Open Close
General Information
Symbol
Dmel\Ubr3
Species
D. melanogaster
Name
Ubr3 ubiquitin ligase
Annotation Symbol
CG42593
Feature Type
FlyBase ID
FBgn0260970
Gene Model Status
Stock Availability
Gene Summary
E3 ubiquitin-protein ligase which is a component of the N-end rule pathway (PubMed:26383956, PubMed:27195754). Recognizes and binds to proteins bearing specific N-terminal residues, leading to their ubiquitination and subsequent degradation (PubMed:26383956, PubMed:27195754). Binds to the E3 ubiquitin-protein ligase Diap1 and enhances its ubiquitination and anti-apoptotic functions (PubMed:25146930). Essential during trichome development for the ubiquitination of the N-terminus of ovo isoform B (svb), converting it from a transcriptional inhibitor to an activator (PubMed:26383956). Positively regulates a hh-signaling pathway which functions in photoreceptor differentiation (PubMed:27195754). Activation of hh up-regulates transcription of Ubr3, which in turn promotes hh signaling by mediating the ubiquitination and degradation of cos (PubMed:27195754). Necessary for auditory transduction: plays a role in Johnston's organ organization by acting in the regulation of zip and ck function in scolopidial apical attachment (PubMed:27331610). Likely to function by acting in a pathway that negatively regulates the ubiquitination of zip, consequently affecting its interaction with ck (PubMed:27331610). May also negatively regulate a component of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex Cul1, which also appears to function in the negative regulation of the zip-ck interaction and scolopidial apical attachment (PubMed:27331610). (UniProt, Q9W3M3)
Contribute a Gene Snapshot for this gene.
Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
1-21
RefSeq locus
NC_004354 REGION:7935896..7953883
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (14 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from physical interaction with FLYBASE:cos; FB:FBgn0000352
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000486924
(assigned by GO_Central )
inferred from electronic annotation with InterPro:IPR001841, InterPro:IPR003126
(assigned by InterPro )
inferred from sequence model
Biological Process (7 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
inferred from mutant phenotype
inferred from mutant phenotype
inferred from direct assay
inferred from direct assay
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000486924
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000486924
(assigned by GO_Central )
Cellular Component (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
located_in cytosol
inferred from direct assay
is_active_in neuronal cell body
inferred from mutant phenotype
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000486924
(assigned by GO_Central )
inferred from biological aspect of ancestor with PANTHER:PTN000486924
(assigned by GO_Central )
Protein Family (UniProt)
Belongs to the UBR1 family. (Q9W3M3)
Summaries
Gene Group (FlyBase)
OTHER RING DOMAIN UBIQUITIN LIGASES -
The RING (Really Interesting New Gene) finger domain co-ordinates two Zn2+ ions via conserved Cys and His residues. Most proteins which contain a RING finger are assumed to be ubiquitin (E3) ligases. The RING finger binds ubiquitin-conjugating enzymes (E2) and promotes direct transfer of ubiquitin to the target protein. (Adapted from FBrf0215242 and PMID:19489725).
Pathway (FlyBase)
Positive Regulators of Hedgehog Signaling Pathway -
Positive regulators of hedgehog signaling up-regulate the pathway, resulting in the activation of transcription of hh-responsive genes.
Protein Function (UniProtKB)
E3 ubiquitin-protein ligase which is a component of the N-end rule pathway (PubMed:26383956, PubMed:27195754). Recognizes and binds to proteins bearing specific N-terminal residues, leading to their ubiquitination and subsequent degradation (PubMed:26383956, PubMed:27195754). Binds to the E3 ubiquitin-protein ligase Diap1 and enhances its ubiquitination and anti-apoptotic functions (PubMed:25146930). Essential during trichome development for the ubiquitination of the N-terminus of ovo isoform B (svb), converting it from a transcriptional inhibitor to an activator (PubMed:26383956). Positively regulates a hh-signaling pathway which functions in photoreceptor differentiation (PubMed:27195754). Activation of hh up-regulates transcription of Ubr3, which in turn promotes hh signaling by mediating the ubiquitination and degradation of cos (PubMed:27195754). Necessary for auditory transduction: plays a role in Johnston's organ organization by acting in the regulation of zip and ck function in scolopidial apical attachment (PubMed:27331610). Likely to function by acting in a pathway that negatively regulates the ubiquitination of zip, consequently affecting its interaction with ck (PubMed:27331610). May also negatively regulate a component of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex Cul1, which also appears to function in the negative regulation of the zip-ck interaction and scolopidial apical attachment (PubMed:27331610).
(UniProt, Q9W3M3)
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
3

Please see the JBrowse view of Dmel\Ubr3 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 5.44

Low-frequency RNA-Seq exon junction(s) not annotated.

Stop-codon suppression (UGA) postulated; FBrf0216884.

Gene model reviewed during 5.46

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0301748
9371
2219
FBtr0331298
9371
2236
FBtr0331299
9308
2218
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
FBpp0290962
247.1
2219
5.72
FBpp0303730
249.0
2236
5.66
FBpp0303731
247.0
2218
5.72
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)

Selectively interacts (via UBR-type zinc finger) with the cleaved form of Diap1; this interaction is enhanced by tal (PubMed:25146930, PubMed:26383956). Interacts with tal and Rrp1 (PubMed:26383956). Interacts with ovo isoform B (via N-terminus) (PubMed:26383956). Interacts with Cad99C (via the cytoplasmic domain) (PubMed:27331610). Interacts with ck and Sans (PubMed:27331610). Interacts with cos (via Kinesin motor domain) (PubMed:27195754).

(UniProt, Q9W3M3)
Post Translational Modification

In vitro, self-ubiquitination in the presence of E1, E2 and ubiquitin.

(UniProt, Q9W3M3)
Domain

The UBR-type zinc finger domain is necessary for interaction with Diap1 and anti-apoptotic activity (PubMed:25146930). Domain is also sufficient for interaction with cos (PubMed:27195754).

The RING-type zinc finger domain is not necessary for interaction with Diap1 and anti-apoptotic activity.

(UniProt, Q9W3M3)
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\Ubr3 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
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
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

Ubr3 is broadly expressed in developing eye discs and is enriched in the morphogenetic furrow.

Ubr3 is expressed broadly in the second and third antennalsegments. In Johnston's organ, Ubr3 is enriched in the apical tips of neurons and in scolopale cells.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytosol
inferred from direct assay
is_active_in neuronal cell body
inferred from mutant phenotype
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Ubr3 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
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
Flygut - An atlas of the Drosophila adult midgut
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 12 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 14 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Ubr3
Transgenic constructs containing regulatory region of Ubr3
Aberrations (Deficiencies and Duplications) ( 1 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
12 of 15
Yes
Yes
1  
Model Organism Orthologs (via DIOPT v8.0)
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)
7 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
5 of 12
Yes
Yes
Danio rerio (Zebrafish) (1)
6 of 15
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
11 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
2 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
3 of 15
Yes
No
2 of 15
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
2 of 12
Yes
No
1 of 12
No
No
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919009B )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
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) ( EOG0915005K )
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) ( EOG090W05CW )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
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
Tribolium castaneum
Red flour beetle
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0594 )
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
Stegodyphus mimosarum
African social velvet spider
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G01MT )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
2 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    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 v8.0 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
    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)
    Selectively interacts (via UBR-type zinc finger) with the cleaved form of Diap1; this interaction is enhanced by tal (PubMed:25146930, PubMed:26383956). Interacts with tal and Rrp1 (PubMed:26383956). Interacts with ovo isoform B (via N-terminus) (PubMed:26383956). Interacts with Cad99C (via the cytoplasmic domain) (PubMed:27331610). Interacts with ck and Sans (PubMed:27331610). Interacts with cos (via Kinesin motor domain) (PubMed:27195754).
    (UniProt, Q9W3M3 )
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Positive Regulators of Hedgehog Signaling Pathway -
    Positive regulators of hedgehog signaling up-regulate the pathway, resulting in the activation of transcription of hh-responsive genes.
    Metabolic Pathways
    External Data
    Linkouts
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-21
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    7C9-7D1
    Limits computationally determined from genome sequence between P{EP}EP1243 and P{EP}snEP1217
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    7C7-7C9
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (17)
    Genomic Clones (21)
    cDNA Clones (9)
     

    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 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
            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: Ubr3 CG42593

            Source for database merge of

            Source for merge of: CG1531 CG1530

            Additional comments

            Annotations CG1531 and CG1530 merged as CG42593 in release 5.18 of the genome annotation.

            Original annotation in this location (CG1531) utilized wrong ORF; current ORF (CG34339) supported by conservation across Drosophila species.

            Other Comments

            dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.

            Origin and Etymology
            Discoverer
            Etymology

            Named 'Ubr3' after its mammalian homolog.

            Identification
            External Crossreferences and Linkouts ( 35 )
            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
            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
            Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
            FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
            FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
            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
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            KEGG Genes - Molecular building blocks of life in the genomic space.
            MARRVEL_MODEL - MARRVEL (model organism gene)
            modMine - A data warehouse for the modENCODE project
            Linkouts
            BioGRID - A database of protein and genetic interactions.
            DroID - A comprehensive database of gene and protein interactions.
            DRSC - Results frm RNAi screens
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Synonyms and Secondary IDs (7)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            References (47)