FB2024_03 , released April 23, 2024
Gene: Dmel\trbd
Open Close
General Information
Symbol
Dmel\trbd
Species
D. melanogaster
Name
trabid
Annotation Symbol
CG9448
Feature Type
protein_coding_gene
FlyBase ID
FBgn0037734
Gene Model Status
Current
Stock Availability
3 publicly available
Enzyme Name (EC)
ubiquitinyl hydrolase 1 (3.4.19.12)
Gene Summary
trabid (trbd) encodes a OTU family member that interacts with the product of Apc when ubiquitinated. It affects the activity of the product of Apc in transcription. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
85E5-85E5
Sequence location
Recombination map
3-49
RefSeq locus
NT_033777 REGION:9705996..9711037
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 (15 terms)
Molecular Function (4 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
enables K63-linked deubiquitinase activity
inferred from direct assay
(Hua et al., 2022)
inferred from mutant phenotype
(Fernando et al., 2014)
enables protein binding
inferred from physical interaction with UniProtKB:P91667
(Tran et al., 2008)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables cysteine-type deubiquitinase activity
inferred from sequence or structural similarity with HGNC:18224
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN001001090
(GO Reference Genome Project, 2011-)
enables K63-linked polyubiquitin modification-dependent protein binding
inferred from biological aspect of ancestor with PANTHER:PTN001001090
(GO Reference Genome Project, 2011-)
Biological Process (9 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in negative regulation of peptidoglycan recognition protein signaling pathway
inferred from mutant phenotype
(Hua et al., 2022, Fernando et al., 2014)
involved_in positive regulation of canonical Wnt signaling pathway
inferred from genetic interaction with FLYBASE:arm; FB:FBgn0000117
(Tran et al., 2008)
inferred from genetic interaction with FLYBASE:wg; FB:FBgn0284084
(Tran et al., 2008)
involved_in positive regulation of Wnt signaling pathway
inferred from mutant phenotype
(Tran et al., 2008)
Terms Based on Predictions or Assertions (7 terms)
CV Term
Evidence
References
involved_in cell migration
inferred from biological aspect of ancestor with PANTHER:PTN000332188
(GO Reference Genome Project, 2011-)
involved_in cytoskeleton organization
inferred from biological aspect of ancestor with PANTHER:PTN000332188
(GO Reference Genome Project, 2011-)
involved_in positive regulation of Wnt signaling pathway
inferred from biological aspect of ancestor with PANTHER:PTN000332188
(GO Reference Genome Project, 2011-)
involved_in protein deubiquitination involved in ubiquitin-dependent protein catabolic process
inferred from biological aspect of ancestor with PANTHER:PTN001001090
(GO Reference Genome Project, 2011-)
involved_in protein K29-linked deubiquitination
inferred from biological aspect of ancestor with PANTHER:PTN000332188
(GO Reference Genome Project, 2011-)
involved_in protein K33-linked deubiquitination
inferred from biological aspect of ancestor with PANTHER:PTN000332188
(GO Reference Genome Project, 2011-)
involved_in protein K63-linked deubiquitination
inferred from sequence or structural similarity with UniProtKB:Q9UGI0
(Gene Ontology Curators, 2002-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN001001090
(GO Reference Genome Project, 2011-)
located_in cytoplasm
inferred from sequence or structural similarity with HGNC:18224
(Gene Ontology Curators, 2002-)
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN001001090
(GO Reference Genome Project, 2011-)
located_in nucleus
inferred from sequence or structural similarity with HGNC:18224
(Gene Ontology Curators, 2002-)
Gene Group (FlyBase)
Pathway (FlyBase)
Protein Family (UniProt)
Belongs to the peptidase C64 family. (Q9VH90)
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
cysteine-type deubiquitinase activity
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal) (3.4.19.12)
Summaries
Gene Snapshot
trabid (trbd) encodes a OTU family member that interacts with the product of Apc when ubiquitinated. It affects the activity of the product of Apc in transcription. [Date last reviewed: 2019-03-14]
Pathway (FlyBase)
Positive Regulators of Wnt-TCF Signaling Pathway -
Positive regulators of Wnt-TCF (canonical Wnt) signaling up-regulate the pathway, resulting in the enhancement of transcriptional regulation mediated by β-catenin (arm).
Negative Regulators of Imd Signaling Pathway -
Negative regulators of the immune deficiency (Imd) pathway result in the decreased activity of the NFκB-like transcription factor Rel in the nucleus. Negative regulators are important in preventing damage to the host from over-activation of the pathway; preventing inappropriate triggering or terminating the response. (Adapted from FBrf0224587 and FBrf0238555.)
Gene Group (FlyBase)
CYSTEINE-TYPE OTU DEUBIQUITINASES -
Cysteine-type OTU deubiquitinases belong to the ovarian tumour (OTU) sub-family of deubiquitinases and catalyze the removal of ubiquitin from ubiquitin chains and ubiquitinated proteins. They have a central cysteine in the catalytic triad within their OTU domain. (Adapted from FBrf0230214.)
Protein Function (UniProtKB)
Positive regulator of the Wnt signaling pathway. Specifically cleaves 'Lys-63'-linked ubiquitin chains. May act by deubiquitinating APC protein, a negative regulator of Wnt-mediated transcription (By similarity). Required for an efficient wg response, but not for other signaling responses, in the eye.
(UniProt, Q9VH90)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\trbd 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 Q9VH90)

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

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

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

Gene model reviewed during 5.49

Sequence Ontology: Class of Gene
gene_with_edited_transcript
(Graveley et al., 2011)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
trbd-RA
FBtr0082091
NM_141674
3679
778
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
UniProt
RefSeq ID
GenBank
trbd-PA
FBpp0081569
88.2
778
6.24
Q9VH90
NP_649931
AAF54429
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)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts with Apc.

(UniProt, Q9VH90)
Domain

The OTU domain mediates the deubiquitinating activity.

The RanBP2-type zinc fingers mediate the specific interaction with 'Lys-63'-linked ubiquitin.

(UniProt, Q9VH90)
Crossreferences
InterPro - A database of protein families, domains and functional sites
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\trbd 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).

4.03

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 13 -- 16
embryonic dorsal epidermis
(Fisher et al., 2012)
embryonic foregut
(Fisher et al., 2012)
embryonic ventral epidermis
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
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\trbd 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
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
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
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of trbd
Transgenic constructs containing regulatory region of trbd
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 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) (5)
Hsap\ZRANB1
14 of 14
Yes
Yes
Hsap\TNFAIP3
4 of 14
No
Yes
1  
Hsap\OTUD7A
3 of 14
No
Yes
Hsap\OTUD7B
3 of 14
No
Yes
Hsap\VCPIP1
2 of 14
No
Yes
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) (5)
Rnor\Zranb1
14 of 14
Yes
Yes
Rnor\Otud7b
3 of 14
No
Yes
Rnor\Tnfaip3
3 of 14
No
Yes
Rnor\Otud7a
2 of 14
No
Yes
Rnor\Vcpip1
2 of 14
No
Yes
Mus musculus (laboratory mouse) (5)
Mmus\Zranb1
14 of 14
Yes
Yes
Mmus\Tnfaip3
4 of 14
No
Yes
Mmus\Otud7a
3 of 14
No
Yes
Mmus\Otud7b
2 of 14
No
Yes
Mmus\Vcpip1
2 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (5)
Xtro\zranb1
11 of 13
Yes
Yes
Xtro\LOC100486032
10 of 13
No
Yes
Xtro\otud7a
2 of 13
No
No
Xtro\otud7b
1 of 13
No
Yes
Xtro\vcpip1
1 of 13
No
Yes
Danio rerio (Zebrafish) (6)
Drer\zranb1b
14 of 14
Yes
Yes
Drer\zranb1a
12 of 14
No
Yes
Drer\otud7a
3 of 14
No
Yes
Drer\tnfaip3
3 of 14
No
Yes
Drer\otud7b
2 of 14
No
Yes
Drer\vcpip1
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\otub-2
5 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (2)
Agam\AgaP_AGAP003853
12 of 12
Yes
Yes
Agam\AgaP_AGAP010345
3 of 12
No
Yes
Arabidopsis thaliana (thale-cress) (0)
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:trbd. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
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 ( 1 )
    Modifiers Based on Experimental Evidence ( 1 )
    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?
    ZRANB1; zinc finger RANBP2-type containing 1
    14 of 14
    611749
        TNFAIP3; TNF alpha induced protein 3
        4 of 14
        191163
         
        OTUD7A; OTU deubiquitinase 7A
        3 of 14
        612024
          OTUD7B; OTU deubiquitinase 7B
          3 of 14
          611748
              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
              Show/hide secondary interactors 
              (data from AllianceMine provided by esyN)
              esyN Network Key:
              Suppression
              Enhancement
              Other Interaction Browsers
              View in FlyBase 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
              Starting gene(s)
              Interaction type
              Interacting gene(s)
              Reference
              arm
              suppressible
              trbd
              (Tran et al., 2008)
              wg
              suppressible
              trbd
              (Tran et al., 2008)
              External Data
              Subunit Structure (UniProtKB)
              Interacts with Apc.
              (UniProt, Q9VH90 )
              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 Wnt-TCF Signaling Pathway -
              Positive regulators of Wnt-TCF (canonical Wnt) signaling up-regulate the pathway, resulting in the enhancement of transcriptional regulation mediated by β-catenin (arm).
              Negative Regulators of Imd Signaling Pathway -
              Negative regulators of the immune deficiency (Imd) pathway result in the decreased activity of the NFκB-like transcription factor Rel in the nucleus. Negative regulators are important in preventing damage to the host from over-activation of the pathway; preventing inappropriate triggering or terminating the response. (Adapted from FBrf0224587 and FBrf0238555.)
              Metabolic Pathways
              External Data
              Linkouts
              Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
              Genomic Location and Detailed Mapping Data
              Chromosome (arm)
              3R
              Recombination map
              3-49
              Cytogenetic map
              85E5-85E5
              Sequence location
              FlyBase Computed Cytological Location
              Cytogenetic map
              Evidence for location
              85E5-85E5
              Limits computationally determined from genome sequence between P{EP}CrcEP3006 and P{lacW}s2681
              Experimentally Determined Cytological Location
              Cytogenetic map
              Notes
              References
              Experimentally Determined Recombination Data
              Location

              3-49

              (FlyBase, 2016)

              3-46.2

              (Comeron et al., 2012)
              Left of (cM)
              Right of (cM)
              Notes
              Stocks and Reagents
              Stocks (3)
              Genomic Clones (18)
               

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

              cDNA Clones (149)
               

              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

                (Hua et al., 2022)
                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

                    Source for identity of: trbd CG9448

                    (Tran et al., 2008)
                    Nomenclature comments
                    Etymology
                    Synonyms and Secondary IDs (7)
                    Datasets (0)
                    Study focus (0)
                    Experimental Role
                    Project
                    Project Type
                    Title
                    Study result (0)
                    Result
                    Result Type
                    Title
                    External Crossreferences and Linkouts ( 41 )
                    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
                    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.
                    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
                    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
                    FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
                    iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
                    MIST (protein-protein) - An integrated Molecular Interaction Database
                    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
                    References (58)