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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
  • 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 (Topoisomerase (DNA) III Beta) is a Protein Coding gene. Diseases associated with TOP3B include Chromosome 22Q11.2 Microduplication Syndrome. Among its related pathways are Homologous recombination and Fanconi anemia pathway. 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

Enhancers for TOP3B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

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

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

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:0003677 DNA binding IEA --
GO:0003916 DNA topoisomerase activity IBA,TAS --
GO:0003917 DNA topoisomerase type I activity IEA --
GO:0005515 protein binding IPI 25416956
GO:0044822 poly(A) RNA binding IDA 22658674
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

Flow Cytometry Products

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

Gene Ontology (GO) - Cellular Components for TOP3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000793 condensed chromosome IEA --
GO:0005634 nucleus IDA --
GO:0005829 cytosol IBA --
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 IEA,IBA --
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 1062
Topotecan Approved, Investigational Pharma Topoisomerase 1 inhibitor, TOPO I inhibitor, Topoisomerase 1 Inhibitors 336
Camptothecin Experimental Pharma Topoisomerase I inhibitor,prototypic 569
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

Transcripts for TOP3B Gene

Unigene Clusters for TOP3B Gene

Topoisomerase (DNA) III beta:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

Primer 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
cow
(Bos Taurus)
Mammalia TOP3B 34
  • 87.96 (n)
  • 93.73 (a)
dog
(Canis familiaris)
Mammalia TOP3B 34
  • 90.18 (n)
  • 95.71 (a)
TOP3B 35
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Top3b 34
  • 86.93 (n)
  • 95.59 (a)
Top3b 16
Top3b 35
  • 96 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia TOP3B 34
  • 99.38 (n)
  • 99.88 (a)
TOP3B 35
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Top3b 34
  • 87.2 (n)
  • 94.66 (a)
oppossum
(Monodelphis domestica)
Mammalia TOP3B 35
  • 92 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 90 (a)
OneToMany
-- 35
  • 82 (a)
OneToMany
chicken
(Gallus gallus)
Aves TOP3B 34
  • 76.3 (n)
  • 87.47 (a)
TOP3B 35
  • 87 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TOP3B 35
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia top3b 34
  • 75.02 (n)
  • 85.2 (a)
African clawed frog
(Xenopus laevis)
Amphibia MGC53016 34
zebrafish
(Danio rerio)
Actinopterygii LOC793414 34
  • 74.95 (n)
  • 82.23 (a)
top3b 35
  • 82 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Top3bgr 36
  • 58 (a)
Top3beta 34
  • 61.72 (n)
  • 58.13 (a)
Top3beta 35
  • 56 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y48C3A.14 36
  • 59 (a)
Y48C3A.14 34
  • 56.64 (n)
  • 55.98 (a)
Y48C3A.14 35
  • 52 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TOP3 35
  • 32 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G32000 34
  • 55.28 (n)
  • 54.66 (a)
rice
(Oryza sativa)
Liliopsida Os09g0500600 34
  • 55.25 (n)
  • 54.47 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5407 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 60 (a)
OneToOne
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
rs9610728 - 21,964,166(+) CGTGT(C/T)GGCCC nc-transcript-variant, reference, missense
rs732466 -- 21,975,375(+) TAATA(G/T)CCCCA intron-variant
rs5995329 -- 21,977,531(+) ctcaa(A/C)caaaa intron-variant, upstream-variant-2KB
rs5995334 -- 21,981,017(+) GACTC(A/C/T)CCTTC intron-variant
rs743525 -- 21,972,239(-) TTATC(A/C)TTTAG 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: DISEASES

Disorder Aliases PubMed IDs
chromosome 22q11.2 microduplication syndrome
  • chromosome 22q11.2 duplication 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 Res. 1997) 2 3 4 65
  2. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins J.E. … Dunham I. (Genome Biol. 2004) 3 4 65
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 65
  4. A new human topoisomerase III that interacts with SGS1 protein. (PMID: 9927731) Ng S.-W. … Berkowitz R.S. (Nucleic Acids Res. 1999) 3 4 65
  5. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3 65

Products for TOP3B Gene

Sources for TOP3B Gene

Content