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    Tdg thymine-DNA glycosylase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 114521, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Tdgprovided by RGD
    Official Full Name
    thymine-DNA glycosylaseprovided by RGD
    Primary source
    RGD:620959
    See related
    Ensembl:ENSRNOG00000027124 AllianceGenome:RGD:620959
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables DNA-binding transcription factor binding activity and protein domain specific binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nucleus. Orthologous to human TDG (thymine DNA glycosylase). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 281.5), Spleen (RPKM 162.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    7q13
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (22965388..22990311, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (21077853..21097617, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (27194000..27213676, complement)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene nuclear transcription factor Y subunit beta Neighboring gene host cell factor C2 Neighboring gene glycosyltransferase 8 domain containing 2 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 6 Neighboring gene heat shock protein 90 beta family member 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Thymine DNA glycosylase is a key regulator of CaMKIIγ expression and vascular smooth muscle phenotype. Liu Y, et al. Am J Physiol Heart Circ Physiol, 2019 Nov 1. PMID 31518169, Free PMC Article
    2. Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA. Maiti A, et al. Proc Natl Acad Sci U S A, 2012 May 22. PMID 22573813, Free PMC Article
    3. Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Zhang L, et al. Nat Chem Biol, 2012 Feb 12. PMID 22327402, Free PMC Article
    4. Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites. Maiti A, et al. J Biol Chem, 2011 Oct 14. PMID 21862836, Free PMC Article
    5. Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability. Cortázar D, et al. Nature, 2011 Feb 17. PMID 21278727

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Thymine DNA glycosylase plays a key role in regulating CaMKIIgamma expression in vascular smooth muscle cells through promoter cytosine methylation/demethylation.
      Title: Thymine DNA glycosylase is a key regulator of CaMKIIγ expression and vascular smooth muscle phenotype.
    2. a previously unsuspected role for the repair enzyme TDG as a repressor of smooth muscle differentiation via competing with SRF for binding to myocardin.
      Title: Thymine DNA glycosylase represses myocardin-induced smooth muscle cell differentiation by competing with serum response factor for myocardin binding.
    3. Expression and activity of the DNA repair enzyme uracil DNA glycosylase during organogenesis in the rat conceptus
      Title: Expression and activity of the DNA repair enzyme uracil DNA glycosylase during organogenesis in the rat conceptus and following methotrexate exposure in vitro.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA N-glycosylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables G/U mismatch-specific uracil-DNA glycosylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables SUMO binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chloride ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables magnesium ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mismatched DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nucleic acid binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase C binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables pyrimidine-specific mismatch base pair DNA N-glycosylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables pyrimidine-specific mismatch base pair DNA N-glycosylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sodium ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription coregulator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables uracil DNA N-glycosylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables uracil DNA N-glycosylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in base-excision repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in base-excision repair, AP site formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in epigenetic regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of embryonic development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in PML body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    G/T mismatch-specific thymine DNA glycosylase
    NP_001375432.1
    NP_446181.2
    XP_038934169.1
    XP_038934170.1

    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_001388503.1 → NP_001375432.1  G/T mismatch-specific thymine DNA glycosylase isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      A0A096MIY3, A0A096MK32
      Related
      ENSRNOP00000067921.1, ENSRNOT00000077041.3
      Conserved Domains (2) summary
      TIGR00584
      Location:2 → 325
      mug; mismatch-specific thymine-DNA glycosylate (mug)
      cd10028
      Location:134 → 138
      UDG-F2_TDG_MUG; motif A [structural motif]

    2. NM_053729.2 → NP_446181.2  G/T mismatch-specific thymine DNA glycosylase isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      A6IFI8, Q99NG8
      Related
      ENSRNOP00000068361.2, ENSRNOT00000076468.3
      Conserved Domains (2) summary
      TIGR00584
      Location:1 → 301
      mug; mismatch-specific thymine-DNA glycosylate (mug)
      cd10028
      Location:110 → 114
      UDG-F2_TDG_MUG; motif A [structural motif]

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086025.1 Reference GRCr8

      Range
      22965388..22990311 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039078241.2 → XP_038934169.1  G/T mismatch-specific thymine DNA glycosylase isoform X1

      UniProtKB/TrEMBL
      A0A096MK32
      Conserved Domains (2) summary
      TIGR00584
      Location:2 → 325
      mug; mismatch-specific thymine-DNA glycosylate (mug)
      cd10028
      Location:134 → 138
      UDG-F2_TDG_MUG; motif A [structural motif]

    2. XM_039078242.2 → XP_038934170.1  G/T mismatch-specific thymine DNA glycosylase isoform X2

      UniProtKB/TrEMBL
      A1L1J2, Q99NG8
      Conserved Domains (2) summary
      TIGR00584
      Location:1 → 301
      mug; mismatch-specific thymine-DNA glycosylate (mug)
      cd10028
      Location:110 → 114
      UDG-F2_TDG_MUG; motif A [structural motif]
    Nucleotide Protein Strain
    Heading Accession and Version

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