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Aliases for TOP3B Gene

Aliases for TOP3B Gene

  • Topoisomerase (DNA) III Beta 2 3 5
  • DNA Topoisomerase III Beta-1 3 4
  • TOP3B1 3 4
  • 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 (Topoisomerase (DNA) III Beta) is a Protein Coding gene. Diseases associated with TOP3B include brain stem cancer and brain stem glioma. Among its related pathways are Fanconi anemia pathway and Homologous recombination. 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

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

Genomics for TOP3B Gene

Regulatory Elements for TOP3B Gene

Promoters for TOP3B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around TOP3B on UCSC Golden Path with GeneCards custom track

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};

    Alternative splice isoforms for TOP3B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TOP3B Gene

Proteomics data for TOP3B Gene at MOPED

Post-translational modifications for TOP3B Gene

  • Ubiquitination at Lys 19 and Lys 100
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TOP3B Gene

Domains & Families for TOP3B Gene

Gene Families for TOP3B Gene

Suggested Antigen Peptide Sequences for TOP3B Gene

Graphical View of Domain Structure for InterPro Entry

O95985

UniProtKB/Swiss-Prot:

TOP3B_HUMAN :
  • Contains 1 Toprim domain.
  • Belongs to the type IA topoisomerase family.
Domain:
  • Contains 1 Toprim domain.
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

Gene Ontology (GO) - Molecular Function for TOP3B Gene

GO ID Qualified GO term Evidence PubMed IDs
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

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
Jensen Localization Image for TOP3B Gene COMPARTMENTS Subcellular localization image for TOP3B gene
Compartment Confidence
nucleus 5
mitochondrion 3
cytosol 2

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components 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

None

No data available for SIGNOR curated interactions for TOP3B Gene

Drugs & Compounds for TOP3B Gene

(8) 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 1044
Topotecan Approved, Investigational Pharma Topoisomerase 1 inhibitor, TOPO I inhibitor, Topoisomerase 1 Inhibitors 330
Camptothecin Experimental Pharma Topoisomerase I inhibitor,prototypic, DNA topoisomerase inhibitor 203
beta-Lapachone Pharma DNA topoisomerase I inhibitor,selective, DNA topoisomerase I inhibitor 11
Epirubicin HCl Pharma Antibiotic antitumor agent 0
genes like me logo Genes that share compounds with TOP3B: view

Transcripts for TOP3B Gene

Unigene Clusters for TOP3B Gene

Topoisomerase (DNA) III beta:
Representative Sequences:

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 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, MOPED, and MaxQB for TOP3B Gene



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.
genes like me logo Genes that share expression patterns with TOP3B: view

Protein tissue co-expression partners for TOP3B Gene

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues 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 36
  • 100 (a)
OneToOne
TOP3B 35
  • 99.38 (n)
  • 99.88 (a)
cow
(Bos Taurus)
Mammalia TOP3B 35
  • 87.96 (n)
  • 93.73 (a)
dog
(Canis familiaris)
Mammalia TOP3B 35
  • 90.18 (n)
  • 95.71 (a)
TOP3B 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Top3b 16
Top3b 36
  • 96 (a)
OneToOne
Top3b 35
  • 86.93 (n)
  • 95.59 (a)
oppossum
(Monodelphis domestica)
Mammalia TOP3B 36
  • 92 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 90 (a)
OneToMany
-- 36
  • 82 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Top3b 35
  • 87.2 (n)
  • 94.66 (a)
chicken
(Gallus gallus)
Aves TOP3B 36
  • 87 (a)
OneToOne
TOP3B 35
  • 76.3 (n)
  • 87.47 (a)
lizard
(Anolis carolinensis)
Reptilia TOP3B 36
  • 88 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia MGC53016 35
tropical clawed frog
(Silurana tropicalis)
Amphibia top3b 35
  • 75.02 (n)
  • 85.2 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC793414 35
  • 74.95 (n)
  • 82.23 (a)
top3b 36
  • 82 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Top3beta 36
  • 56 (a)
OneToOne
Top3bgr 37
  • 58 (a)
Top3beta 35
  • 61.72 (n)
  • 58.13 (a)
worm
(Caenorhabditis elegans)
Secernentea Y48C3A.14 37
  • 59 (a)
Y48C3A.14 36
  • 52 (a)
OneToOne
Y48C3A.14 35
  • 56.64 (n)
  • 55.98 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TOP3 36
  • 32 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G32000 35
  • 55.28 (n)
  • 54.66 (a)
rice
(Oryza sativa)
Liliopsida Os09g0500600 35
  • 55.25 (n)
  • 54.47 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5407 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 60 (a)
OneToOne
Species with no ortholog for TOP3B:
  • 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
rs9610728 - 21,964,166(+) CGTGT(C/T)GGCCC nc-transcript-variant, reference, missense
rs238777 -- 21,978,504(-) GTCCC(A/G)TTTAA intron-variant
rs238778 -- 21,978,896(-) cttct(C/T)gccag intron-variant
rs238779 -- 21,980,114(+) GTGAT(C/G)ACACA intron-variant
rs239914 -- 21,962,965(-) CGAGC(A/G)AGAGT intron-variant, reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
nsv7350 OTHER Inversion 18451855
dgv20e196 CNV Duplication 17116639
esv2422374 CNV Duplication 17116639
dgv22e196 CNV Deletion 17116639
esv2422338 CNV Deletion 17116639
dgv23e196 CNV Deletion 17116639
nsv469782 CNV Gain 16826518
nsv834146 CNV Gain 17160897
dgv4884n71 CNV Loss 21882294
nsv914473 CNV Loss 21882294
nsv828966 CNV Loss 20364138
nsv516394 CNV Gain+Loss 19592680
dgv1388e1 CNV Complex 17122850
nsv914475 CNV Gain 21882294
dgv4885n71 CNV Gain 21882294
dgv4886n71 CNV Gain 21882294
dgv4887n71 CNV Gain+Loss 21882294
nsv914492 CNV Loss 21882294
esv27307 CNV Gain 19812545
dgv545n27 CNV Gain 19166990
dgv546n27 CNV Loss 19166990
nsv526328 CNV Gain 19592680
dgv4888n71 CNV Gain 21882294
nsv914499 CNV Gain 21882294
nsv459421 CNV Gain 19166990
nsv914504 CNV Gain 21882294

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

HapMap Linkage Disequilibrium report
TOP3B
Human Gene Mutation Database (HGMD)
TOP3B

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

Disorders for TOP3B Gene

MalaCards: The human disease database

(7) MalaCards diseases for TOP3B Gene - From: DISEASES

Disorder Aliases PubMed IDs
brain stem cancer
  • malignant neoplasm of brain stem
brain stem glioma
  • brainstem neuroglial tumor
opportunistic bacterial infectious disease
nocardiosis
  • nocardia infectious disease
ovarian benign neoplasm
- 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 Res. 1997) 2 3 4 67
  2. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3
  3. Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. (PMID: 24507716) Yang Y. … Bedford M.T. (Mol. Cell 2014) 3
  4. TRIM65 regulates microRNA activity by ubiquitination of TNRC6. (PMID: 24778252) Li S. … Dorf M.E. (Proc. Natl. Acad. Sci. U.S.A. 2014) 3
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3

Products for TOP3B Gene

Sources for TOP3B Gene

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