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Aliases for UBE3B Gene

Aliases for UBE3B Gene

  • Ubiquitin Protein Ligase E3B 2 3 5
  • HECT-Type Ubiquitin Transferase E3B 3 4
  • Ubiquitin-Protein Ligase E3B 3
  • EC 4
  • EC 6.3.2 61
  • BPIDS 3
  • KOS 3

External Ids for UBE3B Gene

Previous GeneCards Identifiers for UBE3B Gene

  • GC12P108973
  • GC12P109754
  • GC12P108378
  • GC12P109915
  • GC12P106933

Summaries for UBE3B Gene

Entrez Gene Summary for UBE3B Gene

  • The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes, and E3 ubiquitin-protein ligases. This gene encodes a member of the E3 ubiquitin-conjugating enzyme family which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme and transfers the ubiquitin to the targeted substrates. A HECT (homology to E6-AP C-terminus) domain in the C-terminus of the longer isoform of this protein is the catalytic site of ubiquitin transfer and forms a complex with E2 conjugases. Shorter isoforms of this protein which lack the C-terminal HECT domain are therefore unlikely to bind E2 enzymes. Alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2012]

GeneCards Summary for UBE3B Gene

UBE3B (Ubiquitin Protein Ligase E3B) is a Protein Coding gene. Diseases associated with UBE3B include Kaufman Oculocerebrofacial Syndrome and Blepharophimosis-Intellectual Disability Syndrome Due To Ube3b Deficiency. Among its related pathways are Innate Immune System and Class I MHC mediated antigen processing and presentation. GO annotations related to this gene include ligase activity and ubiquitin-protein transferase activity. An important paralog of this gene is UBE3C.

UniProtKB/Swiss-Prot for UBE3B Gene

  • E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UBE3B Gene

Genomics for UBE3B Gene

Regulatory Elements for UBE3B Gene

Enhancers for UBE3B 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
GH12G109827 1.6 FANTOM5 Ensembl ENCODE 45.6 +351.2 351161 1.7 HDGF CREB3L1 ZFP64 FEZF1 TCF12 ZNF121 GLIS2 ZNF766 GATA2 ZNF263 UBE3B FAM216A KCTD10 GIT2 ANKRD13A ALKBH2 RNU4-32P PPP1CC MYO1H ANAPC7
GH12G108793 1.2 ENCODE dbSUPER 45.5 -683.3 -683309 1.5 ZNF473 ZFP64 ARID4B RAD21 RARA ZNF121 ZNF366 ZNF354C PCBP1 ZNF202 SART3 UBE3B KCTD10 CORO1C SELPLG ALKBH2 RNU4-32P MYO1H LOC101929204 PIR53281
GH12G109501 0.9 dbSUPER 56.9 +26.3 26279 3.5 NFIB ZFP64 ZNF121 ZNF366 ZNF138 ZNF354C ZNF350 ZNF202 ZNF680 ZNF654 SART3 UBE3B KCTD10 FAM216A RNU4-32P ANAPC7 MYO1H ENSG00000255655 MVK MMAB
GH12G108587 1 ENCODE 42.7 -888.4 -888386 2.4 HDGF ATF1 ZNF493 YBX1 TCF12 GATA2 FOS ZNF548 YY2 ZNF488 SART3 PWP1 UBE3B ALKBH2 PRDM4 RNU4-32P WSCD2 USP30 LOC101929162 SELPLG
GH12G108626 2.1 FANTOM5 Ensembl ENCODE dbSUPER 20.1 -838.5 -838539 24.2 CREB3L1 MLX ZFP64 DMAP1 FEZF1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 PWP1 CORO1C SART3 PRDM4 UBE3B FICD KCTD10 SELPLG TMEM119 RPL17P38
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around UBE3B on UCSC Golden Path with GeneCards custom track

Promoters for UBE3B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for UBE3B Gene

109,477,402 bp from pter
109,543,628 bp from pter
66,227 bases
Plus strand

Genomic View for UBE3B Gene

Genes around UBE3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UBE3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UBE3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UBE3B Gene

Proteins for UBE3B Gene

  • Protein details for UBE3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Ubiquitin-protein ligase E3B
    Protein Accession:
    Secondary Accessions:
    • A5D8Z3
    • Q05BX9
    • Q659F7
    • Q7Z7Q1
    • Q9BXZ4

    Protein attributes for UBE3B Gene

    1068 amino acids
    Molecular mass:
    123098 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for UBE3B Gene


neXtProt entry for UBE3B Gene

Selected DME Specific Peptides for UBE3B Gene


Post-translational modifications for UBE3B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for UBE3B Gene

Protein Domains for UBE3B Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with UBE3B: view

No data available for Gene Families and UniProtKB/Swiss-Prot for UBE3B Gene

Function for UBE3B Gene

Molecular function for UBE3B 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 an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Enzyme Numbers (IUBMB) for UBE3B Gene

Gene Ontology (GO) - Molecular Function for UBE3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IEA --
GO:0016740 transferase activity IEA --
GO:0016874 ligase activity IEA --
genes like me logo Genes that share ontologies with UBE3B: view
genes like me logo Genes that share phenotypes with UBE3B: view

Human Phenotype Ontology for UBE3B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for UBE3B Gene

Inhibitory RNA Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for UBE3B Gene

Localization for UBE3B Gene

Subcellular locations from

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 UBE3B gene
Compartment Confidence
mitochondrion 3
nucleus 3
cytosol 2
plasma membrane 1
extracellular 1
peroxisome 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for UBE3B Gene

Pathways & Interactions for UBE3B Gene

genes like me logo Genes that share pathways with UBE3B: view

UniProtKB/Swiss-Prot Q7Z3V4-UBE3B_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for UBE3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with UBE3B: view

No data available for SIGNOR curated interactions for UBE3B Gene

Drugs & Compounds for UBE3B Gene

(3) Drugs for UBE3B Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
Adenosine triphosphate Approved Nutra 0

(1) Additional Compounds for UBE3B Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
genes like me logo Genes that share compounds with UBE3B: view

Transcripts for UBE3B Gene

Unigene Clusters for UBE3B Gene

Ubiquitin protein ligase E3B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for UBE3B Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^
SP1: - - - - - -
SP2: - - - -
SP3: - - - -
SP4: - -
SP5: - - -
SP6: -
SP7: - - - -
SP8: - -

ExUns: 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29

Relevant External Links for UBE3B Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for UBE3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for UBE3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for UBE3B Gene

This gene is overexpressed in Heart (22.7), Platelet (10.7), and Frontal cortex (8.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for UBE3B Gene

NURSA nuclear receptor signaling pathways regulating expression of UBE3B Gene:


SOURCE GeneReport for Unigene cluster for UBE3B Gene:


mRNA Expression by UniProt/SwissProt for UBE3B Gene:

Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for UBE3B Gene

  • Nervous system(4.8)
  • Lung(4.3)
  • Skin(4.3)
  • Kidney(2.3)
  • Muscle(2.1)
  • Heart(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for UBE3B Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • epiglottis
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • skull
  • tooth
  • vocal cord
  • aorta
  • chest wall
  • clavicle
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • trachea
  • biliary tract
  • duodenum
  • intestine
  • large intestine
  • pancreas
  • small intestine
  • stomach
  • pelvis
  • rectum
  • vagina
  • vulva
  • digit
  • femur
  • finger
  • foot
  • hand
  • hip
  • lower limb
  • thigh
  • toe
  • upper limb
  • blood
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with UBE3B: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for UBE3B Gene

Orthologs for UBE3B Gene

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

Orthologs for UBE3B Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia UBE3B 34 35
  • 99.5 (n)
(Canis familiaris)
Mammalia UBE3B 34 35
  • 91.23 (n)
(Bos Taurus)
Mammalia UBE3B 34 35
  • 89.7 (n)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 88 (a)
-- 35
  • 75 (a)
-- 35
  • 70 (a)
(Rattus norvegicus)
Mammalia Ube3b 34
  • 86.36 (n)
(Mus musculus)
Mammalia Ube3b 34 16 35
  • 86.11 (n)
(Monodelphis domestica)
Mammalia UBE3B 35
  • 84 (a)
(Gallus gallus)
Aves -- 35
  • 97 (a)
-- 35
  • 96 (a)
-- 35
  • 88 (a)
LOC776286 34
  • 78.03 (n)
(Anolis carolinensis)
Reptilia UBE3B 35
  • 67 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ube3b 34
  • 74.44 (n)
(Danio rerio)
Actinopterygii ube3b 34 35
  • 73.76 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005897 34
  • 55.28 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5087 36 34 35
  • 54.9 (n)
(Caenorhabditis elegans)
Secernentea oxi-1 34 35
  • 47.65 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HUL5 35
  • 26 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 9 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.14141 34
Species where no ortholog for UBE3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)

Evolution for UBE3B Gene

Gene Tree for UBE3B (if available)
Gene Tree for UBE3B (if available)

Paralogs for UBE3B Gene

Paralogs for UBE3B Gene

(5) SIMAP similar genes for UBE3B Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with UBE3B: view

Variants for UBE3B Gene

Sequence variations from dbSNP and Humsavar for UBE3B Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs398123023 Pathogenic, Kaufman oculocerebrofacial syndrome (KOS) [MIM:244450] 109,521,251(+) TGATC(A/C)AGACG nc-transcript-variant, reference, missense
rs398123020 Pathogenic 109,509,716(+) GTAGG(C/T)AAGAG downstream-variant-500B, splice-donor-variant
rs398123021 Pathogenic 109,521,294(+) AAGAG(-/AG)TTTTT nc-transcript-variant, reference, frameshift-variant
rs398123022 Pathogenic 109,489,917(+) TCTTT(A/G)GGTGA splice-acceptor-variant
rs672601304 Pathogenic 109,483,552(+) CAAAC(A/G)TGTTC nc-transcript-variant, reference, missense, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for UBE3B Gene

Variant ID Type Subtype PubMed ID
esv3630719 CNV gain 21293372
nsv560118 CNV loss 21841781

Variation tolerance for UBE3B Gene

Residual Variation Intolerance Score: 1.16% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.85; 48.09% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for UBE3B Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UBE3B Gene

Disorders for UBE3B Gene

MalaCards: The human disease database

(10) MalaCards diseases for UBE3B Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
kaufman oculocerebrofacial syndrome
  • blepharophimosis-ptosis-intellectual disability
blepharophimosis-intellectual disability syndrome due to ube3b deficiency
  • blepharophimosis, ptosis, and epicanthus inversus
  • blepharoptosis
wilson-turner syndrome
  • wilson-turner x-linked mental retardation syndrome
- elite association - COSMIC cancer census association via MalaCards
Search UBE3B in MalaCards View complete list of genes associated with diseases


  • Kaufman oculocerebrofacial syndrome (KOS) [MIM:244450]: A syndrome characterized by blepharophimosis, ptosis, mild upslanting of the palpebral fissures, epicanthus, ectodermal anomalies, developmental delay, and severe intellectual disability with absent speech. Proportionate growth retardation with a small head circumference/microcephaly, congenital malformations, muscular hypotonia, anomalies on brain imaging with hypoplasia of the corpus callosum, and low cholesterol levels are variably present. {ECO:0000269 PubMed:23200864}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for UBE3B

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with UBE3B: view

No data available for Genatlas for UBE3B Gene

Publications for UBE3B Gene

  1. Deficiency for the ubiquitin ligase UBE3B in a blepharophimosis-ptosis-intellectual-disability syndrome. (PMID: 23200864) Basel-Vanagaite L. … Borck G. (Am. J. Hum. Genet. 2012) 3 4 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. Characterization of the human UBE3B gene: structure, expression, evolution, and alternative splicing. (PMID: 12837265) Gong T.-W.L. … Lomax M.I. (Genomics 2003) 3 4 64
  5. UBE3B Is a Calmodulin-regulated, Mitochondrion-associated E3 Ubiquitin Ligase. (PMID: 28003368) Braganza A. … Sobol R.W. (J. Biol. Chem. 2017) 3 64

Products for UBE3B Gene

Sources for UBE3B Gene

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