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

    Gene ID: 54790, updated on 14-Nov-2024

    Summary

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    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; AllianceGenome:HGNC:25941
    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; IMD75; 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
    mouse all
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    Genomic context

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    See TET2 in Genome Data Viewer
    Location:
    4q24
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (105145875..105279803)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (108456807..108590746)
    RS_2024_09 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 ATAC-STARR-seq lymphoblastoid active region 21773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21775 Neighboring gene nucleoporin Nup43-like Neighboring gene uncharacterized LOC124900868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21776 Neighboring gene NANOG hESC enhancer GRCh37_chr4:106064399-106064900 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21778 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:106083203-106083911 Neighboring gene TET2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21779 Neighboring gene RNA, 7SL, cytoplasmic 89, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr4:106307176-106307329 Neighboring gene inorganic pyrophosphatase 2 Neighboring gene RNA, U6 small nuclear 553, pseudogene

    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 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?
    1. RNA m[5]C oxidation by TET2 regulates chromatin state and leukaemogenesis.
      Title: RNA m(5)C oxidation by TET2 regulates chromatin state and leukaemogenesis.
    2. Effects of TET2-mediated methylation reconstruction on A2058 melanoma cell sensitivity to matrix stiffness in a 3D culture system.
      Title: Effects of TET2-mediated methylation reconstruction on A2058 melanoma cell sensitivity to matrix stiffness in a 3D culture system.
    3. Organ involvement in adults with BPDCN is associated with sun exposure history, TET2 and RAS mutations, and survival.
      Title: Organ involvement in adults with BPDCN is associated with sun exposure history, TET2 and RAS mutations, and survival.
    4. NF-kappaB and TET2 promote macrophage reprogramming in hypoxia that overrides the immunosuppressive effects of the tumor microenvironment.
      Title: NF-κB and TET2 promote macrophage reprogramming in hypoxia that overrides the immunosuppressive effects of the tumor microenvironment.
    5. Hypermethylated RASAL1's promotive role in chemoresistance and tumorigenesis of choriocarcinoma was regulated by TET2 but not DNMTs.
      Title: Hypermethylated RASAL1's promotive role in chemoresistance and tumorigenesis of choriocarcinoma was regulated by TET2 but not DNMTs.
    6. Chronic TNF in the aging microenvironment exacerbates Tet2 loss-of-function myeloid expansion.
      Title: Chronic TNF in the aging microenvironment exacerbates Tet2 loss-of-function myeloid expansion.
    7. TET2 Is Downregulated in Early Esophageal Squamous Cell Carcinoma and Promotes Esophageal Squamous Cell Malignant Behaviors.
      Title: TET2 Is Downregulated in Early Esophageal Squamous Cell Carcinoma and Promotes Esophageal Squamous Cell Malignant Behaviors.
    8. [Relationship between DTA Mutations and Thromboembolism in Patients with Myeloproliferative Neoplasms].
      Title: [Relationship between DTA Mutations and Thromboembolism in Patients with Myeloproliferative Neoplasms].
    9. Uncovering the role of TET2-mediated ENPEP activation in trophoblast cell fate determination.
      Title: Uncovering the role of TET2-mediated ENPEP activation in trophoblast cell fate determination.
    10. DNA dioxygenases TET2 deficiency promotes cigarette smoke induced chronic obstructive pulmonary disease by inducing ferroptosis of lung epithelial cell.
      Title: DNA dioxygenases TET2 deficiency promotes cigarette smoke induced chronic obstructive pulmonary disease by inducing ferroptosis of lung epithelial cell.
    Submit: New GeneRIF Correction See all GeneRIFs (415)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Immunodeficiency 75
    MedGen: C5436860 OMIM: 619126 GeneReviews: Not available
    		not available
    Myelodysplastic syndrome
    MedGen: C3463824 OMIM: 614286 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    A genome-wide association study of host genetic determinants of the antibody response to Anthrax Vaccine Adsorbed.
    EBI GWAS Catalog
    Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Identification of a melanoma susceptibility locus and somatic mutation in TET2.
    EBI GWAS Catalog
    Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
    EBI GWAS Catalog
    Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    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)

    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

    • FLJ20032, KIAA1546, MGC125715

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5-methylcytosine dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 5-methylcytosine dioxygenase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 5-methylcytosine dioxygenase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables 5-methylcytosine dioxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ferrous iron binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 chromosomal 5-methylcytosine DNA demethylation, oxidation pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in leukocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in myeloid cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in myeloid cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of gene expression via chromosomal CpG island demethylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein O-linked glycosylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to organic cyclic compound IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    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 TET2
    Names
    probable methylcytosine dioxygenase TET2
    ten-eleven translocation 2
    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
    XP_047271795.1
    XP_047271796.1
    XP_047271797.1
    XP_047271798.1
    XP_047271799.1
    XP_054206247.1
    XP_054206248.1
    XP_054206249.1
    XP_054206250.1
    XP_054206251.1
    XP_054206252.1
    XP_054206253.1
    XP_054206254.1
    XP_054206255.1
    XP_054206256.1

    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.

    Genomic

    1. NG_028191.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001127208.3 → NP_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)
      AC004069, AC026029
      Consensus CDS
      CCDS47120.1
      UniProtKB/Swiss-Prot
      B5MDU0, Q2TB88, Q3LIB8, Q6N021, Q96JX5, Q9HCM6, Q9NXW0
      UniProtKB/TrEMBL
      A0A158SIU0, E7EQS8
      Related
      ENSP00000369351.4, ENST00000380013.9
      Conserved Domains (1) summary
      pfam12851
      Location:1290 → 1417
      Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

    2. NM_017628.4 → NP_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/TrEMBL
      E7EPB1
      Related
      ENSP00000306705.2, ENST00000305737.6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_024454103.2 → XP_024309871.1  methylcytosine dioxygenase TET2 isoform X1

      UniProtKB/Swiss-Prot
      B5MDU0, Q2TB88, Q3LIB8, Q6N021, Q96JX5, Q9HCM6, Q9NXW0
      UniProtKB/TrEMBL
      A0A158SIU0, E7EQS8
      Conserved Domains (1) summary
      pfam12851
      Location:1290 → 1417
      Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

    2. XM_024454102.2 → XP_024309870.1  methylcytosine dioxygenase TET2 isoform X1

      UniProtKB/Swiss-Prot
      B5MDU0, Q2TB88, Q3LIB8, Q6N021, Q96JX5, Q9HCM6, Q9NXW0
      UniProtKB/TrEMBL
      A0A158SIU0, E7EQS8
      Conserved Domains (1) summary
      pfam12851
      Location:1290 → 1417
      Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

    3. XM_006714242.4 → XP_006714305.1  methylcytosine dioxygenase TET2 isoform X2

      UniProtKB/TrEMBL
      E7EQS8
      Conserved Domains (1) summary
      pfam12851
      Location:1190 → 1317
      Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

    4. XM_005263082.4 → XP_005263139.1  methylcytosine dioxygenase TET2 isoform X1

      See identical proteins and their annotated locations for XP_005263139.1

      UniProtKB/Swiss-Prot
      B5MDU0, Q2TB88, Q3LIB8, Q6N021, Q96JX5, Q9HCM6, Q9NXW0
      UniProtKB/TrEMBL
      A0A158SIU0, E7EQS8
      Conserved Domains (1) summary
      pfam12851
      Location:1290 → 1417
      Tet_JBP; Oxygenase domain of the 2OGFeDO superfamily

    5. XM_047415839.1 → XP_047271795.1  methylcytosine dioxygenase TET2 isoform X3

    6. XM_047415840.1 → XP_047271796.1  methylcytosine dioxygenase TET2 isoform X4

    7. XM_047415841.1 → XP_047271797.1  methylcytosine dioxygenase TET2 isoform X5

      Related
      ENSP00000265149.5, ENST00000265149.9

    8. XM_047415842.1 → XP_047271798.1  methylcytosine dioxygenase TET2 isoform X6

    9. XM_017008319.2 → XP_016863808.1  methylcytosine dioxygenase TET2 isoform X6

      UniProtKB/TrEMBL
      E7EPB1

    10. XM_047415843.1 → XP_047271799.1  methylcytosine dioxygenase TET2 isoform X6

    RNA

    1. XR_007057933.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      108456807..108590746
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350273.1 → XP_054206248.1  methylcytosine dioxygenase TET2 isoform X1

    2. XM_054350274.1 → XP_054206249.1  methylcytosine dioxygenase TET2 isoform X1

    3. XM_054350275.1 → XP_054206250.1  methylcytosine dioxygenase TET2 isoform X2

    4. XM_054350272.1 → XP_054206247.1  methylcytosine dioxygenase TET2 isoform X1

    5. XM_054350276.1 → XP_054206251.1  methylcytosine dioxygenase TET2 isoform X3

    6. XM_054350277.1 → XP_054206252.1  methylcytosine dioxygenase TET2 isoform X4

    7. XM_054350278.1 → XP_054206253.1  methylcytosine dioxygenase TET2 isoform X5

    8. XM_054350280.1 → XP_054206255.1  methylcytosine dioxygenase TET2 isoform X6

    9. XM_054350279.1 → XP_054206254.1  methylcytosine dioxygenase TET2 isoform X6

    10. XM_054350281.1 → XP_054206256.1  methylcytosine dioxygenase TET2 isoform X6

    RNA

    1. XR_008486995.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6N021.3 GenPept UniProtKB/Swiss-Prot:Q6N021

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