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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
  • HECT-Type E3 Ubiquitin Transferase E3D 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 2.3.2.26 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. Among its related pathways are Class I MHC mediated antigen processing and presentation and Innate Immune System. 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.

Additional gene information for UBE3D Gene

No data available for Entrez Gene Summary , CIViC 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
GH06H083866 1.7 FANTOM5 Ensembl ENCODE 31 -802.1 -802082 2 PKNOX1 FEZF1 ZNF2 CBX5 ZNF302 ZNF416 ZNF143 FOS ZNF548 CEBPZ CEP162 DOPEY1 UBE3D RWDD2A RIPPLY2 CYB5R4 PIR41363 GC06P083900
GH06H082259 1 ENCODE 21.2 +804.1 804143 3 PKNOX1 ARNT FEZF1 ZNF2 ZNF121 GLIS2 ZNF302 KLF7 FOS SP3 DOPEY1 UBE3D LOC100132659 IBTK TPBG PGM3 GC06P082262
GH06H082396 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10 +667.7 667714 3 TBP INSM2 FEZF1 ZNF2 ZBTB40 ZNF366 FOS ZNF391 RUNX3 SP3 DOPEY1 TPBG UBE3D GC06M082379 GC06M082439
GH06H083215 1.1 Ensembl ENCODE 11.7 -149.9 -149868 1 RB1 INSM2 ARID4B ZNF2 RAD21 YY1 ZNF143 RCOR1 RUNX3 ZNF654 PRSS35 RWDD2A PGM3 DOPEY1 UBE3D GC06M083097 GC06P083243
GH06H083127 0.4 ENCODE 11.3 -62.1 -62127 0 MAFK DOPEY1 UBE3D PGM3 RWDD2A
- Elite enhancer and/or Elite enhancer-gene association 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
ENSR00000199475 340 1400 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 CBX5

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

Gene Families for UBE3D Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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

Function for UBE3D Gene

Molecular function for UBE3D Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.
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

Phenotypes From GWAS Catalog for UBE3D Gene

Gene Ontology (GO) - Molecular Function for UBE3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016740 transferase activity IEA --
GO:0030332 cyclin binding IPI 15749827
GO:0044390 ubiquitin-like protein conjugating enzyme binding IPI 15749827
GO:0061630 ubiquitin protein ligase activity IDA 15749827
genes like me logo Genes that share ontologies with UBE3D: view
genes like me logo Genes that share phenotypes with UBE3D: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for UBE3D
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for UBE3D gene
Compartment Confidence
nucleus 2
cytosol 2
plasma membrane 1
extracellular 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for UBE3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000151 ubiquitin ligase complex IDA 15749827
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:0000209 protein polyubiquitination IDA 15749827
GO:0006513 protein monoubiquitination IDA 15749827
GO:0016567 protein ubiquitination IEA --
GO:0051865 protein autoubiquitination IDA 15749827
genes like me logo Genes that share ontologies with UBE3D: view

No data available for SIGNOR curated interactions for UBE3D Gene

Drugs & Compounds for UBE3D Gene

No Compound Related Data Available

Transcripts for UBE3D Gene

Unigene Clusters for UBE3D Gene

Ubiquitin protein ligase E3D:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for UBE3D
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 CGAP 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

Evidence on tissue expression from TISSUES for UBE3D Gene

  • Bone marrow(4.2)
  • Blood(4)
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 , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 98.89 (n)
dog
(Canis familiaris)
Mammalia UBE3D 33 34
  • 87.73 (n)
cow
(Bos Taurus)
Mammalia UBE3D 33 34
  • 83.2 (n)
mouse
(Mus musculus)
Mammalia Ube2cbp 33 16 34
  • 82.07 (n)
rat
(Rattus norvegicus)
Mammalia Ube3d 33
  • 80.81 (n)
oppossum
(Monodelphis domestica)
Mammalia UBE3D 34
  • 65 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia UBE3D 34
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves UBE2CBP 33
  • 62.18 (n)
UBE3D 34
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia UBE3D 34
  • 51 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ube3d 33
  • 57.64 (n)
zebrafish
(Danio rerio)
Actinopterygii ube3d 33 34
  • 48.88 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes IPA1 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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
rs1000019849 -- 83,056,922(+) TTGAC(A/G)TAATT intron-variant
rs1000030866 -- 83,009,595(+) AGTAG(A/G)AATAC intron-variant
rs1000032400 -- 82,921,211(+) GGCCT(C/T)CCAAA intron-variant
rs1000074211 -- 83,015,068(+) CACAA(C/G)TTGGC intron-variant
rs1000121421 -- 82,928,801(+) TCCAT(A/G)TGGTA intron-variant

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

Relevant External Links for UBE3D

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
UBE3D

No disorders were found for UBE3D Gene.

No data available for MalaCards , 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 (Journal of biochemistry 2005) 2 3 4 60
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  3. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. (PMID: 27173435) Boldt K … UK10K Rare Diseases Group (Nature communications 2016) 3 60
  4. Genome-wide association study of biologically informed periodontal complex traits offers novel insights into the genetic basis of periodontal disease. (PMID: 26962152) Offenbacher S … North KE (Human molecular genetics 2016) 3 60
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 60

Products for UBE3D Gene

Sources for UBE3D Gene

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