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TOP3A Gene(Protein Coding)

DNA Topoisomerase III Alpha

GCID:
GC17M018271
GIFtS:
49
Genes Participants
UDN Logo

Aliases for TOP3A Gene

Aliases for TOP3A Gene

  • DNA Topoisomerase III Alpha 2 3 4 5
  • Zinc Finger, GRF-Type Containing 7 2 3
  • Topoisomerase (DNA) III Alpha 2 3
  • TOP3 3 4
  • DNA Topoisomerase 3-Alpha 3
  • Topo III-Alpha 3
  • EC 5.99.1.2 4
  • ZGRF7 3

External Ids for TOP3A Gene

Previous HGNC Symbols for TOP3A Gene

  • TOP3

Previous GeneCards Identifiers for TOP3A Gene

  • GC17M018422
  • GC17M019769
  • GC17M018117
  • GC17M018377
  • GC17M017930
  • GC17M018175

Summaries for TOP3A Gene

Entrez Gene Summary for TOP3A Gene

  • This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. This enzyme catalyzes the transient breaking and rejoining of a single strand of DNA which allows the strands to pass through one another, thus reducing the number of supercoils and altering the topology of DNA. This enzyme forms a complex with BLM which functions in the regulation of recombination in somatic cells. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]

GeneCards Summary for TOP3A Gene

TOP3A (DNA Topoisomerase III Alpha) is a Protein Coding gene. Diseases associated with TOP3A include Occupational Dermatitis. Among its related pathways are Homologous DNA Pairing and Strand Exchange and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and DNA topoisomerase activity. An important paralog of this gene is TOP3B.

UniProtKB/Swiss-Prot for TOP3A Gene

  • Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. Has DNA decatenation activity.

Gene Wiki entry for TOP3A Gene

Additional gene information for TOP3A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TOP3A Gene

Genomics for TOP3A Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for TOP3A Gene

Promoters and enhancers for TOP3A Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH17I018313 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 568.7 -0.7 -743 5.2 HDGF PKNOX1 CLOCK ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 E2F8 SMCR8 TOP3A DRG2 FLII SHMT1 FOXO3B ENSG00000262202 FAM106A ENSG00000264885 TVP23B
GH17I018223 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 23.4 +89.8 89750 2.8 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF48 ETS1 GLIS2 LLGL1 PIR34011 SMCR8 TOP3A SHMT1 FAM106A MIEF2 ENSG00000273018 ENSG00000262202 DRG2
GH17I017833 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 15.2 +476.6 476552 8.9 CLOCK MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF213 ZNF143 SP3 NFYC GC17P017838 SREBF1 ENSG00000264885 DRG2 SMCR8 RAI1 TOM1L2 TOP3A CCDC144B FOXO3B
GH17I018780 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 19.3 -466.3 -466302 2.2 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 POLR2B TVP23B MAPK7 FOXO3B SMCR8 DRG2 ENSG00000262202 ZNF286B LOC100419436 ENSG00000264885 ENSG00000264932
GH17I018181 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.5 +129.9 129927 8 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 CBX5 ALKBH5 ENSG00000266677 PIR34966 SMCR8 MYO15A MIEF2 FAM106A FOXO3B SHMT1 ZNF286B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TOP3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TOP3A gene promoter:

Genomic Locations for TOP3A Gene

Genomic Locations for TOP3A Gene
chr17:18,271,428-18,315,007
(GRCh38/hg38)
Size:
43,580 bases
Orientation:
Minus strand
chr17:18,174,742-18,218,321
(GRCh37/hg19)

Genomic View for TOP3A Gene

Genes around TOP3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TOP3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TOP3A Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TOP3A Gene

Proteins for TOP3A Gene

Products:

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  2. Protein
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  • Protein details for TOP3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13472-TOP3A_HUMAN
    Recommended name:
    DNA topoisomerase 3-alpha
    Protein Accession:
    Q13472
    Secondary Accessions:
    • A8KA61
    • B4DK80
    • D3DXC7
    • Q13473

    Protein attributes for TOP3A Gene

    Size:
    1001 amino acids
    Molecular mass:
    112372 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Interacts (via N-terminal region) with BLM; the interaction is direct. Directly interacts with RMI1. Component of the RMI complex, containing at least TOP3A, RMI1 and RMI2. The RMI complex interacts with BLM.

    Three dimensional structures from OCA and Proteopedia for TOP3A Gene

    Alternative splice isoforms for TOP3A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TOP3A Gene

Protein Expression for TOP3A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TOP3A Gene

  • Ubiquitination at isoforms=3, 2257 and posLast=557557
  • Modification sites at PhosphoSitePlus

Other Protein References for TOP3A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TOP3A Gene

Domains & Families for TOP3A Gene

Gene Families for TOP3A Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for TOP3A Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TOP3A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q13472

UniProtKB/Swiss-Prot:

TOP3A_HUMAN :
  • Belongs to the type IA topoisomerase family.
Family:
  • Belongs to the type IA topoisomerase family.
genes like me logo Genes that share domains with TOP3A: view

Function for TOP3A Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for TOP3A Gene

GENATLAS Biochemistry:
DNA topoisomerase III,putatively involved in suppression of mitotic recombination between repetitive sequences,deleted in SMCR
UniProtKB/Swiss-Prot CatalyticActivity:
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
UniProtKB/Swiss-Prot Function:
Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells. Has DNA decatenation activity.

Enzyme Numbers (IUBMB) for TOP3A Gene

Phenotypes From GWAS Catalog for TOP3A Gene

Gene Ontology (GO) - Molecular Function for TOP3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding TAS,IEA --
GO:0003916 DNA topoisomerase activity IEA --
GO:0003917 DNA topoisomerase type I activity IDA 20445207
GO:0005515 protein binding IPI 10728666
genes like me logo Genes that share ontologies with TOP3A: view
genes like me logo Genes that share phenotypes with TOP3A: view

Animal Models for TOP3A Gene

MGI Knock Outs for TOP3A:

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TOP3A Gene

Localization for TOP3A Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TOP3A gene
Compartment Confidence
nucleus 5
cytosol 3
mitochondrion 2

Gene Ontology (GO) - Cellular Components for TOP3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 8622991
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0016605 PML body IDA 10728666
genes like me logo Genes that share ontologies with TOP3A: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for TOP3A Gene

Pathways & Interactions for TOP3A Gene

genes like me logo Genes that share pathways with TOP3A: view

Pathways by source for TOP3A Gene

2 KEGG pathways for TOP3A Gene

Gene Ontology (GO) - Biological Process for TOP3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000731 DNA synthesis involved in DNA repair TAS --
GO:0000732 strand displacement TAS --
GO:0006260 DNA replication TAS --
GO:0006265 DNA topological change IDA 20445207
GO:0051321 meiotic cell cycle TAS 8622991
genes like me logo Genes that share ontologies with TOP3A: view

No data available for SIGNOR curated interactions for TOP3A Gene

Drugs & Compounds for TOP3A Gene

Products:

  1. Drug

(1) Drugs for TOP3A Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for TOP3A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TOP3A: view

Transcripts for TOP3A Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for TOP3A Gene

(3) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(135) Selected AceView cDNA sequences:
(20) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TOP3A Gene

Topoisomerase (DNA) III alpha:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TOP3A Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^
SP1: - - - - -
SP2: - - - - -
SP3: - - -
SP4: - - - - - - -
SP5: - - - - - -
SP6: - - - - - -
SP7: -
SP8:
SP9: - -
SP10:
SP11:

ExUns: 17a · 17b ^ 18a · 18b ^ 19 ^ 20a · 20b
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for TOP3A Gene

GeneLoc Exon Structure for
TOP3A
ECgene alternative splicing isoforms for
TOP3A

Expression for TOP3A Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TOP3A Gene

mRNA expression in normal human tissues for TOP3A Gene
mRNA expression by GTEx for TOP3A GenemRNA expression by BioGPS for TOP3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TOP3A Gene

This gene is overexpressed in Retina (57.3) and Testis (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TOP3A Gene



Protein tissue co-expression partners for TOP3A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TOP3A Gene:

TOP3A

SOURCE GeneReport for Unigene cluster for TOP3A Gene:

Hs.592115

mRNA Expression by UniProt/SwissProt for TOP3A Gene:

Q13472-TOP3A_HUMAN
Tissue specificity: High expression is found in testis, heart, skeletal muscle and pancreas.

Evidence on tissue expression from TISSUES for TOP3A Gene

  • Nervous system(4.9)
  • Skin(2.7)
  • Lung(2.2)
genes like me logo Genes that share expression patterns with TOP3A: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TOP3A Gene

Orthologs for TOP3A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TOP3A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia TOP3A 33 34
  • 99.3 (n)
dog
(Canis familiaris)
 Mammalia TOP3A 33 34
  • 87.86 (n)
mouse
(Mus musculus)
 Mammalia Top3a 33 16 34
  • 85.18 (n)
rat
(Rattus norvegicus)
 Mammalia Top3a 33
  • 83.26 (n)
cow
(Bos Taurus)
 Mammalia TOP3A 33 34
  • 82.93 (n)
oppossum
(Monodelphis domestica)
 Mammalia TOP3A 34
  • 79 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia TOP3A 34
  • 79 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves TOP3A 33 34
  • 71.1 (n)
lizard
(Anolis carolinensis)
 Reptilia TOP3A 34
  • 72 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia top3a 33
  • 71.61 (n)
Str.19892 33
African clawed frog
(Xenopus laevis)
 Amphibia Xl.8942 33
zebrafish
(Danio rerio)
 Actinopterygii top3a 33 34
  • 64.78 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Top3alpha 35 33 34
  • 56.23 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP010028 33
  • 53.15 (n)
worm
(Caenorhabditis elegans)
 Secernentea top-3 35 33 34
  • 53.79 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes TOP3 34
  • 40 (a)
 OneToMany
thale cress
(Arabidopsis thaliana)
 eudicotyledons TOP3A 33
  • 51.86 (n)
rice
(Oryza sativa)
 Liliopsida Os03g0165000 33
  • 51.87 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 53 (a)
 OneToOne
Species where no ortholog for TOP3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TOP3A Gene

ENSEMBL:
Gene Tree for TOP3A (if available)
TreeFam:
Gene Tree for TOP3A (if available)

Paralogs for TOP3A Gene

Paralogs for TOP3A Gene

(1) SIMAP similar genes for TOP3A Gene using alignment to 11 proteins:

genes like me logo Genes that share paralogs with TOP3A: view

Variants for TOP3A Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for TOP3A Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000125969 -- 18,311,524(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000176296 -- 18,315,742(-) G/A upstream_transcript_variant
rs1000289068 -- 18,301,633(-) T/C intron_variant
rs1000299292 -- 18,276,141(-) G/T intron_variant
rs1000349437 -- 18,305,567(-) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for TOP3A Gene

Variant ID Type Subtype PubMed ID
esv1743367 CNV insertion 17803354
esv2657654 CNV deletion 23128226
esv3554219 CNV deletion 23714750
esv3640144 CNV loss 21293372
esv3640146 CNV gain 21293372
nsv1116191 CNV deletion 24896259
nsv1134605 CNV deletion 24896259
nsv155 OTHER inversion 15895083
nsv428333 CNV gain 18775914
nsv499114 OTHER inversion 21111241
nsv833386 CNV gain 17160897
nsv833387 CNV loss 17160897
nsv962274 CNV duplication 23825009

Variation tolerance for TOP3A Gene

Residual Variation Intolerance Score: 16.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.54; 77.81% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TOP3A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TOP3A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TOP3A Gene

Disorders for TOP3A Gene

MalaCards: The human disease database

(1) MalaCards diseases for TOP3A Gene - From: DISEASES

Disorder Aliases PubMed IDs
occupational dermatitis
  • occupational allergic contact dermatitis
- elite association - COSMIC cancer census association via MalaCards
Search TOP3A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TOP3A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TOP3A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TOP3A Gene

Publications for TOP3A Gene

  1. Human TOP3: a single-copy gene encoding DNA topoisomerase III. (PMID: 8622991) Hanai R … Wang JC (Proceedings of the National Academy of Sciences of the United States of America 1996) 3 4 22 58
  2. Scaffolding protein SPIDR/KIAA0146 connects the Bloom syndrome helicase with homologous recombination repair. (PMID: 23509288) Wan L … Huang J (Proceedings of the National Academy of Sciences of the United States of America 2013) 3 4 58
  3. Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing. (PMID: 20843780) Wang W … Scharfe C (Nucleic acids research 2011) 3 4 58
  4. Human topoisomerase IIIalpha is a single-stranded DNA decatenase that is stimulated by BLM and RMI1. (PMID: 20445207) Yang J … Brown GW (The Journal of biological chemistry 2010) 3 4 58
  5. Association between polymorphisms in RMI1, TOP3A, and BLM and risk of cancer, a case-control study. (PMID: 19432957) Broberg K … Höglund M (BMC cancer 2009) 3 44 58

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