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General Information
Symbol
Dmel\Blm
Species
D. melanogaster
Name
Bloom syndrome helicase
Annotation Symbol
CG6920
Feature Type
FlyBase ID
FBgn0002906
Gene Model Status
Stock Availability
Enzyme Name (EC)
DNA helicase (3.6.4.12)
Gene Snapshot
Bloom syndrome helicase (Blm) encodes a protein that plays important roles in repairing replication fork damage and double-strand breaks. It promotes repair through non-crossover mechanisms, though it also has roles in meiotic recombination. [Date last reviewed: 2019-03-07]
Also Known As
mus309, DmBlm, gesta1, Bloom syndrome helicase ortholog, Bloom helicase
Key Links
Genomic Location
Cytogenetic map
Sequence location
3R:11,736,810..11,741,783 [-]
Recombination map
3-51
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the helicase family. RecQ subfamily. (Q9VGI8)
Catalytic Activity (EC)
Experimental Evidence
-
Predictions / Assertions
ATP + H(2)O = ADP + phosphate (3.6.4.12)
Summaries
Protein Function (UniProtKB)
Participates in DNA replication and repair. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction (By similarity). ATP-dependent DNA helicase that unwinds single- and double-stranded DNA in a 3'-5' direction. Participates in DNA replication and repair. Negatively regulates sister chromatid exchange (SCE). Stimulates DNA 4-way junction branch migration and DNA Holliday junction dissolution. Binds single-stranded DNA (ssDNA), forked duplex DNA and DNA Holliday junction.
(UniProt, Q9VGI8)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
mus309 (J.B. Boyd)
Larval survival hypersensitive to exposure to methyl methanesulfonate and nitrogen mustard.
Summary (Interactive Fly)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the GBrowse view of Dmel\Blm or the JBrowse view of Dmel\Blm 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 5.47
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0082434
4806
1487
Additional Transcript Data and Comments
Reported size (kB)
4.835 (compiled cDNA)
2.4 (northern blot)
2.1 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0081910
166.1
1487
8.71
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
631 (aa); 65-70 (kD observed); 72 (kD predicted)
631 (aa); 69 (kD observed)
Comments
External Data
Subunit Structure (UniProtKB)
Monomer. Homodimer (via N-terminus). Homotetramer (via N-terminus); dimer of dimers. Homohexamer (via N-terminus). Self-association negatively regulates DNA unwinding amplitude and rate. Oligomer forms dissociate into monomer in presence of ATP.
(UniProt, Q9VGI8)
Domain
The N-terminal region mediates dimerization and homooligomerization. Both the helicase ATP-binding domain and the helicase C-terminal domain form intramolecular interactions with the HRDC domain in a ATP-dependent manner. The HRDC domain is required for single-stranded DNA (ssDNA) and DNA Holliday junction binding.
(UniProt, Q9VGI8)
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\Blm 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 (25 terms)
Molecular Function (7 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR011545
(assigned by InterPro )
inferred from sequence or structural similarity with HGNC:1058
inferred from biological aspect of ancestor with PANTHER:PTN000344873
(assigned by GO_Central )
inferred from sequence or structural similarity
Biological Process (15 terms)
Terms Based on Experimental Evidence (13 terms)
CV Term
Evidence
References
inferred from genetic interaction with SGD:S000004802
inferred from mutant phenotype
inferred from direct assay
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:Gen; FB:FBgn0263831
inferred from direct assay
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000344873
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000344873
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000344873
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000344874
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000344874
(assigned by GO_Central )
Cellular Component (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000344873
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000344873
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000749808
(assigned by GO_Central )
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Blm transcripts are observed at a low level through most of development on northern blots. They are abundant in ovaries, 0-2hr embryos, and adult females.
The Blm transcript is present in all stages, but is most abundant in early embryos and in ovaries.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Blm 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, and Transgenic Constructs
Classical and Insertion Alleles ( 11 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 6 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Blm
Transgenic constructs containing regulatory region of Blm
Deletions and Duplications ( 20 )
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
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (4)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
9 of 15
Yes
Yes
3 of 15
Yes
No
2 of 15
No
No
2 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (5)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
9 of 15
Yes
Yes
3 of 15
Yes
No
2 of 15
No
No
2 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (5)
6 of 13
Yes
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (4)
5 of 12
Yes
Yes
1 of 12
No
No
1 of 12
No
Yes
1 of 12
No
No
Danio rerio (Zebrafish) (5)
7 of 15
Yes
Yes
2 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (4)
9 of 15
Yes
Yes
3 of 15
No
Yes
2 of 15
No
No
2 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (5)
4 of 9
Yes
Yes
4 of 9
Yes
Yes
2 of 9
No
Yes
2 of 9
No
No
1 of 9
No
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
8 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (4)
6 of 12
Yes
Yes
1 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091901M7 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091501YI )
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
Mayetiola destructor
Hessian fly
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) ( EOG090W01QN )
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
Nasonia vitripennis
Parasitic wasp
Nasonia vitripennis
Parasitic wasp
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
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X01ON )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
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) ( EOG091G021X )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (2)
4 of 10
3 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Model Summary Ribbon
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 1 )
Allele
Disease
Evidence
References
Potential Models Based on Orthology ( 1 )
Human Ortholog
Disease
Evidence
References
Modifiers Based on Experimental Evidence ( 0 )
Allele
Disease
Interaction
References
Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
 
Disease Associations of Human Orthologs (via DIOPT v7.1 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?
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 see the Physical Interaction reports below for full details
RNA-RNA
Physical Interaction
Assay
References
protein-protein
Physical Interaction
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)
Monomer. Homodimer (via N-terminus). Homotetramer (via N-terminus); dimer of dimers. Homohexamer (via N-terminus). Self-association negatively regulates DNA unwinding amplitude and rate. Oligomer forms dissociate into monomer in presence of ATP.
(UniProt, Q9VGI8 )
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.
MIST (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Gene Group - Pathway Membership (FlyBase)
External Data
Linkouts
KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
3R
Recombination map
3-51
Cytogenetic map
Sequence location
3R:11,736,810..11,741,783 [-]
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
86E17-86E17
Limits computationally determined from genome sequence between P{PZ}tho1&P{PZ}l(3)0462905275 and P{EP}Lk6EP886
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
86F1-86F8
86F1-86F8
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (13)
Genomic Clones (13)
 

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

cDNA Clones (24)
 

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
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
    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
    Commercially Available Antibodies
     
    Other Information
    Relationship to Other Genes
    Source for database identify of
    Source for identity of: Blm mus309
    Source for database merge of
    Source for merge of: mus309 blm
    Additional comments
    FlyBase Curator comment: 'mus309' renamed to 'Blm' to reflect the preferred usage in the primary literature (see FBrf0155463, FBrf0216460, FBrf0193899, FBrf0207350, FBrf0107832, FBrf0135945, FBrf0180647, FBrf0200344, FBrf0179341, FBrf0191828, FBrf0202212, FBrf0193858, FBrf0209368). Moreover, symbols with 'mus' prefixes (for 'mutagen-sensitive') are deemed placeholders, to be replaced with a more meaningful symbol when available.
    It had previously been suggested that mus309 corresponds to Irbp (FBrf0086898). Detailed deletion mapping suggests that this was incorrect and mus309 actually corresponds to blm, which is supported by the identification of mutations in the blm coding sequence for two mus309 alleles.
    mus309 stated to correspond to Irbp. Subsequent information suggests that this is not the case (see Kusano et al., 2001, Science 291(5513): 2600--2602).
    'Note added in proof' in FBrf0080432 was in error; mus309, l(3)87Ae and lds are not, in fact, allelic.
    Other Comments
    mus309 suppresses single strand annealing between divergent repeats (termed homologous SA), thereby preventing potentially deleterious recombination events.
    mus309, in collaboration with Top3α can resolve a mobile double Holliday junction substrate through convergent branch migration (in contrast to classic resolvase activities that use a structure-specific endonuclease to cleave the Holliday junctions).
    mus309 mutants are severely impaired in their ability to carry out repair DNA synthesis during synthesis-dependent strand annealing in double-strand break repair.
    Designation as "DmKu70" was in error.
    mus309 gene product is required for the repair of P-element induced double-strand DNA chromosome breaks, both in the presence and absence of a homologous sequence. Plasmid based P-element mobility assay demonstrates that the processing of double strand DNA breaks after P-element excision is severely affected in mus309 mutant embryos.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 47 )
    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/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
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    Flygut - An atlas of the Drosophila adult midgut
    GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
    KEGG Genes - Molecular building blocks of life in the genomic space.
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    modMine - A data warehouse for the modENCODE project
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    FlyMine - An integrated database for Drosophila genomics
    Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (28)
    Reported As
    Symbol Synonym
    mus 309
    Name Synonyms
    Bloom syndrome helicase
    Bloom syndrome helicase ortholog
    Bloom's helicase
    Drosophila Blm
    bloom syndrome helicase
    genome stabilizer 1
    mutagen-sensitive 309
    Secondary FlyBase IDs
    • FBgn0015800
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (131)