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Aliases for HDDC3 Gene

Aliases for HDDC3 Gene

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

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 Pyrimidine metabolism (KEGG). GO annotations related to this gene include guanosine-3,5-bis(diphosphate) 3-diphosphatase activity.

UniProtKB/Swiss-Prot for HDDC3 Gene

  • ppGpp hydrolyzing enzyme involved in starvation response.

Additional gene information for HDDC3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HDDC3 Gene

Genomics for HDDC3 Gene

Regulatory Elements for HDDC3 Gene

Enhancers for HDDC3 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
GH15H090835 1.9 FANTOM5 Ensembl ENCODE dbSUPER 11.4 +93.2 93246 6.8 HDGF FOXA2 ARNT ZNF766 CBX5 FOS REST ZNF592 MEF2D SMARCA4 UNC45A FES BLM FURIN VPS33B-DT LOC100631255 MAN2A2 HDDC3 ENSG00000200677 VPS33B
GH15H090829 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.4 +102.0 101993 2.6 BCOR HDGF ZMYM3 RELA ZNF316 EED NFE2 IKZF2 MAZ ZNF687 FES UNC45A FURIN VPS33B-DT HDDC3 ENSG00000200677 IQGAP1 LOC105370969 GC15M090794
GH15H090834 0.9 ENCODE dbSUPER 11.4 +97.7 97692 0.5 BCOR STAT1 SOX6 NR4A1 CEBPB ZEB2 CTBP1 ZNF316 MTA3 IKZF1 FURIN FES VPS33B-DT UNC45A HDDC3 ENSG00000200677 LOC105370969 GC15M090794
GH15H090986 0.6 ENCODE 10.9 -54.4 -54437 0.2 ZNF362 ZSCAN5C NBN CREB1 ATF7 MLLT1 DPF2 VPS33B-DT VPS33B ENSG00000224441 HDDC3 UNC45A PRC1 GC15M090978 ENSG00000200142
GH15H090928 1.4 Ensembl ENCODE 0.7 +2.0 1989 5.2 HDGF PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 UNC45A RCCD1 ENSG00000259212 ENSG00000259314 MAN2A2 FES HDDC3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HDDC3 on UCSC Golden Path with GeneCards custom track

Promoters for HDDC3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000278966 369 801 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF207 ZNF143

Genomic Locations for HDDC3 Gene

Genomic Locations for HDDC3 Gene
2,606 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 isoforms=2123
  • 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

Suggested Antigen Peptide Sequences for HDDC3 Gene

GenScript: Design optimal peptide antigens:

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 CatalyticActivity:
Guanosine 3,5-bis(diphosphate) + H(2)O = guanosine 5-diphosphate + diphosphate.
UniProtKB/Swiss-Prot Function:
ppGpp hydrolyzing enzyme involved in starvation response.

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 IEA --
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:

Animal Model Products

miRNA for HDDC3 Gene

miRTarBase miRNAs that target HDDC3

Clone Products

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

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

SuperPathways for HDDC3 Gene

SuperPathway Contained pathways
1 Pyrimidine metabolism (KEGG)
genes like me logo Genes that share pathways with HDDC3: view

Pathways by source for HDDC3 Gene

1 KEGG pathway 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)
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
genes like me logo Genes that share compounds with HDDC3: view

Transcripts for HDDC3 Gene

Unigene Clusters for HDDC3 Gene

HD domain containing 3:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for HDDC3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HDDC3 Gene

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

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, PaxDb, MaxQB, and MOPED for HDDC3 Gene

Protein tissue co-expression partners for HDDC3 Gene

NURSA nuclear receptor signaling pathways regulating expression of HDDC3 Gene:


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 expression in embryonic tissues and stem cells from LifeMap Discovery , 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 34 33
  • 99.44 (n)
(Bos Taurus)
Mammalia HDDC3 34 33
  • 91.99 (n)
(Canis familiaris)
Mammalia HDDC3 34 33
  • 91.06 (n)
(Mus musculus)
Mammalia Hddc3 34 16 33
  • 87.71 (n)
(Rattus norvegicus)
Mammalia Hddc3 33
  • 86.78 (n)
(Monodelphis domestica)
Mammalia HDDC3 34
  • 61 (a)
(Gallus gallus)
Aves HDDC3 34
  • 41 (a)
(Anolis carolinensis)
Reptilia HDDC3 34
  • 57 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hddc3 33
  • 68.9 (n)
(Danio rerio)
Actinopterygii hddc3 34 33
  • 66.29 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10177 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012646 33
  • 62.59 (n)
fruit fly
(Drosophila melanogaster)
Insecta Mesh1 33 34
  • 59.92 (n)
(Caenorhabditis elegans)
Secernentea ZK909.3 33 34
  • 57.92 (n)
Species where no ortholog for HDDC3 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)
  • 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 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 HDDC3 Gene

Gene Tree for HDDC3 (if available)
Gene Tree for HDDC3 (if available)

Paralogs for HDDC3 Gene

No data available for Paralogs for HDDC3 Gene

Variants for HDDC3 Gene

Sequence variations from dbSNP and Humsavar for HDDC3 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs1001590636 -- 90,930,458(+) CTCCC(A/G)GGTTC intron-variant
rs1002812608 -- 90,932,598(+) CAGCG(-/C)CCCCT intron-variant, upstream-variant-2KB
rs1002885222 -- 90,931,142(+) AAAAA(A/T)GCAAG intron-variant, nc-transcript-variant, utr-variant-3-prime
rs1003083414 -- 90,933,276(+) TGTGG(A/G)CCCCT intron-variant, upstream-variant-2KB
rs1004029773 -- 90,932,900(+) GAGCG(G/T)GAAGA intron-variant, upstream-variant-2KB

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

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

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)

Relevant External Links for HDDC3 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 HDDC3 Gene

Disorders for HDDC3 Gene

Relevant External Links for HDDC3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

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) 3 4 60
  2. Analysis of the DNA sequence and duplication history of human chromosome 15. (PMID: 16572171) Zody MC … Nusbaum C (Nature 2006) 3 4 60
  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 60
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 60
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60

Products for HDDC3 Gene

Sources for HDDC3 Gene

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