRP neurons.
  4. Targeted erasure of DNA methylation by TET3 drives adipogenic reprogramming and differentiation.
    Title: Targeted erasure of DNA methylation by TET3 drives adipogenic reprogramming and differentiation.
  5. Maternal inheritance of glucose intolerance via oocyte TET3 insufficiency.
    Title: Maternal inheritance of glucose intolerance via oocyte TET3 insufficiency.
  6. Two families with TET3-related disorder showing neurodevelopmental delay with craniofacial dysmorphisms.
    Title: Two families with TET3-related disorder showing neurodevelopmental delay with craniofacial dysmorphisms.
  7. TET3 promotes AML growth and epigenetically regulates glucose metabolism and leukemic stem cell associated pathways.
    Title: TET3 promotes AML growth and epigenetically regulates glucose metabolism and leukemic stem cell associated pathways.
  8. Stage-specific regulation of DNA methylation by TET enzymes during human cardiac differentiation.
    Title: Stage-specific regulation of DNA methylation by TET enzymes during human cardiac differentiation.
  9. TET3- and OGT-Dependent Expression of Genes Involved in Epithelial-Mesenchymal Transition in Endometrial Cancer.
    Title: TET3- and OGT-Dependent Expression of Genes Involved in Epithelial-Mesenchymal Transition in Endometrial Cancer.
  10. Oxygen regulation of TET enzymes.
    Title: Oxygen regulation of TET enzymes.
Submit: New GeneRIF Correction See all GeneRIFs (63)

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: TET3-Related Beck-Fahrner Syndrome
Compare labs

EBI GWAS Catalog

Description
Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes.
EBI GWAS Catalog
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
EBI GWAS Catalog

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
  
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
  
involved_in DNA demethylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in epigenetic programing of male pronucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  

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_011530989.1
XP_011530990.1
XP_011530992.1
XP_016859055.1
XP_024308513.1
XP_024308514.1
XP_047299615.1
XP_047299616.1
XP_047299618.1
XP_047299620.1
XP_054196924.1
XP_054196925.1
XP_054196926.1
XP_054196927.1
XP_054196928.1
XP_054196929.1
XP_054196930.1
XP_054196931.1
XP_054196932.1
XP_054196933.1
XP_054196934.1
XP_054196935.1
XP_054196936.1
XP_054196937.1

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
    A6NEI3, J3KNF3, K9JJH7, O43151, Q86Z24, Q8TBM9
    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
    Consensus CDS
    CCDS92780.1
    UniProtKB/TrEMBL
    A0A5H1ZRP3
    Related
    ENSP00000307803.8, ENST00000305799.8
    Conserved Domains (3) summary
    PHA03247
    Location:290 → 659
    PHA03247; large tegument protein UL36; Provisional
    cd18897
    Location:735 → 1059
    TET3; oxygenase domain of ten-eleven translocation (TET)3 methylcytosine dioxygenase and similar proteins
    cl40427
    Location:1545 → 1673
    Tet_JBP; oxygenase domain of ten-eleven translocation (TET) enzymes, J-binding proteins (JBPs), and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    73983631..74135498
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532683.3 → 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

  2. XM_047443659.1 → XP_047299615.1  methylcytosine dioxygenase TET3 isoform X2

    UniProtKB/Swiss-Prot
    A6NEI3, J3KNF3, K9JJH7, O43151, Q86Z24, Q8TBM9

  3. XM_017003566.2 → 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

  4. XM_011532684.3 → 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

  5. XM_011532682.3 → 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

  6. XM_011532685.3 → 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

  7. XM_047443660.1 → XP_047299616.1  methylcytosine dioxygenase TET3 isoform X2

    UniProtKB/Swiss-Prot
    A6NEI3, J3KNF3, K9JJH7, O43151, Q86Z24, Q8TBM9

  8. XM_024452745.2 → XP_024308513.1  methylcytosine dioxygenase TET3 isoform X6

    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

  9. XM_024452746.2 → XP_024308514.1  methylcytosine dioxygenase TET3 isoform X7

    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

  10. XM_011532688.3 → XP_011530990.1  methylcytosine dioxygenase TET3 isoform X8

    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

  11. XM_047443662.1 → XP_047299618.1  methylcytosine dioxygenase TET3 isoform X4

  12. XM_011532690.2 → XP_011530992.1  methylcytosine dioxygenase TET3 isoform X9

    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)/ ...

  13. XM_011532687.3 → XP_011530989.1  methylcytosine dioxygenase TET3 isoform X5

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

  14. XM_047443664.1 → XP_047299620.1  methylcytosine dioxygenase TET3 isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    73991778..74143844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054340950.1 → XP_054196925.1  methylcytosine dioxygenase TET3 isoform X1

  2. XM_054340953.1 → XP_054196928.1  methylcytosine dioxygenase TET3 isoform X2

    UniProtKB/Swiss-Prot
    A6NEI3, J3KNF3, K9JJH7, O43151, Q86Z24, Q8TBM9

  3. XM_054340951.1 → XP_054196926.1  methylcytosine dioxygenase TET3 isoform X1

  4. XM_054340952.1 → XP_054196927.1  methylcytosine dioxygenase TET3 isoform X1

  5. XM_054340959.1 → XP_054196934.1  methylcytosine dioxygenase TET3 isoform X7

  6. XM_054340958.1 → XP_054196933.1  methylcytosine dioxygenase TET3 isoform X6

  7. XM_054340949.1 → XP_054196924.1  methylcytosine dioxygenase TET3 isoform X1

  8. XM_054340955.1 → XP_054196930.1  methylcytosine dioxygenase TET3 isoform X3

  9. XM_054340956.1 → XP_054196931.1  methylcytosine dioxygenase TET3 isoform X4

  10. XM_054340960.1 → XP_054196935.1  methylcytosine dioxygenase TET3 isoform X8

  11. XM_054340954.1 → XP_054196929.1  methylcytosine dioxygenase TET3 isoform X2

    UniProtKB/Swiss-Prot
    A6NEI3, J3KNF3, K9JJH7, O43151, Q86Z24, Q8TBM9

  12. XM_054340962.1 → XP_054196937.1  methylcytosine dioxygenase TET3 isoform X9

  13. XM_054340957.1 → XP_054196932.1  methylcytosine dioxygenase TET3 isoform X5

  14. XM_054340961.1 → XP_054196936.1  methylcytosine dioxygenase TET3 isoform X9

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43151.4 GenPept UniProtKB/Swiss-Prot:O43151

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