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DNPH1 Gene

protein-coding   GIFtS: 43
GCID: GC06M043193

2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1

(Previous name: chromosome 6 open reading frame 108)
(Previous symbol: C6orf108)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 11 2     dJ330M21.32
C6orf1081 2 3     Deoxyribonucleoside 5'-Monophosphate N-Glycosidase2
C-Myc-Responsive Protein RCL2 3     Putative C-Myc-Responsive2
RCL2 3     EC 3.2.2.-3
Chromosome 6 Open Reading Frame 1081     

External Ids:    HGNC: 212181   Entrez Gene: 105912   Ensembl: ENSG000001126677   UniProtKB: O435983   

Export aliases for DNPH1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for DNPH1 Gene:
This gene was identified on the basis of its stimulation by c-Myc protein. The latter is a transcription factor
that participates in the regulation of cell proliferation, differentiation, and apoptosis. The exact function of
this gene is not known but studies in rat suggest a role in cellular proliferation and c-Myc-mediated
transformation. Two alternative transcripts encoding different proteins have been described. (provided by RefSeq,
Jul 2008)

GeneCards Summary for DNPH1 Gene:
DNPH1 (2'-deoxynucleoside 5'-phosphate N-hydrolase 1) is a protein-coding gene. GO annotations related to this gene include nucleoside deoxyribosyltransferase activity and deoxyribonucleoside 5'-monophosphate N-glycosidase activity.

UniProtKB/Swiss-Prot: DNPH1_HUMAN, O43598
Function: Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield
deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine
bases are preferred to those containing pyrimidine bases (By similarity)




(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000006.11  NC_018917.2  NT_007592.16  
Regulatory elements:
   Search for regulatory transcription factor binding sites for DNPH1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDNPH1 promoter sequence
   Search Chromatin IP Primers for DNPH1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DNPH1


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

Entrez Gene cytogenetic band: 6p21.1   Ensembl cytogenetic band:  6p21.1   HGNC cytogenetic band: 6p21.1

DNPH1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DNPH1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M043193:  view genomic region     (about GC identifiers)

Start:
43,193,367 bp from pter      End:
43,197,222 bp from pter
Size:
3,856 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: DNPH1_HUMAN, O43598 (See protein sequence)
Recommended Name: 2'-deoxynucleoside 5'-phosphate N-hydrolase 1  
Size: 174 amino acids; 19108 Da
Subunit: Monomer and homodimer (By similarity)
Secondary accessions: B2LUJ9
Alternative splicing: 2 isoforms:  O43598-1   O43598-2   

Explore the universe of human proteins at neXtProt for DNPH1: NX_O43598

Explore proteomics data for DNPH1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See DNPH1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_006434.1  NP_954653.1  

    ENSEMBL proteins: 
     ENSP00000230431   ENSP00000422440   ENSP00000377556  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR007710 Nucleoside_deoxyribTrfase
     IPR028607 DNPH1

    Graphical View of Domain Structure for InterPro Entry O43598

    ProtoNet protein and cluster: O43598

    UniProtKB/Swiss-Prot: DNPH1_HUMAN, O43598
    Similarity: Belongs to the 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 family


    Find genes that share domains with DNPH1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DNPH1_HUMAN, O43598
    Function: Catalyzes the cleavage of the N-glycosidic bond of deoxyribonucleoside 5'-monophosphates to yield
    deoxyribose 5-phosphate and a purine or pyrimidine base. Deoxyribonucleoside 5'-monophosphates containing purine
    bases are preferred to those containing pyrimidine bases (By similarity)
    Catalytic activity: A deoxyribonucleoside 5'-monophosphate + H(2)0 = deoxyribose 5-monophosphate + a purine or
    pyrimidine base
    Induction: Expression is induced by ETV1

         Enzyme Number (IUBMB): EC 3.2.2.-1

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0042803protein homodimerization activity IEA--
    GO:0050144nucleoside deoxyribosyltransferase activity IEA--
    GO:0070694deoxyribonucleoside 5'-monophosphate N-glycosidase activity ISS--
         
    Find genes that share ontologies with DNPH1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for DNPH1:
     Increased gamma-H2AX phosphory 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for DNPH1

    miRNA
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    miRTarBase miRNAs that target DNPH1:
    hsa-mir-92a-3p (MIRT049552)

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    DNPH1_HUMAN, O43598: Cytoplasm. Nucleus (By similarity)

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ISS--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--
    GO:0070062extracellular vesicular exosome IDA19056867

    Find genes that share ontologies with DNPH1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for DNPH1
    Interactions:

        Search GeneGlobe Interaction Network for DNPH1

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    Selected Interacting proteins for DNPH1 (O435982, 3 ENSP000002304314) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FTSJ1Q9UET63, ENSP000003269484I2D: score=1 STRING: ENSP00000326948
    PLAC8Q9NZF13I2D: score=1 
    DNPH1O435982MINT-67338
    POT1ENSP000003502494STRING: ENSP00000350249
    TERF1ENSP000002766034STRING: ENSP00000276603
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008283cell proliferation TAS9271375
    GO:0009116nucleoside metabolic process IEA--
    GO:0009117nucleotide metabolic process IEA--
    GO:0009159deoxyribonucleoside monophosphate catabolic process ISS--
    GO:0030307positive regulation of cell growth ISS--

    Find genes that share ontologies with DNPH1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for DNPH1



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for DNPH1 gene (2 alternative transcripts): 
    NM_006443.2  NM_199184.1  

    Unigene Cluster for DNPH1:

    2'-deoxynucleoside 5'-phosphate N-hydrolase 1
    Hs.109752  [show with all ESTs]
    Unigene Representative Sequence: BU599901
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000230431(uc003ouo.3) ENST00000509253 ENST00000393987(uc003oup.3)
    ENST00000505042
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    Additional mRNA sequence: 

    AF040105.1 BC011683.2 EU585603.1 

    5 DOTS entries:

    DT.85104614  DT.100776598  DT.100025393  DT.92430723  DT.92430725 

    Selected AceView cDNA sequences (see all 157):

    BM738701 AI352372 AI832691 AI709142 BQ052226 CB991417 BM042391 AA887281 
    AI201663 BF062519 BU553299 AI185914 AW051519 AI144340 AW613915 AI820044 
    BC011683 BE263489 AF040105 BQ267982 AA305573 AI203346 NM_006443 BF431894 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for DNPH1    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c
    SP1:                    -                                 
    SP2:                                                      
    SP3:                    -                                 


    ECgene alternative splicing isoforms for DNPH1

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    DNPH1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    DNPH1 Expression
    About this image


    DNPH1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Hippocampus
     
     Ovary (Reproductive System)
             Oviduct
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
     
     Bone (Muscoskeletal System)
             Bone Marrow
    DNPH1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DNPH1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.109752

    UniProtKB/Swiss-Prot: DNPH1_HUMAN, O43598
    Tissue specificity: Expressed at low levels in brain, colon, lung, peripheral blood leukocytes, placenta, small
    intestine, and thymus. Expressed at high levels in heart, kidney, liver, skeletal muscle and spleen.
    Overexpressed in a significant proportion of breast cancers

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    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for DNPH1 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Dnph11 , 5 cDNA sequence BC0483555
    2'-deoxynucleoside 5'-phosphate N-hydrolase 11
    80.48(n)1
    78.95(a)1
      17 (22.90 cM)5
    3811011  NM_207161.31  NP_997044.21 
     464967895 
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.296972 Xenopus laevis transcribed sequence 75.77(n)    CF286636.1 
    zebrafish
    (Danio rerio)
    Actinopterygii dnph11 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 63.99(n)
    64.23(a)
      561810  NM_001163199.1  NP_001156671.1 


    ENSEMBL Gene Tree for DNPH1 (if available)
    TreeFam Gene Tree for DNPH1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for DNPH1 gene

    Find genes that share paralogs with DNPH1           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for DNPH1
    PGOHUM00000250342


    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for DNPH1 (see all 151)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1164266931,2
    F--43192894(+) CTTCCT/ACCCAA 2 -- ds50011Minor allele frequency- A:0.05WA 118
    rs1488680181,2
    --43192900(+) CCCAAC/GTCTTT 2 -- ds50010--------
    rs1808355541,2
    --43193049(+) TACAGA/GCGCTC 2 -- ds50010--------
    rs97661181,2
    C,F--43193059(+) caccaC/Actcgc 2 -- ds50011Minor allele frequency- A:0.50CSA 2
    rs1851951941,2
    --43193140(+) GACCTC/TGTGAT 2 -- ds50010--------
    rs1884016411,2
    --43193148(+) GATCCA/GCCCAT 2 -- ds50010--------
    rs77482801,2
    C--43193200(+) gcgccC/TggccC 2 -- ds50010--------
    rs1814692141,2
    --43193266(+) CTCTCA/GGCCTA 2 -- ds50010--------
    rs756600241,2
    C,F--43193281(+) TTTCTA/GAAGCA 2 -- ds50013Minor allele frequency- G:0.05NA EA 242
    rs1158427651,2
    C,F--43193318(+) AAAGGG/TTATTA 2 -- ds50012Minor allele frequency- T:0.04WA NA 238

    HapMap Linkage Disequilibrium report for DNPH1 (43193367 - 43197222 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for DNPH1: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing DNPH1
    DNA2.0 Custom Variant and Variant Library Synthesis for DNPH1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (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)
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    PubMed articles for DNPH1 gene, integrated from 10 sources (see all 24):
    (articles sorted by number of sources associating them with DNPH1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of putative c-Myc-responsive genes: characterization of rcl, a novel growth-related gene. (PubMed id 9271375)1, 2, 3, 9 Lewis B.C.... Dang C.V. (Mol. Cell. Biol. 1997)
    2. Rcl is a novel ETV1/ER81 target gene upregulated in breast tumors. (PubMed id 18726892)1, 2 Shin S.... Janknecht R. (J. Cell. Biochem. 2008)
    3. The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase. (PubMed id 17234634)1, 3 Ghiorghi Y.K....Kaminski P.A. (J. Biol. Chem. 2007)
    4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    5. 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. (Genome Res. 2004)
    6. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
    7. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    8. Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-I+-acetylation features. (PubMed id 22223895)2 Bienvenut W.V....Giglione C. (amp 2012)
    9. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 10591 HGNC: 21218 AceView: C6orf108 Ensembl:ENSG00000112667 euGenes: HUgn10591
    ECgene: DNPH1 H-InvDB: DNPH1

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for DNPH1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for DNPH1 gene:
    Search GeneIP for patents involving DNPH1

    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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