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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 4
  • EC 4
  • EC 6.3.2 56
  • 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. Among its related pathways are Innate Immune System and Class I MHC mediated antigen processing and presentation. Gene Ontology (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.

Additional gene information for UBE3B Gene

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

GeneHancer (GH) Regulatory Elements for UBE3B Gene

Promoters and enhancers for UBE3B Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J109475 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 620.8 -0.6 -601 4.4 ZFX CC2D1A MNT SIX5 ZNF148 NKRF ZNF121 POLR2A GTF2F1 CSDE1 KCTD10 UBE3B SART3 IFT81 RNU4-32P ALKBH2 FAM216A USP30 ARPC3 CORO1C
GH12J109993 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 28.2 +522.8 522826 12.7 SP1 ZFX CC2D1A ELF3 MNT SIX5 CBFA2T2 ZNF148 NKRF POLR2A ANKRD13A GIT2 ENSG00000280426 IFT81 RNU4-32P UBE3B ALKBH2 FAM216A ANAPC7 ARPC3
GH12J108626 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 20.1 -844.0 -843956 13.4 SP1 CC2D1A ZFX ELF3 ZKSCAN8 CBFA2T2 ZNF148 NKRF MLLT1 ZNF121 SELPLG GC12P108633 SART3 PWP1 PRDM4 UBE3B CORO1C FICD LOC101929162 TMEM119
GH12J109051 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 19.6 -424.0 -423977 3.3 ZNF473 SP1 ZFX ELF3 MNT SIX5 ZNF148 NKRF ZNF121 MLLT1 USP30 USP30-AS1 SART3 RNU4-32P UBE3B WSCD2 CORO1C TCHP KCTD10
GH12J109091 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 19.5 -384.4 -384415 2.3 SP1 CC2D1A CTCF ELF3 MNT ZNF148 NKRF POLR2A MLLT1 ZNF121 ALKBH2 SART3 UBE3B ACACB RNU4-32P GC12M109089 RNA5SP372 GC12P109058 GC12P109057
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around UBE3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the UBE3B gene promoter:
  • FAC1
  • GCNF
  • GCNF-1
  • GCNF-2
  • HOXA3
  • Nkx5-1
  • YY1

Genomic Locations for UBE3B Gene

Genomic Locations for UBE3B Gene
66,227 bases
Plus strand
59,301 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

Gene Families for UBE3B Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for UBE3B Gene

Suggested Antigen Peptide Sequences for UBE3B Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ51547, moderately similar to Homo sapiens ubiquitin protein ligase E3B (UBE3B), transcript variant 3, mRNA (B7Z6V9_HUMAN)
  • Ubiquitin protein ligase E3B (B9EK57_HUMAN)
  • Ubiquitin-protein ligase E3B (UBE3B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

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

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

Function for UBE3B Gene

Molecular function for UBE3B Gene

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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=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.; EC=;.

Enzyme Numbers (IUBMB) for UBE3B Gene

Phenotypes From GWAS Catalog 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:0005515 protein binding IEA --
GO:0016740 transferase activity IEA --
GO:0016874 ligase activity IEA --
GO:0061631 ubiquitin conjugating enzyme activity IBA 21873635
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 Models for UBE3B Gene

MGI Knock Outs for UBE3B:
  • Ube3b Ube3b<tm1a(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

miRNA for UBE3B Gene

Clone Products

  • Applied Biological Materials (abm): Clones for UBE3B - Now 50% OFF >
  • * UBE3B as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * UBE3B tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All
  • Addgene plasmids for UBE3B

No data available for 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nuclear speckles (2)
See all subcellular structures

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:0000209 protein polyubiquitination IBA 21873635
GO:0006511 ubiquitin-dependent protein catabolic process IBA 21873635
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, Investigational Nutra 0
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Pore Blocker, Potentiation 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE
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

Clone Products

  • Applied Biological Materials (abm): Clones for UBE3B - Now 50% OFF >
  • * UBE3B as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * UBE3B tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All
  • Addgene plasmids for UBE3B

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, 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(2.2)
  • Heart(2.1)
  • Eye(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

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 35 34
  • 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 17 34 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 35 34
  • 73.76 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005897 34
  • 55.28 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5087 35 36 34
  • 54.9 (n)
(Caenorhabditis elegans)
Secernentea oxi-1 35 34
  • 47.65 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HUL5 35
  • 26 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 9 (a)
Cin.14141 34
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)
Evolutionary constrained regions (ECRs) for UBE3B: view image

Paralogs for UBE3B Gene

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

  • B7Z6V9_HUMAN
  • B9EK57_HUMAN
  • F5H5T5_HUMAN
  • F5H6D6_HUMAN
  • S4R3H8_HUMAN
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 Variation AA Info Type
rs1304422857 pathogenic, Inborn genetic diseases 109,511,304(+) G/A/T genic_downstream_transcript_variant, splice_donor_variant
rs1555269815 pathogenic, Kaufman oculocerebrofacial syndrome 109,524,504(+) G/A downstream_transcript_variant, genic_downstream_transcript_variant, splice_donor_variant
rs398123020 pathogenic, Kaufman oculocerebrofacial syndrome 109,509,716(+) T/C genic_downstream_transcript_variant, splice_donor_variant
rs398123021 pathogenic, Kaufman oculocerebrofacial syndrome 109,521,290(+) AGAGAG/AGAG coding_sequence_variant, frameshift, genic_downstream_transcript_variant, non_coding_transcript_variant
rs398123022 pathogenic, Kaufman oculocerebrofacial syndrome 109,489,917(+) A/G splice_acceptor_variant

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)

Additional Variant Information for UBE3B Gene

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

SNP Genotyping and Copy Number Assay Products

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: HGMD, OMIM, ClinVar, GTR, Swiss-Prot, DISEASES, and GeneCards

- 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.

Additional Disease Information for UBE3B

Genetic Association Database
Human Genome Epidemiology 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 (American journal of human genetics 2012) 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Characterization of the human UBE3B gene: structure, expression, evolution, and alternative splicing. (PMID: 12837265) Gong TW … Lomax MI (Genomics 2003) 3 4 58
  5. Kaufman oculocerebrofacial syndrome: Novel UBE3B mutations and clinical features in four unrelated patients. (PMID: 29160006) Yilmaz R … Borck G (American journal of medical genetics. Part A 2018) 3 58

Products for UBE3B Gene

Sources for UBE3B Gene