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

Gene ID: 114521, updated on 2-Nov-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
EnsemblRapid: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. Predicted to be located in PML body and plasma membrane. Predicted to be active in nucleus. Orthologous to human TDG (thymine DNA glycosylase). [provided by Alliance of Genome Resources, Nov 2024]
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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See Tdg in Genome Data Viewer
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 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. 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
  2. Expression of long-patch and short-patch DNA mismatch repair proteins in the embryonic and adult mammalian brain. Marietta C, et al. Brain Res Mol Brain Res, 1998 Jan. PMID 9473709
  3. The thymine-DNA glycosylase regulatory domain: residual structure and DNA binding. Smet-Nocca C, et al. Biochemistry, 2008 Jun 24. PMID 18512959
  4. Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability. Cortázar D, et al. Nature, 2011 Feb 17. PMID 21278727
  5. 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

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, ENSRNOT00000077041.4
    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, ENSRNOT00000076468.4
    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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