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    URM1 ubiquitin related modifier 1 [ Homo sapiens (human) ]

    Gene ID: 81605, updated on 10-Dec-2024

    Summary

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    Official Symbol
    URM1provided by HGNC
    Official Full Name
    ubiquitin related modifier 1provided by HGNC
    Primary source
    HGNC:HGNC:28378
    See related
    Ensembl:ENSG00000167118 MIM:612693; AllianceGenome:HGNC:28378
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C9orf74
    Summary
    Enables sulfur carrier activity. Involved in tRNA thio-modification and tRNA wobble uridine modification. Predicted to be located in cytosol. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in spleen (RPKM 8.1), lymph node (RPKM 7.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See URM1 in Genome Data Viewer
    Location:
    9q34.11
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (128371319..128392016)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (140578420..140599118)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (131133598..131154295)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr9:131102183-131102824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29079 Neighboring gene tRNA-Arg (anticodon TCT) 3-1 Neighboring gene solute carrier family 27 member 4 Neighboring gene TMSB4X pseudogene 4 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131126318-131127208 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131127209-131128100 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131131960-131132824 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131132825-131133688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29080 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:131145413-131146057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131147991-131148635 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131155313-131156018 Neighboring gene MIR219A2 host gene Neighboring gene microRNA 219a-2 Neighboring gene microRNA 219b Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131167036-131167836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131173621-131174240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29081 Neighboring gene cerebral endothelial cell adhesion molecule

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1. Singh S, et al. Protein Sci, 2005 Aug. PMID 16046629, Free PMC Article
    2. Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation. Pabis M, et al. EMBO J, 2020 Oct 1. PMID 32901956, Free PMC Article
    3. Solution structure of Urm1 and its implications for the origin of protein modifiers. Xu J, et al. Proc Natl Acad Sci U S A, 2006 Aug 1. PMID 16864801, Free PMC Article
    4. Urm1 couples sulfur transfer to ubiquitin-like protein function in oxidative stress. Petroski MD, et al. Proc Natl Acad Sci U S A, 2011 Feb 1. PMID 21245332, Free PMC Article
    5. The emerging roles of ubiquitin-like protein Urm1 in eukaryotes. Zhang X, et al. Cell Signal, 2021 May. PMID 33548388

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The emerging roles of ubiquitin-like protein Urm1 in eukaryotes.
      Title: The emerging roles of ubiquitin-like protein Urm1 in eukaryotes.
    2. Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation.
      Title: Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation.
    3. ubiquitin-like Urm1.Uba4 systems are conserved and exchangeable between human and yeast cells
      Title: Urmylation and tRNA thiolation functions of ubiquitin-like Uba4·Urm1 systems are conserved from yeast to man.
    4. observations suggest that Urm1 activation is more similar to that of a prokaryotic sulfur carrier protein than that of a ubiquitin-like protein
      Title: Urm1 couples sulfur transfer to ubiquitin-like protein function in oxidative stress.
    5. Urm1 has a conserved dual role by integrating the functions of prokaryotic sulfur carriers with those of eukaryotic protein modifiers of the Ub family
      Title: Role of the ubiquitin-like protein Urm1 as a noncanonical lysine-directed protein modifier.
    6. Urm1 is activated by an unusual mechanism to yield a thiocarboxylate intermediate that serves as sulfur donor in tRNA thiolation reactions
      Title: A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway.
    7. The UBA4-URM1 system represents the evolutionary link between protein conjugation and protein modification by sulfur carrier proteins.
      Title: The sulfurtransferase activity of Uba4 presents a link between ubiquitin-like protein conjugation and activation of sulfur carrier proteins.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC2668

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein tag activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables sulfur carrier activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein urmylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA thio-modification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tRNA wobble uridine modification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    ubiquitin-related modifier 1
    Names
    ubiquitin-related modifier 1 homolog

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001135947.2 → NP_001129419.1  ubiquitin-related modifier 1 isoform b

      See identical proteins and their annotated locations for NP_001129419.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) encodes the longest isoform (B)
      Source sequence(s)
      AK300877, AL359091, BI823604
      Consensus CDS
      CCDS48035.1
      UniProtKB/Swiss-Prot
      Q9BTM9
      Related
      ENSP00000501135.1, ENST00000483206.2
      Conserved Domains (1) summary
      pfam09138
      Location:6 → 79
      Urm1; Urm1 (Ubiquitin related modifier)

    2. NM_001265582.1 → NP_001252511.1  ubiquitin-related modifier 1 isoform c

      See identical proteins and their annotated locations for NP_001252511.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has an additional segment in the 3' end, compared to variant 2, which reults in a protein (isoform C) with a shorter C-terminus, compared to isoform B.
      Source sequence(s)
      AL359091, BC011620, BI823604
      Consensus CDS
      CCDS59148.1
      UniProtKB/Swiss-Prot
      Q9BTM9
      Related
      ENSP00000361941.1, ENST00000372850.5
      Conserved Domains (1) summary
      cl25424
      Location:6 → 63
      TGS; The TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs, is structurally similar to ubiquitin. TGS is a small domain of about 50 amino acid residues with a predominantly beta-sheet structure. There is no direct information ...

    3. NM_030914.4 → NP_112176.1  ubiquitin-related modifier 1 isoform a

      See identical proteins and their annotated locations for NP_112176.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) lacks a segment in the 3' coding region, compared to variant 2, which results in a protein (isoform 1) with a distinct C-terminus, compared to isoform 2.
      Source sequence(s)
      AL359091, BC003581
      Consensus CDS
      CCDS6900.1
      UniProtKB/Swiss-Prot
      B3KMH3, B4DV08, Q5T4B4, Q9BTM9
      Related
      ENSP00000361944.4, ENST00000372853.9
      Conserved Domains (1) summary
      cd01764
      Location:7 → 101
      Ubl_Urm1; ubiquitin-like (Ubl) domain found in ubiquitin-related modifier 1 (Urm1)

    RNA

    1. NR_049743.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 5' coding region, compared to variant 2, which results in a frameshift and early stop codon. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because the product is significiantly truncated and the transcript is a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL359091, DA691216

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      128371319..128392016
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      140578420..140599118
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BTM9.1 GenPept UniProtKB/Swiss-Prot:Q9BTM9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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