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Aliases for TOP3B Gene

Aliases for TOP3B Gene

  • DNA Topoisomerase III Beta 2 3
  • Topoisomerase (DNA) III Beta 3 5
  • DNA Topoisomerase III Beta-1 3 4
  • TOP3B1 3 4
  • DNA Topoisomerase 3-Beta-1 3
  • Topoisomerase III Beta 3
  • EC 5.99.1.2 4

External Ids for TOP3B Gene

Previous GeneCards Identifiers for TOP3B Gene

  • GC22M019010
  • GC22M020635
  • GC22M021075
  • GC22M005268
  • GC22M022309

Summaries for TOP3B Gene

Entrez Gene Summary for TOP3B 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 relaxing the supercoils and altering the topology of DNA. The enzyme interacts with DNA helicase SGS1 and plays a role in DNA recombination, cellular aging and maintenance of genome stability. Low expression of this gene may be related to higher survival rates in breast cancer patients. This gene has a pseudogene on chromosome 22. Alternate splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Aug 2013]

GeneCards Summary for TOP3B Gene

TOP3B (DNA Topoisomerase III Beta) is a Protein Coding gene. Diseases associated with TOP3B include Chromosome 22Q11.2 Microduplication Syndrome. Among its related pathways are Fanconi anemia pathway and Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA). GO annotations related to this gene include poly(A) RNA binding and DNA topoisomerase activity. An important paralog of this gene is TOP3A.

UniProtKB/Swiss-Prot for TOP3B 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 than 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 (By similarity). Possesses negatively supercoiled DNA relaxing activity.

Gene Wiki entry for TOP3B Gene

Additional gene information for TOP3B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TOP3B Gene

Genomics for TOP3B Gene

Regulatory Elements for TOP3B Gene


Enhancers around TOP3B on UCSC Golden Path with GeneCards custom track

Promoters for TOP3B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000144080 243 1201 PKNOX1 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9

Genomic Location for TOP3B Gene

Chromosome:
22
Start:
21,957,025 bp from pter
End:
21,982,843 bp from pter
Size:
25,819 bases
Orientation:
Minus strand

Genomic View for TOP3B Gene

Genes around TOP3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TOP3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TOP3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TOP3B Gene

Proteins for TOP3B Gene

  • Protein details for TOP3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95985-TOP3B_HUMAN
    Recommended name:
    DNA topoisomerase 3-beta-1
    Protein Accession:
    O95985
    Secondary Accessions:
    • A0M8Q3
    • Q9BUP5

    Protein attributes for TOP3B Gene

    Size:
    862 amino acids
    Molecular mass:
    96662 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA20009.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TOP3B Gene

    Alternative splice isoforms for TOP3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TOP3B Gene

Post-translational modifications for TOP3B Gene

  • Ubiquitination at Lys19 and Lys100
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TOP3B Gene

Domains & Families for TOP3B Gene

Gene Families for TOP3B Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for TOP3B Gene

Graphical View of Domain Structure for InterPro Entry

O95985

UniProtKB/Swiss-Prot:

TOP3B_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 TOP3B: view

Function for TOP3B Gene

Molecular function for TOP3B Gene

GENATLAS Biochemistry:
DNA topoisomerase III,highly expressed in testis,possessing negatively supercoiled DNA relaxing activity
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 than 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 (By similarity). Possesses negatively supercoiled DNA relaxing activity.

Enzyme Numbers (IUBMB) for TOP3B Gene

Phenotypes From GWAS Catalog for TOP3B Gene

Gene Ontology (GO) - Molecular Function for TOP3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IDA 22658674
GO:0003916 DNA topoisomerase activity TAS,IEA 9786843
GO:0003917 DNA topoisomerase type I activity IEA --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with TOP3B: view
genes like me logo Genes that share phenotypes with TOP3B: view

Animal Models for TOP3B Gene

MGI Knock Outs for TOP3B:

Animal Model Products

  • Taconic Biosciences Mouse Models for TOP3B

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TOP3B
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for TOP3B Gene

Localization for TOP3B 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 TOP3B gene
Compartment Confidence
nucleus 5
mitochondrion 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TOP3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000793 condensed chromosome IEA --
GO:0005634 nucleus TAS 9786843
genes like me logo Genes that share ontologies with TOP3B: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for TOP3B Gene

Pathways & Interactions for TOP3B Gene

genes like me logo Genes that share pathways with TOP3B: view

Pathways by source for TOP3B Gene

2 KEGG pathways for TOP3B Gene

Gene Ontology (GO) - Biological Process for TOP3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006265 DNA topological change IBA,IEA --
GO:0007059 chromosome segregation IEA --
genes like me logo Genes that share ontologies with TOP3B: view

No data available for SIGNOR curated interactions for TOP3B Gene

Drugs & Compounds for TOP3B Gene

(9) Drugs for TOP3B Gene - From: ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Irinotecan Approved, Investigational Pharma Topoisomerase I inhibitor, TOPO I inhibitor, Topoisomerase 1 Inhibitors 1148
Topotecan Approved, Investigational Pharma Topoisomerase 1 inhibitor, TOPO I inhibitor, Topoisomerase 1 Inhibitors 354
Camptothecin Experimental Pharma Topoisomerase I inhibitor,prototypic 718
Beta-Lapachone Pharma DNA topoisomerase I inhibitor,selective 11
Epirubicin HCl Pharma Antibiotic antitumor agent 0

(9) ApexBio Compounds for TOP3B Gene

Compound Action Cas Number
Beta-Lapachone DNA topoisomerase I inhibitor,selective 4707-32-8
Camptothecin Topoisomerase I inhibitor,prototypic 7689-03-4
Epirubicin HCl Antibiotic antitumor agent 56390-09-1
Idarubicin HCl Anthracycline and daunorubicin analog,topoisomerase inhibitor 57852-57-0
Irinotecan Topoisomerase I inhibitor 97682-44-5
Moxifloxacin HCl Fluoroquinolone antibiotic 186826-86-8
Topotecan HCl Topoisomerase 1 inhibitor 119413-54-6
Voreloxin Topo II inhibitor 175414-77-4
Voreloxin Hydrochloride Antineoplastic naphthyridine analogue 175519-16-1
genes like me logo Genes that share compounds with TOP3B: view

Drug Products

Transcripts for TOP3B Gene

Unigene Clusters for TOP3B Gene

Topoisomerase (DNA) III beta:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TOP3B
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for TOP3B Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c · 6d · 6e ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^
SP1: - - - - -
SP2: - - - - -
SP3:
SP4: - - - - - -
SP5: - - - - - - -
SP6: - - - - - - -
SP7: - - - -
SP8: - - - -
SP9: -
SP10:
SP11: - - - - -
SP12: - - - - -
SP13: - - - - - - - - -
SP14:
SP15:
SP16: -
SP17: - - -
SP18: - -
SP19: - -
SP20:
SP21:

ExUns: 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21a · 21b · 21c ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26
SP1: - -
SP2: - -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: - -
SP11:
SP12:
SP13:
SP14: -
SP15: -
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:

Relevant External Links for TOP3B Gene

GeneLoc Exon Structure for
TOP3B
ECgene alternative splicing isoforms for
TOP3B

Expression for TOP3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TOP3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TOP3B Gene

This gene is overexpressed in Lymph node (16.9) and CD8 Tcells (10.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TOP3B Gene



Protein tissue co-expression partners for TOP3B Gene

NURSA nuclear receptor signaling pathways regulating expression of TOP3B Gene:

TOP3B

SOURCE GeneReport for Unigene cluster for TOP3B Gene:

Hs.436401

mRNA Expression by UniProt/SwissProt for TOP3B Gene:

O95985-TOP3B_HUMAN
Tissue specificity: Isoform 1 is found in testis, heart and skeletal muscle. A 4 kb transcript which probably represents isoform 2 is found in thymus, kidney and pancreas.

Evidence on tissue expression from TISSUES for TOP3B Gene

  • Skin(4)
genes like me logo Genes that share expression patterns with TOP3B: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TOP3B Gene

Orthologs for TOP3B Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TOP3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TOP3B 34 33
  • 99.38 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TOP3B 34
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TOP3B 34 33
  • 90.18 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 90 (a)
OneToMany
-- 34
  • 82 (a)
OneToMany
cow
(Bos Taurus)
Mammalia TOP3B 33
  • 87.96 (n)
rat
(Rattus norvegicus)
Mammalia Top3b 33
  • 87.2 (n)
mouse
(Mus musculus)
Mammalia Top3b 16 34 33
  • 86.93 (n)
chicken
(Gallus gallus)
Aves TOP3B 34 33
  • 76.3 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TOP3B 34
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia top3b 33
  • 75.02 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC53016 33
zebrafish
(Danio rerio)
Actinopterygii top3b 34
  • 82 (a)
OneToOne
LOC793414 33
  • 74.95 (n)
fruit fly
(Drosophila melanogaster)
Insecta Top3beta 33 34
  • 61.72 (n)
Top3bgr 35
  • 58 (a)
worm
(Caenorhabditis elegans)
Secernentea Y48C3A.14 35 33 34
  • 56.64 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TOP3 34
  • 32 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G32000 33
  • 55.28 (n)
rice
(Oryza sativa)
Liliopsida Os09g0500600 33
  • 55.25 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 60 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5407 33
Species where no ortholog for TOP3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 TOP3B Gene

ENSEMBL:
Gene Tree for TOP3B (if available)
TreeFam:
Gene Tree for TOP3B (if available)

Paralogs for TOP3B Gene

Paralogs for TOP3B Gene

Pseudogenes.org Pseudogenes for TOP3B Gene

genes like me logo Genes that share paralogs with TOP3B: view

Variants for TOP3B Gene

Sequence variations from dbSNP and Humsavar for TOP3B Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs1000062436 -- 21,976,663(+) TACTT(C/T)ACCCC intron-variant
rs1000094814 -- 21,962,096(+) GACTC(-/AG)GGGAC intron-variant
rs1000106361 -- 21,984,388(+) ATTAA(A/G)GTTTG upstream-variant-2KB
rs1000233244 -- 21,959,254(+) TGCAG(A/G)AGTCA intron-variant
rs1000239107 -- 21,959,776(+) CACTC(A/G)CACCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TOP3B Gene

Variant ID Type Subtype PubMed ID
dgv1294e212 CNV gain 25503493
dgv20e196 CNV duplication 17116639
dgv22e196 CNV deletion 17116639
dgv23e196 CNV deletion 17116639
dgv4492n100 CNV gain 25217958
dgv4493n100 CNV gain 25217958
dgv4494n100 CNV gain 25217958
dgv4495n100 CNV gain 25217958
dgv4496n100 CNV loss 25217958
dgv4497n100 CNV gain+loss 25217958
dgv545n27 CNV gain 19166990
dgv546n27 CNV loss 19166990
dgv7997n54 CNV gain 21841781
dgv7998n54 CNV loss 21841781
dgv7999n54 CNV loss 21841781
esv2422338 CNV deletion 17116639
esv2422374 CNV duplication 17116639
esv27307 CNV gain 19812545
esv2758826 CNV gain+loss 17122850
esv2760726 CNV gain+loss 21179565
esv2763701 CNV gain+loss 21179565
esv3568285 CNV loss 25503493
esv3647324 CNV loss 21293372
esv3647325 CNV gain 21293372
esv3647326 CNV loss 21293372
esv3647327 CNV gain 21293372
esv3893445 CNV gain+loss 25118596
esv3893447 CNV gain 25118596
nsv1059265 CNV gain 25217958
nsv1062641 CNV gain 25217958
nsv1067554 CNV loss 25217958
nsv1160731 CNV duplication 26073780
nsv1160733 CNV duplication 26073780
nsv459421 CNV gain 19166990
nsv469782 CNV gain 16826518
nsv516394 CNV gain+loss 19592680
nsv526328 CNV gain 19592680
nsv588336 CNV gain+loss 21841781
nsv588348 CNV gain 21841781
nsv7350 OTHER inversion 18451855
nsv828966 CNV loss 20364138
nsv834146 CNV gain 17160897

Variation tolerance for TOP3B Gene

Residual Variation Intolerance Score: 10.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.44; 77.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TOP3B Gene

Human Gene Mutation Database (HGMD)
TOP3B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TOP3B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TOP3B Gene

Disorders for TOP3B Gene

MalaCards: The human disease database

(1) MalaCards diseases for TOP3B Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
chromosome 22q11.2 microduplication syndrome
  • 22q11.2 microduplication syndrome
- elite association - COSMIC cancer census association via MalaCards
Search TOP3B in MalaCards View complete list of genes associated with diseases

Relevant External Links for TOP3B

Genetic Association Database (GAD)
TOP3B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TOP3B
genes like me logo Genes that share disorders with TOP3B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TOP3B Gene

Publications for TOP3B Gene

  1. One-megabase sequence analysis of the human immunoglobulin lambda gene locus. (PMID: 9074928) Kawasaki K … Shimizu N (Genome research 1997) 2 3 4 60
  2. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4 60
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  4. A new human topoisomerase III that interacts with SGS1 protein. (PMID: 9927731) Ng SW … Berkowitz RS (Nucleic acids research 1999) 3 4 60
  5. Arginine methylation of USP9X promotes its interaction with TDRD3 and its anti-apoptotic activities in breast cancer cells. (PMID: 28101374) Narayanan N … Yang Y (Cell discovery 2017) 3 60

Products for TOP3B Gene

Sources for TOP3B Gene

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