FB2024_02 , released April 23, 2024
Gene: Dmel\Top3β
Open Close
General Information
Symbol
Dmel\Top3β
Species
D. melanogaster
Name
Topoisomerase 3β
Annotation Symbol
CG3458
Feature Type
protein_coding_gene
FlyBase ID
FBgn0026015
Gene Model Status
Current
Stock Availability
15 publicly available
Enzyme Name (EC)
DNA topoisomerase (5.6.2.1)
Gene Summary
Topoisomerase 3β (Top3β) encodes an RNA topoisomerase that participates in both transcription and translation. It promotes transcription by being recruited by the product of Tdrd3, an epigenetic reader recognizing dimethylarginine motifs in core histones. It contributes to translation by complexing with the product of Fmr1, an RNA-binding protein deficient in fragile X mental retardation syndrome. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Also Known As

topo IIIβ, dTop3β, Topoisomerase 3

Key Links
Genomic Location
Cytogenetic map
5E5-5E5
Sequence location
Recombination map
1-16
RefSeq locus
NC_004354 REGION:6284138..6287990
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (7 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables DNA topoisomerase type I (single strand cut, ATP-independent) activity
inferred from direct assay
(Wilson-Sali and Hsieh, 2002)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables DNA binding
(InterPro Project Members, 2004-)
inferred from electronic annotation with InterPro:IPR000380, InterPro:IPR013497
(InterPro Project Members, 2004-)
enables DNA topoisomerase type I (single strand cut, ATP-independent) activity
inferred from biological aspect of ancestor with PANTHER:PTN000149468
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR000380, InterPro:IPR023406
(InterPro Project Members, 2004-)
Biological Process (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in DNA topological change
inferred from direct assay
(Wilson-Sali and Hsieh, 2002)
involved_in positive regulation of synapse assembly
inferred from mutant phenotype
(Xu et al., 2013)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in DNA recombination
inferred from biological aspect of ancestor with PANTHER:PTN000149468
(GO Reference Genome Project, 2011-)
involved_in DNA repair
inferred from biological aspect of ancestor with PANTHER:PTN000149468
(GO Reference Genome Project, 2011-)
involved_in DNA topological change
(InterPro Project Members, 2004-)
inferred from electronic annotation with InterPro:IPR000380, InterPro:IPR013497
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000149468
(GO Reference Genome Project, 2011-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000149470
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the type IA topoisomerase family. (O96651)
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
DNA topoisomerase type I (single strand cut, ATP-independent) activity
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining (5.6.2.1)
Summaries
Gene Snapshot
Topoisomerase 3β (Top3β) encodes an RNA topoisomerase that participates in both transcription and translation. It promotes transcription by being recruited by the product of Tdrd3, an epigenetic reader recognizing dimethylarginine motifs in core histones. It contributes to translation by complexing with the product of Fmr1, an RNA-binding protein deficient in fragile X mental retardation syndrome. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
DNA TOPOISOMERASES TYPE I -
DNA topoisomerases perform topological transformations of DNA by generating a transient DNA break through which strand passage can occur. These enzymes are grouped into types I and II based on structure and mechanism: type I enzymes carry out strand passage through a reversible single-strand break. DNA topoisomerases have critical roles in DNA replication, transcription, recombination, repair, and chromatin remodeling. (Adapted from PMID:23495937.)
Protein Function (UniProtKB)
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). Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA.
(UniProt, O96651)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Top3β for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry O96651)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.50

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Top3β-RA
FBtr0070930
NM_078504
2963
875
Top3β-RB
FBtr0340028
NM_001298009
3296
875
Additional Transcript Data and Comments
Reported size (kB)

2.979 (longest cDNA)

(Wilson et al., 2000)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Top3β-PA
FBpp0070891
97.0
875
8.25
O96651
NP_511059
AAF46144
Top3β-PB
FBpp0309042
97.0
875
8.25
O96651
NP_001284938
AHN59409
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

875 aa isoforms: Top3β-PA, Top3β-PB
Additional Polypeptide Data and Comments
Reported size (kDa)

875 (aa); 97 (kD observed); 97 (kD predicted)

(Wilson et al., 2000)
Comments

Top3β protein has relaxation activity against hypernegatively supercoiled DNA but not against negatively supercoiled DNA. Divalent cations are required for activity. The enzyme forms a covalent linkage to 5' DNA phosphoryl groups, and the DNA cleavage reaction prefers single-stranded templates to double-stranded templates.

(Wilson et al., 2000)
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Top3β using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

0.37

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage -- adult stage
(Wilson et al., 2000)
Additional Descriptive Data

Top3β protein is detected at all stages of development with the highest levels in 0-6hr embryos.

(Wilson et al., 2000)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Top3β in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 14 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 16 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Top3β
Transgenic constructs containing regulatory region of Top3β
Aberrations (Deficiencies and Duplications) ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (2)
Hsap\TOP3B
14 of 14
Yes
Yes
Hsap\TOP3A
4 of 14
No
No
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (2)
Rnor\Top3b
14 of 14
Yes
Yes
Rnor\Top3a
4 of 14
No
No
Mus musculus (laboratory mouse) (2)
Mmus\Top3b
14 of 14
Yes
Yes
Mmus\Top3a
4 of 14
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\top3b
11 of 13
Yes
Yes
Xtro\top3a
4 of 13
No
No
Xtro\egfl7
1 of 13
No
Yes
Xtro\tbc1d9b
1 of 13
No
No
Danio rerio (Zebrafish) (2)
Drer\top3b
13 of 14
Yes
Yes
Drer\top3a
4 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\Y48C3A.14
13 of 14
Yes
Yes
Cele\top-3
5 of 14
No
No
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP010028
5 of 12
Yes
No
Arabidopsis thaliana (thale-cress) (3)
Atha\AT2G32000
13 of 13
Yes
Yes
Atha\TOP3A
5 of 13
No
No
Atha\AT4G31210
4 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\TOP3
5 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\top3
5 of 12
Yes
No
Escherichia coli (enterobacterium) (2)
Ecol\topA
7 of 11
Yes
Yes
Ecol\topB
4 of 11
No
No
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Top3β. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (1)
Top3α
9 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 0 )
Allele
Disease
Evidence
References
Potential Models Based on Orthology ( 0 )
Human Ortholog
Disease
Evidence
References
Modifiers Based on Experimental Evidence ( 0 )
Allele
Disease
Interaction
References
Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
Homo sapiens (Human)
Gene name
Score
OMIM
OMIM Phenotype
DO term
Complementation?
Transgene?
TOP3B; DNA topoisomerase III beta
14 of 14
603582
      TOP3A; DNA topoisomerase III alpha
      4 of 14
      601243
      Functional Complementation Data
      Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
      Interactions
      Summary of Physical Interactions
      esyN Network Diagram
      Show neighbor-neighbor interactions:
      Show/hide secondary interactors 
      (data from AllianceMine provided by esyN)
      Select Layout:
      Legend:
      Protein
      RNA
      Selected Interactor(s)
      Interactions Browser
      View in Interactions Browser
      Please see the Physical Interaction reports below for full details
      MIST Molecular Interaction Search Tool
      View in MIST tool (external link)
      Please see the Physical Interaction reports below for full details
      protein-protein
      Physical Interaction
      Assay
      References
      Top3β - Fmr1
      anti bait coimmunoprecipitation, Identification by mass spectrometry, western blot, anti tag coimmunoprecipitation
      (Lee et al., 2018, Xu et al., 2013)
      Top3β - Rm62
      anti tag coimmunoprecipitation, Identification by mass spectrometry, western blot
      (Lee et al., 2018)
      Top3β - Tdrd3
      anti bait coimmunoprecipitation, anti tag western blot, anti tag coimmunoprecipitation, Identification by mass spectrometry, coimmunoprecipitation, western blot, experimental knowledge based
      (Lee et al., 2018, Xu et al., 2013, Guruharsha et al., 2011)
      Summary of Genetic Interactions
      esyN Network Diagram
      Show/hide secondary interactors 
      (data from AllianceMine provided by esyN)
      esyN Network Key:
      Suppression
      Enhancement
      View in Interactions Browser   View in MIST tool (external link)
      Please look at the allele data for full details of the genetic interactions
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Top3β
      suppressible
      Fmr1
      (Xu et al., 2013)
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Fmr1
      suppressible
      Top3β
      (Xu et al., 2013)
      Fmr1
      enhanceable
      Top3β
      (Xu et al., 2013)
      External Data
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      MIST (genetic) - An integrated Molecular Interaction Database
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      X
      Recombination map
      1-16
      Cytogenetic map
      5E5-5E5
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      5E5-5E5
      Limits computationally determined from genome sequence between P{EP}EP1311&P{EP}EP1384 and P{EP}EP1402&P{EP}CG15893EP1634
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      5E-5F
      (determined by in situ hybridisation)
      (Wilson et al., 2000)
      5E-5F
      (Wilson, 1998.10.20)
      Experimentally Determined Recombination Data
      Location

      1-16

      (FlyBase, 2016)

      1-16.3

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (15)
      Genomic Clones (9)
       

      Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

      cDNA Clones (182)
       

      Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

      cDNA clones, fully sequenced
      BDGP DGC clones
      Other clones
        Drosophila Genomics Resource Center cDNA clones

        For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

        cDNA Clones, End Sequenced (ESTs)
        BDGP DGC clones
        Other clones
        RNAi and Array Information
        Linkouts
        DRSC - Results frm RNAi screens
        Antibody Information
        Laboratory Generated Antibodies
         

        polyclonal

        (Wilson et al., 2000)
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
            Other Comments
            Relationship to Other Genes
            Source for database merge of
            Additional comments
            Nomenclature History
            Source for database identify of
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (17)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 54 )
            Sequence Crossreferences
            NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
            GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
            GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
            RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
            UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
            UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
            UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
            Other crossreferences
            AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
            DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
            EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
            FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
            FlyMine - An integrated database for Drosophila genomics
            InterPro - A database of protein families, domains and functional sites
            KEGG Genes - Molecular building blocks of life in the genomic space.
            MARRVEL_MODEL - MARRVEL (model organism gene)
            Linkouts
            BioGRID - A database of protein and genetic interactions.
            Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
            DroID - A comprehensive database of gene and protein interactions.
            DRSC - Results frm RNAi screens
            Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
            FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
            FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
            Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
            Flygut - An atlas of the Drosophila adult midgut
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
            MIST (genetic) - An integrated Molecular Interaction Database
            MIST (protein-protein) - An integrated Molecular Interaction Database
            References (55)