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

Gene ID: 200424, updated on 1-Aug-2020

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

Genomic context

See TET3 in Genome Data Viewer
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_000002.12Genomic 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 BOLA3 divergent transcript Neighboring gene bolA family member 3

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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
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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0401, MGC22014, AC073046.25

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

Preferred Names
methylcytosine dioxygenase TET3
Names
probable methylcytosine dioxygenase TET3
putative methylcytosine dioxygenase
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)

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_001287491.2NP_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:5089
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:9851112
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  2. NM_001366022.1NP_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:8921019
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
    cl26464
    Location:290659
    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

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

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

    Conserved Domains (2) summary
    pfam02008
    Location:5089
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:9851128
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  2. XM_011532684.2XP_011530986.1  methylcytosine dioxygenase TET3 isoform X1

    See identical proteins and their annotated locations for XP_011530986.1

    Conserved Domains (2) summary
    pfam02008
    Location:5089
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:9851128
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  3. XM_011532683.2XP_011530985.1  methylcytosine dioxygenase TET3 isoform X1

    See identical proteins and their annotated locations for XP_011530985.1

    Conserved Domains (2) summary
    pfam02008
    Location:5089
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:9851128
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  4. XM_024452746.1XP_024308514.1  methylcytosine dioxygenase TET3 isoform X8

    Conserved Domains (3) summary
    pfam02008
    Location:5089
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:9851089
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
    cl26464
    Location:383752
    Atrophin-1; Atrophin-1 family
  5. XM_024452745.1XP_024308513.1  methylcytosine dioxygenase TET3 isoform X7

    Conserved Domains (3) summary
    pfam02008
    Location:5089
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:9851105
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
    cl26464
    Location:383752
    Atrophin-1; Atrophin-1 family
  6. XM_011532682.2XP_011530984.1  methylcytosine dioxygenase TET3 isoform X1

    See identical proteins and their annotated locations for XP_011530984.1

    Conserved Domains (2) summary
    pfam02008
    Location:5089
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:9851128
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  7. XM_011532685.2XP_011530987.1  methylcytosine dioxygenase TET3 isoform X3

    Conserved Domains (2) summary
    pfam02008
    Location:5089
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:9661109
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  8. XM_011532686.2XP_011530988.1  methylcytosine dioxygenase TET3 isoform X4

    Conserved Domains (2) summary
    pfam02008
    Location:5089
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:9661093
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  9. XM_011532688.2XP_011530990.1  methylcytosine dioxygenase TET3 isoform X9

    Conserved Domains (2) summary
    pfam02008
    Location:5089
    zf-CXXC; CXXC zinc finger domain
    pfam12851
    Location:9851045
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  10. XM_011532690.1XP_011530992.1  methylcytosine dioxygenase TET3 isoform X10

    See identical proteins and their annotated locations for XP_011530992.1

    Conserved Domains (3) summary
    pfam05956
    Location:520644
    APC_basic; APC basic domain
    pfam12851
    Location:127270
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
    cl00109
    Location:418553
    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_011532687.2XP_011530989.1  methylcytosine dioxygenase TET3 isoform X5

    Conserved Domains (1) summary
    pfam12851
    Location:8921035
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  12. XM_024452747.1XP_024308515.1  methylcytosine dioxygenase TET3 isoform X10

    Conserved Domains (3) summary
    pfam05956
    Location:520644
    APC_basic; APC basic domain
    pfam12851
    Location:127270
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
    cl00109
    Location:418553
    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)/ ...
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