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UBXN1 UBX domain protein 1 [ Homo sapiens (human) ]

Gene ID: 51035, updated on 10-Dec-2024

Summary

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Official Symbol
UBXN1provided by HGNC
Official Full Name
UBX domain protein 1provided by HGNC
Primary source
HGNC:HGNC:18402
See related
Ensembl:ENSG00000162191 MIM:616378; AllianceGenome:HGNC:18402
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
2B28; SAKS1; UBXD10
Summary
Enables several functions, including enzyme binding activity; polyubiquitin modification-dependent protein binding activity; and proteasome regulatory particle binding activity. Involved in negative regulation of protein metabolic process. Located in cytosol; endoplasmic reticulum; and nucleoplasm. Part of VCP-NPL4-UFD1 AAA ATPase complex. [provided by Alliance of Genome Resources, Dec 2024]
Expression
Ubiquitous expression in ovary (RPKM 47.6), fat (RPKM 40.5) and 25 other tissues See more
Orthologs
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Genomic context

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See UBXN1 in Genome Data Viewer
Location:
11q12.3
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (62676500..62679073, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (62665920..62668532, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (62443972..62446545, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4837 Neighboring gene LBH domain containing 1 Neighboring gene small nucleolar RNA, H/ACA box 57 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:62437829-62438570 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:62438571-62439310 Neighboring gene citrate synthase lysine methyltransferase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:62439311-62440052 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4839 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:62455030-62455530 Neighboring gene HNRNPUL2-BSCL2 readthrough (NMD candidate) Neighboring gene LRRN4 C-terminal like Neighboring gene BSCL2 lipid droplet biogenesis associated, seipin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:62465704-62466296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:62473607-62474280 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:62475600-62476799 Neighboring gene G protein subunit gamma 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. UBXN1 promotes liver tumorigenesis by regulating mitochondrial homeostasis. Jiao K, et al. J Transl Med, 2024 May 21. PMID 38773518, Free PMC Article
  2. VCP/p97 cofactor UBXN1/SAKS1 regulates mitophagy by modulating MFN2 removal from mitochondria. Mengus C, et al. Autophagy, 2022 Jan. PMID 33966597, Free PMC Article
  3. Diubiquitin-Based NMR Analysis: Interactions Between Lys6-Linked diUb and UBA Domain of UBXN1. Shahul Hameed D, et al. Front Chem, 2019. PMID 32039147, Free PMC Article
  4. SUB1 promotes colorectal cancer metastasis by activating NF-κB signaling via UBR5-mediated ubiquitination of UBXN1. Wang H, et al. Sci China Life Sci, 2024 Jun. PMID 38240906
  5. YTHDF2 facilitates UBXN1 mRNA decay by recognizing METTL3-mediated m(6)A modification to activate NF-κB and promote the malignant progression of glioma. Chai RC, et al. J Hematol Oncol, 2021 Jul 10. PMID 34246306, Free PMC Article

See all (94) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SUB1 promotes colorectal cancer metastasis by activating NF-kappaB signaling via UBR5-mediated ubiquitination of UBXN1.
    Title: SUB1 promotes colorectal cancer metastasis by activating NF-κB signaling via UBR5-mediated ubiquitination of UBXN1.
  2. UBXN1 promotes liver tumorigenesis by regulating mitochondrial homeostasis.
    Title: UBXN1 promotes liver tumorigenesis by regulating mitochondrial homeostasis.
  3. YTHDF2 facilitates UBXN1 mRNA decay by recognizing METTL3-mediated m(6)A modification to activate NF-kappaB and promote the malignant progression of glioma.
    Title: YTHDF2 facilitates UBXN1 mRNA decay by recognizing METTL3-mediated m(6)A modification to activate NF-κB and promote the malignant progression of glioma.
  4. LncRNA PRADX-mediated recruitment of PRC2/DDX5 complex suppresses UBXN1 expression and activates NF-kappaB activity, promoting tumorigenesis.
    Title: LncRNA PRADX-mediated recruitment of PRC2/DDX5 complex suppresses UBXN1 expression and activates NF-κB activity, promoting tumorigenesis.
  5. Our results identify how VCP is specifically targeted to ubiquitylated substrates in the BAG6 triage pathway and suggest that the degradation of ubiquitylated clients by the proteasome is reliant on the association of UBXN1 with ubiquitylated substrates and the catalytic activity of VCP.
    Title: The VCP-UBXN1 Complex Mediates Triage of Ubiquitylated Cytosolic Proteins Bound to the BAG6 Complex.
  6. The ability of UBXN1 and other family members to negatively regulate the NFkappaB pathway may be important for dampening the host immune response in disease processes and also re-activating quiescent HIV from latent viral reservoirs in chronically infected individuals
    Title: Multiple UBXN family members inhibit retrovirus and lentivirus production and canonical NFκΒ signaling by stabilizing IκBα.
  7. p47 promotes, whereas SASK1 delays the degradation of a single ERAD substrate, alpha-TCR. Additionally, we found that SAKS1 selectively inhibits the degradation of ERAD substrates without affecting cytosolic proteasomal substrates.
    Title: The opposite role of two UBA-UBX containing proteins, p47 and SAKS1 in the degradation of a single ERAD substrate, α-TCR.
  8. UBXN1 is a negative regulator of NF-kappaB signaling.
    Title: Ubiquitin-associated domain-containing ubiquitin regulatory X (UBX) protein UBXN1 is a negative regulator of nuclear factor κB (NF-κB) signaling.
  9. UBXN1 is induced and recruited to MAVS after virus infection, serving as a brake to prevent excessive RLR signaling, most likely at a late stage of infection.
    Title: UBXN1 interferes with Rig-I-like receptor-mediated antiviral immune response by targeting MAVS.
  10. SAKS1 inhibits protein degradation mediated by p97 complexes in the cytosol with a component of the mechanism being the ability to shield polyubiquitin chains from ubiquitin-processing factors.
    Title: The UBX protein SAKS1 negatively regulates endoplasmic reticulum-associated degradation and p97-dependent degradation.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables K48-linked polyubiquitin modification-dependent protein binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables K48-linked polyubiquitin modification-dependent protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables K6-linked polyubiquitin modification-dependent protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables polyubiquitin modification-dependent protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables proteasome regulatory particle binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin protein ligase binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of ERAD pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of protein K48-linked deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of protein K48-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of ubiquitin-specific protease activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of VCP-NPL4-UFD1 AAA ATPase complex IDA
Inferred from Direct Assay
more info
 PubMed 
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 cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm 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
UBX domain-containing protein 1
Names
SAPK substrate protein 1
UBA/UBX 33.3 kDa protein

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)

  1. NM_001286077.2 → NP_001273006.1  UBX domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001273006.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate exon structure in the 3' region, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC040129
    Consensus CDS
    CCDS66105.1
    UniProtKB/Swiss-Prot
    Q04323, Q9BV93, Q9BVV5
    UniProtKB/TrEMBL
    E9PJ81
    Related
    ENSP00000303991.5, ENST00000301935.10
    Conserved Domains (2) summary
    cd01772
    Location:210 → 293
    SAKS1_UBX; SAKS1-like UBX domain
    cd14302
    Location:5 → 45
    UBA_UBXN1; UBA domain found in UBX domain-containing protein 1 (UBXN1) and similar proteins

  2. NM_001286078.2 → NP_001273007.1  UBX domain-containing protein 1 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two alternate in-frame exons in the 5' region and contains an alternate exon structure in the 3' region, compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC040129, BI855821, BP329601
    Consensus CDS
    CCDS73307.1
    UniProtKB/TrEMBL
    A0A087WTZ5, B4E0P8
    Related
    ENSP00000478250.1, ENST00000616865.4
    Conserved Domains (2) summary
    cd01772
    Location:151 → 234
    SAKS1_UBX; SAKS1-like UBX domain
    cd14302
    Location:5 → 41
    UBA_UBXN1; UBA domain found in UBX domain-containing protein 1 (UBXN1) and similar proteins

  3. NM_015853.5 → NP_056937.2  UBX domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_056937.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    BC001372, BP329601
    Consensus CDS
    CCDS8029.1
    UniProtKB/TrEMBL
    E9PJ81
    Related
    ENSP00000294119.2, ENST00000294119.6
    Conserved Domains (2) summary
    cd14302
    Location:5 → 45
    UBA_UBXN1; UBA domain found in UBX domain-containing protein 1 (UBXN1) and similar proteins
    cl00155
    Location:210 → 283
    UBQ; Ubiquitin-like proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    62676500..62679073 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017017874.2 → XP_016873363.1  UBX domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q04323, Q9BV93, Q9BVV5
    UniProtKB/TrEMBL
    E9PJ81
    Related
    ENSP00000435625.1, ENST00000534176.1
    Conserved Domains (2) summary
    cd01772
    Location:210 → 293
    SAKS1_UBX; SAKS1-like UBX domain
    cd14302
    Location:5 → 45
    UBA_UBXN1; UBA domain found in UBX domain-containing protein 1 (UBXN1) and similar proteins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    62665920..62668532 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369044.1 → XP_054225019.1  UBX domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q04323, Q9BV93, Q9BVV5
    UniProtKB/TrEMBL
    E9PJ81
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q04323.2 GenPept UniProtKB/Swiss-Prot:Q04323

Gene LinkOut

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