Human Gene NUDT2 (uc022bga.1)
  Description: Homo sapiens nudix (nucleoside diphosphate linked moiety X)-type motif 2 (NUDT2), transcript variant 4, mRNA.
RefSeq Summary (NM_001244390): This gene encodes a member of the MutT family of nucleotide pyrophosphatases, a subset of the larger NUDIX hydrolase family. The gene product possesses a modification of the MutT sequence motif found in certain nucleotide pyrophosphatases. The enzyme asymmetrically hydrolyzes Ap4A to yield AMP and ATP and is responsible for maintaining the intracellular level of the dinucleotide Ap4A, the function of which has yet to be established. This gene may be a candidate tumor suppressor gene. Alternative splicing has been observed at this locus and four transcript variants, all encoding the same protein, have been identified. [provided by RefSeq, Sep 2011].
Transcript (Including UTRs)
   Position: hg19 chr9:34,329,504-34,343,711 Size: 14,208 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr9:34,339,038-34,343,438 Size: 4,401 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:34,329,504-34,343,711)mRNA (may differ from genome)Protein (147 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: AP4A_HUMAN
DESCRIPTION: RecName: Full=Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]; EC=3.6.1.17; AltName: Full=Diadenosine 5',5'''-P1,P4-tetraphosphate asymmetrical hydrolase; Short=Ap4A hydrolase; Short=Ap4Aase; Short=Diadenosine tetraphosphatase; AltName: Full=Nucleoside diphosphate-linked moiety X motif 2; Short=Nudix motif 2;
FUNCTION: Asymmetrically hydrolyzes Ap4A to yield AMP and ATP. Plays a major role in maintaining homeostasis.
CATALYTIC ACTIVITY: P(1),P(4)-bis(5'-guanosyl) tetraphosphate + H(2)O = GTP + GMP.
COFACTOR: Divalent ions (By similarity).
SIMILARITY: Belongs to the Nudix hydrolase family.
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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NUDT2
CDC HuGE Published Literature: NUDT2

-  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: 22.83 RPKM in Pituitary
Total median expression: 709.02 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -26.70110-0.243 Picture PostScript Text
3' UTR -83.70273-0.307 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
IPR003565 - Tetra_PHTase

Pfam Domains:
PF00293 - NUDIX domain

SCOP Domains:
55811 - Nudix

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1XSA - NMR MuPIT 1XSB - NMR MuPIT 1XSC - NMR MuPIT 3U53 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P50583
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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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004081 bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0008796 bis(5'-nucleosyl)-tetraphosphatase activity
GO:0008803 bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity
GO:0016787 hydrolase activity

Biological Process:
GO:0006139 nucleobase-containing compound metabolic process
GO:0006915 apoptotic process
GO:0034599 cellular response to oxidative stress

Cellular Component:
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  AK310574 - Homo sapiens cDNA, FLJ17616.
U30313 - Human diadenosine tetraphosphatase mRNA, complete cds.
BC004926 - Homo sapiens nudix (nucleoside diphosphate linked moiety X)-type motif 2, mRNA (cDNA clone MGC:10404 IMAGE:3623134), complete cds.
DQ892973 - Synthetic construct clone IMAGE:100005603; FLH191305.01X; RZPDo839B1077D nudix (nucleoside diphosphate linked moiety X)-type motif 2 (NUDT2) gene, encodes complete protein.
DQ896221 - Synthetic construct Homo sapiens clone IMAGE:100010681; FLH191301.01L; RZPDo839B1067D nudix (nucleoside diphosphate linked moiety X)-type motif 2 (NUDT2) gene, encodes complete protein.
CU678810 - Synthetic construct Homo sapiens gateway clone IMAGE:100020120 5' read NUDT2 mRNA.
KJ890680 - Synthetic construct Homo sapiens clone ccsbBroadEn_00074 NUDT2 gene, encodes complete protein.
JD464181 - Sequence 445205 from Patent EP1572962.
JD477462 - Sequence 458486 from Patent EP1572962.
JD420648 - Sequence 401672 from Patent EP1572962.
JD565300 - Sequence 546324 from Patent EP1572962.
JD469265 - Sequence 450289 from Patent EP1572962.
JD359120 - Sequence 340144 from Patent EP1572962.
JD038160 - Sequence 19184 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00230 - Purine metabolism
hsa00240 - Pyrimidine metabolism

Reactome (by CSHL, EBI, and GO)

Protein P50583 (Reactome details) participates in the following event(s):

R-HSA-5696197 NUDT2 hydrolyses GP4G to GTP, GMP
R-HSA-3299685 Detoxification of Reactive Oxygen Species
R-HSA-2262752 Cellular responses to stress
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: AP4A_HUMAN, APAH1, D3DRM0, NM_001244390, NP_671702, P50583, Q5T589
UCSC ID: uc022bga.1
RefSeq Accession: NM_001244390
Protein: P50583 (aka AP4A_HUMAN)
CCDS: CCDS6552.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001244390.1
exon count: 3CDS single in 3' UTR: no RNA size: 843
ORF size: 444CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1058.00frame shift in genome: no % Coverage: 98.10
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.