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Aliases for URM1 Gene

Aliases for URM1 Gene

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

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. Among its related pathways are Sulfur relay system and Gene Expression. GO annotations related to this gene include sulfurtransferase activity.

UniProtKB/Swiss-Prot 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.

Additional gene information for URM1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for URM1 Gene

Genomics for URM1 Gene

Regulatory Elements for URM1 Gene

Enhancers for URM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09H129338 1.4 Ensembl ENCODE dbSUPER 38.4 +968.1 968093 1 NFIB KLF17 ZNF2 TCF12 HSF1 ZNF207 KLF7 ZNF548 RCOR1 EGR2 NUP188 URM1 SPOUT1 GPR107 GLE1 LOC101929314 UBE2V1P4 PKN3 IER5L LOC105376289
GH09H129340 1.4 Ensembl ENCODE dbSUPER 28.3 +969.8 969848 1 NFIB ZSCAN4 KLF17 GLI4 ZNF2 TCF12 ZSCAN5C ZNF207 ZNF548 SMARCA5 NUP188 URM1 SPOUT1 GPR107 ODF2 LOC101929314 UBE2V1P4 PKN3 GLE1 IER5L
GH09H128837 1 ENCODE 38.4 +467.0 467049 1 FOXA2 ZNF493 ZFP64 ARID4B GLIS2 ZNF202 SP5 ZC3H11A REST PPARG NUP188 SPOUT1 ODF2 CIZ1 GOLGA2 URM1 GLE1 LOC101929314 NAIF1 SWI5
GH09H128549 1.7 Ensembl ENCODE dbSUPER 18.2 +183.5 183476 10 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 YY1 ZNF766 CBX5 ZNF207 URM1 TOR2A MIGA2 LRRC8A KYAT1 ENSG00000273186 SPTAN1 ENSG00000280474
GH09H128370 1.6 FANTOM5 ENCODE dbSUPER 17.3 +1.4 1440 5 HDGF PKNOX1 ATF1 ARID4B SIN3A YY1 ETS1 TCF12 SLC30A9 ELK1 URM1 SLC27A4 PTGES2-AS1 ENSG00000272593
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around URM1 on UCSC Golden Path with GeneCards custom track

Promoters for URM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000241865 81 1601 HDGF PKNOX1 ATF1 ARID4B SIN3A YY1 ETS1 TCF12 SLC30A9 ELK1

Genomic Location for URM1 Gene

Chromosome:
9
Start:
128,371,319 bp from pter
End:
128,392,016 bp from pter
Size:
20,698 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.
    SequenceCaution:
    • Sequence=CAI13492.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    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:

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:0016783 contributes_to sulfurtransferase 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

Animal Model Products

CRISPR Products

miRNA for URM1 Gene

miRTarBase miRNAs that target URM1

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for URM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
extracellular 5
cytosol 5
cytoskeleton 3
nucleus 2

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:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA 23376485
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 IEA --
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

Unigene Clusters for URM1 Gene

Ubiquitin related modifier 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for URM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
ECgene alternative splicing isoforms for
URM1

Expression for URM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for URM1 Gene



NURSA nuclear receptor signaling pathways regulating expression of URM1 Gene:

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(4.1)
  • Lung(2.8)
genes like me logo Genes that share expression patterns with URM1: view

Primer Products

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 33 34
  • 99.67 (n)
cow
(Bos Taurus)
Mammalia URM1 33 34
  • 91.75 (n)
dog
(Canis familiaris)
Mammalia URM1 33 34
  • 91.42 (n)
mouse
(Mus musculus)
Mammalia Urm1 33 16 34
  • 89.11 (n)
rat
(Rattus norvegicus)
Mammalia Urm1 33
  • 89.11 (n)
oppossum
(Monodelphis domestica)
Mammalia URM1 34
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia URM1 34
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves URM1 33 34
  • 76.24 (n)
lizard
(Anolis carolinensis)
Reptilia URM1 34
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia urm1 33
  • 70.96 (n)
Str.12011 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.5791 33
zebrafish
(Danio rerio)
Actinopterygii urm1 33 34
  • 71.95 (n)
Dr.9887 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10830 33
fruit fly
(Drosophila melanogaster)
Insecta CG33276 33 34
  • 62 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta URM1_ANOGA 33
  • 61.4 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes URM1 34 36
  • 29 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G45695 33
  • 57.73 (n)
rice
(Oryza sativa)
Liliopsida Os07g0466300 33
  • 56.36 (n)
Species where no ortholog for URM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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)

Paralogs for URM1 Gene

No data available for Paralogs for URM1 Gene

Variants for URM1 Gene

Sequence variations from dbSNP and Humsavar for URM1 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs1000044256 -- 128,387,142(+) CAGTG(C/T)TAGCT intron-variant
rs1000322117 -- 128,385,551(+) GAGTC(A/T)CCAGC intron-variant
rs1000499153 -- 128,372,917(+) AAAAA(A/G/T)AAAAA intron-variant
rs1000581783 -- 128,370,440(+) GCTTA(C/G/T)AAGGC upstream-variant-2KB
rs1000635785 -- 128,370,067(+) TAGCT(A/G)GGACT upstream-variant-2KB

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)

Relevant External Links for URM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
URM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for URM1 Gene

Disorders for URM1 Gene

Relevant External Links for URM1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
URM1

No disorders were found for URM1 Gene.

No data available for MalaCards , 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 60
  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 60
  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 60
  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 60
  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 60

Products for URM1 Gene

Sources for URM1 Gene

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