FB2024_03 , released June 25, 2024
Gene: Dmel\Urm1
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General Information
Symbol
Dmel\Urm1
Species
D. melanogaster
Name
Ubiquitin-related modifier 1
Annotation Symbol
CG33276
Feature Type
protein_coding_gene
FlyBase ID
FBgn0053276
Gene Model Status
Current
Stock Availability
19 publicly available
Gene Summary
Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln) (By similarity). Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by MOCS3 (By similarity). The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U (By similarity). Also acts as a ubiquitin-like protein (UBL) that is covalently conjugated via an isopeptide bond to lysine residues of target proteins such as Prx2/Jafrac1, Ciao1, Eip71CD and GILT1 (PubMed:26715182, PubMed:28953965). The thiocarboxylated form serves as substrate for conjugation and oxidative stress specifically induces the formation of UBL-protein conjugates (By similarity). Plays a role in the regulation of JNK signaling in response to oxidative stress (PubMed:26715182). (UniProt, Q7KU86)
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
66A8-66A8
Sequence location
Recombination map
3-21
RefSeq locus
NT_037436 REGION:7639811..7640446
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 (6 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables protein tag activity
inferred from biological aspect of ancestor with PANTHER:PTN000384753
(GO Reference Genome Project, 2011-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in negative regulation of JNK cascade
inferred from mutant phenotype
(Khoshnood et al., 2016)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in protein urmylation
inferred from biological aspect of ancestor with PANTHER:PTN000384753
(GO Reference Genome Project, 2011-)
involved_in tRNA thio-modification
inferred from electronic annotation with InterPro:IPR015221
(InterPro Project Members, 2004-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Khoshnood et al., 2016)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from electronic annotation with InterPro:IPR015221
(InterPro Project Members, 2004-)
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000384753
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the URM1 family. (Q7KU86)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
URM1 PROTEINS -
Urm1 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 Urm1 to target proteins (urmylation) regulates their activity, stability, subcellular localization, or macromolecular interactions. The urmylation process can be significantly enhanced by oxidative stress. Urm1 also acts as a sulfur carrier in the thiolation of eukaryotic tRNA. (Adapted from PMID:28234446 and PMID:21904977.)
Protein Function (UniProtKB)
Acts as a sulfur carrier required for 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of cytosolic tRNA(Lys), tRNA(Glu) and tRNA(Gln) (By similarity). Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by MOCS3 (By similarity). The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U (By similarity). Also acts as a ubiquitin-like protein (UBL) that is covalently conjugated via an isopeptide bond to lysine residues of target proteins such as Prx2/Jafrac1, Ciao1, Eip71CD and GILT1 (PubMed:26715182, PubMed:28953965). The thiocarboxylated form serves as substrate for conjugation and oxidative stress specifically induces the formation of UBL-protein conjugates (By similarity). Plays a role in the regulation of JNK signaling in response to oxidative stress (PubMed:26715182).
(UniProt, Q7KU86)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Urm1 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 Q7KU86)

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 5.46

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Urm1-RB
FBtr0114530
NM_206296
391
101
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
Urm1-PB
FBpp0113022
11.5
101
4.48
Q7KU86
NP_996018
AAS65063
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 cer.

(UniProt, Q7KU86)
Post Translational Modification

C-terminal thiocarboxylation occurs in 2 steps, it is first acyl-adenylated (-COAMP) via the hesA/moeB/thiF part of the MOCS3 homolog, then thiocarboxylated (-COSH) via the rhodanese domain of the MOCS3 homolog.

(UniProt, Q7KU86)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Urm1 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).

-1.35

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage
organism
(Khoshnood et al., 2016)
pupal stage

Comment: larval/pupal transition

(Khoshnood et al., 2016)
adult stage | male
(Khoshnood et al., 2016)
adult stage | female
(Khoshnood et al., 2016)
Additional Descriptive Data

Urm1 protein is abundant in embryonic stages, particular early embryos, drops off in larval stages, peaks again at the larval/pupal transition, and is observed again in adult males and females.

(Khoshnood et al., 2016)
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasm
inferred from direct assay
(Khoshnood et al., 2016)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Urm1 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
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
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 4 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Urm1
Transgenic constructs containing regulatory region of Urm1
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) (1)
Hsap\URM1
12 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\Urm1
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Urm1
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\urm1
7 of 13
Yes
Yes
Danio rerio (Zebrafish) (1)
Drer\urm1
14 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\urm-1
12 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\URM1_ANOGA
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\AT2G45695
13 of 13
Yes
Yes
Atha\AT3G61113
13 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\URM1
12 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\urm1
11 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Urm1. 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 ( 0 )
    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?
    URM1; ubiquitin related modifier 1
    12 of 14
    612693
        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)
        Other Interaction Browsers
        View in FlyBase Interactions Browser   View in MIST tool (external link)
        Please see the Physical Interaction reports below for full details
        protein-protein
        Physical Interaction
        Assay
        References
        Urm1 - Gsc
        two hybrid
        (Hu et al., 2017.6.13)
        Urm1 - Mocs3
        pull down, western blot, anti tag coimmunoprecipitation, anti tag western blot
        (Khoshnood et al., 2016)
        Urm1 - Prx5
        anti tag coimmunoprecipitation, western blot
        (Khoshnood et al., 2016)
        Urm1 - cer
        anti tag coimmunoprecipitation, western blot
        (Khoshnood et al., 2017)
        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
        Urm1
        enhanceable
        Mocs3
        (Khoshnood et al., 2016)
        Urm1
        suppressible
        Prx2
        (Khoshnood et al., 2016)
        Starting gene(s)
        Interaction type
        Interacting gene(s)
        Reference
        Mocs3
        enhanceable
        Urm1
        (Khoshnood et al., 2016)
        External Data
        Subunit Structure (UniProtKB)
        Interacts with cer.
        (UniProt, Q7KU86 )
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        MIST (genetic) - An integrated Molecular Interaction Database
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        External Data
        Linkouts
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3L
        Recombination map
        3-21
        Cytogenetic map
        66A8-66A8
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        66A8-66A8
        Limits computationally determined from genome sequence between P{PZ}l(3)0721708223&P{EP}Rac2EP3118 and P{lacW}Nmtj1C7 66A8
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        3-21

        (FlyBase, 2016)

        3-17.7

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (19)
        Genomic Clones (18)
         

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

        cDNA Clones (2)
         

        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

              (Khoshnood et al., 2016)
              Commercially Available Antibodies
               
              Cell Line Information
              Publicly Available Cell Lines
               
                Other Stable Cell Lines
                 
                  Other Comments

                  New annotation (CG33276) in release 3.2 of the genome annotation.

                  (FlyBase Genome Annotators, 2004)
                  Relationship to Other Genes
                  Source for database merge of
                  Additional comments
                  Nomenclature History
                  Source for database identify of

                  Source for identity of: Urm1 CG33276

                  (Khoshnood et al., 2016)
                  Nomenclature comments
                  Etymology

                  Named 'Urm1' after its homologues in other species.

                  (FlyBase, 2009-)
                  Synonyms and Secondary IDs (5)
                  Reported As
                  Symbol Synonym
                  CG33276
                  (Pirone et al., 2017, Khoshnood et al., 2016, Ni et al., 2010.12.1, Perkins et al., 2009)
                  Urm1
                  (Harnish et al., 2021, Hleihel et al., 2018, Hu et al., 2017.6.13, Khoshnood et al., 2017, Khoshnood et al., 2016)
                  anon-AE003558.1
                  Name Synonyms
                  Ubiquitin-related modifier 1
                  Ubiquitin-related modifier 1 ortholog
                  Secondary FlyBase IDs
                  • FBgn0043540
                  Datasets (0)
                  Study focus (0)
                  Experimental Role
                  Project
                  Project Type
                  Title
                  Study result (0)
                  Result
                  Result Type
                  Title
                  External Crossreferences and Linkouts ( 27 )
                  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
                  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.
                  FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
                  FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
                  Flygut - An atlas of the Drosophila adult midgut
                  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 (genetic) - An integrated Molecular Interaction Database
                  MIST (protein-protein) - An integrated Molecular Interaction Database
                  References (28)