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TDG thymine DNA glycosylase [ Homo sapiens (human) ]

Gene ID: 6996, updated on 6-Jan-2019

Summary

Official Symbol
TDGprovided by HGNC
Official Full Name
thymine DNA glycosylaseprovided by HGNC
Primary source
HGNC:HGNC:11700
See related
Ensembl:ENSG00000139372 MIM:601423
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
hTDG
Summary
The protein encoded by this gene belongs to the TDG/mug DNA glycosylase family. Thymine-DNA glycosylase (TDG) removes thymine moieties from G/T mismatches by hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of DNA and the mispaired thymine. With lower activity, this enzyme also removes thymine from C/T and T/T mispairings. TDG can also remove uracil and 5-bromouracil from mispairings with guanine. This enzyme plays a central role in cellular defense against genetic mutation caused by the spontaneous deamination of 5-methylcytosine and cytosine. This gene may have a pseudogene in the p arm of chromosome 12. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 10.7), appendix (RPKM 8.9) and 25 other tissues See more
Orthologs

Genomic context

See TDG in Genome Data Viewer
Location:
12q23.3
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (103965815..103988878)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (104359593..104382656)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene heat shock protein 90 beta family member 1 Neighboring gene microRNA 3652 Neighboring gene chromosome 12 open reading frame 73 Neighboring gene glycosyltransferase 8 domain containing 2 Neighboring gene phosphoglycerate mutase 1 (brain) pseudogene Neighboring gene host cell factor C2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Base Excision Repair, organism-specific biosystem (from REACTOME)
    Base Excision Repair, organism-specific biosystemOf the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of ...
  • Base excision repair, organism-specific biosystem (from KEGG)
    Base excision repair, organism-specific biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
  • Base excision repair, conserved biosystem (from KEGG)
    Base excision repair, conserved biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
  • Base-Excision Repair, AP Site Formation, organism-specific biosystem (from REACTOME)
    Base-Excision Repair, AP Site Formation, organism-specific biosystemBase excision repair is initiated by DNA glycosylases that hydrolytically cleave the base-deoxyribose glycosyl bond of a damaged nucleotide residue, releasing the damaged base (Lindahl and Wood 1999,...
  • Cleavage of the damaged pyrimidine, organism-specific biosystem (from REACTOME)
    Cleavage of the damaged pyrimidine, organism-specific biosystemDamaged pyrimidines are cleaved by pyrimide-specific glycosylases (Lindahl and Wood 1999).
  • 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...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Depyrimidination, organism-specific biosystem (from REACTOME)
    Depyrimidination, organism-specific biosystemDepyrimidination of a damaged nucleotide in DNA is mediated by a pyrimidine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribos...
  • Displacement of DNA glycosylase by APEX1, organism-specific biosystem (from REACTOME)
    Displacement of DNA glycosylase by APEX1, organism-specific biosystemFollowing cleavage of the damaged base, DNA glycosylase is displaced by APEX1, an AP endonuclease (Parikh et al. 1998).
  • 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...
  • Fluoropyrimidine Activity, organism-specific biosystem (from WikiPathways)
    Fluoropyrimidine Activity, organism-specific biosystemThe main mechanism of 5-FU activation is conversion to fluorodeoxyuridine monophosphate (FdUMP) which inhibits the enzyme thymidylate synthase (TYMS), an important part of the folate-homocysteine cyc...
  • 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...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Recognition and association of DNA glycosylase with site containing an affected pyrimidine, organism-specific biosystem (from REACTOME)
    Recognition and association of DNA glycosylase with site containing an affected pyrimidine, organism-specific biosystemBase excision repair is initiated by a DNA glycosylase which first recognizes and removes a damaged or incorrect (e.g. mismatched) base (Sokhansanj et al. 2002).
  • Resolution of Abasic Sites (AP sites), organism-specific biosystem (from REACTOME)
    Resolution of Abasic Sites (AP sites), organism-specific biosystemResolution of AP sites can occur through the single nucleotide replacement pathway or through the multiple nucleotide patch replacement pathway, also known as the long-patch base excision repair (BER...
  • SUMO E3 ligases SUMOylate target proteins, organism-specific biosystem (from REACTOME)
    SUMO E3 ligases SUMOylate target proteins, organism-specific biosystemSUMO proteins are conjugated to lysine residues of target proteins via an isopeptide bond with the C-terminal glycine of SUMO (reviewed in Zhao 2007, Gareau and Lima 2010, Hannoun et al. 2010, Citro ...
  • SUMOylation, organism-specific biosystem (from REACTOME)
    SUMOylation, organism-specific biosystemSmall Ubiquitin-like MOdifiers (SUMOs) are a family of 3 proteins (SUMO1,2,3) that are reversibly conjugated to lysine residues of target proteins via a glycine-lysine isopeptide bond (reviewed in Ha...
  • SUMOylation of DNA damage response and repair proteins, organism-specific biosystem (from REACTOME)
    SUMOylation of DNA damage response and repair proteins, organism-specific biosystemSeveral factors that participate in DNA damage response and repair are SUMOylated (reviewed in Dou et al. 2011, Bekker-Jensen and Mailand 2011, Ulrich 2012, Psakhye and Jentsch 2012, Bologna and Ferr...
  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA N-glycosylase activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA N-glycosylase activity TAS
Traceable Author Statement
more info
 
DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
G/U mismatch-specific uracil-DNA glycosylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
SUMO binding IPI
Inferred from Physical Interaction
more info
PubMed 
chloride ion binding IDA
Inferred from Direct Assay
more info
PubMed 
damaged DNA binding TAS
Traceable Author Statement
more info
PubMed 
double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
magnesium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
mismatched DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IEA
Inferred from Electronic Annotation
more info
 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
protein kinase C binding IEA
Inferred from Electronic Annotation
more info
 
protein self-association IDA
Inferred from Direct Assay
more info
PubMed 
pyrimidine-specific mismatch base pair DNA N-glycosylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pyrimidine-specific mismatch base pair DNA N-glycosylase activity IDA
Inferred from Direct Assay
more info
PubMed 
pyrimidine-specific mismatch base pair DNA N-glycosylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
sodium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription coregulator activity IEA
Inferred from Electronic Annotation
more info
 
transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
uracil DNA N-glycosylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
uracil DNA N-glycosylase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
DNA demethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
base-excision repair IDA
Inferred from Direct Assay
more info
PubMed 
base-excision repair, AP site formation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
base-excision repair, AP site formation IDA
Inferred from Direct Assay
more info
PubMed 
base-excision repair, AP site formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
depyrimidination TAS
Traceable Author Statement
more info
 
mismatch repair IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of chromatin binding IEA
Inferred from Electronic Annotation
more info
 
negative regulation of protein binding IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
oxidative DNA demethylation TAS
Traceable Author Statement
more info
 
regulation of DNA N-glycosylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of embryonic development ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of gene expression, epigenetic ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
PML body IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
G/T mismatch-specific thymine DNA glycosylase
NP_003202.3
XP_005269182.1
XP_011537016.1
XP_011537017.1

NCBI Reference Sequences (RefSeq)

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_001363612.1NP_001350541.1  G/T mismatch-specific thymine DNA glycosylase isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC078819, AK303631
    Consensus CDS
    CCDS86330.1
    Conserved Domains (1) summary
    cl00483
    Location:1186
    UDG_like; Uracil-DNA glycosylases (UDG) and related enzymes
  2. NM_003211.6NP_003202.3  G/T mismatch-specific thymine DNA glycosylase isoform 1

    See identical proteins and their annotated locations for NP_003202.3

    Status: REVIEWED

    Source sequence(s)
    AI004247, AK303631, BC037557, DN601672
    Consensus CDS
    CCDS9095.1
    UniProtKB/Swiss-Prot
    Q13569
    UniProtKB/TrEMBL
    B4E127
    Related
    ENSP00000376611.3, ENST00000392872.7
    Conserved Domains (1) summary
    TIGR00584
    Location:2329
    mug; mismatch-specific thymine-DNA glycosylate (mug)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    103965815..103988878
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538714.1XP_011537016.1  G/T mismatch-specific thymine DNA glycosylase isoform X1

    UniProtKB/TrEMBL
    B4E127
    Related
    ENSP00000445899.1, ENST00000544861.5
    Conserved Domains (1) summary
    cl00483
    Location:1186
    UDG_like; Uracil-DNA glycosylases (UDG) and related enzymes
  2. XM_011538715.1XP_011537017.1  G/T mismatch-specific thymine DNA glycosylase isoform X2

    See identical proteins and their annotated locations for XP_011537017.1

    UniProtKB/TrEMBL
    B4DI29
    Conserved Domains (1) summary
    cl00483
    Location:20125
    UDG_like; Uracil-DNA glycosylases (UDG) and related enzymes
  3. XM_005269125.2XP_005269182.1  G/T mismatch-specific thymine DNA glycosylase isoform X2

    See identical proteins and their annotated locations for XP_005269182.1

    UniProtKB/TrEMBL
    B4DI29
    Conserved Domains (1) summary
    cl00483
    Location:20125
    UDG_like; Uracil-DNA glycosylases (UDG) and related enzymes

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001008411.1: Suppressed sequence

    Description
    NM_001008411.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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