YOD1 Gene
protein-coding GIFtS: 46
GCID: GC01M207217
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YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)(Previous name: YOD1 OTU deubiquinating enzyme 1 homolog ( yeast) )
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Aliases
for YOD1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| YOD1 OTU Deubiquinating Enzyme 1 Homolog (S. Cerevisiae)1 2 | | PRO09072 | | DUBA81 2 3 5 | | HsHIN73 | | OTUD21 2 3 5 | | OTU Domain Containing 22 | | YOD1 OTU Deubiquinating Enzyme 1 Homolog ( Yeast)1 2 | | Ubiquitin Thioesterase OTU12 | | DUBA-82 3 | | EC 3.4.19.123 | | HIN-72 3 | | HIN73 | | HIV-1-Induced Protease 72 3 | | HsHIN73 | | OTU Domain-Containing Protein 22 3 | | EC 3.1.28 | | DKFZp451J17191 | | |
Export aliases for YOD1 gene to outside databasesPrevious GC identifers: GC01M203608 GC01M205284 GC01M177914 |
Summaries
for YOD1 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for YOD1:
Protein ubiquitination controls many intracellular processes, including cell cycle progression, transcriptionalactivation, and signal transduction. This dynamic process, involving ubiquitin conjugating enzymes anddeubiquitinating enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are cysteine proteases thatspecifically cleave ubiquitin from ubiquitin-conjugated protein substrates. The protein encoded by this gene belongsto a DUB subfamily characterized by an ovarian tumor (OTU) domain. Alternative splicing results in multiple transcriptvariants. (provided by RefSeq, Jan 2013)
UniProtKB/Swiss-Prot: OTU1_HUMAN, Q5VVQ6Function: Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmicreticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on theassociated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates maypresent a steric impediment to the threading process when the substrate is transferred to the VCP pore and threadedthrough VCP's axial channel. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.Able to cleave both polyubiquitin and di-ubiquitin
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Genomic Views
for YOD1 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000001.10 NC_018912.1 NT_167186.1
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the YOD1 gene promoter:
E2F-4 E2F-3a E2F-5 HTF E2F-2 GATA-2 GATA-1 E2F-1 E2F HSF2
Other transcription factors
Search SABiosciences Chromatin IP Primers for YOD1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat YOD1 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 1q32.2 Ensembl cytogenetic band: 1q32.2 HGNC cytogenetic band: 1q32.2YOD1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 1 GeneLoc Exon Structure GeneLoc location for GC01M207217: view genomic region
(about GC identifiers)
Start:
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207,217,194 bp from pter |
End:
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207,226,325 bp from pter |
Size:
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9,132 bases |
Orientation:
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minus strand |
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Proteins
for YOD1 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: OTU1_HUMAN, Q5VVQ6 (See
protein sequence)Recommended Name: Ubiquitin thioesterase OTU1 Size: 348 amino acids; 38322 Da
Subunit: Interacts with VCP; the interaction is direct. Interacts with FAF2/UBXD8. Interacts with DERL1; howeverinteraction is dependent on the UBAX-like region, suggesting that it may be indirect
Sequence caution: Sequence=AAF71033.1; Type=Erroneous translation; Note=Wrong choice of frame; Sequence=EAW93510.1;Type=Erroneous gene model prediction;
Secondary accessions: B2RNX3 Q5VVQ5 Q6ZRS6 Q86T63 Q9P1L8Alternative splicing: 2 isoforms: Q5VVQ6-1 Q5VVQ6-2 (No experimental confirmation available)Explore the universe of human proteins at neXtProt for YOD1: NX_Q5VVQ6
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q5VVQ6
4/7 DME Specific Peptides for YOD1 (Q5VVQ6) (see all 7)
YOD1 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (2 alternative transcripts):
NP_001263249.1 NP_061036.3
ENSEMBL proteins: ENSP00000356051 ENSP00000326813 ENSP00000375793
Human Recombinant Protein Products:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005622 | intracellular |
IEA | -- |
YOD1 for ontologies About GeneDecksing
YOD1 Antibody Products:
Assay Products for YOD1: |
Protein
Domains /
Families
for YOD1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
YOD1 for domains About GeneDecksing
3 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q5VVQ6ProtoNet protein and cluster: Q5VVQ6 UniProtKB/Swiss-Prot: OTU1_HUMAN, Q5VVQ6Domain: The UBAX-like region mediates the interaction with VCP. According to PubMed:19818707, it corresponds to a UBXdomain, which is a hallmark for VCP-associated proteins. However, no canonical UBX is detected by prediction toolssuch as Pfam or PROSITESimilarity: Contains 1 C2H2-type zinc fingerSimilarity: Contains 1 OTU domain |
Function
for YOD1 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Function Summary:
UniProtKB/Swiss-Prot: OTU1_HUMAN, Q5VVQ6Function: Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmicreticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on theassociated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates maypresent a steric impediment to the threading process when the substrate is transferred to the VCP pore and threadedthrough VCP's axial channel. Mediates deubiquitination of both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains.Able to cleave both polyubiquitin and di-ubiquitinCatalytic activity: Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by theC-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal)Enzyme Numbers (IUBMB): EC 3.1.22 EC 3.4.19.121
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for YOD1
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YOD1 |
Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view): About this table
YOD1 for ontologies About GeneDecksing
|
Pathways & Interactions
for YOD1 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
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Unified GeneCards pathways About this table
See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | Protein processing in endoplasmic reticulum | |
Pathway sources
See GeneCards unified pathways
Show all pathways
1 
Kegg Pathway (Kegg details for YOD1):
YOD1 for pathways About GeneDecksing
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for YOD1
STRING Interaction
Network Preview (showing 5 interactants - click image to see 17)
5/41 Interacting proteins for YOD1 (Q5VVQ63 ENSP000003268134) via UniProtKB, MINT, STRING, and/or I2D (see all 41)About this table
Gene Ontology (GO): 5 biological process terms (GO ID links to tree view): About this table
YOD1 for ontologies About GeneDecksing
|
Drugs & Compounds
for YOD1 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for YOD1
Search CenterWatch for drugs/clinical trials and news about YOD1 / OTU1
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Transcripts
for YOD1 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for YOD1 gene (2 alternative transcripts): NM_001276320.1 NM_018566.3 Unigene Clusters for YOD1: YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae) Hs.567533 [show with all ESTs], Hs.711982 [show with all ESTs]Unigene Representative Sequences: NM_018566, AK1280143 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000367084(uc001hff.1) ENST00000315927(uc001hfe.1) ENST00000391927
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for YOD1 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for YOD1
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: YOD1 (NM_002478) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for YOD1 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YOD1 |
Additional cDNA sequence: AK128014.1 5 DOTS entries: DT.95151639 DT.100651383 DT.87017586 DT.410129 DT.91809420 24/60 AceView cDNA sequences (see all 60): AA830040 AA338005 CR590739 AF116608 CB136300 BX281286 BU677062 BX325304 CB120592 CF143691 AA279267 CA443491 AL833081 BU754342 AK128014 AA687363 BX324620 BG035362 BF436566 AL121343 CD653082 AI690940 AI888335 BX643543
GeneLoc Exon Structure
|
Expression
for YOD1 gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| YOD1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AGTCTACTTT
About this image
See YOD1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for YOD1
SOURCE GeneReport for Unigene clusters: Hs.567533 Hs.711982
SABiosciences Custom PCR Arrays for YOD1
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for YOD1
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat YOD1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat YOD1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat YOD1 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YOD1 |
Orthologs
for YOD1 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of eukaryotes.
Orthologs for YOD1 gene from 8/29 species (see all 29) About this table
ENSEMBL Gene Tree for YOD1 (if available)
TreeFam Gene Tree for YOD1 (if available) |
Paralogs
for YOD1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| -- |
Genomic Variants
for YOD1 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 1 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for YOD1 (207217194 - 207226325 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for YOD1: -- | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing YOD1 |
|
Disorders
/ Diseases
for YOD1 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
 YOD1 for disorders About MalaCards
YOD1 for disorders About GeneDecksing
OMIM gene information: 612023
OMIM disorders: --
Export disorders for YOD1 gene to outside databases
|
Publications
for YOD1 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for YOD1 gene, integrated from 9 sources (see all 17):
(articles sorted by number of sources associating them with YOD1) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- The otubain YOD1 is a deubiquitinating enzyme that associates with p97 to facilitate protein dislocation from the ER. (PubMed id 19818707)1, 2 Ernst R.... Schlieker C. (2009)
- The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- A microarray of ubiquitylated proteins for profiling d eubiquitylase activity reveals the critical roles of both chain and substrate. (PubMed id 22626734)1 Loch C.M. and Strickler J.E. (2012)
- Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
- Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
- Activity-based chemical proteomics accelerates inhibi tor development for deubiquitylating enzymes. (PubMed id 22118674)1 Altun M....Kessler B.M. (2011)
- Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
- Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
- The transmembrane segment of a tail-anchored protein d etermines its degradative fate through dislocation from the endoplasmic reticulu m. (PubMed id 20435896)1 Claessen J.H....Ploegh H.L. (2010)
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External Searches for YOD1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing YOD1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing YOD1 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing YOD1 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for YOD1 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for YOD1 gene:
Search GeneIP for patents involving YOD1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for YOD1 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
 | |
 | |
 |
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat YOD1 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing YOD1 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat YOD1 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat YOD1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat YOD1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat YOD1 |
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| |  |  |  |  | | | | |
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 | | | YOD1 Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YOD1 |
|  |  |  | | | | Search ThermoFisher Antibodies for YOD1 |
| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YOD1 |
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