UFM1 ubiquitin fold modifier 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: UFM1provided by HGNC
Official Full Name: ubiquitin fold modifier 1provided by HGNC
Primary source: HGNC:HGNC:20597
See related: Ensembl:ENSG00000120686 MIM:610553; AllianceGenome:HGNC:20597
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: HLD14; BM-002; C13orf20
Summary: UFM1 is a ubiquitin-like protein that is conjugated to target proteins by E1-like activating enzyme UBA5 (UBE1DC1; MIM 610552) and E2-like conjugating enzyme UFC1 (MIM 610554) in a manner analogous to ubiquitylation (see UBE2M; MIM 603173) (Komatsu et al., 2004 [PubMed 15071506]).[supplied by OMIM, Dec 2008]
Expression: Ubiquitous expression in thyroid (RPKM 26.2), endometrium (RPKM 24.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q13.3

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (38349851..38363619)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (37569505..37583274)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (38923988..38937756)

Chromosome 13 - NC_000013.11 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 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?

Inhibition of UFM1 expression suppresses cancer progression and is linked to the dismal prognosis and immune infiltration in oral squamous cell carcinoma.
Title: Inhibition of UFM1 expression suppresses cancer progression and is linked to the dismal prognosis and immune infiltration in oral squamous cell carcinoma.
Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control.
Title: Mechanistic insights into the roles of the UFM1 E3 ligase complex in ufmylation and ribosome-associated protein quality control.
Modification of PLAC8 by UFM1 affects tumorous proliferation and immune response by impacting PD-L1 levels in triple-negative breast cancer.
Title: Modification of PLAC8 by UFM1 affects tumorous proliferation and immune response by impacting PD-L1 levels in triple-negative breast cancer.
Emerging role of protein modification by UFM1 in cancer.
Title: Emerging role of protein modification by UFM1 in cancer.
Human UFSP1 is an active protease that regulates UFM1 maturation and UFMylation.
Title: Human UFSP1 is an active protease that regulates UFM1 maturation and UFMylation.
Modification of ERalpha by UFM1 Increases Its Stability and Transactivity for Breast Cancer Development.
Title: Modification of ERα by UFM1 Increases Its Stability and Transactivity for Breast Cancer Development.
Structure and dynamics of UBA5-UFM1 complex formation showing new insights in the UBA5 activation mechanism.
Title: Structure and dynamics of UBA5-UFM1 complex formation showing new insights in the UBA5 activation mechanism.
Structural basis for UFM1 transfer from UBA5 to UFC1.
Title: Structural basis for UFM1 transfer from UBA5 to UFC1.
Decrypting UFMylation: How Proteins Are Modified with UFM1.
Title: Decrypting UFMylation: How Proteins Are Modified with UFM1.
A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1.
Title: A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1.

Submit: New GeneRIF Correction See all GeneRIFs (35)

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

Associated conditions

Description	Tests
Leukodystrophy, hypomyelinating, 14 MedGen: C4693535 OMIM: 617899 GeneReviews: Not available	Compare labs

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

NIB712 (e-PCR)
- UniSTS:29502

STS-Z70222 (e-PCR)
- UniSTS:27046

RH26802 (e-PCR)
- UniSTS:88004

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of protein import into nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein K69-linked ufmylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ufmylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ufmylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of intracellular estrogen receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in response to endoplasmic reticulum stress	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within response to endoplasmic reticulum stress	IDA Inferred from Direct Assay more info	PubMed
involved_in response to endoplasmic reticulum stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in reticulophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in reticulophagy	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: ubiquitin-fold modifier 1

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_001286703.2 → NP_001273632.1 ubiquitin-fold modifier 1 isoform 2

See identical proteins and their annotated locations for NP_001273632.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AL356863

UniProtKB/TrEMBL

H0Y614

Conserved Domains (1) summary

cl00155
Location:2 → 81

UBQ; Ubiquitin-like proteins
NM_001286704.2 → NP_001273633.1 ubiquitin-fold modifier 1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region and initiates translation from an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is longer than isoform 1.

Source sequence(s)

AL356863

Consensus CDS

CCDS66533.1

UniProtKB/Swiss-Prot

P61960

Related

ENSP00000368970.1, ENST00000379649.5

Conserved Domains (1) summary

cl28922
Location:39 → 96

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
NM_001286705.2 → NP_001273634.1 ubiquitin-fold modifier 1 isoform 4

See identical proteins and their annotated locations for NP_001273634.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) contains an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is shorter than isoform 1. Variants 4 and 5 encode the same isoform (4).

Source sequence(s)

AL356863

UniProtKB/Swiss-Prot

P61960

Conserved Domains (1) summary

cl28922
Location:4 → 64

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
NM_001286706.2 → NP_001273635.1 ubiquitin-fold modifier 1 isoform 4

See identical proteins and their annotated locations for NP_001273635.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is shorter than isoform 1. Variants 4 and 5 encode the same isoform (4).

Source sequence(s)

AL356863

UniProtKB/Swiss-Prot

P61960

Conserved Domains (1) summary

cl28922
Location:4 → 64

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
NM_016617.4 → NP_057701.1 ubiquitin-fold modifier 1 isoform 1

See identical proteins and their annotated locations for NP_057701.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AL356863

Consensus CDS

CCDS9366.1

UniProtKB/Swiss-Prot

P61960, Q14346, Q5VXS0, Q6IAG6, Q9CPX2, Q9NZF2

UniProtKB/TrEMBL

H0Y614

Related

ENSP00000239878.4, ENST00000239878.9

Conserved Domains (1) summary

cd01766
Location:4 → 78

Ubl_UFM1; ubiquitin-like (Ubl) domain found in ubiquitin fold modifier 1 (UFM1)

RNA

NR_104584.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (6) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL356863
NR_104585.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (7) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the predicted ORF does not meet RefSeq quality criteria.

Source sequence(s)

AL356863