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    NUDT4 nudix hydrolase 4 [ Homo sapiens (human) ]

    Gene ID: 11163, updated on 26-Nov-2024

    Summary

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    Official Symbol
    NUDT4provided by HGNC
    Official Full Name
    nudix hydrolase 4provided by HGNC
    Primary source
    HGNC:HGNC:8051
    See related
    Ensembl:ENSG00000173598 MIM:609229; AllianceGenome:HGNC:8051
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DIPP2; NUDT4B; DIPP-2B; HDCMB47P; DIPP2beta; DIPP2alpha
    Summary
    The protein encoded by this gene regulates the turnover of diphosphoinositol polyphosphates. The turnover of these high-energy diphosphoinositol polyphosphates represents a molecular switching activity with important regulatory consequences. Molecular switching by diphosphoinositol polyphosphates may contribute to regulating intracellular trafficking. Several alternatively spliced transcript variants have been described, but the full-length nature of some variants has not been determined. Isoforms DIPP2alpha and DIPP2beta are distinguishable from each other solely by DIPP2beta possessing one additional amino acid due to intron boundary skidding in alternate splicing. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in ovary (RPKM 30.0), kidney (RPKM 25.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NUDT4 in Genome Data Viewer
    Location:
    12q22
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (93377925..93408146)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (93358899..93389124)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (93771701..93801922)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC643339 Neighboring gene small nucleolar RNA SNORD74 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6767 Neighboring gene HNF4 motif-containing MPRA enhancer 125 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:93729207-93729708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:93729709-93730208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:93731209-93731709 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:93741082-93741250 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4704 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:93764071-93765034 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:93771297-93772236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4709 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:93835621-93836258 Neighboring gene ubiquitin conjugating enzyme E2 N Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6770 Neighboring gene mitochondrial ribosomal protein L42 Neighboring gene uncharacterized LOC124902985 Neighboring gene RNA, 7SL, cytoplasmic 737, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Discovery of molecular and catalytic diversity among human diphosphoinositol-polyphosphate phosphohydrolases. An expanding Nudt family. Caffrey JJ, et al. J Biol Chem, 2000 Apr 28. PMID 10777568
    2. Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising Nudix hydrolases. Leslie NR, et al. BMC Biochem, 2002 Jul 16. PMID 12121577, Free PMC Article
    3. Genetic rationale for microheterogeneity of human diphosphoinositol polyphosphate phosphohydrolase type 2. Caffrey JJ, et al. Gene, 2001 May 16. PMID 11376937
    4. Nudix hydrolases that degrade dinucleoside and diphosphoinositol polyphosphates also have 5-phosphoribosyl 1-pyrophosphate (PRPP) pyrophosphatase activity that generates the glycolytic activator ribose 1,5-bisphosphate. Fisher DI, et al. J Biol Chem, 2002 Dec 6. PMID 12370170
    5. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. Seki N, et al. DNA Res, 1997 Oct 31. PMID 9455484

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. This paper demonstrates that KIAA0487 (AB007956) is the 3'-UTR for human diphosphoinositol polyphosphate phosphohydrolase type II
      Title: Discovery of molecular and catalytic diversity among human diphosphoinositol-polyphosphate phosphohydrolases. An expanding Nudt family.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of nudix (nucleoside diphosphate linked moiety X)-type motif 4 (NUDT4) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables bis(5'-adenosyl)-hexaphosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables bis(5'-adenosyl)-pentaphosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables diphosphoinositol-polyphosphate diphosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables diphosphoinositol-polyphosphate diphosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables endopolyphosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables inositol-5-diphosphate-1,3,4,6-tetrakisphosphate diphosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables snoRNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in adenosine 5'-(hexahydrogen pentaphosphate) catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in calcium-mediated signaling TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in diadenosine hexaphosphate catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in diadenosine pentaphosphate catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in diphosphoinositol polyphosphate metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular signal transduction NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    diphosphoinositol polyphosphate phosphohydrolase 2
    Names
    DIPP-2
    Diphosphoinositol polyphosphate phosphohydrolase NUDT4B
    Nucleoside diphosphate-linked moiety X motif 4B
    Nudix hydrolase 4B
    Nudix motif 4B
    diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase 2
    diphosphoinositol polyphosphate phosphohydrolase type 2
    nudix (nucleoside diphosphate linked moiety X)-type motif 4
    NP_001287951.1
    NP_001287952.1
    NP_001287953.1
    NP_061967.3
    NP_950241.1
    XP_047284091.1
    XP_047284092.1
    XP_047284093.1
    XP_047284094.1
    XP_054226836.1
    XP_054226837.1
    XP_054226838.1
    XP_054226839.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_029507.2 RefSeqGene

      Range
      5002..35223
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001301022.2 → NP_001287951.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform 3

      See identical proteins and their annotated locations for NP_001287951.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon, resulting in the use of a downstream start codon compared to variant 2. The encoded isoform (3) has a shorter N-terminus compared to isoform beta.
      Source sequence(s)
      AC025260, AK304296
      Consensus CDS
      CCDS73504.1
      UniProtKB/TrEMBL
      F8VRR0
      Related
      ENSP00000448032.1, ENST00000547014.5
      Conserved Domains (1) summary
      cl00447
      Location:1 → 86
      Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

    2. NM_001301023.2 → NP_001287952.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform 4

      See identical proteins and their annotated locations for NP_001287952.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 5' terminal exon, and uses an alternate splice site in the 5' coding region, resulting in the use of a downstream start codon compared to variant 2. The encoded isoform (4) has a shorter N-terminus compared to isoform beta. Variants 4 and 5 encode the same isoform.
      Source sequence(s)
      AC025260, CR749445
      Consensus CDS
      CCDS76584.1
      UniProtKB/TrEMBL
      A0A0C4DGJ4, F8VRR0
      Related
      ENSP00000449552.1, ENST00000549992.5
      Conserved Domains (1) summary
      cl00447
      Location:1 → 85
      Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

    3. NM_001301024.2 → NP_001287953.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform 4

      See identical proteins and their annotated locations for NP_001287953.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an alternate 5' terminal exon, and uses an alternate splice site in the 5' coding region, resulting in the use of a downstream start codon compared to variant 2. The encoded isoform (4) has a shorter N-terminus compared to isoform beta. Variants 4 and 5 encode the same isoform.
      Source sequence(s)
      AC025260, BP315657, CN335956
      Consensus CDS
      CCDS76584.1
      UniProtKB/TrEMBL
      A0A0C4DGJ4, F8VRR0
      Related
      ENSP00000449724.1, ENST00000548662.5
      Conserved Domains (1) summary
      cl00447
      Location:1 → 85
      Nudix_Hydrolase; Nudix hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ ...

    4. NM_019094.6 → NP_061967.3  diphosphoinositol polyphosphate phosphohydrolase 2 isoform alpha

      See identical proteins and their annotated locations for NP_061967.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate in-frame splice site in the 5' coding region, compared to variant 2. The encoded protein is the predominant isoform (alpha), and is shorter than isoform beta.
      Source sequence(s)
      AC025260, AC124947, AF191649
      Consensus CDS
      CCDS44952.1
      UniProtKB/Swiss-Prot
      B7Z916, Q4AEJ6, Q53EZ2, Q68DD7, Q9NPC5, Q9NS30, Q9NZJ9, Q9NZK0, Q9NZK1
      UniProtKB/TrEMBL
      B2RE29
      Related
      ENSP00000406612.2, ENST00000415493.7
      Conserved Domains (1) summary
      cd04666
      Location:19 → 137
      Nudix_Hydrolase_9; Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly ...

    5. NM_199040.4 → NP_950241.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform beta

      See identical proteins and their annotated locations for NP_950241.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (beta).
      Source sequence(s)
      AC025260, AC090050, AC124947, AK223497
      Consensus CDS
      CCDS9044.1
      UniProtKB/Swiss-Prot
      A0A024RBG1
      UniProtKB/TrEMBL
      B2RE29
      Related
      ENSP00000338352.5, ENST00000337179.9
      Conserved Domains (1) summary
      cd04666
      Location:19 → 138
      Nudix_Hydrolase_9; Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      93377925..93408146
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428136.1 → XP_047284092.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    2. XM_047428137.1 → XP_047284093.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    3. XM_047428135.1 → XP_047284091.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    4. XM_047428138.1 → XP_047284094.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X2

      UniProtKB/TrEMBL
      A0A0C4DGJ4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      93358899..93389124
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370862.1 → XP_054226837.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    2. XM_054370863.1 → XP_054226838.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    3. XM_054370861.1 → XP_054226836.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    4. XM_054370864.1 → XP_054226839.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X2

      UniProtKB/TrEMBL
      A0A0C4DGJ4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZJ9.2 GenPept UniProtKB/Swiss-Prot:Q9NZJ9

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