General Information
Symbol
Dmel\Irbp
Species
D. melanogaster
Name
Inverted repeat-binding protein
Annotation Symbol
CG5247
Feature Type
FlyBase ID
FBgn0011774
Gene Model Status
Stock Availability
Enzyme Name (EC)
Adenosinetriphosphatase (3.6.1.3)
Gene Snapshot
Inverted repeat-binding protein (Irbp) encodes a protein that, together with the product of Ku80, forms part of the Ku protein complex, which is involved in double-strand break repair via non-homologous end joining and telomere maintenance. [Date last reviewed: 2018-09-13]
Also Known As
Ku70, YPF1, DmKu70, Ku, YPF1β
Genomic Location
Cytogenetic map
Sequence location
3R:11,410,047..11,412,440 [+]
Recombination map
3-51
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 ku70 family. (Q23976)
Molecular Function (see GO section for details)
Catalytic Activity (EC)
Experimental Evidence
-
Predictions / Assertions
ATP + H(2)O = ADP + phosphate (3.6.1.3)
Summaries
Gene Group Membership
5'-DEOXYRIBOSE-5-PHOSPHATE LYASES -
5'-deoxyribose-5-phosphate lyases catalyze the excision of the 5' deoxyribose-5-phosphate at an abasic site in DNA where a DNA-(apurinic or apyrimidinic site) lyase has already cleaved the C-O-P bond 3' to the apurinic or apyrimidinic site. These enzymes play an important role in base excision repair pathway responsible for the repair of DNA lesions. (Adapted from PMID:11457865).
UniProt Contributed Function Data
Single-stranded DNA-dependent ATP-dependent helicase. Involved in non-homologous end joining (NHEJ) DNA double strand break repair (By similarity). Sequence-specific DNA-binding protein that has a high affinity for a 31 bp sequence in the Yp1 gene. Site-specific DNA binding to 31 bp P element inverted repeats.
(UniProt, Q23976)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\Irbp or the JBrowse view of Dmel\Irbp 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
Low-frequency RNA-Seq exon junction(s) not annotated.
Multiphase exon postulated: exon reading frame differs in alternative transcripts.
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0082385
2149
631
FBtr0334308
2048
265
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0081861
72.5
631
6.66
FBpp0306423
29.7
265
4.33
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)
Heterodimer of a 70 kDa and a 80 kDa subunit.
(UniProt, Q23976)
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\Irbp 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 (13 terms)
Molecular Function (7 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
contributes_to DNA binding
inferred from direct assay
Terms Based on Predictions or Assertions (6 terms)
CV Term
Evidence
References
inferred from sequence or structural similarity with UniProtKB:P12956
inferred from electronic annotation with InterPro:IPR005160
(assigned by InterPro )
inferred from electronic annotation with InterPro:IPR006165
(assigned by InterPro )
inferred from sequence or structural similarity with HGNC:4055
inferred from biological aspect of ancestor with PANTHER:PTN000288287
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000288287
(assigned by GO_Central )
Biological Process (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (4 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000288287
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000288287
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000288287
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000288287
(assigned by GO_Central )
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000288287
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000288287
(assigned by GO_Central )
Expression Data
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

Additional Descriptive Data
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\Irbp 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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
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 ( 3 )
For All Classical and Insertion Alleles Show
 
Allele of Irbp
Class
Mutagen
Associated Insertion
Stocks
Known lesion
Other relevant insertions
Transgenic Constructs ( 12 )
Deletions and Duplications ( 2 )
Summary of Phenotypes
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
15 of 15
Yes
Yes
 
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
12 of 15
Yes
Yes
Rattus norvegicus (Norway rat) (1)
9 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
10 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
14 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
12 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
9 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
9 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
11 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG0919042H )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150362 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W02Y3 )
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
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X05EI )
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) ( EOG091G04AI )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
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 ( 1 )
    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)
    Heterodimer of a 70 kDa and a 80 kDa subunit.
    (UniProt, Q23976 )
    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
    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:11,410,047..11,412,440 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    86E4-86E4
    Limits computationally determined from genome sequence between P{EP}EP3340EP3340 and P{PZ}tho1&P{PZ}l(3)0462905275
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    86E2-86E3
    86E2-86E3
    (determined by in situ hybridisation)
    34C-34C
    (determined by in situ hybridisation)
    Not 34C1--34C7 as reported in FBrf0068542.
    Experimentally Determined Recombination Data
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (7)
    Genomic Clones (11)
     

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

    cDNA Clones (68)
     

    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 database merge of
    Source for merge of: Irbp Ypf1b
    Additional comments
    snoRNA:Irbp-a is encoded in an intron of Irbp.
    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.
    Identity of "Irbp" to "Ypf1b" based on DNA sequence identity.
    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).
    Other Comments
    Irbp has a role in length regulation of telomeres.
    A decrease in Irbp gene dosage causes a sharp increase in the frequency of HeT-A and TART-element attachments to a broken chromosome end and strongly enhances terminal DNA elongation by gene conversion. However, reduction in Irbp function also reduces the stability of terminally deficient chromosomes.
    The DNA binding properties of YPF1, a heterodimeric protein encoded by Ypf1a and Irbp, have been investigated.
    Irbp may act to preserve P-element ends when transposition produces a double strand gap. This allows the terminus to serve as a template upon which DNA synthesis can act to repair the gap.
    Irbp gene product specifically interacts with the outer half of the 31bp terminal inverted repeats.
    Isolated from an ovarian cDNA expression library.
    Irbp has been cloned. The purified Irbp subunit binds DNA.
    The Irbp protein is a sequence-specific DNA-binding protein that has a high affinity for a 31bp sequence in the Yp1 gene necessary for normal steady state levels of Yp1 RNA in vivo.
    DNase I footprinting has identified a protein from Kc cells that binds to the P-element 31bp inverted repeats. UV photochemical crosslinking and purification of protein identifies the DNA binding activity within a polypeptide of 66kD.
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 41 )
    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
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    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 (16)
    Reported As
    Symbol Synonym
    Ypf1b
    Name Synonyms
    Inverted repeat-binding protein
    Yolk protein factor 1b
    Secondary FlyBase IDs
    • FBgn0004048
    • FBgn0011292
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (100)