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TET2 tet methylcytosine dioxygenase 2 [ Homo sapiens (human) ]

Gene ID: 54790, updated on 3-Jun-2018
Official Symbol
TET2provided by HGNC
Official Full Name
tet methylcytosine dioxygenase 2provided by HGNC
Primary source
HGNC:HGNC:25941
See related
Ensembl:ENSG00000168769 MIM:612839; Vega:OTTHUMG00000131213
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MDS; KIAA1546
Summary
The protein encoded by this gene is a methylcytosine dioxygenase that catalyzes the conversion of methylcytosine to 5-hydroxymethylcytosine. The encoded protein is involved in myelopoiesis, and defects in this gene have been associated with several myeloproliferative disorders. Two variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]
Expression
Ubiquitous expression in bone marrow (RPKM 5.5), appendix (RPKM 4.6) and 25 other tissues See more
Orthologs
See TET2 in Genome Data Viewer
Location:
4q24
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (105145875..105279803)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (106067032..106200960)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 351, pseudogene Neighboring gene nucleoporin Nup43-like Neighboring gene TET2 antisense RNA 1 Neighboring gene RNA, 7SL, cytoplasmic 89, pseudogene Neighboring gene pyrophosphatase (inorganic) 2 Neighboring gene RNA, U6 small nuclear 553, pseudogene

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Myelodysplastic syndrome
MedGen: C3463824 OMIM: 614286 GeneReviews: Not available
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NHGRI GWAS Catalog

Description
A genome-wide association study of host genetic determinants of the antibody response to Anthrax Vaccine Adsorbed.
NHGRI GWA Catalog
Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog
Identification of a melanoma susceptibility locus and somatic mutation in TET2.
NHGRI GWA Catalog
Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
NHGRI GWA Catalog
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog
  • Cytosine methylation, organism-specific biosystem (from WikiPathways)
    Cytosine methylation, organism-specific biosystemDNA, namely cytosine, methylation is the key event in epigentics. The degree of methylation influences gene expression and methylation disorders are known to be major causes of some diseases like Ret...
  • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
    Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • MECP2 and Associated Rett Syndrome, organism-specific biosystem (from WikiPathways)
    MECP2 and Associated Rett Syndrome, organism-specific biosystemMecp2 is in many mammals an important regulator of neuronal function and development. It affects all cell types, especially neurons but also astrocytes, oligodendrocytes, and glial cells. Mecp2 plays...
  • TET1,2,3 and TDG demethylate DNA, organism-specific biosystem (from REACTOME)
    TET1,2,3 and TDG demethylate DNA, organism-specific biosystemAbout 2-6% of all cytosine residues and 70-80% of cytosine residues in CG dinucleotides in mammalian cells are methylated at the 5 position of the pyrimidine ring. The cytosine residues are methylate...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ20032, KIAA1546, MGC125715

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
ferrous iron binding IDA
Inferred from Direct Assay
more info
PubMed 
iron ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
methylcytosine dioxygenase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
methylcytosine dioxygenase activity IDA
Inferred from Direct Assay
more info
PubMed 
methylcytosine dioxygenase activity IMP
Inferred from Mutant Phenotype
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
5-methylcytosine catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
DNA demethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA demethylation IDA
Inferred from Direct Assay
more info
PubMed 
cell cycle IEA
Inferred from Electronic Annotation
more info
 
histone H3-K4 trimethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
myeloid cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
myeloid cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
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 IDA
Inferred from Direct Assay
more info
PubMed 
protein O-linked glycosylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to organic cyclic compound IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Preferred Names
methylcytosine dioxygenase TET2
Names
probable methylcytosine dioxygenase TET2
tet oncogene family member 2
NP_001120680.1
NP_060098.3
XP_005263139.1
XP_006714305.1
XP_016863808.1
XP_024309870.1
XP_024309871.1

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.

Genomic

  1. NG_028191.1 RefSeqGene

    Range
    5001..138929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_626

mRNA and Protein(s)

  1. NM_001127208.2NP_001120680.1  methylcytosine dioxygenase TET2 isoform a

    See identical proteins and their annotated locations for NP_001120680.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    BQ006500, BX640738, DR005542, FM992369
    Consensus CDS
    CCDS47120.1
    UniProtKB/Swiss-Prot
    Q6N021
    UniProtKB/TrEMBL
    A0A158SIU0
    Related
    ENSP00000369351.4, OTTHUMP00000161870, ENST00000380013.8, OTTHUMT00000253952
    Conserved Domains (1) summary
    pfam12851
    Location:12901417
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  2. NM_017628.4NP_060098.3  methylcytosine dioxygenase TET2 isoform b

    See identical proteins and their annotated locations for NP_060098.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC026029, BX640738
    Consensus CDS
    CCDS3666.1
    UniProtKB/Swiss-Prot
    Q6N021
    UniProtKB/TrEMBL
    A0A024RDF7
    Related
    ENSP00000306705.2, OTTHUMP00000161869, ENST00000305737.6, OTTHUMT00000253951

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    105145875..105279803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024454103.1XP_024309871.1  methylcytosine dioxygenase TET2 isoform X1

    Conserved Domains (1) summary
    pfam12851
    Location:12901417
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  2. XM_024454102.1XP_024309870.1  methylcytosine dioxygenase TET2 isoform X1

    Conserved Domains (1) summary
    pfam12851
    Location:12901417
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  3. XM_006714242.3XP_006714305.1  methylcytosine dioxygenase TET2 isoform X2

    Conserved Domains (1) summary
    pfam12851
    Location:11901317
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily
  4. XM_017008319.1XP_016863808.1  methylcytosine dioxygenase TET2 isoform X3

  5. XM_005263082.3XP_005263139.1  methylcytosine dioxygenase TET2 isoform X1

    See identical proteins and their annotated locations for XP_005263139.1

    UniProtKB/Swiss-Prot
    Q6N021
    UniProtKB/TrEMBL
    A0A158SIU0
    Conserved Domains (1) summary
    pfam12851
    Location:12901417
    Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

RNA

  1. XR_244633.3 RNA Sequence

    Related
    ENST00000265149.9
  2. XR_427546.4 RNA Sequence

  3. XR_001741246.1 RNA Sequence

  4. XR_938746.2 RNA Sequence

  5. XR_938747.3 RNA Sequence

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