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

NT5DC3 Gene

protein-coding   GIFtS: 49
GCID: GC12M104164

5'-Nucleotidase Domain Containing 3

Microbiology & Infectious Diseases Congress
  See related diseases
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
5'-Nucleotidase Domain Containing 31 2     5'-Nucleotidase Domain-Containing Protein 32
TU12B1-TY2 3     EC 3.1.3.-3
TU12B1TY2 5     GRP94-Neighboring Nucleotidase3
GNN3 5     

External Ids:    HGNC: 308261   Entrez Gene: 515592   Ensembl: ENSG000001116967   OMIM: 6110765   UniProtKB: Q86UY83   

Export aliases for NT5DC3 gene to outside databases

Previous GC identifers: GC12M102669 GC12M101226


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

GeneCards Summary for NT5DC3 Gene: 
NT5DC3 (5'-nucleotidase domain containing 3) is a protein-coding gene. Diseases associated with NT5DC3 include acute myeloid leukemia, and pancreatic cancer. GO annotations related to this gene include hydrolase activity and metal ion binding. An important paralog of this gene is NT5C2.


(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_000012.11  NC_018923.2  NT_029419.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NT5DC3 gene promoter:
         HEN1   ISGF-3   POU2F1   POU2F1a   Arnt   RORalpha2   GATA-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNT5DC3 promoter sequence
   Search SABiosciences Chromatin IP Primers for NT5DC3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NT5DC3


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

Entrez Gene cytogenetic band: 12q22-q23.1   Ensembl cytogenetic band:  12q23.3   HGNC cytogenetic band: 12q22-q23.1

NT5DC3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NT5DC3 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M104164:  view genomic region     (about GC identifiers)

Start:
104,164,231 bp from pter      End:
104,234,975 bp from pter
Size:
70,745 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: NT5D3_HUMAN, Q86UY8 (See protein sequence)
Recommended Name: 5'-nucleotidase domain-containing protein 3  
Size: 548 amino acids; 63420 Da
Cofactor: Binds 1 magnesium ion per subunit (By similarity)
Sequence caution: Sequence=BAA92095.1; Type=Erroneous initiation; Sequence=BAA93053.1; Type=Frameshift;
Positions=62;
Secondary accessions: Q9NUM7 Q9P2T2 Q9P2T3
Alternative splicing: 2 isoforms:  Q86UY8-1   Q86UY8-2   

Explore the universe of human proteins at neXtProt for NT5DC3: NX_Q86UY8

Explore proteomics data for NT5DC3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q86UY8

  • NT5DC3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    NT5DC3 Protein Expression
    REFSEQ proteins: NP_001026871.1  
    ENSEMBL proteins: 
     ENSP00000413657   ENSP00000376615   ENSP00000399171  

    Human Recombinant Protein Products for NT5DC3: 
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    Novus Biologicals NT5DC3 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for NT5DC3 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IEA--
    GO:0005829cytosol IEA--

    NT5DC3 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    3 InterPro protein domains:
     IPR023214 HAD-like_dom
     IPR008380 HAD-SF_hydro_IG_5-nucl
     IPR016695 Pur_nucleotidase

    Graphical View of Domain Structure for InterPro Entry Q86UY8

    ProtoNet protein and cluster: Q86UY8

    UniProtKB/Swiss-Prot: NT5D3_HUMAN, Q86UY8
    Similarity: Belongs to the 5'(3')-deoxyribonucleotidase family


    NT5DC3 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

         Enzyme Number (IUBMB): EC 3.1.3.-1

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016787hydrolase activity IEA--
    GO:0046872metal ion binding IEA--
         
    NT5DC3 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for NT5DC3 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for NT5DC3 
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    miRNA
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    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NT5DC3


    (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



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NT5DC3

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

    5/8 Interacting proteins for NT5DC3 (Q86UY83 ENSP000003766154) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000204490P013753I2D: score=1 
    ENSG00000206439P013753I2D: score=1 
    ENSG00000223952P013753I2D: score=1 
    ENSG00000228321P013753I2D: score=1 
    ENSG00000228849P013753I2D: 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 NT5DC3 (NT5D3)

    1 HMDB Compound for NT5DC3    About this table
    CompoundSynonyms CAS #PubMed Ids
    MagnesiumMagnesium (see all 2)7439-95-4--

    Search CenterWatch for drugs/clinical trials and news about NT5DC3 / NT5D3

    (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 NT5DC3 gene (2 alternative transcripts): 
    NM_016575.1  NM_001031701.2  

    Unigene Cluster for NT5DC3:

    5'-nucleotidase domain containing 3
    Hs.48428  [show with all ESTs]
    Unigene Representative Sequence: NM_001031701
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000447799 ENST00000392876(uc010swe.1) ENST00000415849 ENST00000474268
    ENST00000465502
    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 NT5DC3
    8/25 QIAGEN miScript miRNA Assays for microRNAs that regulate NT5DC3 (see all 25):
    hsa-miR-485-5p hsa-miR-1271 hsa-miR-515-5p hsa-miR-3142 hsa-miR-23a hsa-miR-3121-3p hsa-miR-330-3p hsa-miR-96
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for NT5DC3
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat NT5DC3
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat NT5DC3

    Additional mRNA sequence: 

    AB032773.1 AK130442.1 BC052293.1 

    5 DOTS entries:

    DT.416750  DT.101963203  DT.95286617  DT.95300035  DT.121176108 

    24/138 AceView cDNA sequences (see all 138):

    CA396370 BU838097 BF476138 AW205506 BM562753 BQ684492 CA420627 AI784548 
    BM855976 CD672505 AI744176 BC052293 AI865829 AJ706163 AI041733 BF593836 
    BQ682708 BM795871 BU155544 AI800679 BU535248 BQ681191 AI497757 BF340737 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for NT5DC3    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18 ^ 19
    SP1:        -                       -                                                           -                                             
    SP2:                                                                                                                                          
    SP3:                                -                                                                                                         
    SP4:                                                                                                                                          
    SP5:                                                                                                                                          


    ECgene alternative splicing isoforms for NT5DC3

    (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

    NT5DC3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    NT5DC3 Expression
    About this image


    See NT5DC3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for NT5DC3

    SOURCE GeneReport for Unigene cluster: Hs.48428

    UniProtKB/Swiss-Prot: NT5D3_HUMAN, Q86UY8
    Tissue specificity: Expressed in brain, placenta, skeletal muscle, pancreas, testis, uterus, and small intestine.
    Reduced expression in pancreatic cancer cells

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    In Situ
    Assay Products:
     

     
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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for NT5DC3 gene from 6/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Nt5dc31 , 5 5'-nucleotidase domain containing 31, 5 86.46(n)1
    92.28(a)1
      10 (43.11 cM)5
    1034661  NM_175331.31  NP_780540.21 
     867790055 
    chicken
    (Gallus gallus)
    Aves NT5DC31 5'-nucleotidase domain containing 3 82.52(n)
    91.26(a)
      427914  XM_425487.3  XP_425487.3 
    lizard
    (Anolis carolinensis)
    Reptilia NT5DC36
    5'-nucleotidase domain containing 3
    82(a)
    1 ↔ 1
    5(18119318-18154208)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia BX712298.12   -- 78.04(n)    BX712298.1 
    zebrafish
    (Danio rerio)
    Actinopterygii nt5dc31 5'-nucleotidase domain containing 3 71.91(n)
    77.09(a)
      558469  XM_681686.2  XP_686778.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG18141 CG1814 53.36(n)
    48.02(a)
      35984  NM_136655.3  NP_610499.2 


    ENSEMBL Gene Tree for NT5DC3 (if available)
    TreeFam Gene Tree for NT5DC3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for NT5DC3 gene
    NT5C22  NT5DC12  NT5DC22  NT5DC42  
    2 SIMAP similar genes for NT5DC3 using alignment to 3 protein entries:     NT5D3_HUMAN (see all proteins):
    NT5DC2    NT5DC1

    NT5DC3 for paralogs           About GeneDecksing



    (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

    10/1524 SNPs in NT5DC3 are shown (see all 1524)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs778382561,2
    F--104165648(+) TTAGAT/AGACAT 1 -- ds50012Minor allele frequency- A:0.03CSA WA 120
    rs79774591,2
    C,F,H--104165666(+) TTCCAA/G/TAAAAT 1 -- ds50016NS EA CSA WA 524
    rs1510016891,2
    --104165673(+) AAATCA/GCCCCC 1 -- ds50010--------
    rs1159353081,2
    C,F--104165736(+) ACAGGT/AACACA 1 -- ds50011Minor allele frequency- A:0.03WA 118
    rs49810331,2
    H--104165781(-) CCTCCC/TATGGA 1 -- ds50014Minor allele frequency- T:0.00NS EA 420
    rs751099751,2
    C,F--104165783(+) CATGGG/AAGGAA 1 -- ds50011Minor allele frequency- A:0.02WA 118
    rs1408939141,2
    --104165790(+) GGAATC/GACAGT 1 -- ds50010--------
    rs49810321,2
    C,F,A,H--104165864(-) CAAAGG/ATTTCT 1 -- ds500111Minor allele frequency- A:0.29EA NS NA WA CSA 519
    rs42488271,2
    C,F,A--104165870(-) AAAGCC/TCAAAG 1 -- ds500110Minor allele frequency- T:0.26NA WA CSA EA 371
    rs1173658991,2
    C,F--104165976(+) AATAAC/TCTCAA 1 -- ds50011Minor allele frequency- T:0.03EA 120

    HapMap Linkage Disequilibrium report for NT5DC3 (104164231 - 104234975 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for NT5DC3:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv34031CNV Loss18971310
    nsv52873CNV Loss16902084
    dgv1488n71CNV Gain21882294
    nsv899486CNV Gain21882294
    dgv1486n71CNV Gain21882294
    dgv1489n71CNV Gain21882294

    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing NT5DC3
    DNA2.0 Custom Variant and Variant Library Synthesis for NT5DC3

    (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
    OMIM gene information: 611076    OMIM disorders: --

    5 diseases for NT5DC3:    About MalaCards
    acute myeloid leukemia    pancreatic cancer    myeloid leukemia    pancreatitis
    leukemia


    NT5DC3 for disorders           About GeneDecksing

    Genetic Association Database (GAD): NT5DC3

    Export disorders for NT5DC3 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 NT5DC3 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with NT5DC3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. (PubMed id 18839057)1, 4 Lesch K.P....Jacob C. (2008)
    2. TU12B1-TY, a novel gene in the region at 12q22-q23.1 frequently deleted in pancreatic cancer, shows reduced expression in pancreatic cancer cells. (PubMed id 15547748)1, 2 Yatsuoka T....Horii A. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. A genome-wide association study identifies a region at chromosome 12 as a potential susceptibility locus for restenosis after percutan eous coronary intervention. (PubMed id 21878436)1 Sampietro M.L....Jukema J.W. (2011)
    5. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
    6. The common viral insertion site Evi12 is located in the 5'-noncoding region of Gnn, a novel gene with enhanced expression in two subclasses of human acute myeloid leukemia. (PubMed id 15827139)1 van den Akker E....Delwel R. (2005)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 51559 HGNC: 30826 AceView: TU12B1-TY Ensembl:ENSG00000111696 euGenes: HUgn51559
    ECgene: NT5DC3 H-InvDB: NT5DC3

    (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 NT5DC3 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 NT5DC3 gene:
    Search GeneIP for patents involving NT5DC3

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



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