Aliases for URM1 Gene

Aliases for URM1 Gene

  • Ubiquitin Related Modifier 1 2 3 5
  • Ubiquitin-Related Modifier 1 3 4
  • C9orf74 3 4
  • Ubiquitin Related Modifier 1 Homolog (S. Cerevisiae) 2
  • Ubiquitin-Related Modifier 1 Homolog 3
  • Chromosome 9 Open Reading Frame 74 2
  • MGC2668 2
  • URM1 5

External Ids for URM1 Gene

Previous HGNC Symbols for URM1 Gene

  • C9orf74

Previous GeneCards Identifiers for URM1 Gene

  • GC09P130174
  • GC09P131133
  • GC09P100747

Summaries for URM1 Gene

GeneCards Summary for URM1 Gene

URM1 (Ubiquitin Related Modifier 1) is a Protein Coding gene. Diseases associated with URM1 include Benign Epilepsy With Centrotemporal Spikes. Among its related pathways are Sulfur relay system and tRNA processing. Gene Ontology (GO) annotations related to this gene include sulfurtransferase activity.

UniProtKB/Swiss-Prot Summary for URM1 Gene

  • 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). Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by MOCS3. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Also acts as a ubiquitin-like protein (UBL) that is covalently conjugated via an isopeptide bond to lysine residues of target proteins such as MOCS3, ATPBD3, CTU2, USP15 and CAS. The thiocarboxylated form serves as substrate for conjugation and oxidative stress specifically induces the formation of UBL-protein conjugates.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for URM1 Gene

Genomics for URM1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for URM1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around URM1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for URM1

Top Transcription factor binding sites by QIAGEN in the URM1 gene promoter:
  • C/EBPalpha
  • E47
  • ER-alpha
  • NF-1
  • Nkx2-5
  • POU2F1
  • POU2F1a
  • PPAR-alpha

Genomic Locations for URM1 Gene

Latest Assembly
chr9:128,371,319-128,392,016
(GRCh38/hg38)
Size:
20,698 bases
Orientation:
Plus strand

Previous Assembly
chr9:131,133,598-131,154,295
(GRCh37/hg19 by Entrez Gene)
Size:
20,698 bases
Orientation:
Plus strand

chr9:131,133,598-131,153,015
(GRCh37/hg19 by Ensembl)
Size:
19,418 bases
Orientation:
Plus strand

Genomic View for URM1 Gene

Genes around URM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
URM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for URM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for URM1 Gene

Proteins for URM1 Gene

  • Protein details for URM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BTM9-URM1_HUMAN
    Recommended name:
    Ubiquitin-related modifier 1
    Protein Accession:
    Q9BTM9
    Secondary Accessions:
    • B3KMH3
    • B4DV08
    • Q5T4B4

    Protein attributes for URM1 Gene

    Size:
    101 amino acids
    Molecular mass:
    11380 Da
    Quaternary structure:
    • Component of a complex at least composed of URM1, CTU2/NCS2 and CTU1/ATPBD3.

    Alternative splice isoforms for URM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for URM1 Gene

Post-translational modifications for URM1 Gene

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

Other Protein References for URM1 Gene

No data available for DME Specific Peptides for URM1 Gene

Domains & Families for URM1 Gene

Gene Families for URM1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for URM1 Gene

Suggested Antigen Peptide Sequences for URM1 Gene

GenScript: Design optimal peptide antigens:
  • Ubiquitin-related modifier 1 homolog (URM1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BTM9

UniProtKB/Swiss-Prot:

URM1_HUMAN :
  • Belongs to the URM1 family.
Family:
  • Belongs to the URM1 family.
genes like me logo Genes that share domains with URM1: view

Function for URM1 Gene

Molecular function for URM1 Gene

UniProtKB/Swiss-Prot Function:
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). Serves as sulfur donor in tRNA 2-thiolation reaction by being thiocarboxylated (-COSH) at its C-terminus by MOCS3. The sulfur is then transferred to tRNA to form 2-thiolation of mcm(5)S(2)U. Also acts as a ubiquitin-like protein (UBL) that is covalently conjugated via an isopeptide bond to lysine residues of target proteins such as MOCS3, ATPBD3, CTU2, USP15 and CAS. The thiocarboxylated form serves as substrate for conjugation and oxidative stress specifically induces the formation of UBL-protein conjugates.

Phenotypes From GWAS Catalog for URM1 Gene

Gene Ontology (GO) - Molecular Function for URM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19017811
GO:0031386 protein tag IBA 21873635
GO:0097163 sulfur carrier activity IDA 19017811
genes like me logo Genes that share ontologies with URM1: view
genes like me logo Genes that share phenotypes with URM1: view

miRNA for URM1 Gene

miRTarBase miRNAs that target URM1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for URM1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for URM1 Gene

Localization for URM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for URM1 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for URM1 gene
Compartment Confidence
cytosol 5
nucleus 4
cytoskeleton 3
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for URM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with URM1: view

Pathways & Interactions for URM1 Gene

genes like me logo Genes that share pathways with URM1: view

Pathways by source for URM1 Gene

1 KEGG pathway for URM1 Gene

UniProtKB/Swiss-Prot Q9BTM9-URM1_HUMAN

  • Pathway: tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA biosynthesis.

Gene Ontology (GO) - Biological Process for URM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002098 tRNA wobble uridine modification IMP 19017811
GO:0006400 tRNA modification TAS --
GO:0008033 tRNA processing IEA --
GO:0032447 protein urmylation IBA 21873635
GO:0034227 tRNA thio-modification IMP 19017811
genes like me logo Genes that share ontologies with URM1: view

No data available for SIGNOR curated interactions for URM1 Gene

Drugs & Compounds for URM1 Gene

No Compound Related Data Available

Transcripts for URM1 Gene

mRNA/cDNA for URM1 Gene

3 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for URM1

Alternative Splicing Database (ASD) splice patterns (SP) for URM1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c · 6d ^ 7a · 7b
SP1: - - - - -
SP2: - - - -
SP3: - - - -
SP4: - - - -
SP5: - - -
SP6: - -
SP7: -
SP8: - -

Relevant External Links for URM1 Gene

GeneLoc Exon Structure for
URM1

Expression for URM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for URM1 Gene

Protein differential expression in normal tissues from HIPED for URM1 Gene

This gene is overexpressed in Ovary (10.3), Prostate (8.0), and Platelet (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for URM1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for URM1

SOURCE GeneReport for Unigene cluster for URM1 Gene:

Hs.495229

Evidence on tissue expression from TISSUES for URM1 Gene

  • Intestine(4.3)
  • Nervous system(4.3)
  • Lung(2.8)
  • Skin(2.5)
genes like me logo Genes that share expression patterns with URM1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for URM1 Gene

Orthologs for URM1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for URM1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia URM1 29 30
  • 99.67 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia URM1 29 30
  • 91.75 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia URM1 29 30
  • 91.42 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Urm1 29 16 30
  • 89.11 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Urm1 29
  • 89.11 (n)
Oppossum
(Monodelphis domestica)
Mammalia URM1 30
  • 70 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia URM1 30
  • 61 (a)
OneToOne
Chicken
(Gallus gallus)
Aves URM1 29 30
  • 76.24 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia URM1 30
  • 65 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia urm1 29
  • 70.96 (n)
Str.12011 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.5791 29
Zebrafish
(Danio rerio)
Actinopterygii urm1 29 30
  • 71.95 (n)
OneToOne
Dr.9887 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10830 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG33276 29 30
  • 62 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta URM1_ANOGA 29
  • 61.4 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes URM1 30 32
  • 29 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT2G45695 29
  • 57.73 (n)
Rice
(Oryza sativa)
Liliopsida Os07g0466300 29
  • 56.36 (n)
Species where no ortholog for URM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for URM1 Gene

ENSEMBL:
Gene Tree for URM1 (if available)
TreeFam:
Gene Tree for URM1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for URM1: view image
Alliance of Genome Resources:
Additional Orthologs for URM1

Paralogs for URM1 Gene

No data available for Paralogs for URM1 Gene

Variants for URM1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for URM1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for URM1 Gene

Variant ID Type Subtype PubMed ID
nsv831728 CNV loss 17160897

Variation tolerance for URM1 Gene

Residual Variation Intolerance Score: 34% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.13; 3.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for URM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
URM1
Leiden Open Variation Database (LOVD)
URM1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for URM1 Gene

Disorders for URM1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for URM1 Gene - From: COP

Disorder Aliases PubMed IDs
benign epilepsy with centrotemporal spikes
  • bcects
- elite association - COSMIC cancer census association via MalaCards
Search URM1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for URM1

genes like me logo Genes that share disorders with URM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for URM1 Gene

Publications for URM1 Gene

  1. Urmylation and tRNA thiolation functions of ubiquitin-like Uba4·Urm1 systems are conserved from yeast to man. (PMID: 25747390) Jüdes A … Schaffrath R (FEBS letters 2015) 2 3
  2. Role of the ubiquitin-like protein Urm1 as a noncanonical lysine-directed protein modifier. (PMID: 21209336) Van der Veen AG … Jentsch S (Proceedings of the National Academy of Sciences of the United States of America 2011) 3 4
  3. A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway. (PMID: 19017811) Schlieker CD … Ploegh HL (Proceedings of the National Academy of Sciences of the United States of America 2008) 3 4
  4. Solution structure of Urm1 and its implications for the origin of protein modifiers. (PMID: 16864801) Xu J … Shi Y (Proceedings of the National Academy of Sciences of the United States of America 2006) 2 3
  5. Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1. (PMID: 16046629) Singh S … Markley JL (Protein science : a publication of the Protein Society 2005) 2 3

Products for URM1 Gene

Sources for URM1 Gene