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

Summary

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: mouse all

Genomic context

Location:: 2p13.1

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
109.20200522	current	GRCh38.p13 (GCF_000001405.39)	2	NC_000002.12 (73982036..74135394)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (74212211..74335303)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

C35-mediated TET inactivation increased the efficiency of somatic cell programming without affecting TET complexes.
Title: Selective targeting of TET catalytic domain promotes somatic cell reprogramming.
TET3 is a direct target gene of miR-27a-5p, and induces hypomethylation of CpG sites causing overexpression of Synaptophysin (SYP). The miR-27a-5p - TET3 - SYP signaling pathway may regulate proliferation and cortisol secretion in H295R cells and thus play a key role in the development of cortisol-producing adenoma.
Title: Aberrant DNA methylation of synaptophysin is involved in adrenal cortisol-producing adenoma.
TET3 deficiency is associated with Mendelian disorders of the epigenetic machinery.
Title: Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency.
elevated expression of TET3 is associated with poor clinic-pathological functions, poor prognosis, wherein TET3, which presents epigenetic changes or methylation changes, might be served as a diagnostic marker or therapeutic target for ovarian cancer.
Title: Increased expression of TET3 predicts unfavorable prognosis in patients with ovarian cancer-a bioinformatics integrative analysis.
Epigenetic drugs increased expression of TET3 in glioblastoma cells and ectopic overexpression of TET3 impaired in vitro cell growth and markedly reduced tumor formation in immunodeficient mice models. Elevated TET3 mRNA levels were correlated with better prognosis in glioma samples. Results suggest that epigenetic repression of TET3 might promote glioblastoma tumorigenesis through the genome-wide alteration of 5hmC.
Title: Epigenetic downregulation of TET3 reduces genome-wide 5hmC levels and promotes glioblastoma tumorigenesis.
Hyperglycemia appeared to promote the mRNA expression of SIRT6, TET2 and TE3, which in turn might cause the dynamic changes of 5mC and 5hmC in white blood cells from type 2 diabetes mellitus patients.
Title: Hyperglycemia affects global 5-methylcytosine and 5-hydroxymethylcytosine in blood genomic DNA through upregulation of SIRT6 and TETs.
Study data, for the first time, demonstrated an association of the expression levels of TET3 in endothelial progenitor cells (EPCs) with the development of peripheral artery disease (PAD) in diabetic patients. The expression pattern of TET3 mRNA and TET3 protein in EPCs may be a biomarker of angiopathy in diabetic patients.
Title: Reduced mRNA and Protein Expression Levels of Tet Methylcytosine Dioxygenase 3 in Endothelial Progenitor Cells of Patients of Type 2 Diabetes With Peripheral Artery Disease.
We report a comparison of the specificities of the human MLL1 and TET3 CXXC domains bound to dsDNA containing either cytosine, 5mC, or an enzymatically oxidized 5mC derivatives, in CpG or non-CpG context. With respect to CXXC domain specificity towards non-modified DNA, our work extends a recent analysis, but accounts more carefully for possible confounding influences of cytosine bases away from the site of interest.
Title: Specificity of MLL1 and TET3 CXXC domains towards naturally occurring cytosine modifications.
Results indicate that TET3 expression regulated cell proliferation, which is associated with 5hmC in HepG2 cells.
Title: The expression of TET3 regulated cell proliferation in HepG2 cells.
abnormal expression in eutopic endometrium from infertile women with endometriosis
Title: Alternation of ten-eleven translocation 1, 2, and 3 expression in eutopic endometrium of women with endometriosis-associated infertility.

Submit: New GeneRIF Correction See all GeneRIFs (42)

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: CN263349 OMIM: 618798 GeneReviews: Not available	not available

NHGRI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-16880 (e-PCR)
- UniSTS:46860

SHGC-145629 (e-PCR)
- UniSTS:174692

SHGC-62008 (e-PCR)
- UniSTS:70545

MGC22014__7690 (e-PCR)
- UniSTS:466321

D2S1726E (e-PCR)
- UniSTS:150755

Homology

Homologs of the TET3 gene: The TET3 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 289 organisms have orthologs with human gene TET3
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
methyl-CpG binding	IDA Inferred from Direct Assay more info	PubMed
methylcytosine dioxygenase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
methylcytosine dioxygenase activity	ISS Inferred from Sequence or Structural Similarity more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
5-methylcytosine catabolic process	IEA Inferred from Electronic Annotation more info
DNA demethylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
DNA demethylation	ISS Inferred from Sequence or Structural Similarity more info
DNA demethylation of male pronucleus	ISS Inferred from Sequence or Structural Similarity more info
histone H3-K4 trimethylation	IMP Inferred from Mutant Phenotype more info	PubMed
oxidative demethylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
protein O-linked glycosylation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
chromosome	IEA Inferred from Electronic Annotation more info
cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
female pronucleus	IEA Inferred from Electronic Annotation more info
male pronucleus	ISS Inferred from Sequence or Structural Similarity more info
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; tet oncogene family member 3

NP_001274420.1

EC 1.14.11.n2

NP_001352951.1

EC 1.14.11.n2

XP_011530984.1

EC 1.14.11.n2

XP_011530985.1

EC 1.14.11.n2

XP_011530986.1

EC 1.14.11.n2

XP_011530987.1

EC 1.14.11.n2

XP_011530988.1

EC 1.14.11.n2

XP_011530989.1

EC 1.14.11.n2

XP_011530990.1

EC 1.14.11.n2

XP_011530992.1

EC 1.14.11.n2

XP_016859055.1

EC 1.14.11.n2

XP_024308513.1

EC 1.14.11.n2

XP_024308514.1

EC 1.14.11.n2

XP_024308515.1

EC 1.14.11.n2

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)

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, ENST00000409262.7

Conserved Domains (2) summary

pfam02008
Location:50 → 89

zf-CXXC; CXXC zinc finger domain

pfam12851
Location:985 → 1112

Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
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 Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p13 Primary Assembly

Range

73982036..74135394

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
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
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
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)/ ...
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
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)/ ...