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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

OTUD4 Gene

protein-coding   GIFtS: 48
GCID: GC04M146054

OTU domain containing 4

  Search for OTUD4
in our new
 Human Malady Compendium 
Biological research products
for OTUD4
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
OTU Domain Containing 41 2     HSHIN11 2
KIAA10461 3 5     HIV-1-Induced Protein HIN-12 3
HIN12 3 5     HIV-1 Induced Protein HIN-12
DUBA61 2     OTU Domain-Containing Protein 42

External Ids:    HGNC: 249491   Entrez Gene: 547262   Ensembl: ENSG000001641647   OMIM: 6117445   UniProtKB: Q018043   

Export aliases for OTUD4 gene to outside databases

Previous GC identifers: GC04M146413 GC04M146274 GC04M141787


(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 OTUD4:
Alternatively spliced transcript variants have been found for this gene. The smaller protein isoform encoded by the
shorter transcript variant is found only in HIV-1 infected cells. (provided by RefSeq, Jul 2010)

Gene Wiki entry for OTUD4


(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_000004.11  NC_018915.1  NT_016354.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the OTUD4 gene promoter:
         HOXA9B   HOXA9   p300   Tal-1beta   Meis-1b   E47   GATA-2   N-Myc   Sox9   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidOTUD4 promoter sequence
   Search SABiosciences Chromatin IP Primers for OTUD4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat OTUD4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4q31.21   Ensembl cytogenetic band:  4q31.21   HGNC cytogenetic band: 4q31.21

OTUD4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
OTUD4 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M146054:  view genomic region     (about GC identifiers)

Start:
146,031,990 bp from pter      End:
146,101,313 bp from pter
Size:
69,324 bases      Orientation:
minus strand

(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: OTUD4_HUMAN, Q01804 (See protein sequence)
Recommended Name: OTU domain-containing protein 4  
Size: 1113 amino acids; 123916 Da
Sequence caution: Sequence=AAI18573.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAI18654.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=ABD72605.1;
Type=Erroneous gene model prediction; Sequence=BAA82998.2; Type=Miscellaneous discrepancy; Note=Intron retention;
Sequence=BAB71229.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAA48313.1;
Type=Miscellaneous discrepancy; Note=Contaminating sequence. Originates from a chimeric transcript in HIV-1-infected
cells. The premature stop may be due to intron retention;
Secondary accessions: B4DYS4 Q147U2 Q1ZYK1 Q6PG39 Q96MQ5 Q9NT94 Q9UPV6
Alternative splicing: 4 isoforms:  Q01804-1   Q01804-2   Q01804-4   Q01804-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for OTUD4: NX_Q01804

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q01804

  • OTUD4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001096123.1  NP_059963.1  

    ENSEMBL proteins: 
     ENSP00000409279   ENSP00000395487   ENSP00000425972   ENSP00000424192   ENSP00000423453  
     ENSP00000296579  

    Human Recombinant Protein Products: 
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    Novus Biologicals OTUD4 Proteins
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    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins
    Uscn Proteins for OTUD4

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--


    OTUD4 for ontologies           About GeneDecksing



    OTUD4 Antibody Products: 
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    Uscn ELISAs and CLIAs for OTUD4


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    OTUD4 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR003323 OTU

    Graphical View of Domain Structure for InterPro Entry Q01804

    ProtoNet protein and cluster: Q01804

    1 Blocks protein family: IPB003323 OTU-like cysteine protease

    UniProtKB/Swiss-Prot: OTUD4_HUMAN, Q01804
    Similarity: Contains 1 OTU domain


    (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: OTUD4_HUMAN, Q01804
    Induction: By HIV-1 insertion

    miRNA
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    hsa-miR-100* hsa-miR-4272 hsa-miR-15a hsa-miR-485-3p hsa-miR-138-2* hsa-miR-3142 hsa-miR-376c hsa-miR-92b
    SwitchGear 3'UTR luciferase reporter plasmidOTUD4 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for OTUD4 (see all 4)
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for OTUD4

    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--


    OTUD4 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for OTUD4:
     Increased HPV18 LCR reporter a 


    (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



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for OTUD4

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/38 Interacting proteins for OTUD4 (Q018043 ENSP000004092794) via UniProtKB, MINT, STRING, and/or I2D (see all 38)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    AGO3Q9H9G73, ENSP000003622874I2D: score=2 STRING: ENSP00000362287
    ATG12O948173, ENSP000002744594I2D: score=2 STRING: ENSP00000274459
    BAG5Q9UL153, ENSP000003388144I2D: score=2 STRING: ENSP00000338814
    DSG1Q024133, ENSP000002571924I2D: score=2 STRING: ENSP00000257192
    FXR2P511163, ENSP000002501134I2D: score=2 STRING: ENSP00000250113
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--


    OTUD4 for ontologies           About GeneDecksing



    (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 Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for OTUD4
    Search CenterWatch for drugs/clinical trials and news about OTUD4 

    (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 OTUD4 gene (3 alternative transcripts): 
    NM_001102653.1  NM_017493.6  NM_199324.2  

    Unigene Cluster for OTUD4:

    OTU domain containing 4
    Hs.270851  [show with all ESTs]
    Unigene Representative Sequence: NM_001102653
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000455611 ENST00000454497(uc003ika.4) ENST00000447906 ENST00000509517
    ENST00000514973 ENST00000505976 ENST00000509620(uc021xsl.1) ENST00000504501
    ENST00000509985 ENST00000504331 ENST00000296579

    miRNA
    Products:
         
    OriGene 3'-UTR Clone (see all 2): OTUD4
    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat OTUD4
    8/88 QIAGEN miScript miRNA Assays for microRNAs that regulate OTUD4 (see all 88):
    hsa-miR-100* hsa-miR-4272 hsa-miR-15a hsa-miR-485-3p hsa-miR-138-2* hsa-miR-3142 hsa-miR-376c hsa-miR-92b
    SwitchGear 3'UTR luciferase reporter plasmidOTUD4 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for OTUD4 (see all 4)
    OriGene shRNA RFP: OTUD4
    OriGene siRNA: OTUD4
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat OTUD4
    Clone
    Products:
         
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for OTUD4 (see all 4)
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat OTUD4
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat OTUD4

    Additional cDNA sequence: 

    AK056597.1 AK302581.1 AL137460.1 BC020682.1 BC057242.1 BC118572.1 BC118653.1 X68242.1 

    11 DOTS entries:

    DT.311285  DT.447767  DT.40312008  DT.202656  DT.121178469  DT.70102334  DT.95114464  DT.95168685 
    DT.100652143  DT.92408187  DT.95094459 

    24/192 AceView cDNA sequences (see all 192):

    BF726608 AI074703 AA382637 AI081558 AA634121 BM471766 BX489372 BF126137 
    AK056597 AB028969 AA371189 CA397434 BQ435300 AI139983 AI081525 BQ436647 
    AA363754 AA888030 AI076277 AI417087 CK429593 AI683771 CR592200 AW612484 

    GeneLoc Exon Structure


    (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

    OTUD4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GTGTGATGCT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    OTUD4 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    SomiteThoracic Ventrolateral Dermomyotome LipMuscle Progenitor CellsSkeletal Muscle
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See OTUD4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for OTUD4

    SOURCE GeneReport for Unigene cluster: Hs.270851
        SABiosciences Custom PCR Arrays for OTUD4
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for OTUD4

    (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 animals.

    Orthologs for OTUD4 gene from 6/16 species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Otud41 , 5 OTU domain containing 41, 5 88.21(n)1
    87.69(a)1
      8 (37.74 cM)5
    739451  NM_001081164.11  NP_001074633.11 
     796396185 
    chicken
    (Gallus gallus)
    Aves OTUD41 OTU domain containing 4 69.27(n)
    62.01(a)
      422463  XM_420427.2  XP_420427.2 
    lizard
    (Anolis carolinensis)
    Reptilia OTUD46
    --
    48(a)
    1 ↔ 1
    5(117906527-117943058)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.195812 Transcribed sequence with moderate similarity to protein more 77.63(n)    BX781054.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC057511.12   -- 74.05(n)    BC057511.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG32516
    otu6
    ovarian tumor
    16(a)
    15(a)
    many ↔ many
    many ↔ many
    2L(4688965-4690702)
    X(8379041-8383568)


    ENSEMBL Gene Tree for OTUD4 (if available)
    TreeFam Gene Tree for OTUD4 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for OTUD4 gene
    ALG132  
    2 SIMAP similar genes for OTUD4 using alignment to 6 protein entries:     OTUD4_HUMAN (see all proteins):
    HIN1L    ALG13

    OTUD4 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for OTUD4
    PGOHUM00000258652


    (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
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing OTUD4
    DNA2.0 Custom Variant and Variant Library Synthesis for OTUD4

    (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

    OTUD4 for disorders           About MalaCards

    OTUD4 for disorders           About GeneDecksing

    OMIM gene information: 611744    OMIM disorders: --


    Export disorders for OTUD4 gene to outside databases

    (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 OTUD4 gene, integrated from 9 sources (see all 28):
    (articles sorted by number of sources associating them with OTUD4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. HIV-1 promotor insertion revealed by selective detection of chimeric provirus-host gene transcripts. (PubMed id 1475186)1, 2, 3 Raineri I. and Senn H.-P. (1992)
    2. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (2006)
    3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
    4. Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. (PubMed id 15144186)1, 2 Brill L.M....Peters E.C. (2004)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10470851)1, 2 Kikuno R....Ohara O. (1999)
    8. Targeted ubiquitination and degradation of G-protein-c oupled receptor kinase 5 by the DDB1-CUL4 ubiquitin ligase complex. (PubMed id 22952844)1 Wu Z....Ma L. (2012)
    9. Functional dissection of lysine deacetylases reveals t hat HDAC1 and p300 regulate AMPK. (PubMed id 22318606)1 Lin Y.Y....Boeke J.D. (2012)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)

    (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)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 54726 HGNC: 24949 AceView: HSHIN1 Ensembl:ENSG00000164164 euGenes: HUgn54726
    ECgene: OTUD4 H-InvDB: OTUD4

    (According to HUGE)
    About This Section
    HUGE: KIAA1046

    (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
    NameDescription
    PharmGKB entry for OTUD4 Pharmacogenomics, SNPs, Pathways
    SeattleSNPshttp://pga.gs.washington.edu/data/otud4/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for OTUD4 gene:
    Search GeneIP for patents involving OTUD4

    GeneCards and IP:
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     OriGene Antibodies for OTUD4   OriGene shRNA RFP for OTUD4  
     OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for OTUD4   OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for OTUD4  
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     GenScript Custom Purified and Recombinant Proteins Services for OTUD4 GenScript cDNA clones with any tag delivered in your preferred vector for OTUD4
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     Regulatory tfbs in OTUD4 promoter
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     OTUD4 Proteins, Antibodies, CLIAs, and ELISAs
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     Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for OTUD4
     SwitchGear 3'UTR luciferase reporter plasmids for OTUD4
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     ThermoFisher Antibodies for OTUD4
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat OTUD4
           
    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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