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UBTD1 Gene

protein-coding   GIFtS: 48
GCID: GC10P099248

Ubiquitin Domain Containing 1

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Ubiquitin Domain Containing 11 2
Ubiquitin Domain-Containing Protein 12

External Ids:    HGNC: 256831   Entrez Gene: 800192   Ensembl: ENSG000001658867   UniProtKB: Q9HAC83   

Export aliases for UBTD1 gene to outside databases

Previous GC identifers: GC10P098924 GC10P092884


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for UBTD1 Gene:
The degradation of many proteins is carried out by the ubiquitin pathway in which proteins are targeted for
degradation by covalent conjugation of the polypeptide ubiquitin. This gene encodes a protein that belongs to the
ubiquitin family of proteins. The encoded protein is thought to regulate E2 ubiquitin conjugating enzymes
belonging to the UBE2D family. (provided by RefSeq, Mar 2014)

GeneCards Summary for UBTD1 Gene:
UBTD1 (ubiquitin domain containing 1) is a protein-coding gene. An important paralog of this gene is UBTD2.




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000010.10  NC_018921.2  NT_030059.14  
Regulatory elements:
   Regulatory transcription factor binding sites in the UBTD1 gene promoter:
         p53   Pax-6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUBTD1 promoter sequence
   Search Chromatin IP Primers for UBTD1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat UBTD1


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

Entrez Gene cytogenetic band: 10q24.2   Ensembl cytogenetic band:  10q24.1   HGNC cytogenetic band: 10q24.2

UBTD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UBTD1 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P099248:  view genomic region     (about GC identifiers)

Start:
99,258,625 bp from pter      End:
99,330,966 bp from pter
Size:
72,342 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: UBTD1_HUMAN, Q9HAC8 (See protein sequence)
Recommended Name: Ubiquitin domain-containing protein 1  
Size: 227 amino acids; 25938 Da
Secondary accessions: D3DR57 Q53HI3

Explore the universe of human proteins at neXtProt for UBTD1: NX_Q9HAC8

Explore proteomics data for UBTD1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys37, Lys50
  • Modification sites at PhosphoSitePlus

  • See UBTD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_079230.1  
    ENSEMBL proteins: 
     ENSP00000359698  

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    antibodies-online proteins for UBTD1 (7 products) 

     
    antibodies-online peptides for UBTD1

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    Cloud-Clone Corp. ELISAs for UBTD1
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    antibodies-online kits for UBTD1 (8 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR000626 Ubiquitin_dom
     IPR019956 Ubiquitin

    Graphical View of Domain Structure for InterPro Entry Q9HAC8

    ProtoNet protein and cluster: Q9HAC8

    1 Blocks protein domain: IPB000626 Ubiquitin domain

    UniProtKB/Swiss-Prot: UBTD1_HUMAN, Q9HAC8
    Similarity: Contains 1 ubiquitin-like domain


    Find genes that share domains with UBTD1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    Find genes that share ontologies with UBTD1           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for UBTD1

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate UBTD1 (see all 17):
    hsa-miR-644 hsa-miR-146b-3p hsa-miR-125a-5p hsa-miR-218 hsa-miR-3161 hsa-miR-125b hsa-miR-1914 hsa-miR-1827
    SwitchGear 3'UTR luciferase reporter plasmidUBTD1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat UBTD1

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    Browse Sino Biological Human cDNA Clones
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus2
    cytosol1
    plasma membrane1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for UBTD1
    Interactions:

        Search GeneGlobe Interaction Network for UBTD1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    Selected Interacting proteins for UBTD1 (Q9HAC82, 3 ENSP000003596984) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000224994Q9HCM92, 3, ENSP000004119494MINT-66738 I2D: score=4 STRING: ENSP00000411949
    ENSG00000232839Q9HCM92, 3, ENSP000003983554MINT-66738 I2D: score=4 STRING: ENSP00000398355
    ENSG00000206495Q9HCM92, 3MINT-66738 I2D: score=4 
    ENSG00000226437Q9HCM92, 3MINT-66738 I2D: score=4 
    ENSG00000229929Q9HCM92, 3MINT-66738 I2D: score=4 
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for UBTD1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for UBTD1 gene: 
    NM_024954.4  

    Unigene Cluster for UBTD1:

    Ubiquitin domain containing 1
    Hs.500724  [show with all ESTs]
    Unigene Representative Sequence: BM906603
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000370664(uc001knv.1)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate UBTD1 (see all 17):
    hsa-miR-644 hsa-miR-146b-3p hsa-miR-125a-5p hsa-miR-218 hsa-miR-3161 hsa-miR-125b hsa-miR-1914 hsa-miR-1827
    SwitchGear 3'UTR luciferase reporter plasmidUBTD1 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for UBTD1
    Predesigned siRNA for gene silencing in human, mouse, rat UBTD1
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    GenScript: all cDNA clones in your preferred vector: UBTD1 (NM_024954)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat UBTD1
    Primer
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    OriGene qPCR primer pairs and template standards for UBTD1
    OriGene qSTAR qPCR primer pairs in human, mouse for UBTD1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat UBTD1
      QuantiTect SYBR Green Assays in human, mouse, rat UBTD1
      QuantiFast Probe-based Assays in human, mouse, rat UBTD1

    Additional mRNA sequence: 

    AK021869.1 AK222597.1 BC007331.2 

    3 DOTS entries:

    DT.313017  DT.91910353  DT.100785995 

    Selected AceView cDNA sequences (see all 118):

    BM919838 BM695060 BQ934823 BI825413 BI823467 BM725240 BF035667 BM782106 
    BE276842 BM695795 CB216539 BI830834 BG420962 AI057114 BQ949749 BI909560 
    AV721116 CA454506 CF265057 BI757230 BI831190 BM922594 AI024786 CB306542 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    UBTD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCCTCCACAG
    UBTD1 Expression
    About this image


    UBTD1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Neurons
             Mature Rod Cells Outer Nuclear Layer
     
     Eye (Sensory Organs)
             Mature Rod Cells Outer Nuclear Layer
     
     Testis (Reproductive System)
    UBTD1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    UBTD1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.500724
        Custom PCR Arrays for UBTD1
    Primer
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    OriGene qPCR primer pairs and template standards for UBTD1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for UBTD1

    (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)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for UBTD1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ubtd11 , 5 ubiquitin domain containing 11, 5 90.9(n)1
    98.68(a)1
      19 (35.56 cM)5
    2261221  NM_145500.31  NP_663475.11 
     419817635 
    chicken
    (Gallus gallus)
    Aves UBTD11 ubiquitin domain containing 1 81.86(n)
    83.72(a)
      431558  XM_429110.4  XP_429110.4 
    lizard
    (Anolis carolinensis)
    Reptilia UBTD16
    ubiquitin domain containing 1
    83(a)
    1 ↔ 1
    3(39258014-39263800)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia 1419997472   -- 77.72(n)    141999747 
    zebrafish
    (Danio rerio)
    Actinopterygii ubtd1b1 ubiquitin domain containing 1b 69.79(n)
    74.55(a)
      571832  NM_001030265.1  NP_001025436.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG11726
    --
    44(a)
    1 → many
    3R(1219628-1225235)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G457401 AT5G45740 52.22(n)
    50(a)
      834613  NM_123941.2  NP_199386.2 


    ENSEMBL Gene Tree for UBTD1 (if available)
    TreeFam Gene Tree for UBTD1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for UBTD1 gene
    UBTD22  
    2 SIMAP similar genes for UBTD1 using alignment to 1 protein entry:     UBTD1_HUMAN:
    DC-UbP    UBTD2

    Find genes that share paralogs with UBTD1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for UBTD1 (see all 1386)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs611287141,2
    C--92893444(+) AAAAA-/A/AAA 
            
    GAGAG
    1 -- int11NA 2
    rs111892601,2
    C--99287953(+) CCTCCC/TGGACG 1 -- int1 trp31Minor allele frequency- T:0.00NA 2
    rs111892611,2
    C--99288133(+) CGGACG/AGGGCG 1 -- int12Minor allele frequency- A:0.00NA 4
    rs111892631,2
    C--99288333(+) GGGCTG/CACCCC 1 -- int12Minor allele frequency- C:0.00NA 4
    rs748860371,2
    C--99288354(+) TCCCGG/AACGGG 1 -- int11Minor allele frequency- A:0.00NA 2
    rs46064131,2
    C--99288835(+) tcaccC/Tcccag 1 -- int10--------
    rs1807710701,2
    --99288843(+) CAGACA/GGGGTC 1 -- int10--------
    rs1143153801,2
    F--99288855(+) CGGCCG/AGCCGA 1 -- int11Minor allele frequency- A:0.06WA 118
    rs1138214191,2
    C--99288884(+) GACGGA/GGCAGC 1 -- int10--------
    rs2020182601,2
    C--99288979(+) AGAGGC/TGCTCC 1 -- int10--------

    HapMap Linkage Disequilibrium report for UBTD1 (99258625 - 99330966 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for UBTD1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv992861CNV Deletion20482838
    esv1218822CNV Deletion17803354
    nsv7509CNV Insertion18451855
    nsv7508CNV Loss18451855

    Site Specific Mutation Identification with PCR Assays
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    (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.)
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      --

    (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)
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    PubMed articles for UBTD1 gene, integrated from 10 sources (see all 16):
    (articles sorted by number of sources associating them with UBTD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)1, 2 Deloukas P.... Rogers J. (Nature 2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    5. The UbL protein UBTD1 stably interacts with the UBE2D family of E2 ubiquitin conjugating enzymes. (PubMed id 24211586)1 Uhler J.P....Gustafsson C.M. (Biochem. Biophys. Res. Commun. 2014)
    6. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    7. The P-body component USP52/PAN2 is a novel regulator of HIF1A mRNA stability. (PubMed id 23398456)1 Bett J.S....Hay R.T. (Biochem. J. 2013)
    8. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    9. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)
    10. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 80019 HGNC: 25683 AceView: UBTD1 Ensembl:ENSG00000165886 euGenes: HUgn80019
    ECgene: UBTD1 H-InvDB: UBTD1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for UBTD1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for UBTD1 gene:
    Search GeneIP for patents involving UBTD1

    GeneCards and IP:
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    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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     OriGene Antibodies for UBTD1   OriGene RNAi products in human, mouse, rat for UBTD1  
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     Block miRNA regulation of human, mouse, rat UBTD1 using miScript Target Protectors SeqTarget long-range PCR primers for resequencing UBTD1
     DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat UBTD1 Predesigned siRNA for gene silencing in human, mouse, rat UBTD1
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     Novus Tissue Slides
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     Browse ESI BIO Cell Lines and PureStem Progenitors for UBTD1
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     Browse compounds at ApexBio
     Search Addgene for plasmids for UBTD1
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     genOway: Develop your customized and physiologically relevant rodent model for UBTD1
     antibodies-online antibodies for UBTD1 (47 products)
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     antibodies-online proteins for UBTD1 (7 products)
           
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