FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Ufd1
Open Close
General Information
Symbol
Dmel\Ufd1
Species
D. melanogaster
Name
Ubiquitin fusion-degradation 1-like
Annotation Symbol
CG6233
Feature Type
protein_coding_gene
FlyBase ID
FBgn0036136
Gene Model Status
Current
Stock Availability
5 publicly available
Gene Summary
Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway. (UniProt, Q9VTF9)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

Ufd1-like

Key Links
Genomic Location
Cytogenetic map
68A7-68A7
Sequence location
Recombination map
3-34
RefSeq locus
NT_037436 REGION:11121966..11123216
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 (11 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables ubiquitin protein ligase binding
inferred from physical interaction with FLYBASE:Roc1a; FB:FBgn0025638
(Zhang et al., 2013)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables polyubiquitin modification-dependent protein binding
inferred from biological aspect of ancestor with PANTHER:PTN000285104
(GO Reference Genome Project, 2011-)
Biological Process (7 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
involved_in cellular response to virus
inferred from mutant phenotype
(Panda et al., 2013)
involved_in negative regulation of smoothened signaling pathway
inferred from mutant phenotype
(Zhang et al., 2013)
involved_in positive regulation of proteasomal ubiquitin-dependent protein catabolic process
inferred from mutant phenotype
(Lundgren et al., 2005)
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process
inferred from genetic interaction with FLYBASE:sordd1; FB:FBgn0030693
(Xu et al., 2020)
involved_in proteolysis
inferred from mutant phenotype
(Lundgren et al., 2005)
involved_in ubiquitin-dependent protein catabolic process
inferred from mutant phenotype
(Beskow et al., 2009)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in ERAD pathway
inferred from biological aspect of ancestor with PANTHER:PTN000285104
(GO Reference Genome Project, 2011-)
involved_in ubiquitin-dependent protein catabolic process
inferred from electronic annotation with InterPro:IPR004854
(InterPro Project Members, 2004-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
part_of proteasome complex
non-traceable author statement
(Lundgren et al., 2005)
part_of VCP-NPL4-UFD1 AAA ATPase complex
inferred from biological aspect of ancestor with PANTHER:PTN000285104
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Pathway (FlyBase)
Protein Family (UniProt)
Belongs to the UFD1 family. (Q9VTF9)
Protein Signatures (InterPro)
Summaries
Pathway (FlyBase)
NEGATIVE REGULATORS OF HEDGEHOG SIGNALING PATHWAY -
Negative regulators of hedgehog signaling down-regulate the pathway, resulting in the repression of transcription of hh-responsive genes.
Protein Function (UniProtKB)
Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway.
(UniProt, Q9VTF9)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Ufd1 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 Q9VTF9)

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

Gene model reviewed during 5.44

Gene model reviewed during 5.42

Gene model reviewed during 5.45

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Ufd1-RA
FBtr0076223
NM_079299
1194
316
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
Ufd1-PA
FBpp0075952
34.8
316
6.18
Q9VTF9
NP_524023
AAF50090
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
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\Ufd1 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).

3.40

Transcript Expression
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
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\Ufd1 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) 4-6
  • Stages(s) 7-8
  • Stages(s) 11-12
  • Stages(s) 13-16
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Ufd1
Transgenic constructs containing regulatory region of Ufd1
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 5 )
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) (1)
Hsap\UFD1
14 of 14
Yes
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) (1)
Rnor\Ufd1
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Ufd1
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\ufd1
11 of 13
Yes
Yes
Xtro\spag6
1 of 13
No
Yes
Danio rerio (Zebrafish) (1)
Drer\ufd1l
14 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\ufd-1
13 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP001307
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (4)
Atha\AT4G38930
13 of 13
Yes
Yes
Atha\UFD1
13 of 13
Yes
Yes
Atha\AT2G29070
12 of 13
No
Yes
Atha\AT4G15420
3 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\UFD1
12 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\ufd1
11 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Ufd1. 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 ( 1 )
    Allele
    Disease
    Evidence
    References
    Ufd1KK108134
    model of  neurodegenerative disease
    CEA
    (Byrne et al., 2017)
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 1 )
    Allele
    Disease
    Interaction
    References
    Ufd1KK108134
    model of  neurodegenerative disease
    is exacerbated by TBPHRNAi.UAS.cDa
    (Byrne et al., 2017)
    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?
    UFD1; ubiquitin recognition factor in ER associated degradation 1
    14 of 14
    601754
        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
        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
        Ufd1
        enhanceable
        TBPH
        (Byrne et al., 2017)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Nsf2
        suppressible
        Ufd1
        (Laviolette et al., 2005)
        TBPH
        enhanceable
        Ufd1
        (Byrne et al., 2017)
        External Data
        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)
        Metabolic Pathways
        FlyBase
        External Links
        External Data
        Linkouts
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3L
        Recombination map
        3-34
        Cytogenetic map
        68A7-68A7
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        68A7-68A7
        Limits computationally determined from genome sequence between P{PZ}l(3)0123901239&P{lacW}l(3)01239j9B4 and P{PZ}CycA02461&P{PZ}CycA03946
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        68B1-68B1
        (Ratti, 2000.1.27)
        Experimentally Determined Recombination Data
        Location

        3-34

        (FlyBase, 2016)

        3-28.7

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (5)
        Genomic Clones (28)
        cDNA Clones (27)
         

        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
         
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
            Other Comments

            Area matching Drosophila EST AA696390. This EST has sequence similarity to Ubiquitin fusion protein genes. Probable intron in gene represented by EST AA696390.

            (Davies, 2001.3.15)
            Relationship to Other Genes
            Source for database merge of

            Source for merge of: Ufd1-like anon-WO0118547.405

            (FlyBase, 1996-)
            Additional comments

            Source for identity of Ufd1-like CG6233 was sequence comparison ( date:010210 ).

            (FlyBase, 1996-)

            Source for merge of Ufd1-like anon-WO0118547.405 was sequence comparison ( date:051113 ).

            (FlyBase, 1996-)
            Nomenclature History
            Source for database identify of

            Source for identity of: Ufd1-like CG6233

            (FlyBase, 1996-)

            Source for identity of: Ufd1 Ufd1-like

            (FlyBase, 2009-)
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (16)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 44 )
            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)
            KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            References (64)