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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 tRNA processing and Sulfur relay system. 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.

No data available for Entrez Gene 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
GH09F127577 0.2 ENCODE 38.3 -791.8 -791845 3.5 PKNOX1 MLX ZFP64 ARID4B SIN3A SLC30A9 ZNF143 FOS DEK SP5 URM1 SNORA65 LOC102723566 CDK9 ZNF79 ENSG00000272696 ANGPTL2 RPL12 ENSG00000272593 CFAP157
GH09F127533 1.3 FANTOM5 Ensembl ENCODE 31.6 -830.9 -830870 13.7 HDGF PKNOX1 ZFP64 ARID4B SIN3A ZNF143 FOS DEK ZNF263 SP5 RPL12 URM1 SNORA65 ENSG00000272593 ZNF79 ENSG00000272696 NAIF1 SLC2A8 LOC102723566 LOC100129352
GH09F129339 0.4 ENCODE 30.4 +968.7 968679 0.1 ZSCAN5A KLF1 ZSCAN18 ZNF792 KLF17 CDC5L ZNF514 ZNF2 ZFHX2 ZNF157 URM1 UBE2V1P4 PKN3 IER5L LOC105376289 SPOUT1 LOC101929314 NTMT1 C9orf50 SPTAN1
GH09F127935 0.2 ENCODE 28.6 -434.0 -433977 4.3 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 SNORA65 SPOUT1 URM1 PIP5KL1 LOC102723566 ZNF79 CDK9 RPL12 ANGPTL2 ENSG00000272696
GH09F128837 0.6 ENCODE 28.6 +467.0 467049 1.3 ZFP64 ZNF493 ARID4B ZNF48 GLIS2 ZNF202 SP5 REST PPARG ZNF518A SPOUT1 URM1 LOC101929314 ENSG00000272696 ENSG00000272593 SPTAN1 SWI5 DOLK WDR34 NAIF1
- Elite enhancer/Elite enhancer-gene association Download Table
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
ENSR00001315132 -19 1801 HDGF PKNOX1 ATF1 WRNIP1 ARID4B SIN3A ZNF48 ETS1 YY1 SLC30A9

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

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

No data available for Gene Families for URM1 Gene

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.

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

miRNA for URM1 Gene

miRTarBase miRNAs that target URM1

Inhibitory RNA Products

Flow Cytometry Products

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
Jensen Localization Image for URM1 Gene COMPARTMENTS Subcellular localization image for URM1 gene
Compartment Confidence
cytosol 5
extracellular 5
cytoskeleton 3
nucleus 2

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

Transcripts for URM1 Gene

Unigene Clusters for URM1 Gene

Ubiquitin related modifier 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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 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
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 and mRNA Expression by UniProt/SwissProt 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 34 35
  • 99.67 (n)
cow
(Bos Taurus)
Mammalia URM1 34 35
  • 91.75 (n)
dog
(Canis familiaris)
Mammalia URM1 34 35
  • 91.42 (n)
mouse
(Mus musculus)
Mammalia Urm1 34 16 35
  • 89.11 (n)
rat
(Rattus norvegicus)
Mammalia Urm1 34
  • 89.11 (n)
oppossum
(Monodelphis domestica)
Mammalia URM1 35
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia URM1 35
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves URM1 34 35
  • 76.24 (n)
lizard
(Anolis carolinensis)
Reptilia URM1 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia urm1 34
  • 70.96 (n)
Str.12011 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.5791 34
zebrafish
(Danio rerio)
Actinopterygii urm1 34 35
  • 71.95 (n)
Dr.9887 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10830 34
fruit fly
(Drosophila melanogaster)
Insecta CG33276 34 35
  • 62 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta URM1_ANOGA 34
  • 61.4 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes URM1 35 37
  • 29 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G45695 34
  • 57.73 (n)
rice
(Oryza sativa)
Liliopsida Os07g0466300 34
  • 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
rs10119630 -- 128,369,987(+) ggagt(G/T)cagtg upstream-variant-2KB
rs10124503 -- 128,391,680(+) CTGGG(C/T)GCTAG nc-transcript-variant, upstream-variant-2KB, utr-variant-3-prime
rs1048340 -- 128,390,665(+) CCCTT(C/T)TGGAA nc-transcript-variant, upstream-variant-2KB, utr-variant-3-prime
rs1048354 -- 128,390,673(+) GAAGT(C/T)TTGGG nc-transcript-variant, upstream-variant-2KB, utr-variant-3-prime
rs10987973 -- 128,388,457(+) TGCCA(A/C)GAAGT intron-variant, utr-variant-3-prime

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 Uba4A^Urm1 systems are conserved from yeast to man. (PMID: 25747390) JA1des A. … Schaffrath R. (FEBS Lett. 2015) 2 3 64
  2. Role of the ubiquitin-like protein Urm1 as a noncanonical lysine-directed protein modifier. (PMID: 21209336) Van der Veen A.G. … Jentsch S. (Proc. Natl. Acad. Sci. U.S.A. 2011) 3 4 64
  3. A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway. (PMID: 19017811) Schlieker C.D. … Ploegh H.L. (Proc. Natl. Acad. Sci. U.S.A. 2008) 3 4 64
  4. Solution structure of Urm1 and its implications for the origin of protein modifiers. (PMID: 16864801) Xu J. … Shi Y. (Proc. Natl. Acad. Sci. U.S.A. 2006) 2 3 64
  5. Three-dimensional structure of the AAH26994.1 protein from Mus musculus, a putative eukaryotic Urm1. (PMID: 16046629) Singh S. … Markley J.L. (Protein Sci. 2005) 2 3 64

Products for URM1 Gene

Sources for URM1 Gene

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