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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HDDC3 Gene

protein-coding   GIFtS: 49
GCID: GC15M091474

HD Domain Containing 3

Microbiology & Infectious Diseases Congress
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
HD Domain Containing 31 2     HD Domain-Containing Protein 32 3
Metazoan SpoT Homolog 12 3     Guanosine-3',5'-Bis(Diphosphate) 3'-Pyrophosphohydrolase MESH12
Penta-Phosphate Guanosine-3'-Pyrophosphohydrolase2 3     Metazoan SpoT Homolog-12
(ppGpp)ase2 3     EC 3.1.7.23
MESH12 3     

External Ids:    HGNC: 305221   Entrez Gene: 3746592   Ensembl: ENSG000001845087   UniProtKB: Q8N4P33   

Export aliases for HDDC3 gene to outside databases

Previous GC identifers: GC15M089276 GC15M067585


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for HDDC3 Gene: 
HDDC3 (HD domain containing 3) is a protein-coding gene. Diseases associated with HDDC3 include pneumonia, and among its related super-pathways are Pyrimidine metabolism. GO annotations related to this gene include guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity and metal ion binding.

UniProtKB/Swiss-Prot: MESH1_HUMAN, Q8N4P3
Function: ppGpp hydrolyzing enzyme involved in starvation response




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000015.9  NT_010274.17  NC_018926.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HDDC3 gene promoter:
         E2F-4   E2F-3a   E2F-5   AML1a   AP-4   E2F-2   Nkx5-1   E2F   E2F-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHDDC3 promoter sequence
   Search SABiosciences Chromatin IP Primers for HDDC3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HDDC3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 15q26.1   Ensembl cytogenetic band:  15q26.1   HGNC cytogenetic band: 15q26.1

HDDC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HDDC3 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15M091474:  view genomic region     (about GC identifiers)

Start:
91,474,148 bp from pter      End:
91,475,799 bp from pter
Size:
1,652 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: MESH1_HUMAN, Q8N4P3 (See protein sequence)
Recommended Name: Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase MESH1  
Size: 179 amino acids; 20329 Da
Cofactor: Manganese
1 PDB 3D structure from and Proteopedia for HDDC3:
3NR1 (3D)    
Alternative splicing: 2 isoforms:  Q8N4P3-1   Q8N4P3-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for HDDC3: NX_Q8N4P3

Explore proteomics data for HDDC3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8N4P3

  • HDDC3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    HDDC3 Protein Expression
    REFSEQ proteins: NP_940929.1  
    ENSEMBL proteins: 
     ENSP00000377814   ENSP00000330721   ENSP00000454103   ENSP00000452937  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR026020 (p)ppGpp_Synthase
     IPR003607 HD/PDEase_dom

    Graphical View of Domain Structure for InterPro Entry Q8N4P3

    ProtoNet protein and cluster: Q8N4P3

    1 Blocks protein domain: IPB006674 Metal-dependent phosphohydrolase

    UniProtKB/Swiss-Prot: MESH1_HUMAN, Q8N4P3
    Similarity: Belongs to the MESH1 family
    Similarity: Contains 1 HD domain


    HDDC3 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: MESH1_HUMAN, Q8N4P3
    Function: ppGpp hydrolyzing enzyme involved in starvation response
    Catalytic activity: Guanosine 3',5'-bis(diphosphate) + H(2)O = guanosine 5'-diphosphate + diphosphate

         Enzyme Number (IUBMB): EC 3.1.7.21

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:0008081phosphoric diester hydrolase activity ----
    GO:0008893guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity IEA--
    GO:0046872metal ion binding IEA--
         
    HDDC3 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for HDDC3:
     Increased G1 DNA content 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for HDDC3 
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    SwitchGear 3'UTR luciferase reporter plasmidHDDC3 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for HDDC3 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Purine metabolism
    Purine metabolism0.38

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    1         Kegg Pathway  (Kegg details for HDDC3):
        Purine metabolism


    HDDC3 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HDDC3

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    3 Interacting proteins for HDDC3 (Q8N4P32, 3 ENSP000003307214) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NMIQ132873, ENSP000002433464I2D: score=3 STRING: ENSP00000243346
    --Q8WTW23, 2MINT-67658 I2D: score=1 
    --Q8WTW23, 2MINT-67658 I2D: score=1 
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for HDDC3 (MESH1)

    Search CenterWatch for drugs/clinical trials and news about HDDC3 / MESH1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HDDC3 gene: 
    NM_198527.2  

    Unigene Cluster for HDDC3:

    HD domain containing 3
    Hs.349979  [show with all ESTs]
    Unigene Representative Sequence: AK057584
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000394272 ENST00000330334(uc002bqe.4) ENST00000494993 ENST00000559898
    ENST00000559834 ENST00000561036
    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
    Products:
         
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat HDDC3
    8/13 QIAGEN miScript miRNA Assays for microRNAs that regulate HDDC3 (see all 13):
    hsa-miR-3690 hsa-miR-125a-5p hsa-miR-3184 hsa-miR-4254 hsa-miR-1236 hsa-miR-197 hsa-miR-423-5p hsa-miR-877*
    SwitchGear 3'UTR luciferase reporter plasmidHDDC3 3' UTR sequence
    Inhib. RNA
    Products:
         
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    OriGene RNAi products in human, mouse, rat for HDDC3
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    Clone
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HDDC3
    Sirion Biotech Customized lentivirus for stable overexpression of HDDC3 
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    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HDDC3

    Additional mRNA sequence: 

    AK057584.1 BC033794.1 

    4 DOTS entries:

    DT.95165968  DT.100036151  DT.95165969  DT.100780829 

    24/92 AceView cDNA sequences (see all 92):

    AA287658 BM787605 BU633661 BM670927 BG033389 AI362805 AI990363 CR625970 
    CN481832 AK057584 BX095354 AI824988 AW005351 BU165799 BM693865 BX363567 
    BE671742 BQ778167 AI799077 BM013692 BI830820 BQ777217 AI266070 AA960973 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    HDDC3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTGGGATCTC
    HDDC3 Expression
    About this image


    See HDDC3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HDDC3

    SOURCE GeneReport for Unigene cluster: Hs.349979
        SABiosciences Custom PCR Arrays for HDDC3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HDDC3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for HDDC3 gene from 5/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves HDDC36
    HD domain containing 3
    54(a)
    1 ↔ 1
    10(19553415-19554362)
    lizard
    (Anolis carolinensis)
    Reptilia HDDC36
    Uncharacterized protein
    57(a)
    1 ↔ 1
    AAWZ02039614(2343-8223)
    zebrafish
    (Danio rerio)
    Actinopterygii hddc36
    HD domain containing 3
    58(a)
    1 ↔ 1
    7(51852844-51854956)
    fruit fly
    (Drosophila melanogaster)
    Insecta Mesh16
    Metazoan SpoT homolog-1
    46(a)
    1 ↔ 1
    3R(25027478-25028247)
    worm
    (Caenorhabditis elegans)
    Secernentea ZK909.36
    Protein ZK909.3
    34(a)
    1 ↔ 1
    I(14953488-14955611)
            Species with no ortholog for HDDC3

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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section
    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for HDDC3:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv833089CNV Loss17160897
    nsv515661CNV Loss19592680
    nsv833090CNV Loss17160897

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    2 diseases for HDDC3:    About MalaCards
    pneumonia    


    HDDC3 for disorders           About GeneDecksing


    Export disorders for HDDC3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for HDDC3 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with HDDC3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses. (PubMed id 20818390)1, 2 Sun D....Chung J. (2010)
    2. Analysis of the DNA sequence and duplication history of human chromosome 15. (PubMed id 16572171)1, 2 Zody M.C....Nusbaum C. (2006)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    5. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    6. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    7. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    8. Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. (PubMed id 19413330)2 Gauci S....Mohammed S. (2009)
    9. Lysine acetylation targets protein complexes and co-regulates major cellular functions. (PubMed id 19608861)2 Choudhary C.... Mann M. (2009)
    10. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 374659 HGNC: 30522 AceView: MGC45386 Ensembl:ENSG00000184508 euGenes: HUgn374659
    ECgene: HDDC3 Kegg: 374659 H-InvDB: HDDC3

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for HDDC3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for HDDC3 gene:
    Search GeneIP for patents involving HDDC3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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