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NUDT4 nudix hydrolase 4 [ Homo sapiens (human) ]

Gene ID: 11163, updated on 17-Jun-2024

Summary

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
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Genomic context

See NUDT4 in Genome Data Viewer
Location:
12q22
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (93377925..93408146)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (93358899..93389124)
105.20220307 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

Expression

  • 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

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA0487, DKFZp686I1281

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 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

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_001301022.2NP_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:186
    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_001301023.2NP_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:185
    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_001301024.2NP_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:185
    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_019094.6NP_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:19137
    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_199040.4NP_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:19138
    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_2023_10

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_047428136.1XP_047284092.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    UniProtKB/TrEMBL
    F8VRR0
  2. XM_047428137.1XP_047284093.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    UniProtKB/TrEMBL
    F8VRR0
  3. XM_047428135.1XP_047284091.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    UniProtKB/TrEMBL
    F8VRR0
  4. XM_047428138.1XP_047284094.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X2

    UniProtKB/TrEMBL
    A0A0C4DGJ4, F8VRR0

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_054370862.1XP_054226837.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    UniProtKB/TrEMBL
    F8VRR0
  2. XM_054370863.1XP_054226838.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    UniProtKB/TrEMBL
    F8VRR0
  3. XM_054370861.1XP_054226836.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X1

    UniProtKB/TrEMBL
    F8VRR0
  4. XM_054370864.1XP_054226839.1  diphosphoinositol polyphosphate phosphohydrolase 2 isoform X2

    UniProtKB/TrEMBL
    A0A0C4DGJ4, F8VRR0