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Aliases for URM1 Gene

Aliases for URM1 Gene

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

External Ids for URM1 Gene

Previous Symbols for URM1 Gene

  • C9orf74

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. 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

Genomic Location for URM1 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for URM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for URM1 Gene

Regulatory Elements 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

Proteomics data for URM1 Gene at MOPED

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 for URM1 Gene

Protein Domains for URM1 Gene

UniProtKB/Swiss-Prot:

URM1_HUMAN
Family:
  • Belongs to the URM1 family.:
    • Q9BTM9
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

miRNA for URM1 Gene

miRTarBase miRNAs that target URM1

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting 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 4
cytoskeleton 3

Gene Ontology (GO) - Cellular Components for URM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm --
GO:0005829 cytosol IC 19017811
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with URM1: view

Pathways for URM1 Gene

SuperPathways for URM1 Gene

Superpath Contained pathways
1 Sulfur relay system
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.

Interacting Proteins for URM1 Gene

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:0032447 protein urmylation IEA --
GO:0034227 tRNA thio-modification IMP 19017811
genes like me logo Genes that share ontologies with URM1: view

Transcripts for URM1 Gene

Unigene Clusters for URM1 Gene

Ubiquitin related modifier 1:
Representative Sequences:

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 for URM1 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for URM1 Gene

SOURCE GeneReport for Unigene cluster for URM1 Gene Hs.495229

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

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 36
  • 99.67 (n)
  • 100 (a)
URM1 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia URM1 36
  • 91.75 (n)
  • 95.05 (a)
URM1 37
  • 73 (a)
OneToOne
dog
(Canis familiaris)
Mammalia URM1 36
  • 91.42 (n)
  • 94.06 (a)
URM1 37
  • 73 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Urm1 36
  • 89.11 (n)
  • 93.07 (a)
Urm1 16
Urm1 37
  • 72 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia URM1 37
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia URM1 37
  • 61 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Urm1 36
  • 89.11 (n)
  • 94.06 (a)
chicken
(Gallus gallus)
Aves URM1 36
  • 76.24 (n)
  • 86.14 (a)
URM1 37
  • 66 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia URM1 37
  • 65 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.5791 36
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.12011 36
urm1 36
  • 70.96 (n)
  • 79.21 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10830 36
zebrafish
(Danio rerio)
Actinopterygii Dr.9887 36
urm1 36
  • 71.95 (n)
  • 77.23 (a)
urm1 37
  • 58 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta URM1_ANOGA 36
  • 61.4 (n)
  • 52.63 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG33276 36
  • 62 (n)
  • 66 (a)
CG33276 37
  • 48 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes URM1 37
  • 29 (a)
OneToOne
URM1 39
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G45695 36
  • 57.73 (n)
  • 55.67 (a)
rice
(Oryza sativa)
Liliopsida Os07g0466300 36
  • 56.36 (n)
  • 56.7 (a)
Species with no ortholog for URM1:
  • 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 MAF
rs2240945 -- 128,390,366(-) GAGCG(A/G)GGCAG utr-variant-3-prime, nc-transcript-variant
rs2240946 -- 128,388,322(-) CGTGC(C/T)GCACT intron-variant, utr-variant-3-prime
rs2240947 -- 128,383,728(-) CAGGC(A/G)TAACA intron-variant
rs2240948 -- 128,383,434(-) TTCGG(A/G)GAGCC intron-variant
rs2240949 -- 128,382,625(-) AACTG(C/T)GCGTG intron-variant

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

Variant ID Type Subtype PubMed ID
dgv8294n71 CNV Loss 21882294
nsv831728 CNV Loss 17160897
dgv8295n71 CNV Loss 21882294
nsv893898 CNV Loss 21882294

Relevant External Links for URM1 Gene

HapMap Linkage Disequilibrium report
URM1

Disorders for URM1 Gene

No disorders were found for URM1 Gene.

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

Publications for URM1 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  2. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray S.J. … Dunham I. (Nature 2004) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  4. 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
  5. 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

Products for URM1 Gene

Sources for URM1 Gene

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