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Aliases for YOD1 Gene

Aliases for YOD1 Gene

  • YOD1 Deubiquitinase 2 3 5
  • 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
  • DUBA8 3 4
  • HIN-7 3 4
  • OTUD2 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 61
  • 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 Brown-Sequard Syndrome. Among its related pathways are Ovarian tumor domain proteases and Metabolism of proteins. GO annotations related to this gene include thiol-dependent ubiquitin-specific protease activity and Lys48-specific deubiquitinase 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

Enhancers for YOD1 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
GH01F207073 1 ENCODE 12.8 -21.0 -21001 1.6 HLF ZNF512 REST PFKFB2 YOD1 C1orf116 C4BPB
GH01F207407 1.2 FANTOM5 Ensembl 1.6 -354.7 -354668 1.6 TBP HDAC1 PKNOX1 DDX20 TAL1 RAD21 YY1 NCOR1 SMC3 RCOR1 CR1 CD55 CR2 C4BPB C4BPA CD46 YOD1 ENSG00000283044 ENSG00000274245
GH01F207048 0.8 Ensembl ENCODE 0.8 +0.2 190 9.7 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A YBX1 DMAP1 ZNF2 YY1 CDCA4P4 MAPKAPK2 C1orf116 CR1 RPL7AP20 PFKFB2 YOD1
GH01F207058 0.4 Ensembl 0.4 -5.8 -5768 0.2 FOSL1 YOD1 C4BPB
GH01F207059 0.6 Ensembl 0.4 -6.6 -6568 1.0 HDAC1 CREB3L1 ZNF766 GATA2 FOS ZBTB11 USF2 ZEB2 MEF2D RAD51 YOD1 C4BPB
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around YOD1 on UCSC Golden Path with GeneCards custom track

Promoters for YOD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001753984 33 1801 HDGF PKNOX1 CREB3L1 ARID4B SIN3A YBX1 ZNF2 YY1 ZNF143 KLF13
ENSR00001753983 1233 201 MXI1 ZNF740 ZFP64 ZFP37 BACH1 HDAC8 ZBTB20

Genomic Location for YOD1 Gene

Chromosome:
1
Start:
207,043,849 bp from pter
End:
207,053,133 bp from pter
Size:
9,285 bases
Orientation:
Minus strand

Genomic View for YOD1 Gene

Genes around YOD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YOD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Selected DME Specific Peptides for YOD1 Gene

Q5VVQ6:
  • DGIHYDPL
  • DDIVLVQALELADEAR
  • SILSKFYQCEICVVDTQTVR
  • CQKGLTGQ
  • LRCMVCQ
  • FPDPDTPPLTIFSS
  • YYVVEGGV

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 & Families for YOD1 Gene

Gene Families for YOD1 Gene

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 :
  • 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.
  • Contains 1 C2H2-type zinc finger.
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 thiol-dependent ubiquitin-specific protease activity IDA 19818707
GO:0005515 protein binding IPI 19818707
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with YOD1: view
genes like me logo Genes that share phenotypes with YOD1: view

Animal Model Products

miRNA for YOD1 Gene

miRTarBase miRNAs that target YOD1

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for YOD1

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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
nucleus 4
cytosol 3
cytoskeleton 2
endoplasmic reticulum 2
plasma membrane 2

Gene Ontology (GO) - Cellular Components for YOD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005829 cytosol IBA --
genes like me logo Genes that share ontologies with YOD1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for YOD1 Gene

Pathways & Interactions for YOD1 Gene

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

Pathways by source for YOD1 Gene

Gene Ontology (GO) - Biological Process for YOD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0006986 response to unfolded protein IEA --
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
genes like me logo Genes that share ontologies with YOD1: view

No data available for SIGNOR curated interactions for YOD1 Gene

Transcripts for YOD1 Gene

mRNA/cDNA for YOD1 Gene

Unigene Clusters for YOD1 Gene

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

Inhibitory RNA Products

Clone Products

  • Addgene plasmids 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 from GTEx, Illumina, BioGPS, and SAGE for YOD1 Gene

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

This gene is overexpressed in Esophagus - Mucosa (x6.7).

Protein differential expression in normal tissues from HIPED for YOD1 Gene

This gene is overexpressed in Cervix (50.9) and Peripheral blood mononuclear cells (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for YOD1 Gene



NURSA nuclear receptor signaling pathways regulating expression of YOD1 Gene:

YOD1

SOURCE GeneReport for Unigene cluster for YOD1 Gene:

Hs.567533
genes like me logo Genes that share expression patterns with YOD1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and 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 34 35
  • 99.43 (n)
cow
(Bos Taurus)
Mammalia YOD1 34 35
  • 91.38 (n)
dog
(Canis familiaris)
Mammalia YOD1 34 35
  • 90.24 (n)
rat
(Rattus norvegicus)
Mammalia Yod1 34
  • 89.66 (n)
mouse
(Mus musculus)
Mammalia Yod1 34 16 35
  • 87.76 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YOD1 35
  • 85 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia YOD1 35
  • 62 (a)
OneToOne
chicken
(Gallus gallus)
Aves YOD1 34 35
  • 69.66 (n)
lizard
(Anolis carolinensis)
Reptilia YOD1 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia yod1 34
  • 65.24 (n)
zebrafish
(Danio rerio)
Actinopterygii yod1 34 35
  • 65.89 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4603 34 35
  • 51.22 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007001 34
  • 49.56 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes OTU1 34 35 37
  • 48.12 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D05599g 34
  • 47.06 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ABR233W 34
  • 44.84 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G50670 34
  • 53.64 (n)
rice
(Oryza sativa)
Liliopsida Os02g0164800 34
  • 56.21 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02353 34
  • 44.68 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes otu1 34
  • 43.76 (n)
Species where no ortholog for YOD1 was found in the sources mined by GeneCards:
  • 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
rs1044145 -- 207,044,014(-) GTAAT(A/G)CACTG utr-variant-3-prime
rs10592048 -- 207,046,965(+) GTAGC(-/AAAG)AAAGG utr-variant-3-prime
rs11120103 -- 207,045,167(+) TCCTT(A/G)TAAGT utr-variant-3-prime
rs11120106 -- 207,046,078(+) ATCTT(A/C)ATAGT utr-variant-3-prime
rs111432079 -- 207,052,739(+) ACGAT(-/GA)GAGTG intron-variant, upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
nsv832426 CNV gain 17160897
nsv946618 CNV duplication 23825009

Variation tolerance for YOD1 Gene

Residual Variation Intolerance Score: 21.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.01; 20.69% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for YOD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
YOD1

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

Disorders for YOD1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for YOD1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
brown-sequard syndrome
  • brown-squard syndrome
- elite association - COSMIC cancer census association via MalaCards
Search YOD1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for YOD1

Genetic Association Database (GAD)
YOD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
YOD1
genes like me logo Genes that share disorders with YOD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas 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 64
  2. 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 64
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. Non-hydrolyzable Diubiquitin Probes Reveal Linkage-Specific Reactivity of Deubiquitylating Enzymes Mediated by S2 Pockets. (PMID: 27066941) Flierman D. … Ovaa H. (Cell Chem Biol 2016) 3 64

Products for YOD1 Gene

Sources for YOD1 Gene

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