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Aliases for YOD1 Gene

Aliases for YOD1 Gene

  • YOD1 Deubiquitinase 2 3
  • DUBA8 3 4 6
  • OTUD2 3 4 6
  • YOD1 OTU Deubiquinating Enzyme 1 Homolog ( Yeast) 2 3
  • OTU Domain-Containing Protein 2 3 4
  • HIV-1-Induced Protease 7 3 4
  • HsHIN7 3 4
  • DUBA-8 3 4
  • HIN-7 3 4
  • YOD1 OTU Deubiquinating Enzyme 1 Homolog (S. Cerevisiae) 2
  • Ubiquitin Thioesterase OTU1 3
  • OTU Domain Containing 2 3
  • EC 3.4.19.12 4
  • EC 3.1.2 63
  • PRO0907 3
  • HIN7 4

External Ids for YOD1 Gene

Previous GeneCards Identifiers for YOD1 Gene

  • GC01M203608
  • GC01M205284
  • GC01M207217
  • GC01M177914

Summaries for YOD1 Gene

Entrez Gene Summary for YOD1 Gene

  • Protein ubiquitination controls many intracellular processes, including cell cycle progression, transcriptional activation, and signal transduction. This dynamic process, involving ubiquitin conjugating enzymes and deubiquitinating enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are cysteine proteases that specifically cleave ubiquitin from ubiquitin-conjugated protein substrates. The protein encoded by this gene belongs to a DUB subfamily characterized by an ovarian tumor (OTU) domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

GeneCards Summary for YOD1 Gene

YOD1 (YOD1 Deubiquitinase) is a Protein Coding gene. Diseases associated with YOD1 include hiv-1. Among its related pathways are Protein processing in endoplasmic reticulum. GO annotations related to this gene include ubiquitin-specific protease activity.

UniProtKB/Swiss-Prot for YOD1 Gene

  • Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on the associated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates may present a steric impediment to the threading process when the substrate is transferred to the VCP pore and threaded through VCPs axial channel. Mediates deubiquitination of Lys-27-, Lys-29- and Lys-33-linked polyubiquitin chains. Also able to hydrolyze Lys-11-linked ubiquitin chains. Cleaves both polyubiquitin and di-ubiquitin.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for YOD1 Gene

Genomics for YOD1 Gene

Regulatory Elements for YOD1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for YOD1 Gene

Start:
207,043,849 bp from pter
End:
207,052,980 bp from pter
Size:
9,132 bases
Orientation:
Minus strand

Genomic View for YOD1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for YOD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YOD1 Gene

Proteins for YOD1 Gene

  • Protein details for YOD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VVQ6-OTU1_HUMAN
    Recommended name:
    Ubiquitin thioesterase OTU1
    Protein Accession:
    Q5VVQ6
    Secondary Accessions:
    • B2RNX3
    • Q5VVQ5
    • Q6ZRS6
    • Q86T63
    • Q9P1L8

    Protein attributes for YOD1 Gene

    Size:
    348 amino acids
    Molecular mass:
    38322 Da
    Quaternary structure:
    • Interacts with VCP; the interaction is direct. Interacts with FAF2/UBXD8. Interacts with DERL1; however interaction is dependent on the UBAX-like region, suggesting that it may be indirect.
    SequenceCaution:
    • Sequence=AAF71033.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305}; Sequence=EAW93510.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for YOD1 Gene

    Alternative splice isoforms for YOD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for YOD1 Gene

Proteomics data for YOD1 Gene at MOPED

Post-translational modifications for YOD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for YOD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains for YOD1 Gene

Gene Families for YOD1 Gene

HGNC:
  • OTUD :OTU domain containing

Protein Domains for YOD1 Gene

Suggested Antigen Peptide Sequences for YOD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q5VVQ6

UniProtKB/Swiss-Prot:

OTU1_HUMAN :
  • Q5VVQ6
Domain:
  • The UBAX-like region mediates the interaction with VCP. According to PubMed:19818707, it corresponds to a UBX domain, which is a hallmark for VCP-associated proteins. However, no canonical UBX is detected by prediction tools such as Pfam or PROSITE
  • The C2H2-type zinc finger mediates specificity for Lys-27-, Lys-29- and Lys-33-linked polyubiquitin chains but not for Lys-11-linked ubiquitin chains. Selectivity for Lys-11-linked ubiquitin chains is provided by recognition of the sequence surrounding Lys-11 in ubiquitin. The S2 site region provides specificity for longer Lys-11-linked ubiquitin chains (PubMed:23827681).
  • Contains 1 OTU domain.
Similarity:
  • Contains 1 C2H2-type zinc finger.
genes like me logo Genes that share domains with YOD1: view

Function for YOD1 Gene

Molecular function for YOD1 Gene

UniProtKB/Swiss-Prot CatalyticActivity: Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
UniProtKB/Swiss-Prot Function: Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on the associated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates may present a steric impediment to the threading process when the substrate is transferred to the VCP pore and threaded through VCPs axial channel. Mediates deubiquitination of Lys-27-, Lys-29- and Lys-33-linked polyubiquitin chains. Also able to hydrolyze Lys-11-linked ubiquitin chains. Cleaves both polyubiquitin and di-ubiquitin.

Enzyme Numbers (IUBMB) for YOD1 Gene

Gene Ontology (GO) - Molecular Function for YOD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004843 ubiquitin-specific protease activity IDA 19818707
GO:0005515 protein binding IPI 19818707
GO:0046872 metal ion binding IEA --
GO:1990380 Lys48-specific deubiquitinase activity IDA 21376232
genes like me logo Genes that share ontologies with YOD1: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for YOD1

In Situ Assay Products

Flow Cytometry Products

No data available for Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for YOD1 Gene

Localization for YOD1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for YOD1 Gene COMPARTMENTS Subcellular localization image for YOD1 gene
Compartment Confidence
cytosol 3
nucleus 3
plasma membrane 3
endoplasmic reticulum 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for YOD1 Gene

Pathways for YOD1 Gene

genes like me logo Genes that share pathways with YOD1: view

Pathways by source for YOD1 Gene

1 KEGG pathway for YOD1 Gene

Gene Ontology (GO) - Biological Process for YOD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006520 cellular amino acid metabolic process --
GO:0030433 ER-associated ubiquitin-dependent protein catabolic process IMP 19818707
GO:0030968 endoplasmic reticulum unfolded protein response IMP 19818707
GO:0035523 protein K29-linked deubiquitination IDA 23827681
GO:0035871 protein K11-linked deubiquitination IDA 23827681
genes like me logo Genes that share ontologies with YOD1: view

Transcripts for YOD1 Gene

mRNA/cDNA for YOD1 Gene

Unigene Clusters for YOD1 Gene

YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for YOD1

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for YOD1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for YOD1 Gene

No ASD Table

Relevant External Links for YOD1 Gene

GeneLoc Exon Structure for
YOD1
ECgene alternative splicing isoforms for
YOD1

Expression for YOD1 Gene

mRNA expression in normal human tissues for YOD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for YOD1 Gene

This gene is overexpressed in Esophagus - Mucosa (6.7).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for YOD1 Gene

SOURCE GeneReport for Unigene cluster for YOD1 Gene Hs.567533

genes like me logo Genes that share expressions with YOD1: view

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for YOD1 Gene

Orthologs for YOD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for YOD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia YOD1 35
  • 99.43 (n)
  • 99.14 (a)
YOD1 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia YOD1 35
  • 91.38 (n)
  • 91.38 (a)
YOD1 36
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia YOD1 35
  • 90.24 (n)
  • 91.01 (a)
YOD1 36
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Yod1 35
  • 87.76 (n)
  • 88.63 (a)
Yod1 16
Yod1 36
  • 88 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia YOD1 36
  • 62 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia YOD1 36
  • 85 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Yod1 35
  • 89.66 (n)
  • 92.41 (a)
chicken
(Gallus gallus)
Aves YOD1 35
  • 69.66 (n)
  • 74.09 (a)
YOD1 36
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia YOD1 36
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia yod1 35
  • 65.24 (n)
  • 69.64 (a)
zebrafish
(Danio rerio)
Actinopterygii yod1 35
  • 65.89 (n)
  • 71.1 (a)
yod1 36
  • 71 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007001 35
  • 49.56 (n)
  • 46 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG4603 35
  • 51.22 (n)
  • 48.67 (a)
CG4603 36
  • 42 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABR233W 35
  • 44.84 (n)
  • 36.51 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes OTU1 35
  • 48.12 (n)
  • 37.66 (a)
OTU1 36
  • 31 (a)
OneToOne
OTU1 38
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D05599g 35
  • 47.06 (n)
  • 32.94 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G50670 35
  • 53.64 (n)
  • 48.73 (a)
rice
(Oryza sativa)
Liliopsida Os02g0164800 35
  • 56.21 (n)
  • 54.9 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU02353 35
  • 44.68 (n)
  • 36.52 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes otu1 35
  • 43.76 (n)
  • 34.71 (a)
Species with no ortholog for YOD1:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for YOD1 Gene

ENSEMBL:
Gene Tree for YOD1 (if available)
TreeFam:
Gene Tree for YOD1 (if available)

Paralogs for YOD1 Gene

No data available for Paralogs for YOD1 Gene

Variants for YOD1 Gene

Sequence variations from dbSNP and Humsavar for YOD1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs1044145 -- 207,044,014(-) GTAAT(A/G)CACTG utr-variant-3-prime
rs1385611 -- 207,048,064(-) GGGGG(A/G)ATTTA utr-variant-3-prime, nc-transcript-variant
rs2054779 -- 207,049,341(-) ACACA(C/G)ACAGT missense, reference, nc-transcript-variant
rs2054780 -- 207,048,267(-) AAAAC(A/G)TAGAA utr-variant-3-prime, nc-transcript-variant
rs2495255 -- 207,046,111(+) AAGAA(A/G)AGTAA utr-variant-3-prime, nc-transcript-variant

Structural Variations from Database of Genomic Variants (DGV) for YOD1 Gene

Variant ID Type Subtype PubMed ID
nsv832426 CNV Gain 17160897

Relevant External Links for YOD1 Gene

HapMap Linkage Disequilibrium report
YOD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for YOD1 Gene

Disorders for YOD1 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for YOD1 Gene including...

Search for YOD1 Gene in MalaCards »

Relevant External Links for YOD1

Genetic Association Database (GAD)
YOD1
genes like me logo Genes that share disorders with YOD1: view

No data available for UniProtKB/Swiss-Prot for YOD1 Gene

Publications for YOD1 Gene

  1. OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis. (PMID: 23827681) Mevissen T.E. … Komander D. (Cell 2013) 3 4
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  4. The otubain YOD1 is a deubiquitinating enzyme that associates with p97 to facilitate protein dislocation from the ER. (PMID: 19818707) Ernst R. … Schlieker C. (Mol. Cell 2009) 3 4
  5. Defining the human deubiquitinating enzyme interaction landscape. (PMID: 19615732) Sowa M.E. … Harper J.W. (Cell 2009) 3

Products for YOD1 Gene

Sources for YOD1 Gene

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