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UBD Gene

protein-coding   GIFtS: 54

GC06M029634
ubiquitin D
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
Diubiquitin 3
FAT10 1, 2, 3, 5
GABBR1 2
OTTHUMP00000029427 2
UBD-3 2
diubiquitin 2
Descriptions
Ubiquitin-like protein FAT10 3
ubiquitin D 2
External Ids
HGNC: 187951
Entrez Gene: 105372
UniProtKB: O152053
Ensembl: ENSG000002138867
Search outside databases for aliases for UBD gene

Previous GC identifers: GC06M029580 GC06M029294 GC06M029632 GC06M029633 GC06Mc29667

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Gene Wiki entry for UBD
(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)
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Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the UBD gene  

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p22.1   HGNC cytogenetic band: 6p21.3

UBD 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 6         GeneLoc Exon Structure

GeneLoc location for GC06M029634:     (about GC identifiers)

Start:
29,631,387 bp from pter
End:
29,635,681 bp from pter
Size:
4,295 bases
Orientation:
minus strand

2 alternative locations:
Chr6-,c6_COX 29,667,268-29,671,562      Chr6-,c6_QBL 29,666,182-29,670,477     
RefSeq DNA sequence:
NC_000006.10  NT_007592.14  NT_113891.1  NT_113893.1  
(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)
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UniProtKB/Swiss-Prot: UBD_HUMAN, O15205 (See protein sequence)
Recommended Name: Ubiquitin D  
Size: 165 amino acids; 18457 Da
Subunit: Interacts with MAD2
Secondary accessions: B0UZT6 Q5SUK2 Q96EC7

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_006389.2  

    ENSEMBL proteins: 
    ENSP00000366249 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Millipore Purified and/or Recombinant UBD Protein
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Enzo Life Sciences proteins for UBD
    Recombinant Proteins from Abcam (Diubiquitin)
    Human Recombinant Proteins from Abnova (UBD)
                  OriGene Purified Recombinant Human Protein: UBD 


    Antibodies for UBD: 
    Browse Antibodies Central at Invitrogen
    Millipore Mono- and Polyclonal Antibodies for the study of UBD
    Sigma-Aldrich Antibodies for UBD
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (Diubiquitin), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (UBD)
    Novus Biologicals Antibody for UBD

    Assays for UBD: 
    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

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

    2 InterPro domains/families:
     IPR000626 Ubiquitin
     IPR019956 Ubiquitin_subgroup


       GeneDecks  UBD for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry O15205

    ProtoNet protein and cluster: O15205

    1 Blocks protein family: IPB000626 Ubiquitin domain

    UniProtKB/Swiss-Prot: UBD_HUMAN, O15205
    Similarity: Contains 2 ubiquitin-like domains

    (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 (UBD)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_006398

                  Applied Biosystems Silencer® siRNAs for UBD

                  Sigma-Aldrich siRNA and siRNA Panels for UBD  
                         Sigma-Aldrich shRNA Panels and shRNA for UBD  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for UBD
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_006398
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_006398
                                     untagged cDNA clone in CMV expression vector: NM_006398 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_006398

    2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Ubd):

    cellularimmune system

    (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


    1 Millipore Pathway for UBD
     Selected targets of p53

       GeneDecks  UBD for the pathways selected above  
    About GeneDecksing

    5/9 Sigma-Aldrich "Your Favorite Gene" Pathways for  UBD  (Your Favorite Gene powered by Ingenuity) (see all 9
     Cell Cycle: G2/M DNA Damage Checkpoint Regulation
     GABA Receptor Signaling
     TGF-&beta
     Hypoxia Signaling in the Cardiovascular System
     Protein Ubiquitination Pathway

       GeneDecks  UBD for the pathways selected above  
    About GeneDecksing

     Gene Network CentralTM Interacting Genes and Proteins Network for  UBD 

      --

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006464 protein modification process NAS9368598
    GO:0006508 proteolysis NAS9368598
    GO:0019941 modification-dependent protein catabolic process IEA--
    About this table
    (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 UBD

    (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 (UBD)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_006398

                  Sigma-Aldrich siRNA and siRNA Panels for UBD  
                         Sigma-Aldrich shRNA Panels and shRNA for UBD  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_006398  

    REFSEQ mRNAs for UBD gene: 

    NM_006398.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_006398  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_006398
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_006398
                                     untagged cDNA clone in CMV expression vector: NM_006398 

    Additional cDNA sequence: 

    AF123050.1 AK311914.1 BC012472.1 Y12653.1 

    6 DOTS entries:

    DT.100645165  DT.112373  DT.121390472  DT.95368176  DT.95359346  DT.92324520 

    24/255 AceView cDNA sequences (see all 255 ):

    BX644916 AA583465 BM717516 AW264022 BM929866 BX431259 BG818076 BE047768 
    AU280038 BM661640 NM_021904 AL602784 BF476724 CF552729 AJ012185 NM_021903 
    Y11044 BX111922 BM702959 BC023336 NM_001470 AJ225029 BG910376 AW105586 

    highest scoring ESTs for UBD:

    AF123050 AI133610 BC012472 BG290370 BX280913 CB985708 Y12653 AW383833 U37231 AW270961 

    Unigene Cluster for UBD:

    Ubiquitin D
    Hs.719331  [show with all ESTs]
    Unigene Representative Sequence: NM_006398


    GeneLoc Exon Structure

    1 Ensembl transcript including schematic representation:
    ENST00000377050  
    (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

    UBD expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for UBD

    1 / 2 / 3

    3 probe-sets matching UBD gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    39959_at2, 3 U95-A 3 1.00 0.34 1.00 1.00 AL031983 0.20 0.25 0.23 1

    205890_s_at2, 3 U133-A 3 1.00 0.33 -- -- NM_006398 0.60 0.83 0.73 1

    205890_s_at2 U133Plus2 3 1.00 0.33 -- -- -- -- -- -- --
    GeneDecks  UBD 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: --

    SOURCE GeneReport for Unigene cluster: Hs.719331

    Expression variation in blood from EXPOLDB for UBD

    (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 UBD gene from 4 species
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    chimpanzee
    (Pan troglodytes)
    UBD1   -- ubiquitin D 98.59(n)
    96.36(a)
    471944  XM_527322.2  XP_527322.2 
    cow
    (Bos taurus)
    UBD1   -- ubiquitin D 79.75(n)
    72.15(a)
    504548  XM_580689.3  XP_580689.1 
    rat
    (Rattus norvegicus)
    Ubd1   -- ubiquitin D 76.67(n)
    76.25(a)
    29168  NM_053299.1  NP_445751.1 
    mouse
    (Mus musculus)
    Ubd1, 5 175
    ubiquitin D1, 5 75.64(n)1
    73.08(a)1
    241081  NM_023137.21  NP_075626.11 
     AF3140885  AK0081165  (see all 10)
    About this table        Species with no ortholog for UBD

    ENSEMBL Gene Tree for UBD
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

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


    10/57 NCBI SNPs in UBD are shown (see all 57 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 88)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 6 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs20764851,2
    A,C,F,H,O29631931(-) TGGCAC/TTGACA 1 I/T mis114Minor allele frequency- N:0.00EU EA WA MN NA 1214
    rs20764841,2
    A,C,F,H29631982(-) TCTTTT/CGCTGG 1 S/L mis118Minor allele frequency- C:0.17NS MN NA EU EA WA 1248
    rs20764871,2
    A,C,F,H29631838(-) TGAGGC/GAAAGA 1 A/G mis113Minor allele frequency- G:0.19MN NA EU EA WA 1144
    rs3625131,2
    A,C,F,H29636297(-) CTCACT/CAAATA 1 -- ng319Minor allele frequency- C:0.31EU EA WA NS 1004
    rs77579311,2
    A,C,F,H29631649(+) CAATAC/AAATAA 1 F/C mis112Minor allele frequency- A:0.30MN NA EA WA EU 1016
    rs83371,2
    A,C,F,H29631655(-) GGCATC/GTTATT 1 S/C mis121Minor allele frequency- N:0.00MN EU EA WA NA 2122
    rs20764861,2
    A,C,F,H29631851(-) TGGAGT/CCAGGT 1 P/S mis19Minor allele frequency- C:0.17MN NA EU EA WA 718
    rs4440131,2
    A,C,F,H29631625(-) CTGGGG/CATGGG 1 -- ut319Minor allele frequency- C:0.34MN EU EA WA NA 788
    rs22729911,2
    A,C,F,H29635578(-) CAAAGA/GGCACA 1 -- ut515Minor allele frequency- G:0.18EA EU WA 1852
    rs9951851,2
    A,C,F,H29637116(-) TGGCTT/ATGGGC 1 -- ng318Minor allele frequency- A:0.43EA NA EU WA 554
    About this table

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

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

    OMIM: 606050

    2 Novoseek disease relationships for UBD gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    cancer 9.21 7 12730673 (4), 10602013 (1), 16495226 (1)
    tumors 0.00 2 18280469 (1), 12730673 (1)
    About this table

    Human Genome Epidemiology Navigator: UBD (2 documents)

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

      --

    (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

    10/59 PubMed articles for UBD gene (see all 59 ):
    (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, and/or H-InvDB)
    About This Section

    Entrez Gene: 10537 HGNC: 18795 AceView: GABBR1andUBD Ensembl:ENSG00000213886 euGenes: HUgn10537
    ECgene: UBD H-InvDB: UBD
    (According to HUGE)
    About This Section

      --
    (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

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

      --
    (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 UBD:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
      Invitrogen Antibodies  Invitrogen Assays
      Invitrogen Clones  Invitrogen Q-PCR Products
      Invitrogen Human Recombinant Kinases  Invitrogen Custom Antibody and Peptide Service
      Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for UBD-related products

     Millipore Custom Antibody & Bulk Services
     Millipore Preclinical / Clinical Development Services
     Millipore Immunoassay Services
     Millipore Target Screening & Profiling Services


     Predesigned and custom siRNAs for UBD Antibodies for UBD
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for UBD Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
     Antibodies   Primer Pairs  
     Cell Culture Products   ELISAs  
     Flow Cytometry Kits   Protease Activity Assays & Reagents  
     Cell Selection/Detection Kits & Reagents   ELISA/Assay Development Kits & Reagents  
     Multiplex/Array Assay Kits & Reagents   ELISpot Kits & Development Modules  
     Recombinant & Natural Proteins  

     Recombinant Proteins (UBD)
     Antibodies (UBD)
     Search for Chimera RNAi
     Custom Service for Mouse Mab
     Custom Service for Rabbit Pab from Full-length Protein
      
     Search for Antibodies & Assays

     Recombinant Proteins
    (Diubiquitin)
     Antibodies (Diubiquitin)
     Tagged/untagged cDNA clones
     Validated SYBR primer pairs
     Purified proteins from HEK293T cells
     Western blot validated antibodies
     shRNA in GFP-retroviral vector
     Search Tocris compounds for UBD




     Proteins for UBD
     Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
     Antibodies for UBD

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