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Aliases for HERC3 Gene

Aliases for HERC3 Gene

  • HECT And RLD Domain Containing E3 Ubiquitin Protein Ligase 3 2 3 5
  • HECT Domain And RCC1-Like Domain-Containing Protein 3 3 4
  • HECT-Type E3 Ubiquitin Transferase HERC3 3 4
  • Hect Domain And RLD 3 2 3
  • Probable E3 Ubiquitin-Protein Ligase HERC3 3
  • EC 4
  • KIAA0032 4

External Ids for HERC3 Gene

Previous GeneCards Identifiers for HERC3 Gene

  • GC04P089671
  • GC04P089815
  • GC04P089906
  • GC04P089972
  • GC04P089870
  • GC04U900479
  • GC04P089513
  • GC04P085266
  • GC04P089444
  • GC04P088521

Summaries for HERC3 Gene

Entrez Gene Summary for HERC3 Gene

  • This gene encodes a member the HERC ubiquitin ligase family. The encoded protein is located in the cytosol and binds ubiquitin via a HECT domain. Mutations in this gene have been associated with colorectal and gastric carcinomas. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]

GeneCards Summary for HERC3 Gene

HERC3 (HECT And RLD Domain Containing E3 Ubiquitin Protein Ligase 3) is a Protein Coding gene. Among its related pathways are Class I MHC mediated antigen processing and presentation and Ubiquitin mediated proteolysis. Gene Ontology (GO) annotations related to this gene include ligase activity and ubiquitin-protein transferase activity. An important paralog of this gene is HERC4.

UniProtKB/Swiss-Prot for HERC3 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 HERC3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HERC3 Gene

Genomics for HERC3 Gene

GeneHancer (GH) Regulatory Elements for HERC3 Gene

Promoters and enhancers for HERC3 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
GH04J088591 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.3 332 3.1 PKNOX1 CLOCK ZFP64 ARID4B SIN3A ZNF2 YY1 ZNF143 FOS SP3 PYURF GC04M088591 HERC3 PIGY LOC100129137 FAM13A-AS1 ENSG00000285385 GC04M088685 RNU6-33P
GH04J088230 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 10.3 -361.0 -361049 1.8 NFIC ABCG2 LOC105369192 PPM1K RNU6-112P LOC100129137 PIGY PYURF RNU6ATAC31P HERC3 RNU6-1298P
GH04J088658 Enhancer 1 Ensembl ENCODE 12.5 +68.3 68343 3.8 ELF3 FOXA2 ARID4B RAD21 ZNF143 RCOR1 FOS ZNF654 RXRA CEBPB HERC3 PIGY PYURF LOC100129137 NAP1L5 FAM13A-AS1 RNU6-33P GC04M088685
GH04J088608 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 7.8 +19.2 19185 6 PKNOX1 SMAD1 FEZF1 IRF4 ATF7 FOS RUNX3 JUNB ZNF518A ATF4 LOC100129137 PIGY PYURF NAP1L5 HERC3 FAM13A-AS1 PPM1K RNU6-33P GC04M088685 ENSG00000285385
GH04J088615 Enhancer 0.9 Ensembl ENCODE dbSUPER 11.4 +24.6 24565 2.2 JUND POLR2A STAT3 CEBPB EP300 HERC3 LOC100129137 PYURF PIGY HERC6 RNU6-33P GC04M088685 ENSG00000285385
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HERC3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HERC3 gene promoter:
  • AREB6
  • FOXL1
  • p53
  • Brachyury
  • Pax-4a
  • POU3F2
  • FOXO4
  • POU6F1 (c2)
  • MEF-2A
  • aMEF-2

Genomic Locations for HERC3 Gene

Genomic Locations for HERC3 Gene
116,875 bases
Plus strand
187,495 bases
Plus strand

Genomic View for HERC3 Gene

Genes around HERC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HERC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HERC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HERC3 Gene

Proteins for HERC3 Gene

  • Protein details for HERC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Probable E3 ubiquitin-protein ligase HERC3
    Protein Accession:
    Secondary Accessions:
    • A8K1S5
    • Q8IXX3

    Protein attributes for HERC3 Gene

    1050 amino acids
    Molecular mass:
    117188 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA04945.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for HERC3 Gene


neXtProt entry for HERC3 Gene

Post-translational modifications for HERC3 Gene

  • Ubiquitinated; which promotes degradation by the proteasome.
  • Ubiquitination at isoforms=920 and Lys63
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HERC3 Gene

Domains & Families for HERC3 Gene

Gene Families for HERC3 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for HERC3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with HERC3: view

No data available for UniProtKB/Swiss-Prot for HERC3 Gene

Function for HERC3 Gene

Molecular function for HERC3 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:
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.

Enzyme Numbers (IUBMB) for HERC3 Gene

Phenotypes From GWAS Catalog for HERC3 Gene

Gene Ontology (GO) - Molecular Function for HERC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016740 transferase activity IEA --
GO:0061630 ubiquitin protein ligase activity IBA --
genes like me logo Genes that share ontologies with HERC3: view
genes like me logo Genes that share phenotypes with HERC3: view

Animal Models for HERC3 Gene

MGI Knock Outs for HERC3:
  • Herc3 Herc3<tm1a(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

miRNA for HERC3 Gene

miRTarBase miRNAs that target HERC3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HERC3

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HERC3 Gene

Localization for HERC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HERC3 Gene

Cytoplasm. Cytoplasmic vesicle. Note=Also found in vesicular-like structures.

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 HERC3 gene
Compartment Confidence
cytosol 5
nucleus 3

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HERC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005829 cytosol IDA --
GO:0031410 cytoplasmic vesicle IEA --
genes like me logo Genes that share ontologies with HERC3: view

Pathways & Interactions for HERC3 Gene

genes like me logo Genes that share pathways with HERC3: view

UniProtKB/Swiss-Prot Q15034-HERC3_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for HERC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with HERC3: view

No data available for SIGNOR curated interactions for HERC3 Gene

Drugs & Compounds for HERC3 Gene

No Compound Related Data Available

Transcripts for HERC3 Gene

mRNA/cDNA for HERC3 Gene

(12) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(10) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HERC3 Gene

HECT and RLD domain containing E3 ubiquitin protein ligase 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HERC3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HERC3 Gene

No ASD Table

Relevant External Links for HERC3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HERC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HERC3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HERC3 Gene

This gene is overexpressed in Urine (13.4), Platelet (13.3), Colon muscle (12.1), Plasma (10.6), and Stomach (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HERC3 Gene

NURSA nuclear receptor signaling pathways regulating expression of HERC3 Gene:


SOURCE GeneReport for Unigene cluster for HERC3 Gene:


Evidence on tissue expression from TISSUES for HERC3 Gene

  • Nervous system(4.7)
  • Bone marrow(4.2)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with HERC3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HERC3 Gene

Orthologs for HERC3 Gene

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

Orthologs for HERC3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HERC3 33
  • 98.16 (n)
(Canis familiaris)
Mammalia HERC3 34 33
  • 93.59 (n)
(Monodelphis domestica)
Mammalia HERC3 34
  • 92 (a)
(Bos Taurus)
Mammalia HERC3 34 33
  • 91.97 (n)
(Mus musculus)
Mammalia Herc3 16 34 33
  • 89.08 (n)
(Rattus norvegicus)
Mammalia Herc3 33
  • 89.08 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 18 (a)
(Gallus gallus)
Aves HERC3 34 33
  • 79.62 (n)
(Anolis carolinensis)
Reptilia HERC3 34
  • 81 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia herc3 33
  • 72.06 (n)
(Danio rerio)
Actinopterygii herc3 34 33
  • 64.91 (n)
Dr.16537 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7420 33
fruit fly
(Drosophila melanogaster)
Insecta CG9153 34 35
  • 44 (a)
(Caenorhabditis elegans)
Secernentea herc-1 34 33
  • 47.12 (n)
Y48G8AL.1 35
  • 33 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HUL4 34
  • 22 (a)
Species where no ortholog for HERC3 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)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 HERC3 Gene

Gene Tree for HERC3 (if available)
Gene Tree for HERC3 (if available)
Evolutionary constrained regions (ECRs) for HERC3: view image

Paralogs for HERC3 Gene

(17) SIMAP similar genes for HERC3 Gene using alignment to 10 proteins:

  • C9J6Z1_HUMAN
  • C9J8E7_HUMAN
  • H0Y8G9_HUMAN
  • Q4W5H5_HUMAN
genes like me logo Genes that share paralogs with HERC3: view

Variants for HERC3 Gene

Sequence variations from dbSNP and Humsavar for HERC3 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000009906 -- 88,623,147(+) C/G genic_upstream_transcript_variant, intron_variant
rs1000078195 -- 88,622,034(+) A/G genic_upstream_transcript_variant, intron_variant
rs10000885 -- 88,665,040(+) C/A genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000110501 -- 88,674,272(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000119420 -- 88,617,154(+) A/C genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HERC3 Gene

Variant ID Type Subtype PubMed ID
dgv2850n106 CNV deletion 24896259
esv1953449 CNV deletion 18987734
esv2278581 CNV deletion 18987734
esv2640318 CNV deletion 19546169
esv2657218 CNV deletion 23128226
esv2727952 CNV deletion 23290073
esv2727953 CNV deletion 23290073
esv3564216 CNV deletion 23714750
esv5387 CNV loss 18987735
nsv1073354 CNV deletion 25765185
nsv291508 CNV deletion 16902084
nsv461575 CNV gain 19166990
nsv461576 CNV gain 19166990
nsv594805 CNV gain 21841781
nsv594806 CNV gain 21841781

Variation tolerance for HERC3 Gene

Residual Variation Intolerance Score: 6.67% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.28; 85.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HERC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HERC3 Gene

Disorders for HERC3 Gene

Additional Disease Information for HERC3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for HERC3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HERC3 Gene

Publications for HERC3 Gene

  1. 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 44 58
  2. HERC3 binding to and regulation by ubiquitin. (PMID: 11163799) Cruz C … Rosa JL (FEBS letters 2001) 3 4 58
  3. The human HERC3 gene maps to chromosome 4q21 by fluorescence in situ hybridization. (PMID: 10702688) Cruz C … Rosa JL (Cytogenetics and cell genetics 1999) 2 3 58
  4. Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1. (PMID: 7584026) Nomura N … Tabata S (DNA research : an international journal for rapid publication of reports on genes and genomes 1994) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for HERC3 Gene

Sources for HERC3 Gene

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