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] See more...

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
  • Probable E3 Ubiquitin-Protein Ligase HERC3 3 4
  • HECT-Type E3 Ubiquitin Transferase HERC3 3 4
  • Hect Domain And RLD 3 2 3
  • KIAA0032 2 4
  • EC 2.3.2.26 4
  • EC 6.3.2 51
  • HERC3 5

External Ids for HERC3 Gene

Previous GeneCards Identifiers for HERC3 Gene

  • GC04P089671
  • GC04P089815
  • GC04P089906
  • GC04P089972
  • GC04P089870
  • GC04U900479
  • GC04P089513
  • GC04P085266
  • GC04P089444
  • GC04P088521
  • GC04P088592
  • GC04P088534

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. Diseases associated with HERC3 include Epidural Abscess. Among its related pathways are Ubiquitin mediated proteolysis and Innate Immune System. 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 Summary 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 , Rfam classification and piRNA Summary for HERC3 Gene

Genomics for HERC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HERC3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
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 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.2 +68.9 68891 3.4 CHD2 TBP MXD4 SP1 MNT SMAD5 ZFP64 MBD2 BHLHE40 ELF1 PYURF lnc-PYURF-2 HERC3 ENSG00000249755 PIGY FAM13A-AS1 RF00017-4362 NAP1L5
GH04J088522 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 -0.5 -531 3 TBP ZBTB10 SP1 MXD4 FEZF1 NR2C1 IKZF1 SMAD5 ETS1 IRF2 HERC3 PYURF PIGY PIGY-DT NAP1L5 MEPE NCOA4P2 lnc-HERC5-3 HERC5
GH04J088608 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 7.6 +87.8 87798 6 ZSCAN16 BCL11A FEZF1 NR2C1 IKZF1 CEBPB MAX IRF4 TRIM22 EP300 ENSG00000249755 PIGY PYURF NAP1L5 HERC3 FAM13A-AS1 PPM1K RF00017-4362 HSALNG0035767
GH04J088757 Promoter/Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 4.5 +234.9 234852 2.8 FEZF1 CEBPA IKZF1 FOXA2 SAP130 TAL1 YY1 ZFP91 BCL6 FOSL1 HSALNG0035772 lnc-NAP1L5-3 FAM13A-AS1 HERC3 NAP1L5 FAM13A TIGD2
GH04J087716 Enhancer 0.5 Ensembl ENCODE 5.9 -806.5 -806493 2.6 ATF2 HNF4A HERC3 IBSP piR-33432-390 piR-36588-318 ENSG00000249001 DMP1
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HERC3

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

Genomic Locations for HERC3 Gene

Latest Assembly
chr4:88,523,810-88,709,303
(GRCh38/hg38)
Size:
185,494 bases
Orientation:
Plus strand

Previous Assembly
chr4:89,444,994-89,629,690
(GRCh37/hg19 by Entrez Gene)
Size:
184,697 bases
Orientation:
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:
    Q15034-HERC3_HUMAN
    Recommended name:
    Probable E3 ubiquitin-protein ligase HERC3
    Protein Accession:
    Q15034
    Secondary Accessions:
    • A8K1S5
    • Q8IXX3

    Protein attributes for HERC3 Gene

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

    Alternative splice isoforms for HERC3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HERC3 Gene

Selected DME Specific Peptides for HERC3 Gene

Q15034:
  • FLLFLTGSDRIPI
  • NLLDLPKY
  • QVAAGGAHSF
  • GGVFTFGAG
  • EETFCLNFTI
  • NRQEFVDAYV
  • FPLALYKKLL

Post-translational modifications for HERC3 Gene

  • Ubiquitinated; which promotes degradation by the proteasome.
  • Ubiquitination at Lys63 and Lys920
  • Modification sites at PhosphoSitePlus

Antibodies for research

  • Abcam antibodies for HERC3
  • Boster Bio Antibodies for HERC3
  • Santa Cruz Biotechnology (SCBT) Antibodies for HERC3

Domains & Families for HERC3 Gene

Gene Families for HERC3 Gene

Protein Domains for HERC3 Gene

InterPro:
Blocks:
  • HECT domain (Ubiquitin-protein ligase)
  • Regulator of chromosome condensation, RCC1
ProtoNet:

Suggested Antigen Peptide Sequences for HERC3 Gene

GenScript: Design optimal peptide antigens:
  • HECT domain and RCC1-like domain-containing protein 3 (HERC3_HUMAN)
genes like me logo Genes that share domains with HERC3: view

No data available for Graphical View of Domain Structure and 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:
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=2.3.2.26;.

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:0004842 ubiquitin-protein transferase activity IEA --
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>

Inhibitory RNAs for research

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

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

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 HERC3 gene
Compartment Confidence
cytosol 5
nucleus 3
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endosome 1
lysosome 1

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: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.

Interacting Proteins for HERC3 Gene

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

10 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

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

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

No ASD Table

Relevant External Links for HERC3 Gene

GeneLoc Exon Structure for
HERC3

Expression for HERC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HERC3

SOURCE GeneReport for Unigene cluster for HERC3 Gene:

Hs.35804

Evidence on tissue expression from TISSUES for HERC3 Gene

  • Nervous system(4.8)
  • Skin(4.3)
  • Bone marrow(4.2)
genes like me logo Genes that share expression patterns with HERC3: view

Primer products for research

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.

Orthologs for HERC3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia HERC3 30
  • 98.16 (n)
Dog
(Canis familiaris)
Mammalia HERC3 30
  • 93.59 (n)
Cow
(Bos Taurus)
Mammalia HERC3 30
  • 91.97 (n)
Mouse
(Mus musculus)
Mammalia Herc3 30 17
  • 89.08 (n)
Rat
(Rattus norvegicus)
Mammalia Herc3 30
  • 89.08 (n)
Chicken
(Gallus gallus)
Aves HERC3 30
  • 79.62 (n)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia herc3 30
  • 72.06 (n)
Zebrafish
(Danio rerio)
Actinopterygii herc3 30
  • 64.91 (n)
Dr.16537 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7420 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG9153 32
  • 44 (a)
Worm
(Caenorhabditis elegans)
Secernentea herc-1 30
  • 47.12 (n)
Y48G8AL.1 32
  • 33 (a)
Species where no ortholog for HERC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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

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

Paralogs for HERC3 Gene

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

  • HERC3_HUMAN
  • C9J6Z1_HUMAN
  • C9J8E7_HUMAN
  • C9JFL2_HUMAN
  • C9JKA7_HUMAN
  • D6RAT5_HUMAN
  • F5GWU0_HUMAN
  • H0Y8G9_HUMAN
  • Q4W5H5_HUMAN
  • Q8IXX3_HUMAN
genes like me logo Genes that share paralogs with HERC3: view

Variants for HERC3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HERC3 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs187220478 Likely Benign: not provided 88,697,328(+) C/T
NM_153757.4(NAP1L5):c.427G>A (p.Glu143Lys)
MISSENSE_VARIANT,INTRON
rs1804080 - p.Glu946Gln

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for HERC3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
HERC3

SNP Genotyping and Copy Number Assays for research

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

Disorders for HERC3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for HERC3 Gene - From: COP

Disorder Aliases PubMed IDs
epidural abscess
  • abscess epidural
- elite association - COSMIC cancer census association via MalaCards
Search HERC3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HERC3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HERC3: view

No data available for 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 41
  2. HERC3 binding to and regulation by ubiquitin. (PMID: 11163799) Cruz C … Rosa JL (FEBS letters 2001) 3 4
  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
  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
  5. The midbody interactome reveals unexpected roles for PP1 phosphatases in cytokinesis. (PMID: 31586073) Capalbo L … D'Avino PP (Nature communications 2019) 3

Products for HERC3 Gene

Sources for HERC3 Gene