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UBD ubiquitin D [ Homo sapiens (human) ]

Gene ID: 10537, updated on 3-Nov-2024

Summary

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Official Symbol
UBDprovided by HGNC
Official Full Name
ubiquitin Dprovided by HGNC
Primary source
HGNC:HGNC:18795
See related
Ensembl:ENSG00000213886 MIM:606050; AllianceGenome:HGNC:18795
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FAT10; UBD-3
Summary
This gene encodes a protein which contains two ubiquitin-like domains and appears to have similar function to ubiquitin. Through covalent attachment, the encoded protein targets other proteins for 26S proteasome degradation. This protein has been implicated to function in many cellular processes, including caspase-dependent apoptosis, formation of aggresomes, mitotic regulation, and dendritic cell maturation. Upregulation of this gene may promote inflammation in chronic kidney disease and has been observed in many cancer types. [provided by RefSeq, Aug 2017]
Expression
Biased expression in lymph node (RPKM 113.8), appendix (RPKM 64.9) and 10 other tissues See more
Orthologs
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Genomic context

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See UBD in Genome Data Viewer
Location:
6p22.1
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (29555515..29559732, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (29430199..29434416, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (29523292..29527509, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1015 Neighboring gene G protein-coupled receptor 53, pseudogene Neighboring gene olfactory receptor family 2 subfamily I member 1 (gene/pseudogene) Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:29530647-29531846 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:29541846-29542105 Neighboring gene TMEM183A pseudogene 1 Neighboring gene olfactory receptor family 2 subfamily H member 5 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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?
  1. FAT10 induces immune suppression by upregulating PD-L1 expression in hepatocellular carcinoma.
    Title: FAT10 induces immune suppression by upregulating PD-L1 expression in hepatocellular carcinoma.
  2. Cytokines-activated nuclear IKKalpha-FAT10 pathway induces breast cancer tamoxifen-resistance.
    Title: Cytokines-activated nuclear IKKα-FAT10 pathway induces breast cancer tamoxifen-resistance.
  3. The ubiquitin-like modifier FAT10 is induced in MASLD and impairs the lipid-regulatory activity of PPARalpha.
    Title: The ubiquitin-like modifier FAT10 is induced in MASLD and impairs the lipid-regulatory activity of PPARα.
  4. UBDP1 pseudogene and UBD network competitively bind miR-6072 to promote glioma progression.
    Title: UBDP1 pseudogene and UBD network competitively bind miR‑6072 to promote glioma progression.
  5. FAT10 differentially stabilizes MYPT2 isoforms.
    Title: FAT10 differentially stabilizes MYPT2 isoforms.
  6. Tumor necrosis factor mediates USE1-independent FAT10ylation under inflammatory conditions.
    Title: Tumor necrosis factor mediates USE1-independent FAT10ylation under inflammatory conditions.
  7. FAT10 and NUB1L cooperate to activate the 26S proteasome.
    Title: FAT10 and NUB1L cooperate to activate the 26S proteasome.
  8. FAT10 Silencing Prevents Liver Fibrosis through Regulating SIRT1 Expression in Hepatic Stellate Cells.
    Title: FAT10 Silencing Prevents Liver Fibrosis through Regulating SIRT1 Expression in Hepatic Stellate Cells.
  9. Ubiquitin D promotes the progression of rheumatoid arthritis via activation of the p38 MAPK pathway.
    Title: Ubiquitin D promotes the progression of rheumatoid arthritis via activation of the p38 MAPK pathway.
  10. Recombinant Human Proteoglycan 4 (rhPRG4) Downregulates TNFalpha-Stimulated NFkappaB Activity and FAT10 Expression in Human Corneal Epithelial Cells.
    Title: Recombinant Human Proteoglycan 4 (rhPRG4) Downregulates TNFα-Stimulated NFκB Activity and FAT10 Expression in Human Corneal Epithelial Cells.
Submit: New GeneRIF Correction See all GeneRIFs (89)

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

EBI GWAS Catalog

Description
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction Pubs
HIV-1 LAI infection downregulates UBD (FAT10) and IFI6 mRNA levels in HeLa cells, which results from IFNG signaling inhibition PubMed

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev is modified by polyubiquitination at Lys-33 and Lys-115; Lys-33 is the most efficient residue for branching of ubiquitin chains PubMed
Tat tat HIV-1 Tat is ubiquitinated on Lys71 by Hdm2 in conjunction with ubiquitin-activating enzyme E1 and ubiquitin-conjugating enzyme E2D 1 (UbcH5) PubMed
Vpr vpr HIV-1 Vpr and FAT10 co-localize to mitochondria with marker protein Cox4 PubMed
vpr HIV-1 Vpr upregulates FAT10 expression and that Vpr-mediated upregulation of FAT10 enhances Vpr-induced apoptosis PubMed
capsid gag Monoubiquitinated forms of the HIV-1 matrix (MA), capsid (CA), and nucleocapsid (NC) proteins are detected in mature virus particles PubMed
matrix gag Monoubiquitinated forms of the HIV-1 matrix (MA), capsid (CA), and nucleocapsid (NC) proteins are detected in mature virus particles PubMed
nucleocapsid gag Monoubiquitinated forms of the HIV-1 matrix (MA), capsid (CA), and nucleocapsid (NC) proteins are detected in mature virus particles PubMed
p1 gag HIV-1 p1 is mono- or di-ubiquitinated at levels comparable to those of the other HIV-2 Gag domains MA, CA, NC, and p6; cumulative replacement of all lysine residues in NC and p1 or in NC and p6 results in an accumulation of late budding structures PubMed
p6 gag Ubiquitination of HIV-1 p6-Gag may be important for proper virus release from cells PubMed
gag The L domain (P(T/S)APP; amino acids 7-11) of HIV-1 p6-Gag interacts with a ubiquitin ligase complex resulting in the monoubiquitination of p6 PubMed

Go to the HIV-1, Human Interaction Database

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 proteasome binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables proteasome binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in aggresome assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in myeloid dendritic cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of canonical NF-kappaB signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of canonical NF-kappaB signal transduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein modification by small protein conjugation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proteolysis NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of mitotic cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to tumor necrosis factor IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to tumor necrosis factor IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in response to type II interferon IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to type II interferon IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in aggresome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in fibrillar center IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
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 D
Names
diubiquitin
ubiquitin-like protein FAT10

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_006398.4 → NP_006389.2  ubiquitin D

    See identical proteins and their annotated locations for NP_006389.2

    Status: REVIEWED

    Source sequence(s)
    AA878968, AL645936, CB111380, DB181897
    Consensus CDS
    CCDS4662.1
    UniProtKB/Swiss-Prot
    B0UZT6, O15205, Q5STL2, Q5SUK2, Q96EC7
    UniProtKB/TrEMBL
    A0A1U9X8S5, A0A1U9X8S6, A0A1U9X8S9
    Related
    ENSP00000366249.4, ENST00000377050.5
    Conserved Domains (2) summary
    smart00213
    Location:8 → 79
    UBQ; Ubiquitin homologues
    cl00155
    Location:104 → 165
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    29555515..29559732 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    821210..825428 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    1041996..1046213 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    821058..825275 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    820674..824892 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    820919..825136 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    821014..825232 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    29430199..29434416 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O15205.2 GenPept UniProtKB/Swiss-Prot:O15205

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