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UBE3D Gene

protein-coding   GIFtS: 39
GCID: GC06M083603

Ubiquitin Protein Ligase E3D

(Previous names: chromosome 6 open reading frame 157, ubiquitin-conjugating...)
(Previous symbols: C6orf157, UBE2CBP)
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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 Protein Ligase E3D1 2     UbcH10-Binding Protein With A HECT-Like Domain2 3
UBE2CBP1 2 3 5     Ubiquitin-Conjugating Enzyme E2C-Binding Protein2 3
C6orf1571 2 3     Chromosome 6 Open Reading Frame 1571
H10BH2 3 5     YJR141W2
Ubiquitin-Conjugating Enzyme E2C Binding Protein1 2     E3 Ubiquitin-Protein Ligase E3D2
UBCH10 Binding Protein With A Hect-Like Domain1 2     EC 6.3.2.-3

External Ids:    HGNC: 213811   Entrez Gene: 900252   Ensembl: ENSG000001184207   OMIM: 6124955   UniProtKB: Q7Z6J83   

Export aliases for UBE3D gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for UBE3D Gene:
UBE3D (ubiquitin protein ligase E3D) is a protein-coding gene. GO annotations related to this gene include ligase activity.

UniProtKB/Swiss-Prot: UBE3D_HUMAN, Q7Z6J8
Function: E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and
transfers it to substrates, generally promoting their degradation by the proteasome




(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_000006.11  NT_025741.16  NC_018917.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for UBE3D
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidUBE3D promoter sequence
   Search Chromatin IP Primers for UBE3D

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat UBE3D


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

Entrez Gene cytogenetic band: 6q14.1   Ensembl cytogenetic band:  6q14.1   HGNC cytogenetic band: 6q15

UBE3D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UBE3D gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M083603:  view genomic region     (about GC identifiers)

Start:
83,602,117 bp from pter      End:
83,775,560 bp from pter
Size:
173,444 bases      Orientation:
minus 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: UBE3D_HUMAN, Q7Z6J8 (See protein sequence)
Recommended Name: E3 ubiquitin-protein ligase E3D  
Size: 389 amino acids; 43657 Da
Subunit: Interacts with UBE2C/UbcH10 (E2 ubiquitin-conjugating enzyme). In vitro, interacts with cyclin-B
Sequence caution: Sequence=AAH53645.1; Type=Erroneous initiation; Sequence=CAI13740.2; Type=Erroneous gene model
prediction; Sequence=CAI15282.2; Type=Erroneous gene model prediction; Sequence=CAM28304.1; Type=Erroneous gene
model prediction;
Secondary accessions: B4DP63 Q5T4W2 Q6IPR4 Q75UG0 Q9NT42

Explore the universe of human proteins at neXtProt for UBE3D: NX_Q7Z6J8

Explore proteomics data for UBE3D at MOPED

Post-translational modifications: 

  • Ubiquitinated by UBCH10 (E2 ubiquitin-conjugating enzyme)1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See UBE3D Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_944602.1  
    ENSEMBL proteins: 
     ENSP00000358762   ENSP00000237186   ENSP00000427101   ENSP00000394749   ENSP00000358761  
     ENSP00000422755   ENSP00000358760  

    UBE3D Human Recombinant Protein Products:

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    Browse Proteins at Cloud-Clone Corp.

     
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    antibodies-online proteins for UBE3D (2 products) 

     
    antibodies-online peptides for UBE3D

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    antibodies-online kits for UBE3D (8 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR019193 UBQ-conj_enz_E2-bd_prot

    Graphical View of Domain Structure for InterPro Entry Q7Z6J8

    ProtoNet protein and cluster: Q7Z6J8

    UniProtKB/Swiss-Prot: UBE3D_HUMAN, Q7Z6J8
    Domain: The C-terminal half (AA 188-389) is able to bind cyclin-B and shows a self-ubiquitination activity (mono-,
    poly, or multi-ubiquitination) in a HECT-like sequence dependent manner


    Find genes that share domains with UBE3D           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: UBE3D_HUMAN, Q7Z6J8
    Function: E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and
    transfers it to substrates, generally promoting their degradation by the proteasome

         Enzyme Number (IUBMB): EC 6.3.2.-1

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016874ligase activity IEA--
         
    Find genes that share ontologies with UBE3D           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for UBE3D

    miRNA
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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 UniProtKB/Swiss-Prot
    UBE3D_HUMAN, Q7Z6J8: Cytoplasm (Potential)

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--

    Find genes that share ontologies with UBE3D           About GenesLikeMe


    (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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    UniProtKB/Swiss-Prot: UBE3D_HUMAN, Q7Z6J8
    Pathway: Protein modification; protein ubiquitination

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for UBE3D
    Interactions:

        Search GeneGlobe Interaction Network for UBE3D

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for UBE3D (ENSP000002371864) via UniProtKB, MINT, STRING, and/or I2D

    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCNB1ENSP000002564424STRING: ENSP00000256442
    UBE2CENSP000003488384STRING: ENSP00000348838
    RRP12ENSP000003600314STRING: ENSP00000360031
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    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016567protein ubiquitination IEA--

    Find genes that share ontologies with UBE3D           About GenesLikeMe



    (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 UBE3D



    (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 UBE3D gene: 
    NM_198920.1  

    Unigene Cluster for UBE3D:

    Ubiquitin protein ligase E3D
    Hs.148609  [show with all ESTs]
    Unigene Representative Sequence: BC036049
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000369747(uc003pjp.2 uc011dyx.1) ENST00000237186 ENST00000503942
    ENST00000509102 ENST00000430071 ENST00000369746(uc003pjq.3) ENST00000505226(uc003pjr.3)
    ENST00000369745
    miRNA
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    Inhib. RNA
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    Primer
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      QuantiFast Probe-based Assays in human, mouse, rat UBE3D

    Additional mRNA sequence: 

    AB126062.1 AF026526.1 AK298205.1 AL137544.1 BC036049.1 BC053645.1 BC057845.1 BC071763.1 
    BC101512.1 BC101538.1 BC143617.1 

    7 DOTS entries:

    DT.101979664  DT.99962609  DT.86998464  DT.92423695  DT.441685  DT.70101584  DT.40278814 

    Selected AceView cDNA sequences (see all 63):

    AB126062 AW469373 CR604323 AI478251 BE552206 AV692609 AA706678 BG150480 
    CR590287 AW611839 BU619285 CR598717 AL137544 AI025408 BQ421993 BF438997 
    NM_198920 AI744564 AI825544 BI771255 AA136385 AI051333 BI906212 BE777478 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for UBE3D    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11
    SP1:              -                 -                                                   
    SP2:                                -                                                   
    SP3:                                                                                    


    ECgene alternative splicing isoforms for UBE3D

    (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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    UBE3D expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTCTTTTGT
    UBE3D Expression
    About this image

    UBE3D Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    UBE3D Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.148609
        Custom PCR Arrays for UBE3D
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    In Situ
    Assay Products:
     

     
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    (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 chordates.

    Orthologs for UBE3D gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ube2cbp1 , 5 ubiquitin-conjugating enzyme E2C binding protein1, 5 82.07(n)1
    78.53(a)1
      9 (46.58 cM)5
    703481  NM_027394.21  NP_081670.11 
     863072345 
    chicken
    (Gallus gallus)
    Aves UBE2CBP1 ubiquitin-conjugating enzyme E2C binding protein 62.18(n)
    54.88(a)
      421843  XM_419864.4  XP_419864.4 
    lizard
    (Anolis carolinensis)
    Reptilia UBE3D6
    ubiquitin protein ligase E3D
    51(a)
    1 ↔ 1
    1(197836370-197857026)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia ube3d1 ubiquitin protein ligase E3D 57.64(n)
    48.26(a)
      100489753  XM_002938455.2  XP_002938501.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ube3d1 ubiquitin protein ligase E3D 48.88(n)
    39.95(a)
      553294  XM_005157858.1  XP_005157915.1 


    ENSEMBL Gene Tree for UBE3D (if available)
    TreeFam Gene Tree for UBE3D (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for UBE3D gene
    1 SIMAP similar gene for UBE3D using alignment to 5 protein entries:     UBE3D_HUMAN (see all proteins):
    UBE2CBP

    Find genes that share paralogs with UBE3D           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 UBE3D (see all 3141)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1481899811,2
    --83601719(+) CGAGAA/GCTAAA 1 -- int10--------
    rs341082791,2
    C--83601734(+) AAAAAA/-GTGTT 1 -- int11Minor allele frequency- -:0.00NA 2
    rs357864551,2
    C--83601734(+) ATCTC-/AAAAAA 1 -- int10--------
    rs69316521,2
    C,F,A,H--83601795(+) AGATAT/CATCAG 1 -- int116Minor allele frequency- C:0.28NA EA NS WA CSA 1147
    rs1508978791,2
    C--83601825(+) GCCAAC/TTGAGC 1 -- int10--------
    rs1590401,2
    C,F,A,H--83601877(-) TTCCTA/GCTCCA 1 -- int122Minor allele frequency- G:0.50NS EA NA WA CSA 2349
    rs1383298191,2
    --83601906(+) GATGGA/GTCAGA 1 -- int10--------
    rs1877091821,2
    --83601924(+) CAGAGA/GAGATG 1 -- int10--------
    rs1439507491,2
    --83601937(+) CATGCC/GTGGCT 1 -- int10--------
    rs1922020851,2
    --83602016(+) GCTAGC/TGTGTA 1 -- int10--------

    HapMap Linkage Disequilibrium report for UBE3D (83602117 - 83775560 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for UBE3D: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing UBE3D
    DNA2.0 Custom Variant and Variant Library Synthesis for UBE3D

    (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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    OMIM gene information: 612495    OMIM disorders: --


    Find genes that share disorders with UBE3D           About GenesLikeMe


    Export disorders for UBE3D 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)
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    PubMed articles for UBE3D gene integrated from 10 sources:
    (articles sorted by number of sources associating them with UBE3D)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A novel UbcH10-binding protein facilitates the ubiquitinylation of cyclin B in vitro. (PubMed id 15749827)1, 2, 3 Kobirumaki F.... Tanaka H. (J. Biochem. 2005)
    2. 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)
    3. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    4. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    5. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    8. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)2 Mungall A.J.... Beck S. (Nature 2003)
    9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 90025 HGNC: 21381 AceView: C6orf157 Ensembl:ENSG00000118420 euGenes: HUgn90025
    ECgene: UBE3D H-InvDB: UBE3D

    (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 UBE3D 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 UBE3D gene:
    Search GeneIP for patents involving UBE3D

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (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
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