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Aliases for UBD Gene

Aliases for UBD Gene

  • Ubiquitin D 2 3 5
  • Ubiquitin-Like Protein FAT10 3 4
  • Diubiquitin 3 4
  • FAT10 3 4
  • GABBR1 3
  • UBD-3 3

External Ids for UBD Gene

Previous GeneCards Identifiers for UBD Gene

  • GC06M029580
  • GC06M029294
  • GC06M029632
  • GC06M029633
  • GC06M029634
  • GC06Mc29667
  • GC06M029330

Summaries for UBD Gene

Entrez Gene Summary for UBD Gene

  • 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]

GeneCards Summary for UBD Gene

UBD (Ubiquitin D) is a Protein Coding gene. Diseases associated with UBD include Kidney Disease and Hepatocellular Carcinoma. Among its related pathways are NF-KappaB Family Pathway and fMLP Pathway. GO annotations related to this gene include proteasome binding. An important paralog of this gene is UBC.

UniProtKB/Swiss-Prot for UBD Gene

  • Ubiquitin-like protein modifier which can be covalently attached to target protein and subsequently leads to their degradation by the 26S proteasome, in a NUB1-dependent manner. Probably functions as a survival factor. Conjugation ability activated by UBA6. Promotes the expression of the proteasome subunit beta type-9 (PSMB9/LMP2). Regulates TNF-alpha-induced and LPS-mediated activation of the central mediator of innate immunity NF-kappa-B by promoting TNF-alpha-mediated proteasomal degradation of ubiquitinated-I-kappa-B-alpha. Required for TNF-alpha-induced p65 nuclear translocation in renal tubular epithelial cells (RTECs). May be involved in dendritic cell (DC) maturation, the process by which immature dendritic cells differentiate into fully competent antigen-presenting cells that initiate T-cell responses. Mediates mitotic non-disjunction and chromosome instability, in long-term in vitro culture and cancers, by abbreviating mitotic phase and impairing the kinetochore localization of MAD2L1 during the prometaphase stage of the cell cycle. May be involved in the formation of aggresomes when proteasome is saturated or impaired. Mediates apoptosis in a caspase-dependent manner, especially in renal epithelium and tubular cells during renal diseases such as polycystic kidney disease and Human immunodeficiency virus (HIV)-associated nephropathy (HIVAN).

Gene Wiki entry for UBD Gene

Additional gene information for UBD Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UBD Gene

Genomics for UBD Gene

Regulatory Elements for UBD Gene

Enhancers for UBD Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H029477 0.6 FANTOM5 10.5 +81.8 81828 0 GATA2 E2F5 USF2 FOXJ2 MAS1L OR12D3 OR5V1 UBD LINC01015 OR2H2 OR14J1 MAS1LP1
GH06H029552 1 FANTOM5 ENCODE 4.6 +7.2 7178 0 ATF1 FEZF1 ZBTB40 RFX5 RFXANK PRDM10 FOS CREM STAT1 OVOL3 IFITM4P UBD LOC105375009 HLA-F HLA-A OR2I1P
GH06H029553 1.1 Ensembl ENCODE 0.4 +6.2 6245 0 ZSCAN5A CTCF MXI1 ZNF777 ATF1 ZIC2 RFX5 HIC1 ZNF121 ZFHX2 ZFP57 LINC01015 ENSG00000237669 HLA-J HLA-K LOC105375009 OR2I1P UBD
GH06H029559 0.6 ENCODE 0.7 +0.2 177 0 SOX13 TBP SAP130 TAF1 RAD21 RELA POLR2A HNF4A IKZF2 CREM UBD OR2I1P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around UBD on UCSC Golden Path with GeneCards custom track

Genomic Location for UBD Gene

Chromosome:
6
Start:
29,555,515 bp from pter
End:
29,559,925 bp from pter
Size:
4,411 bases
Orientation:
Minus strand

Genomic View for UBD Gene

Genes around UBD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UBD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UBD Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for UBD Gene

  • Protein details for UBD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15205-UBD_HUMAN
    Recommended name:
    Ubiquitin D
    Protein Accession:
    O15205
    Secondary Accessions:
    • B0UZT6
    • Q5STL2
    • Q5SUK2
    • Q96EC7

    Protein attributes for UBD Gene

    Size:
    165 amino acids
    Molecular mass:
    18473 Da
    Quaternary structure:
    • Interact directly with the 26S proteasome. The interaction with NUB1 via the N-terminal ubiquitin domain facilitates the linking of UBD-conjugated target protein to the proteasome complex and accelerates its own degradation and that of its conjugates. Interacts (via ubiquitin-like 1 domain) with the spindle checkpoint protein MAD2L1 during mitosis. Present in aggresomes of proteasome inhibited cells. Interacts with HDAC6 under proteasome impairment conditions. Forms a thioester with UBA6 in cells stimulated with tumor necrosis factor-alpha (TNFa) and interferon-gamma (IFNg). Interacts with SQSTM1 and TP53/p53 (PubMed:25422469).
    Miscellaneous:
    • Common types of chronic kidney disease are associated with tubulointerstitial up-regulation of FAT10. FAT10 may mediate NF-kappa-B activation and may promote tubulointerstitial inflammation in chronic kidney diseases.

    Three dimensional structures from OCA and Proteopedia for UBD Gene

neXtProt entry for UBD Gene

Post-translational modifications for UBD Gene

Other Protein References for UBD Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for UBD Gene

Domains & Families for UBD Gene

Gene Families for UBD Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for UBD Gene

Suggested Antigen Peptide Sequences for UBD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with UBD: view

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

Function for UBD Gene

Molecular function for UBD Gene

UniProtKB/Swiss-Prot Function:
Ubiquitin-like protein modifier which can be covalently attached to target protein and subsequently leads to their degradation by the 26S proteasome, in a NUB1-dependent manner. Probably functions as a survival factor. Conjugation ability activated by UBA6. Promotes the expression of the proteasome subunit beta type-9 (PSMB9/LMP2). Regulates TNF-alpha-induced and LPS-mediated activation of the central mediator of innate immunity NF-kappa-B by promoting TNF-alpha-mediated proteasomal degradation of ubiquitinated-I-kappa-B-alpha. Required for TNF-alpha-induced p65 nuclear translocation in renal tubular epithelial cells (RTECs). May be involved in dendritic cell (DC) maturation, the process by which immature dendritic cells differentiate into fully competent antigen-presenting cells that initiate T-cell responses. Mediates mitotic non-disjunction and chromosome instability, in long-term in vitro culture and cancers, by abbreviating mitotic phase and impairing the kinetochore localization of MAD2L1 during the prometaphase stage of the cell cycle. May be involved in the formation of aggresomes when proteasome is saturated or impaired. Mediates apoptosis in a caspase-dependent manner, especially in renal epithelium and tubular cells during renal diseases such as polycystic kidney disease and Human immunodeficiency virus (HIV)-associated nephropathy (HIVAN).
UniProtKB/Swiss-Prot Induction:
Rapidly degraded by the proteasome. Cell-cycle regulation with highest expression during the S-phase (at protein level). Induced during dendritic cell maturation. Negatively regulated by p53/TP53. High levels in various gastrointestinal and gynecological cancer cells. Induced in RTECs in common renal diseases including diabetic nephropathy (DN), IgA nephropathy (IgAN), and hypertensive nephrosclerosis (HN), as well as in hepatocellular carcinoma (HCC) and during HIVAN. Inducible by the proinflammatory cytokines IFNG/IFN-gamma and TNF in cancers of liver and colon. Repressed by NUB1 (at protein level).

Phenotypes From GWAS Catalog for UBD Gene

Gene Ontology (GO) - Molecular Function for UBD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10200259
GO:0070628 proteasome binding IDA 16707496
genes like me logo Genes that share ontologies with UBD: view
genes like me logo Genes that share phenotypes with UBD: view

Animal Models for UBD Gene

MGI Knock Outs for UBD:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for UBD
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for UBD Gene

Localization for UBD Gene

Subcellular locations from UniProtKB/Swiss-Prot for UBD Gene

Nucleus. Cytoplasm. Note=Accumulates in aggresomes under proteasome inhibition conditions.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for UBD gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
lysosome 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Nucleoli fibrillar center (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for UBD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IDA,IEA 12730673
GO:0005737 cytoplasm ISS --
GO:0005829 cytosol TAS --
GO:0016235 aggresome IDA 19033385
genes like me logo Genes that share ontologies with UBD: view

Pathways & Interactions for UBD Gene

genes like me logo Genes that share pathways with UBD: view

Pathways by source for UBD Gene

Gene Ontology (GO) - Biological Process for UBD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis NAS 9368598
GO:0006511 ubiquitin-dependent protein catabolic process IEA,IDA 17889673
GO:0016567 protein ubiquitination IDA,IEA 15831455
GO:0032446 protein modification by small protein conjugation NAS 9368598
GO:0034341 response to interferon-gamma IEP 17889673
genes like me logo Genes that share ontologies with UBD: view

No data available for SIGNOR curated interactions for UBD Gene

Drugs & Compounds for UBD Gene

No Compound Related Data Available

Transcripts for UBD Gene

mRNA/cDNA for UBD Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(255) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for UBD Gene

Ubiquitin D:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for UBD
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for UBD Gene

No ASD Table

Relevant External Links for UBD Gene

GeneLoc Exon Structure for
UBD
ECgene alternative splicing isoforms for
UBD

Expression for UBD Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for UBD Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for UBD Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x6.2), Liver (x5.5), Pancreas (x4.9), and Minor Salivary Gland (x4.8).

Protein differential expression in normal tissues from HIPED for UBD Gene

This gene is overexpressed in Monocytes (32.0), Ovary (16.7), Liver (12.8), and Islet of Langerhans (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for UBD Gene



Protein tissue co-expression partners for UBD Gene

NURSA nuclear receptor signaling pathways regulating expression of UBD Gene:

UBD

SOURCE GeneReport for Unigene cluster for UBD Gene:

Hs.44532

mRNA Expression by UniProt/SwissProt for UBD Gene:

O15205-UBD_HUMAN
Tissue specificity: Constitutively expressed in mature dendritic cells and B-cells. Mostly expressed in the reticuloendothelial system (e.g. thymus, spleen), the gastrointestinal system, kidney, lung and prostate gland.

Evidence on tissue expression from TISSUES for UBD Gene

  • Spleen(4.5)
genes like me logo Genes that share expression patterns with UBD: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for UBD Gene

Orthologs for UBD Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for UBD Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia UBD 33 34
  • 98.59 (n)
dog
(Canis familiaris)
Mammalia LOC100687262 33
  • 79.67 (n)
UBD 34
  • 50 (a)
OneToOne
cow
(Bos Taurus)
Mammalia UBD 33 34
  • 77.64 (n)
-- 34
  • 69 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Ubd 33
  • 76.04 (n)
mouse
(Mus musculus)
Mammalia Ubd 33 16 34
  • 74.28 (n)
oppossum
(Monodelphis domestica)
Mammalia UBD 34
  • 55 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia UBD 34
  • 48 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia UBD 34
  • 42 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Ubi-p63E 34
  • 8 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBI4 34
  • 14 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 8 (a)
OneToOne
Species where no ortholog for UBD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for UBD Gene

ENSEMBL:
Gene Tree for UBD (if available)
TreeFam:
Gene Tree for UBD (if available)

Paralogs for UBD Gene

Paralogs for UBD Gene

(5) SIMAP similar genes for UBD Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with UBD: view

Variants for UBD Gene

Sequence variations from dbSNP and Humsavar for UBD Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000246981 -- 29,558,868(+) CATGA(A/G)GCCAA intron-variant
rs1000612349 -- 29,557,520(+) CCATG(A/G)GTGGT intron-variant
rs1000622253 -- 29,557,873(+) ATGTA(A/G)TTAGT intron-variant
rs1000923103 -- 29,558,332(+) CCAAT(A/C)AGGTA intron-variant
rs1000958775 -- 29,558,580(+) CTTTC(A/G)CTTGC intron-variant

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

Variant ID Type Subtype PubMed ID
esv2759411 CNV gain+loss 17122850
nsv1074389 CNV deletion 25765185
nsv1122126 CNV deletion 24896259
nsv1145096 CNV deletion 24896259
nsv5239 CNV deletion 18451855

Variation tolerance for UBD Gene

Residual Variation Intolerance Score: 90.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.26; 90.58% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for UBD Gene

Human Gene Mutation Database (HGMD)
UBD
SNPedia medical, phenotypic, and genealogical associations of SNPs for
UBD

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UBD Gene

Disorders for UBD Gene

MalaCards: The human disease database

(2) MalaCards diseases for UBD Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
kidney disease
  • nephropathy
hepatocellular carcinoma
  • hepatocellular carcinoma, somatic
- elite association - COSMIC cancer census association via MalaCards
Search UBD in MalaCards View complete list of genes associated with diseases

Relevant External Links for UBD

Genetic Association Database (GAD)
UBD
Human Genome Epidemiology (HuGE) Navigator
UBD
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
UBD
genes like me logo Genes that share disorders with UBD: view

No data available for UniProtKB/Swiss-Prot and Genatlas for UBD Gene

Publications for UBD Gene

  1. A regulatory single nucleotide polymorphism in the ubiquitin D gene associated with celiac disease. (PMID: 19808075) Castellanos-Rubio A … Bilbao JR (Human immunology 2010) 3 22 45 60
  2. The ubiquitin-like modifier FAT10 interacts with HDAC6 and localizes to aggresomes under proteasome inhibition. (PMID: 19033385) Kalveram B … Groettrup M (Journal of cell science 2008) 3 4 22 60
  3. SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians. (PMID: 17971048) Burfoot RK … Rubio JP (Tissue antigens 2008) 3 22 45 60
  4. Role of ubiquitin-like protein FAT10 in epithelial apoptosis in renal disease. (PMID: 16495380) Ross MJ … Klotman PE (Journal of the American Society of Nephrology : JASN 2006) 3 4 22 60
  5. FAT10 plays a role in the regulation of chromosomal stability. (PMID: 16495226) Ren J … Lee CG (The Journal of biological chemistry 2006) 3 4 22 60

Products for UBD Gene

Sources for UBD Gene

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