General Information
Symbol
Dmel\Top1
Species
D. melanogaster
Name
Topoisomerase 1
Annotation Symbol
CG6146
Feature Type
FlyBase ID
FBgn0004924
Gene Model Status
Stock Availability
Enzyme Name (EC)
DNA topoisomerase (5.99.1.2)
Gene Snapshot
Topoisomerase 1 is a topoisomerase with essential functions in cell proliferation during stages of oogenesis, embryogenesis, larva, and pupa. [Date last reviewed: 2016-06-16]
Also Known As
Topo I, l(1)G0229, l(1)G0134, l(1)G0278, l(1)G0201
Genomic Location
Cytogenetic map
Sequence location
X:15,319,479..15,328,029 [+]
Recombination map
1-50
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
Belongs to the type IB topoisomerase family. (P30189)
Molecular Function (see GO section for details)
Catalytic Activity (EC)
Experimental Evidence
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining (5.99.1.2)
Predictions / Assertions
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining (5.99.1.2)
Summaries
Gene Group Membership
DNA TOPOISOMERASES -
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, whereas type II enzymes mediate strand transport through a double-strand DNA gate. DNA topoisomerases have critical roles in DNA replication, transcription, recombination, repair, and chromatin remodeling. (Adapted from PMID:23495937.)
UniProt Contributed Function Data
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 (By similarity). Introduces a single-strand break via transesterification at a target site in duplex DNA (By similarity). The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-OH DNA strand (By similarity). The free DNA strand then undergoes passage around the unbroken strand thus removing DNA supercoils (By similarity). Finally, in the religation step, the DNA 5'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity).
(UniProt, P30189)
Gene Model and Products
Number of Transcripts
5
Number of Unique Polypeptides
4

Please see the GBrowse view of Dmel\Top1 or the JBrowse view of Dmel\Top1 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
Comments on Gene Model
Gene model reviewed during 5.50
Low-frequency RNA-Seq exon junction(s) not annotated.
Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.
Gene model reviewed during 5.39
Gene model reviewed during 5.55
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0074005
4265
974
FBtr0074006
2378
581
FBtr0100294
5325
974
FBtr0308699
4600
970
FBtr0340434
3942
593
Additional Transcript Data and Comments
Reported size (kB)
5.2, 4.0 (northern blot)
5.2, 4.0 (unknown)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0073822
111.9
974
9.55
FBpp0073823
68.6
581
9.56
FBpp0099689
111.9
974
9.55
FBpp0300905
111.6
970
9.59
FBpp0309379
70.0
593
9.91
Polypeptides with Identical Sequences

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

974 aa isoforms: Top1-PA, Top1-PC
Additional Polypeptide Data and Comments
Reported size (kDa)
972 (aa); 135 (kD)
Comments
Homology to other Top1 proteins is concentrated in two regions. The Drosophila enzyme is larger than the enzymes from yeast and human and is uniquely characterized by a Ser/His rich hydrophilic domain of 200aa at its amino terminus. The bacterially expressed protein was shown to have classic eukaryotic DNA topoisomerase I activity, distinguished by the fact that it can relax both positively and negatively supercoiled DNA in the absence of a divalent cation.
Camptothecin-induced Top1 protein cleavage sites were mapped in the Act5C, Act57A, and hsp70 genes. Top1 protein cleavage sites were localized to the transcribed portions of the Hsp70B and Act5C genes, and only when they are transcriptionally active. None were found in a transcriptionally inactive Act57A gene.
External Data
Subunit Structure (UniProtKB)
Interacts with Topors.
(UniProt, P30189)
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Top1 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (21 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
Biological Process (10 terms)
Terms Based on Experimental Evidence (8 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000033230
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000033230
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000033230
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000033230
(assigned by GO_Central )
Cellular Component (8 terms)
Terms Based on Experimental Evidence (7 terms)
CV Term
Evidence
References
inferred from direct assay
inferred from high throughput direct assay
inferred from direct assay
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000033230
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000033230
(assigned by GO_Central )
Expression Data
Transcript Expression
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
No Assay Recorded
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
A substantial amount of maternally derived Top1 protein is present in early embryos. Protein levels peak at 6-12 hours and decline to near zero in pupae. Some expression is observed in the ovary.
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
inferred from high throughput direct assay
inferred from direct assay
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
Stage
Tissue/Position (including subcellular localization)
Reference
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Top1 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs and Phenotypes
Classical and Insertion Alleles ( 26 )
Transgenic Constructs ( 15 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Top1
Allele of Top1
Mutagen
Associated Transgenic Construct
Stocks
Transgenic constructs containing regulatory region of Top1
Deletions and Duplications ( 3 )
Summary of Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
nurse cell & nucleus, with Top177
nurse cell & nucleus, with Top1hs.2
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
10 of 15
No
Yes
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (2)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
13 of 15
Yes
Yes
10 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
10 of 13
Yes
Yes
9 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (2)
10 of 12
Yes
Yes
7 of 12
No
Yes
Danio rerio (Zebrafish) (4)
12 of 15
Yes
Yes
10 of 15
No
Yes
6 of 15
No
Yes
6 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (2)
14 of 15
Yes
Yes
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (3)
9 of 9
Yes
Yes
8 of 9
No
Yes
2 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
14 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
10 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091904CH )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091502JZ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W02BL )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0296 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G02KT )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Human Disease Model Data
FlyBase Human Disease Model Reports
    Alleles Reported to Model Human Disease (Disease Ontology)
    Download
    Models ( 0 )
    Allele
    Disease
    Evidence
    References
    Interactions ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments ( 0 )
     
    Human Orthologs (via DIOPT v7.1)
    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
    Complementation?
    Transgene?
    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:
    Select Layout:
    Legend:
    Protein
    RNA
    Selected Interactor(s)
    Interactions Browser

    Please look at the Interaction Group reports for full details of the physical interactions
    protein-protein
    Interacting group
    Assay
    References
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Subunit Structure (UniProtKB)
    Interacts with Topors.
    (UniProt, P30189 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-50
    Cytogenetic map
    Sequence location
    X:15,319,479..15,328,029 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    13B6-13B6
    Limits computationally determined from genome sequence between P{EP}hiwEP1308 and P{EP}Ahcy13EP1007
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    13B6-13B8
    (determined by in situ hybridisation) 13B5--9 (determined by in situ hybridisation) 13B8--9 (determined by in situ hybridisation) 13C (determined by in situ hybridisation)
    13B8-13B9
    (determined by in situ hybridisation) 13B6--9 (determined by in situ hybridisation)
    13B5-13B9
    (determined by in situ hybridisation) 13C1--2 (determined by in situ hybridisation) 13C (determined by in situ hybridisation)
    13C1-13C1
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (22)
    Genomic Clones (11)
     

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

    cDNA Clones (99)
     

    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 GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequences
    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)
    RNAi and Array Information
    Linkouts
    DRSC - Results frm RNAi screens
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    Antibody Information
    Laboratory Generated Antibodies
     
    polyclonal
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for identity of: Top1 CG6146
    Source for database merge of
    Source for merge of: Top1 l(1)G0229 l(1)G0278 l(1)G0134 l(1)G0201
    Additional comments
    Other Comments
    DNA-protein interactions: genome-wide binding profile assayed for Top1 protein in Kc167 cells; see Chromatin_types_NKI collection report. Individual protein-binding experiments listed under "Samples" at GEO_GSE22069 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22069).
    Top1 plays an essential role in many developmental stages active in cell proliferation.
    The genomic organisation of the Top1 locus has been determined and its expression pattern has been analysed.
    The N-terminal 430 amino acid residues of Top1 are inconsequential for its catalytic activity. The N-terminal region directs Top1-Ecol\lacZ fusion constructs to transcriptionally active loci in the polytene chromosomes.
    Using P element mutagenesis a mutant deficient in topoisomerase 1 was generated: topoisomerase 1 is essential for growth and development.
    Top1 has been isolated and partially characterised.
    DNA topoisomerase 1 was cloned by homology to consensus eukaryotic DNA topoisomerase 1 sequence, and expressed in an E.coli expression system.
    The interaction of Top1 and Top2 gene products with transcriptionally active and inactive Act5C, Act57B and Hsp70B has been compared. Topoisomerase I binding sites are found in the transcribed portions of the Hsp70B and Act5C genes, and only when they are transcriptionally active. It does not associate with a transcriptionally inactive Act57B gene.
    Top1 enzyme has been purified and characterised.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 63 )
    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/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
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center 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.
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    FlyMine - An integrated database for Drosophila genomics
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    Synonyms and Secondary IDs (21)
    Reported As
    Secondary FlyBase IDs
    • FBgn0027237
    • FBgn0027261
    • FBgn0027275
    • FBgn0040195
    Datasets (1)
    Study focus (1)
    Experimental Role
    Project
    Project Type
    Title
    • transgene_used
    Protein profiling reveals five principal chromatin types in Drosophila cells.
    References (109)