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

    Gene ID: 200424, updated on 27-Nov-2024

    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 RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; methyl-CpG binding activity; and zinc ion binding activity. Involved in 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, Nov 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 6.8), skin (RPKM 6.6) and 23 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (73983631..74135498)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (73991778..74143844)
    RS_2024_09 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. Selective Estrogen Receptor Modulators' (SERMs) Influence on TET3 Expression in Breast Cancer Cell Lines with Distinct Biological Subtypes. Linowiecka K, et al. Int J Mol Sci, 2024 Aug 6. PMID 39201247, Free PMC Article
    2. Neurodevelopmental Disorder Defined in TET3-Deficient Individuals. . Am J Med Genet A, 2020 Jun. PMID 32453507
    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. Two families with TET3-related disorder showing neurodevelopmental delay with craniofacial dysmorphisms. Seyama R, et al. J Hum Genet, 2022 Mar. PMID 34719681
    5. TET3 mediates the activation of human hepatic stellate cells via modulating the expression of long non-coding RNA HIF1A-AS1. Zhang QQ, et al. Int J Clin Exp Pathol, 2014. PMID 25550811, Free PMC Article

    See all (100) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MLL4 binds TET3.
      Title: MLL4 binds TET3.
    2. TET3-mediated DNA demethylation modification activates SHP2 expression to promote endometrial cancer progression through the EGFR/ERK pathway.
      Title: TET3-mediated DNA demethylation modification activates SHP2 expression to promote endometrial cancer progression through the EGFR/ERK pathway.
    3. Epigenetic Regulatory Axis MIR22-TET3-MTRNR2L2 Represses Fibroblast-Like Synoviocyte-Mediated Inflammation in Rheumatoid Arthritis.
      Title: Epigenetic Regulatory Axis MIR22-TET3-MTRNR2L2 Represses Fibroblast-Like Synoviocyte-Mediated Inflammation in Rheumatoid Arthritis.
    4. TET3 Protein Represses Proliferation of the MG-63 Human Osteosarcoma Cell Line by Regulating DNA Demethylation: an Epigenetic Study.
      Title: TET3 Protein Represses Proliferation of the MG-63 Human Osteosarcoma Cell Line by Regulating DNA Demethylation: an Epigenetic Study.
    5. Selective Estrogen Receptor Modulators' (SERMs) Influence on TET3 Expression in Breast Cancer Cell Lines with Distinct Biological Subtypes.
      Title: Selective Estrogen Receptor Modulators' (SERMs) Influence on TET3 Expression in Breast Cancer Cell Lines with Distinct Biological Subtypes.
    6. TET3 downregulation and low 5-hydroxymethylcytosine are epigenetic signatures of head and neck carcinoma.
      Title: TET3 downregulation and low 5-hydroxymethylcytosine are epigenetic signatures of head and neck carcinoma.
    7. MiR-26b-5p/TET3 regulates the osteogenic differentiation of human bone mesenchymal stem cells and bone reconstruction in female rats with calvarial defects.
      Title: MiR-26b-5p/TET3 regulates the osteogenic differentiation of human bone mesenchymal stem cells and bone reconstruction in female rats with calvarial defects.
    8. TET3 boosts hepatocyte autophagy and impairs non-alcoholic fatty liver disease by increasing ENPP1 promoter hypomethylation.
      Title: TET3 boosts hepatocyte autophagy and impairs non-alcoholic fatty liver disease by increasing ENPP1 promoter hypomethylation.
    9. Association between SPRY1 and TET3 in skin photoaging and natural aging mechanisms.
      Title: Association between SPRY1 and TET3 in skin photoaging and natural aging mechanisms.
    10. Skeletal muscle TET3 promotes insulin resistance through destabilisation of PGC-1alpha.
      Title: Skeletal muscle TET3 promotes insulin resistance through destabilisation of PGC-1α.
    Submit: New GeneRIF Correction See all GeneRIFs (73)

    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)

    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 5-methylcytosine dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 5-methylcytosine dioxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methyl-CpG 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 epigenetic programing of male pronucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of gene expression via chromosomal CpG island demethylation ISS
    Inferred from Sequence or Structural Similarity
    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 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, ENST00000305799.9
      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_2024_08

    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

      Related
      ENSP00000520736.1, ENST00000718303.1

    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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