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YOD1 Gene

protein-coding   GIFtS: 47

GC01M205284
YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)
(Previous name: YOD1 OTU deubiquinating enzyme 1 homolog ( yeast) )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
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Aliases &
Descriptions
for YOD1

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section
Aliases
DKFZp451J1719 1, 2
DUBA-8 3
DUBA8 1, 2, 3, 5
EC 3.1.2.- 3
HIN-7 3
HIN7 3
HsHIN7 3
OTTHUMP00000034284 2
OTUD2 1, 2, 3, 5
PRO0907 2
Descriptions
HIV-1-induced protease 7 3
OTU domain containing 2 2
OTU domain-containing protein 2 3
YOD1 OTU deubiquinating enzyme 1 homolog 2
YOD1 OTU deubiquinating enzyme 1 homolog ( yeast) 1, 2
YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae) 2
External Ids
HGNC: 250351
Entrez Gene: 554322
UniProtKB: Q5VVQ63
Ensembl: ENSG000001806677
Search outside databases for aliases for YOD1 gene

Previous GC identifer: GC01M203608

Summaries
for YOD1

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

 EntrezGene summary for YOD1:
Deubiquitinating enzymes (DUBs; see MIM 603478) are proteases that specifically cleave ubiquitin
(MIM 191339) linkages, negating the action of ubiquitin ligases. DUBA8 belongs to a DUB subfamily
characterized by an ovarian tumor (OTU) domain.[supplied by OMIM]

UniProtKB/Swiss-Prot: OTU1_HUMAN, Q5VVQ6
Function: Hydrolase that can remove conjugated ubiquitin from proteins and may therefore play an
important regulatory role at the level of protein turnover by preventing degradation (By
similarity)

Genomic Location
for YOD1

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

 Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the YOD1 gene  

Entrez Gene cytogenetic band: 1q32.1   Ensembl cytogenetic band:  1q32.1   HGNC cytogenetic band: 1q32.2

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

GeneLoc gene densities for chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M205284:     (about GC identifiers)

Start:
 205,283,817 bp from pter
End:
 205,292,948 bp from pter
Size:
 9,132 bases
Orientation:
 minus strand
RefSeq DNA sequence:
NC_000001.9  NT_021877.18  

Proteins
for YOD1

(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

 UniProtKB/Swiss-Prot: OTU1_HUMAN, Q5VVQ6 (See protein sequence)
Recommended Name: Ubiquitin thioesterase OTU1  
Size: 348 amino acids; 38322 Da
Sequence caution: Sequence=AAF71033.1; Type=Erroneous translation; Note=Wrong choice of frame;
Sequence=EAW93510.1; Type=Erroneous gene model prediction;
Secondary accessions: Q5VVQ5 Q6ZRS6 Q86T63 Q9P1L8
Alternative splicing: 2 isoforms:  Q5VVQ6-1   Q5VVQ6-2   

REFSEQ proteins: NP_061036.3  

ENSEMBL proteins: 
ENSP00000375793 ENSP00000356051 ENSP00000326813 


Human Recombinant Proteins 
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Browse Abcam for Recombinant Proteins
Browse Abnova for Human Recombinant Proteins
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

1 Gene Ontology (GO) cellular component term (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005622 intracellular IEA--
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Antibodies for YOD1: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Browse Antibodies at Sigma-Aldrich
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Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
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Search Novus for antibodies for YOD1

Assays for YOD1: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

Protein Domains/
Families
for YOD1

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
3 InterPro domains/families:
 IPR003323 OTU
 IPR015880 Znf_C2H2-like
 IPR007087 Znf_C2H2


   GeneDecks  YOD1 for the domains selected above  
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Graphical View of Domain Structure for InterPro Entry Q5VVQ6

ProtoNet protein and cluster: Q5VVQ6

UniProtKB/Swiss-Prot: OTU1_HUMAN, Q5VVQ6
Similarity: Contains 1 C2H2-type zinc finger
Similarity: Contains 1 OTU domain

Gene Function
for YOD1

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section
Inhib.
RNA:		Invitrogen RNAi Products for gene knock-down (YOD1)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (YOD1)
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): XR_000127

              Applied Biosystems Silencer® siRNAs for YOD1

              Sigma-Aldrich siRNA for YOD1  
                     Sigma-Aldrich shRNA for YOD1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Browse Clone Ranger at Invitrogen for clones
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_018566
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_018566
                                 untagged cDNA clone in CMV expression vector: NM_018566 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_018566

UniProtKB/Swiss-Prot: OTU1_HUMAN, Q5VVQ6
Function: Hydrolase that can remove conjugated ubiquitin from proteins and may therefore play an
important regulatory role at the level of protein turnover by preventing degradation (By
similarity)
Enzyme Number (IUBMB): EC 3.1.2.- 

5 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0008233 peptidase activity IEA--
GO:0008234 cysteine-type peptidase activity IEA--
GO:0008270 zinc ion binding IEA--
GO:0016289 CoA hydrolase activity ISS--
GO:0046872 metal ion binding IEA--
About this table

Pathways & Interactions
for YOD1

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section


3 Kegg Pathways  (Kegg details for YOD1):
 hsa00632 Benzoate degradation via CoA ligation
 hsa00903 Limonene and pinene degradation
 hsa01040 Biosynthesis of unsaturated fatty acids

   GeneDecks  YOD1 for the pathways selected above  
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5/14 Interacting proteins for YOD1 (ENSP000003268133) via UniProtKB, MINT, and/or STRING (see all 14 )
InteractantInteraction Details
GeneCardExternal ID(s)
ARD1AENSP000003590323STRING (score=.899)
DHRS1ENSP000002881113STRING (score=.899)
DHRS2ENSP000003446743STRING (score=.899)
DHRS3ENSP000003653973STRING (score=.899)
DHRS7ENSP000003537593STRING (score=.899)
About this table

2 Gene Ontology (GO) biological process terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006519 cellular amino acid and derivative metabolic process ISS--
GO:0019941 modification-dependent protein catabolic process IEA--
About this table

Drugs & Compounds
for YOD1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for YOD1

Transcripts
for YOD1

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section
Inhib.
RNA:		Invitrogen RNAi Products for gene knock-down (YOD1)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (YOD1)
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): XR_000127

              Sigma-Aldrich siRNA for YOD1  
                     Sigma-Aldrich shRNA for YOD1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_018566  

REFSEQ mRNAs for YOD1 gene: 

NM_018566.3   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_018566  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_018566
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_018566
                                 untagged cDNA clone in CMV expression vector: NM_018566 

Additional cDNA sequence: AK128014.1 

5 DOTS entries:

DT.95151639  DT.87017586  DT.100651383  DT.410129  DT.91809420 

24/60 AceView cDNA sequences (see all 60 ):

BX325304 AF116608 CR590739 AA830040 BU677062 AA338005 BX281286 CB120592 
CF143691 CB136300 BX643543 CD653082 AI253636 AA521103 AI888335 AL121343 
BE350156 AI065073 BG035362 CA443491 CA450323 AA687363 BI829009 BU754342 

highest scoring ESTs for YOD1:

AA279267 AA338005 AI982535 AK128014 AL121343 AL833081 BE166835 BE882397 BI829009 BX281286 

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, AK128014


GeneLoc Exon Structure

3 Ensembl transcripts including schematic representations:
ENST00000391927  ENST00000367084  ENST00000315927  

Expression
for YOD1

(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

YOD1 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for YOD1

1 / 2 / 3

5 probe-sets matching YOD1 gene


Affymetrix
probe-set		 Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
52762_at2, 3 U95-B 1 1.00 1.00 1.00 1.00 AI982535 0.60 1.00 0.82 1

227309_at2, 3 U133-B 1 1.00 1.00 -- -- AI982535 0.60 1.00 0.82 1

215150_at2, 3 U133-A 1 1.00 1.00 -- -- AF090896 0.20 0.50 0.38 1

227309_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

215150_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  YOD1 for binary patterns associated with the probe-sets selected above  
About GeneDecksing
About this table    
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: CCTCTTTCTG

SOURCE GeneReport for Unigene clusters: Hs.567533 Hs.711982

Orthologs
for YOD1

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section
Orthologs for YOD1 gene from 5/17 species (see all 17 )
Organism Gene Locus Description Human
Similarity		 NCBI accessions
dog
(Canis familiaris)		 YOD11   -- YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae) 90.24(n)
91.01(a)		 490268  XM_547387.2  XP_547387.1 
chimpanzee
(Pan troglodytes)		 YOD11   -- YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae) 99.43(n)
99.14(a)		 469659  XM_525042.2  XP_525042.2 
cow
(Bos taurus)		 YOD11   -- YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae) 91.38(n)
91.38(a)		 539931  XM_590370.3  XP_590370.1 
rat
(Rattus norvegicus)		 Yod11   -- YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae) 89.66(n)
92.41(a)		 363982  NM_001008889.1  NP_001008889.1 
mouse
(Mus musculus)		 Yod11, 5 15
 YOD1 OTU deubiquitinating enzyme 1 homologue (S. cerevisiae)1, 5 89.55(n)1
91.09(a)1		 2264181  NM_178691.31  NP_848806.11 
 AI4262505  AK0369385  (see all 11)
About this table        Species with no ortholog for YOD1

ENSEMBL Gene Tree for YOD1

Paralogs
for YOD1

(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

  --

SNPs/Variants
for YOD1

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/45 NCBI SNPs in YOD1 are shown (see all 45 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 68)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 1 posSequenceRecsAA
Chg		TypeMoreRecsAllele
freq		PopTotal
sample		More
------------
rs28427411,2
A,C,F,H,O205283318(+) CGTCCA/GTAATT 1 -- ng516Minor allele frequency- G:0.11EA WA NA 440
rs26296651,2
A,C,F,H,O205287423(-) TATCTG/TCCTAG 1 -- ut31 ese38Minor allele frequency- T:0.18EU EA WA NA 2052
--
rs10441451,2
A,C,F,H205283982(-) GTAATA/GCACTG 1 -- ut31 ese36Minor allele frequency- G:0.33MN EU EA WA 1864
rs118020371,2
C,F,H205283685(+) GAGTCC/TGCCTA 1 -- ng514Minor allele frequency- T:0.03EU EA WA 418
rs121231071,2
C,F,H205286905(+) CAAATG/ATCAAC 1 -- ut314Minor allele frequency- A:0.25EU EA WA 418
rs13856111,2
A,C,H205288032(-) GGGGGG/AATTTA 1 -- ut315Minor allele frequency- A:0.00MN EU EA WA 602
rs20547801,2
C,F,H205288235(-) AAAACG/ATAGAA 1 -- ut31 ese35Minor allele frequency- A:0.10EU EA WA 1896
rs24952551,2
A,F,H205286079(+) AAGAAA/GAGTAA 1 -- ut314Minor allele frequency- G:0.08EU EA WA 408
rs172587111,2
C,F,H205286226(+) TCTAGT/CACAAA 1 -- ut31 ese38Minor allele frequency- C:0.24NA EA EU WA 634
rs111201031,2
C,F,H205285135(+) TCCTTA/GTAAGT 1 -- ut31 ese34Minor allele frequency- G:0.03EU EA WA 414
About this table

HapMap Linkage Disequilibrium images for YOD1 (up to first 250kb)

Disorders & Mutations
for YOD1

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

 OMIM: 612023

Medical News
for YOD1

(Possibly Related Articles in Doctor's Guide)
About This Section

   --

Publications
for YOD1

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
About This Section

4 PubMed articles for YOD1 gene:

Search for YOD1

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

 ANDOR
Aliases
Free Text  
  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

Genome Databases showing YOD1

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section
Entrez Gene: 55432 HGNC: 25035 AceView: DKFZp451J1719 Ensembl:ENSG00000180667 euGenes: HUgn55432
ECgene: YOD1 H-InvDB: YOD1

Other Databases showing YOD1

(According to HUGE)
About This Section

   --

Specialized Databases showing YOD1

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

   --

Licensable Technologies
for YOD1

(Available from WIS Yeda, Salk, Tufts)
About This Section

  --

Services
for YOD1

(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for YOD1:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



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  Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for YOD1-related products

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 Millipore Preclinical / Clinical Development Services
 Millipore Immunoassay Services
 Millipore Target Screening & Profiling Services


 Predesigned and custom siRNAs for YOD1 Browse antibodies at Sigma-Aldrich
 Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
 Lentivirus-delivered shRNAs for YOD1 Browse small molecules at Sigma-Aldrich
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