Aliases for HDDC3 Gene

Aliases for HDDC3 Gene

  • HD Domain Containing 3 2 3 5
  • MESH1 2 3 4
  • Guanosine-3',5'-Bis(Diphosphate) 3'-Pyrophosphohydrolase MESH1 3 4
  • Penta-Phosphate Guanosine-3'-Pyrophosphohydrolase 3 4
  • HD Domain-Containing Protein 3 3 4
  • Metazoan SpoT Homolog 1 3 4
  • (PpGpp)Ase 3 4
  • EC 4
  • MGC45386 2
  • HDDC3 5

External Ids for HDDC3 Gene

Previous GeneCards Identifiers for HDDC3 Gene

  • GC15M089276
  • GC15M091474
  • GC15M067585

Summaries for HDDC3 Gene

GeneCards Summary for HDDC3 Gene

HDDC3 (HD Domain Containing 3) is a Protein Coding gene. Among its related pathways are Metabolism and Metabolism of nucleotides. Gene Ontology (GO) annotations related to this gene include guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity.

UniProtKB/Swiss-Prot Summary for HDDC3 Gene

Additional gene information for HDDC3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HDDC3 Gene

Genomics for HDDC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HDDC3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HDDC3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HDDC3

Top Transcription factor binding sites by QIAGEN in the HDDC3 gene promoter:
  • AML1a
  • AP-4
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Nkx5-1

Genomic Locations for HDDC3 Gene

Genomic Locations for HDDC3 Gene
5,229 bases
Minus strand
1,652 bases
Minus strand

Genomic View for HDDC3 Gene

Genes around HDDC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HDDC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HDDC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HDDC3 Gene

Proteins for HDDC3 Gene

  • Protein details for HDDC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1
    Protein Accession:

    Protein attributes for HDDC3 Gene

    179 amino acids
    Molecular mass:
    20329 Da
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for HDDC3 Gene

    Alternative splice isoforms for HDDC3 Gene


neXtProt entry for HDDC3 Gene

Post-translational modifications for HDDC3 Gene

  • Ubiquitination at Lys123
  • Modification sites at PhosphoSitePlus

Other Protein References for HDDC3 Gene

No data available for DME Specific Peptides for HDDC3 Gene

Domains & Families for HDDC3 Gene

Gene Families for HDDC3 Gene

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

Protein Domains for HDDC3 Gene

  • Metal-dependent phosphohydrolase, HD region

Suggested Antigen Peptide Sequences for HDDC3 Gene

GenScript: Design optimal peptide antigens:
  • Penta-phosphate guanosine-3'-pyrophosphohydrolase (MESH1_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the MESH1 family.
  • Belongs to the MESH1 family.
genes like me logo Genes that share domains with HDDC3: view

Function for HDDC3 Gene

Molecular function for HDDC3 Gene

UniProtKB/Swiss-Prot Function:
ppGpp hydrolyzing enzyme involved in starvation response.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=guanosine 3',5'-bis(diphosphate) + H2O = diphosphate + GDP + H(+); Xref=Rhea:RHEA:14253, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:33019, ChEBI:CHEBI:58189, ChEBI:CHEBI:77828; EC=; Evidence={ECO:0000269|PubMed:20818390};.

Enzyme Numbers (IUBMB) for HDDC3 Gene

Gene Ontology (GO) - Molecular Function for HDDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0008893 guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity IBA 21873635
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with HDDC3: view
genes like me logo Genes that share phenotypes with HDDC3: view

Animal Models for HDDC3 Gene

MGI Knock Outs for HDDC3:
  • Hddc3 Hddc3<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

miRNA for HDDC3 Gene

miRTarBase miRNAs that target HDDC3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HDDC3

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HDDC3 Gene

Localization for HDDC3 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 HDDC3 gene
Compartment Confidence
nucleus 3
cytosol 3
mitochondrion 2
plasma membrane 1
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for HDDC3 Gene

Pathways & Interactions for HDDC3 Gene

PathCards logo

SuperPathways for HDDC3 Gene

SuperPathway Contained pathways
1 Metabolism
2 Metabolism of nucleotides
genes like me logo Genes that share pathways with HDDC3: view

Pathways by source for HDDC3 Gene

2 KEGG pathways for HDDC3 Gene

Gene Ontology (GO) - Biological Process for HDDC3 Gene


No data available for SIGNOR curated interactions for HDDC3 Gene

Drugs & Compounds for HDDC3 Gene

(2) Drugs for HDDC3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Guanosine diphosphate Experimental Pharma 0

(2) Additional Compounds for HDDC3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Guanosine 3',5'-bis(diphosphate)
  • Guanosine 3'-diphosphate 5'-diphosphate
  • Guanosine 5'-diphosphate,3'-diphosphate
  • GUANOSINE-5',3'-tetraphosphATE
  • Guanosine 3'-diphosphoric acid 5'-diphosphoric acid
  • Guanosine 3',5'-bis(diphosphoric acid)
  • [(ho)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • PYROphosphATE
genes like me logo Genes that share compounds with HDDC3: view

Transcripts for HDDC3 Gene

mRNA/cDNA for HDDC3 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HDDC3

Alternative Splicing Database (ASD) splice patterns (SP) for HDDC3 Gene

No ASD Table

Relevant External Links for HDDC3 Gene

GeneLoc Exon Structure for

Expression for HDDC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HDDC3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Lung (Respiratory System)

Protein differential expression in normal tissues from HIPED for HDDC3 Gene

This gene is overexpressed in Skin (12.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HDDC3 Gene

Protein tissue co-expression partners for HDDC3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HDDC3

SOURCE GeneReport for Unigene cluster for HDDC3 Gene:

genes like me logo Genes that share expression patterns with HDDC3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HDDC3 Gene

Orthologs for HDDC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for HDDC3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HDDC3 30 31
  • 99.44 (n)
(Bos Taurus)
Mammalia HDDC3 30 31
  • 91.99 (n)
(Canis familiaris)
Mammalia HDDC3 30 31
  • 91.06 (n)
(Mus musculus)
Mammalia Hddc3 30 17 31
  • 87.71 (n)
(Rattus norvegicus)
Mammalia Hddc3 30
  • 86.78 (n)
(Monodelphis domestica)
Mammalia HDDC3 31
  • 61 (a)
(Gallus gallus)
Aves HDDC3 31
  • 41 (a)
(Anolis carolinensis)
Reptilia HDDC3 31
  • 57 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia hddc3 30
  • 68.9 (n)
(Danio rerio)
Actinopterygii hddc3 30 31
  • 66.29 (n)
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10177 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012646 30
  • 62.59 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Mesh1 30 31
  • 59.92 (n)
(Caenorhabditis elegans)
Secernentea ZK909.3 30 31
  • 57.92 (n)
Species where no ortholog for HDDC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • 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 HDDC3 Gene

Gene Tree for HDDC3 (if available)
Gene Tree for HDDC3 (if available)
Evolutionary constrained regions (ECRs) for HDDC3: view image

Paralogs for HDDC3 Gene

No data available for Paralogs for HDDC3 Gene

Variants for HDDC3 Gene

Additional dbSNP identifiers (rs#s) for HDDC3 Gene

Structural Variations from Database of Genomic Variants (DGV) for HDDC3 Gene

Variant ID Type Subtype PubMed ID
nsv515661 CNV loss 19592680
nsv833089 CNV loss 17160897
nsv833090 CNV loss 17160897

Variation tolerance for HDDC3 Gene

Residual Variation Intolerance Score: 76.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.52; 29.53% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HDDC3 Gene

Human Gene Mutation Database (HGMD)
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 and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HDDC3 Gene

Disorders for HDDC3 Gene

No disorders were found for HDDC3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HDDC3 Gene

Publications for HDDC3 Gene

  1. A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses. (PMID: 20818390) Sun D … Chung J (Nature structural & molecular biology 2010) 2 3 4
  2. Analysis of the DNA sequence and duplication history of human chromosome 15. (PMID: 16572171) Zody MC … Nusbaum C (Nature 2006) 3 4
  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
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations. (PMID: 31515488) Fragoza R … Yu H (Nature communications 2019) 3

Products for HDDC3 Gene

  • Signalway Proteins for HDDC3

Sources for HDDC3 Gene