Format

Send to:

Choose Destination

UBD ubiquitin D [ Homo sapiens (human) ]

Gene ID: 10537, updated on 5-Jul-2020

Summary

Official Symbol
UBDprovided by HGNC
Official Full Name
ubiquitin Dprovided by HGNC
Primary source
HGNC:HGNC:18795
See related
Ensembl:ENSG00000213886 MIM:606050
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; GABBR1
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

Genomic context

See UBD in Genome Data Viewer
Location:
6p22.1
Exon count:
2
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (29555515..29559732, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (29523389..29527702, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene G protein-coupled receptor 53, pseudogene Neighboring gene olfactory receptor family 2 subfamily I member 1 pseudogene Neighboring gene olfactory receptor family 2 subfamily H member 5 pseudogene Neighboring gene transmembrane protein 183A pseudogene 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
proteasome binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proteasome binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
aggresome assembly IDA
Inferred from Direct Assay
more info
PubMed 
myeloid dendritic cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of I-kappaB kinase/NF-kappaB signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of I-kappaB kinase/NF-kappaB signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
post-translational protein modification TAS
Traceable Author Statement
more info
 
protein modification by small protein conjugation NAS
Non-traceable Author Statement
more info
PubMed 
protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
proteolysis NAS
Non-traceable Author Statement
more info
PubMed 
regulation of mitotic cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to interferon-gamma IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to interferon-gamma IEP
Inferred from Expression Pattern
more info
PubMed 
response to tumor necrosis factor IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to tumor necrosis factor IEP
Inferred from Expression Pattern
more info
PubMed 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
aggresome IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
cytosol TAS
Traceable Author Statement
more info
 
fibrillar center IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
ubiquitin D
Names
diubiquitin
ubiquitin-like protein FAT10

NCBI Reference Sequences (RefSeq)

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_006398.4NP_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
    O15205
    UniProtKB/TrEMBL
    A0A1U9X8S6
    Related
    ENSP00000366249.4, ENST00000377050.5
    Conserved Domains (2) summary
    smart00213
    Location:879
    UBQ; Ubiquitin homologues
    cl00155
    Location:104165
    UBQ; Ubiquitin-like proteins

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

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

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

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

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

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

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

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

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

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

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

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

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

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