FB2024_02 , released April 23, 2024
Gene: Dmel\Ufm1
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General Information
Symbol
Dmel\Ufm1
Species
D. melanogaster
Name
Ubiquitin-fold modifier 1
Annotation Symbol
CG34191
Feature Type
FlyBase ID
FBgn0085220
Gene Model Status
Stock Availability
Gene Summary
Ubiquitin-like modifier which can be covalently attached via an isopeptide bond to substrate proteins as a monomer or a lysine-linked polymer (By similarity). The so-called ufmylation, requires the UFM1-activating E1 enzyme Uba5, the UFM1-conjugating E2 enzyme Ufc1, and the UFM1-ligase E3 enzyme Ufl1 (By similarity). This post-translational modification on lysine residues of proteins may play a crucial role in a number of cellular processes (By similarity). The Ufm1 cascade might play a role in the development of the neuromuscular junctions (PubMed:26872069). (UniProt, A8DYH2)
Contribute a Gene Snapshot for this gene.
Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
2-81
RefSeq locus
NT_033778 REGION:16951837..16952581
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (7 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (0 terms)
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from mutant phenotype
involved_in protein ufmylation
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in protein ufmylation
inferred from electronic annotation with InterPro:IPR005375
inferred from sequence or structural similarity with HGNC:20597
Cellular Component (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
is_active_in cytosol
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000406181
located_in cytoplasm
inferred from sequence or structural similarity with HGNC:20597
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000406181
located_in nucleus
inferred from sequence or structural similarity with HGNC:20597
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the UFM1 family. (A8DYH2)
Summaries
Gene Group (FlyBase)
UFM1 PROTEINS -
Ufm1 is a ubiquitin-like protein that is conjugated to substrates through a cascade of E1 activating enzymes, E2 conjugating enzymes, and E3 ligases. Conjugation of Ufm1 to target proteins (ufmylation) regulates their activity, stability, subcellular localization, or macromolecular interactions. The ufmylation pathway is key to sustain cell development and tissue homeostasis, and is tightly related to the function of the endoplasmic reticulum. (Adapted from PMID:28234446 and PMID:31703843.)
Protein Function (UniProtKB)
Ubiquitin-like modifier which can be covalently attached via an isopeptide bond to substrate proteins as a monomer or a lysine-linked polymer (By similarity). The so-called ufmylation, requires the UFM1-activating E1 enzyme Uba5, the UFM1-conjugating E2 enzyme Ufc1, and the UFM1-ligase E3 enzyme Ufl1 (By similarity). This post-translational modification on lysine residues of proteins may play a crucial role in a number of cellular processes (By similarity). The Ufm1 cascade might play a role in the development of the neuromuscular junctions (PubMed:26872069).
(UniProt, A8DYH2)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Ufm1 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 A8DYH2)

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

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

Gene model reviewed during 5.50

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0112384
647
87
FBtr0340071
479
87
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
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

87 aa isoforms: Ufm1-PA, Ufm1-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Interacts with Uba5.

(UniProt, A8DYH2)
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\Ufm1 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).

-1.56

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
is_active_in cytosol
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Ufm1 in JBrowse
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
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 1 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 4 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Ufm1
Transgenic constructs containing regulatory region of Ufm1
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Inferred from location ( 0 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (1)
14 of 14
Yes
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
11 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
14 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
14 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
13 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (1)
1 of 11
Yes
Yes
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Ufm1. Refer to their site for version information.
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
Potential Models Based on Orthology ( 1 )
Human Ortholog
Disease
Evidence
References
Modifiers Based on Experimental Evidence ( 0 )
Allele
Disease
Interaction
References
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?
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:
Show/hide secondary interactors 
(data from AllianceMine provided by esyN)
Select Layout:
Legend:
Protein
RNA
Selected Interactor(s)
Interactions Browser

Please see the Physical Interaction reports below for full details
MIST Molecular Interaction Search Tool

Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
Summary of Genetic Interactions
esyN Network Diagram
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
External Data
Subunit Structure (UniProtKB)
Interacts with Uba5.
(UniProt, A8DYH2 )
Linkouts
DroID - A comprehensive database of gene and protein interactions.
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
External Data
Linkouts
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2R
Recombination map
2-81
Cytogenetic map
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
53E2-53E2
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (5)
Genomic Clones (23)
cDNA Clones (7)
 

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
      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

          New annotation (CG34191) in release 5.2 of the genome annotation.

          Relationship to Other Genes
          Source for database merge of
          Additional comments
          Nomenclature History
          Source for database identify of

          Source for identity of: Ufm1 CG34191

          Nomenclature comments
          Etymology
          Synonyms and Secondary IDs (5)
          Datasets (0)
          Study focus (0)
          Experimental Role
          Project
          Project Type
          Title
          Study result (0)
          Result
          Result Type
          Title
          External Crossreferences and Linkouts ( 26 )
          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 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
          UniProt/TrEMBL - Automatically annotated and unreviewed 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.
          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
          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.
          FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
          MIST (protein-protein) - An integrated Molecular Interaction Database
          References (26)