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

Summary

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, Apr 2022]
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

Location:: 9q34.11

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (128371319..128392016)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (140578420..140599118)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (131133598..131154295)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The emerging roles of ubiquitin-like protein Urm1 in eukaryotes.
Title: The emerging roles of ubiquitin-like protein Urm1 in eukaryotes.
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.
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.
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.
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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH78079 (e-PCR)
- UniSTS:11087

RH80307 (e-PCR)
- UniSTS:85124

RH41877 (e-PCR)
- UniSTS:32994

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)

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)
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 ...
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

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