Free for academic non-profit institutions. Other users need a Commercial license

Aliases for UBE3D Gene

Aliases for UBE3D Gene

  • Ubiquitin Protein Ligase E3D 2 3 5
  • Ubiquitin-Conjugating Enzyme E2C-Binding Protein 3 4
  • UBCH10 Binding Protein With A Hect-Like Domain 2 3
  • UbcH10-Binding Protein With A HECT-Like Domain 3 4
  • C6orf157 3 4
  • UBE2CBP 3 4
  • H10BH 3 4
  • Ubiquitin-Conjugating Enzyme E2C Binding Protein 2
  • Chromosome 6 Open Reading Frame 157 2
  • E3 Ubiquitin-Protein Ligase E3D 3
  • EC 6.3.2.- 4
  • YJR141W 3

External Ids for UBE3D Gene

Previous HGNC Symbols for UBE3D Gene

  • C6orf157
  • UBE2CBP

Previous GeneCards Identifiers for UBE3D Gene

  • GC06M083603

Summaries for UBE3D Gene

GeneCards Summary for UBE3D Gene

UBE3D (Ubiquitin Protein Ligase E3D) is a Protein Coding gene. Diseases associated with UBE3D include Periodontitis 1, Juvenile. Among its related pathways are Immune System and Class I MHC mediated antigen processing and presentation. GO annotations related to this gene include ligase activity.

UniProtKB/Swiss-Prot for UBE3D Gene

  • 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.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UBE3D Gene

Genomics for UBE3D Gene

Regulatory Elements for UBE3D Gene

Enhancers for UBE3D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F083215 1.2 Ensembl ENCODE 11.7 -149.9 -149879 1.0 CTCF SAP130 TEAD4 INSM2 ARID4B CEBPG EBF1 ZNF2 RAD21 ZNF101 PRSS35 RWDD2A PGM3 DOPEY1 UBE3D GC06M083097 GC06P083243
GH06F083127 0.6 ENCODE 11.3 -62.1 -62127 0.6 MAFK UBE3D DOPEY1 PGM3 RWDD2A ENSG00000281446
GH06F083221 0.5 FANTOM5 2.3 -155.9 -155934 0.2 ZNF362 ZNF512 PRDM1 PRSS35 PGM3 RWDD2A UBE3D GC06M083097 GC06P083243
GH06F083064 0.5 ENCODE 0.8 +0.2 221 1.7 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 KLF13 RWDD2A UBE3D GC06M083015 PIR40475
GH06F083047 0.2 ENCODE 0.3 +18.3 18272 0.5 RFX1 CBX3 TEAD4 TRIM28 DOPEY1 UBE3D GC06M083015 PIR40475
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around UBE3D on UCSC Golden Path with GeneCards custom track

Promoters for UBE3D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001882588 541 1801 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 KLF13
ENSR00001221369 1740 200 ZNF524 ZBTB33 MLLT1

Genomic Location for UBE3D Gene

Chromosome:
6
Start:
82,892,398 bp from pter
End:
83,065,841 bp from pter
Size:
173,444 bases
Orientation:
Minus strand

Genomic View for UBE3D Gene

Genes around UBE3D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UBE3D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UBE3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UBE3D Gene

Proteins for UBE3D Gene

  • Protein details for UBE3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z6J8-UBE3D_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase E3D
    Protein Accession:
    Q7Z6J8
    Secondary Accessions:
    • B4DP63
    • Q5T4W2
    • Q6IPR4
    • Q75UG0
    • Q9NT42

    Protein attributes for UBE3D Gene

    Size:
    389 amino acids
    Molecular mass:
    43657 Da
    Quaternary structure:
    • Interacts with UBE2C/UbcH10 (E2 ubiquitin-conjugating enzyme). In vitro, interacts with cyclin-B.
    SequenceCaution:
    • Sequence=AAH53645.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAI13740.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAI15282.2; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAM28304.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for UBE3D Gene

Post-translational modifications for UBE3D Gene

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

No data available for DME Specific Peptides for UBE3D Gene

Domains & Families for UBE3D Gene

Protein Domains for UBE3D Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for UBE3D Gene

Graphical View of Domain Structure for InterPro Entry

Q7Z6J8

UniProtKB/Swiss-Prot:

UBE3D_HUMAN :
  • 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.
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.
genes like me logo Genes that share domains with UBE3D: view

No data available for Gene Families for UBE3D Gene

Function for UBE3D Gene

Molecular function for UBE3D Gene

UniProtKB/Swiss-Prot 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 Numbers (IUBMB) for UBE3D Gene

Gene Ontology (GO) - Molecular Function for UBE3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016874 ligase activity IEA --
genes like me logo Genes that share ontologies with UBE3D: view

Phenotypes for UBE3D Gene

genes like me logo Genes that share phenotypes with UBE3D: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for UBE3D Gene

Localization for UBE3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for UBE3D Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for UBE3D Gene COMPARTMENTS Subcellular localization image for UBE3D gene
Compartment Confidence
cytosol 2
nucleus 2
extracellular 1
mitochondrion 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for UBE3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with UBE3D: view

Pathways & Interactions for UBE3D Gene

genes like me logo Genes that share pathways with UBE3D: view

UniProtKB/Swiss-Prot Q7Z6J8-UBE3D_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for UBE3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with UBE3D: view

No data available for SIGNOR curated interactions for UBE3D Gene

Transcripts for UBE3D Gene

Unigene Clusters for UBE3D Gene

Ubiquitin protein ligase E3D:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for UBE3D Gene

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

Relevant External Links for UBE3D Gene

GeneLoc Exon Structure for
UBE3D
ECgene alternative splicing isoforms for
UBE3D

Expression for UBE3D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for UBE3D Gene

Protein differential expression in normal tissues from HIPED for UBE3D Gene

This gene is overexpressed in Liver (47.8) and Platelet (21.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for UBE3D Gene



Protein tissue co-expression partners for UBE3D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of UBE3D Gene:

UBE3D

SOURCE GeneReport for Unigene cluster for UBE3D Gene:

Hs.148609
genes like me logo Genes that share expression patterns with UBE3D: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for UBE3D Gene

Orthologs for UBE3D Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for UBE3D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia UBE2CBP 34 35
  • 98.89 (n)
dog
(Canis familiaris)
Mammalia UBE3D 34 35
  • 87.73 (n)
cow
(Bos Taurus)
Mammalia UBE3D 34 35
  • 83.2 (n)
mouse
(Mus musculus)
Mammalia Ube2cbp 34 16 35
  • 82.07 (n)
rat
(Rattus norvegicus)
Mammalia Ube3d 34
  • 80.81 (n)
oppossum
(Monodelphis domestica)
Mammalia UBE3D 35
  • 65 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia UBE3D 35
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves UBE2CBP 34
  • 62.18 (n)
UBE3D 35
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia UBE3D 35
  • 51 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ube3d 34
  • 57.64 (n)
zebrafish
(Danio rerio)
Actinopterygii ube3d 34 35
  • 48.88 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes IPA1 37
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 25 (a)
OneToOne
Species where no ortholog for UBE3D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for UBE3D Gene

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

Paralogs for UBE3D Gene

(1) SIMAP similar genes for UBE3D Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with UBE3D: view

No data available for Paralogs for UBE3D Gene

Variants for UBE3D Gene

Sequence variations from dbSNP and Humsavar for UBE3D Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs10080327 -- 82,886,242(+) AGACA(A/G)TTTTT intron-variant
rs1016886 -- 82,989,726(+) CCCAT(A/T)TGCCC intron-variant
rs10455136 -- 82,975,729(+) CTAAC(C/T)TAAAA intron-variant
rs10455137 -- 82,985,760(+) cagca(C/T)cccaa intron-variant
rs10455412 -- 82,944,597(+) aaagg(A/G)gactt intron-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for UBE3D Gene

Variant ID Type Subtype PubMed ID
dgv387n21 CNV loss 19592680
esv1525166 CNV insertion 17803354
esv2234898 CNV deletion 18987734
esv2510248 CNV deletion 19546169
esv2674545 CNV deletion 23128226
esv2675870 CNV deletion 23128226
esv2732360 CNV deletion 23290073
esv3426435 CNV insertion 20981092
esv3540070 CNV deletion 23714750
esv3571273 CNV loss 25503493
esv3609770 CNV loss 21293372
esv3609771 CNV loss 21293372
esv3609772 CNV loss 21293372
nsv1022371 CNV loss 25217958
nsv1026095 CNV gain 25217958
nsv1030196 CNV loss 25217958
nsv1073992 CNV deletion 25765185
nsv478729 CNV novel sequence insertion 20440878
nsv528433 CNV loss 19592680

Variation tolerance for UBE3D Gene

Residual Variation Intolerance Score: 56.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.68; 78.51% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for UBE3D Gene

Human Gene Mutation Database (HGMD)
UBE3D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
UBE3D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UBE3D Gene

Disorders for UBE3D Gene

MalaCards: The human disease database

(1) MalaCards diseases for UBE3D Gene - From: DISEASES

Disorder Aliases PubMed IDs
periodontitis 1, juvenile
  • aggressive periodontitis
- elite association - COSMIC cancer census association via MalaCards
Search UBE3D in MalaCards View complete list of genes associated with diseases

Relevant External Links for UBE3D

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
UBE3D
genes like me logo Genes that share disorders with UBE3D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for UBE3D Gene

Publications for UBE3D Gene

  1. A novel UbcH10-binding protein facilitates the ubiquitinylation of cyclin B in vitro. (PMID: 15749827) Kobirumaki F. … Tanaka H. (J. Biochem. 2005) 2 3 4 64
  2. Whole-exome sequencing implicates UBE3D in age-related macular degeneration in East Asian populations. (PMID: 25872646) Huang L.Z. … Li X.X. (Nat Commun 2015) 3 64
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64
  4. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3 64
  5. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PMID: 22814378) Van Damme P. … Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012) 4 64

Products for UBE3D Gene

Sources for UBE3D Gene

Content
Loading form....