Human Gene NUDT3 (ENST00000607016.2_7) from GENCODE V47lift37
  Description: nudix hydrolase 3 (from RefSeq NM_006703.4)
Gencode Transcript: ENST00000607016.2_7
Gencode Gene: ENSG00000272325.2_10
Transcript (Including UTRs)
   Position: hg19 chr6:34,247,456-34,360,446 Size: 112,991 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr6:34,256,530-34,360,139 Size: 103,610 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:34,247,456-34,360,446)mRNA (may differ from genome)Protein (172 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NUDT3_HUMAN
DESCRIPTION: RecName: Full=Diphosphoinositol polyphosphate phosphohydrolase 1; Short=DIPP-1; EC=3.6.1.52; AltName: Full=Diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase 1; EC=3.6.1.-; AltName: Full=Nucleoside diphosphate-linked moiety X motif 3; Short=Nudix motif 3;
FUNCTION: Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate) and [PP]2-InsP4 (bisdiphosphoinositol tetrakisphosphate), suggesting that it may play a role in signal transduction. InsP6 (inositol hexakisphophate) is not a substrate. Acts as a negative regulator of the ERK1/2 pathway. Also able to catalyze the hydrolysis of dinucleoside oligophosphates, with Ap6A and Ap5A being the preferred substrates. The major reaction products are ADP and p4a from Ap6A and ADP and ATP from Ap5A. Also able to hydrolyze 5- phosphoribose 1-diphosphate.
CATALYTIC ACTIVITY: Diphospho-myo-inositol polyphosphate + H(2)O = myo-inositol polyphosphate + phosphate.
COFACTOR: Binds 3 magnesium ions per subunit.
ENZYME REGULATION: Inhibited by fluoride and InsP6.
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=5.9 uM for Ap6A; KM=7.7 uM for Ap5A; KM=38 mM for 5-phosphoribose 1-diphosphate; KM=4.2 nM for PP-InsP5; pH dependence: Optimum pH is 7-7.5;
SUBUNIT: Monomer (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (Probable).
TISSUE SPECIFICITY: Widely expressed. Expressed at higher level in brain, heart, pancreas and liver. Also expressed in placenta, lung and kidney.
SIMILARITY: Belongs to the Nudix hydrolase family. DIPP subfamily.
SIMILARITY: Contains 1 nudix hydrolase domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.40 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 556.51 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -170.50307-0.555 Picture PostScript Text
3' UTR -2746.009074-0.303 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR020084 - NUDIX_hydrolase_CS
IPR000086 - NUDIX_hydrolase_dom
IPR015797 - NUDIX_hydrolase_dom-like

Pfam Domains:
PF00293 - NUDIX domain

SCOP Domains:
55811 - Nudix

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2FVV - X-ray MuPIT 2Q9P - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O95989
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
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    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000287 magnesium ion binding
GO:0000298 endopolyphosphatase activity
GO:0008486 diphosphoinositol-polyphosphate diphosphatase activity
GO:0016787 hydrolase activity
GO:0034431 bis(5'-adenosyl)-hexaphosphatase activity
GO:0034432 bis(5'-adenosyl)-pentaphosphatase activity
GO:0046872 metal ion binding
GO:0050072 m7G(5')pppN diphosphatase activity
GO:0052840 inositol diphosphate tetrakisphosphate diphosphatase activity
GO:0052841 inositol bisdiphosphate tetrakisphosphate diphosphatase activity
GO:0052842 inositol diphosphate pentakisphosphate diphosphatase activity
GO:0052843 inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity
GO:0052844 inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity
GO:0052845 inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity
GO:0052846 inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity
GO:0052847 inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity
GO:0052848 inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity

Biological Process:
GO:0007267 cell-cell signaling
GO:0015961 diadenosine polyphosphate catabolic process
GO:0043647 inositol phosphate metabolic process
GO:0071544 diphosphoinositol polyphosphate catabolic process
GO:1901907 diadenosine pentaphosphate catabolic process
GO:1901909 diadenosine hexaphosphate catabolic process
GO:1901911 adenosine 5'-(hexahydrogen pentaphosphate) catabolic process

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AF062529 - Homo sapiens clone 486790 diphosphoinositol polyphosphate phosphohydrolase mRNA, complete cds.
BC007727 - Homo sapiens nudix (nucleoside diphosphate linked moiety X)-type motif 3, mRNA (cDNA clone MGC:12752 IMAGE:4303483), complete cds.
AF062530 - Homo sapiens clone 469920 diphosphoinositol polyphosphate phosphohydrolase mRNA, complete cds.
AK313440 - Homo sapiens cDNA, FLJ93979, Homo sapiens nudix (nucleoside diphosphate linked moiety X)-type motif 3 (NUDT3), mRNA.
KJ893244 - Synthetic construct Homo sapiens clone ccsbBroadEn_02638 NUDT3 gene, encodes complete protein.
BT019984 - Homo sapiens nudix (nucleoside diphosphate linked moiety X)-type motif 3 mRNA, complete cds.
BT019985 - Homo sapiens nudix (nucleoside diphosphate linked moiety X)-type motif 3 mRNA, complete cds.
DQ893118 - Synthetic construct clone IMAGE:100005748; FLH193906.01X; RZPDo839D0479D nudix (nucleoside diphosphate linked moiety X)-type motif 3 (NUDT3) gene, encodes complete protein.
DQ896391 - Synthetic construct Homo sapiens clone IMAGE:100010851; FLH193902.01L; RZPDo839D0469D nudix (nucleoside diphosphate linked moiety X)-type motif 3 (NUDT3) gene, encodes complete protein.
AB463951 - Synthetic construct DNA, clone: pF1KB6839, Homo sapiens NUDT3 gene for nudix (nucleoside diphosphate linked moiety X)-type motif 3, without stop codon, in Flexi system.
AF052101 - Homo sapiens clone 23872 mRNA sequence.
AK025515 - Homo sapiens cDNA: FLJ21862 fis, clone HEP02321, highly similar to AF052101 Homo sapiens clone 23872 mRNA sequence.
AK026168 - Homo sapiens cDNA: FLJ22515 fis, clone HRC12122, highly similar to AF052101 Homo sapiens clone 23872 mRNA sequence.
DQ572964 - Homo sapiens piRNA piR-41076, complete sequence.
DQ597651 - Homo sapiens piRNA piR-35717, complete sequence.
DQ601646 - Homo sapiens piRNA piR-39712, complete sequence.
AK025759 - Homo sapiens cDNA: FLJ22106 fis, clone HEP17675.
JD118479 - Sequence 99503 from Patent EP1572962.
JD388417 - Sequence 369441 from Patent EP1572962.
JD041438 - Sequence 22462 from Patent EP1572962.
JD274902 - Sequence 255926 from Patent EP1572962.
JD274901 - Sequence 255925 from Patent EP1572962.
JD496998 - Sequence 478022 from Patent EP1572962.
BC043178 - Homo sapiens cDNA clone IMAGE:5287836.
AK057088 - Homo sapiens cDNA FLJ32526 fis, clone SMINT2000073.
JD537705 - Sequence 518729 from Patent EP1572962.
JD546953 - Sequence 527977 from Patent EP1572962.
DQ591995 - Homo sapiens piRNA piR-59107, complete sequence.
JD083206 - Sequence 64230 from Patent EP1572962.
JD117312 - Sequence 98336 from Patent EP1572962.
JD518063 - Sequence 499087 from Patent EP1572962.
JD199555 - Sequence 180579 from Patent EP1572962.
JD038754 - Sequence 19778 from Patent EP1572962.
DQ573515 - Homo sapiens piRNA piR-41627, complete sequence.
JD475836 - Sequence 456860 from Patent EP1572962.
JD516695 - Sequence 497719 from Patent EP1572962.
JD338187 - Sequence 319211 from Patent EP1572962.
JD365859 - Sequence 346883 from Patent EP1572962.
JD432326 - Sequence 413350 from Patent EP1572962.
JD437073 - Sequence 418097 from Patent EP1572962.
JD508523 - Sequence 489547 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95989 (Reactome details) participates in the following event(s):

R-HSA-1855165 (PP)2-IP4 is dephosphorylated to 5-PP-IP5 by NUDT(1) in the cytosol
R-HSA-2023973 (PP)2-IP4 is dephosphorylated to 1/3-PP-IP5 by NUDT(1) in the cytosol
R-HSA-1855198 5-PP-IP5 is dephosphorylated to IP6 by NUDT(1) in the cytosol
R-HSA-2023971 1/3 PP-IP5 is dephosphorylated to IP6 by NUDT(1) in the cytosol
R-HSA-1855167 Synthesis of pyrophosphates in the cytosol
R-HSA-1483249 Inositol phosphate metabolism
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B2R8N4, DIPP, DIPP1, ENST00000607016.1, NM_006703, NUDT3 , NUDT3_HUMAN, O95989, uc327kdy.1, uc327kdy.2
UCSC ID: ENST00000607016.2_7
RefSeq Accession: NM_006703.4
Protein: O95989 (aka NUDT3_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.