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    NUDT16 nudix hydrolase 16 [ Homo sapiens (human) ]

    Gene ID: 131870, updated on 9-Dec-2024

    Summary

    Official Symbol
    NUDT16provided by HGNC
    Official Full Name
    nudix hydrolase 16provided by HGNC
    Primary source
    HGNC:HGNC:26442
    See related
    Ensembl:ENSG00000198585 MIM:617381; AllianceGenome:HGNC:26442
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables several functions, including RNA binding activity; metal ion binding activity; and pyrophosphatase activity. Involved in RNA metabolic process and positive regulation of cell cycle process. Located in cytoplasm; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in fat (RPKM 14.5), kidney (RPKM 13.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NUDT16 in Genome Data Viewer
    Location:
    3q22.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (131381671..131388830)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (134125463..134132622)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (131100515..131107674)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene NIMA related kinase 11 Neighboring gene RNA, U6 small nuclear 726, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr3:130935591-130936092 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:131050541-131051088 Neighboring gene NUDT16 divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:131080535-131081079 Neighboring gene nudix hydrolase 16 like 2, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:131100488-131101057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:131101058-131101626 Neighboring gene uncharacterized LOC107986025 Neighboring gene uncharacterized LOC105374110

    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

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ31265, FLJ34034, FLJ36248

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables IDP phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA NAD-cap (NMN-forming) hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables chloride ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cobalt ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables dIDP phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables dITP diphosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables manganese ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metalloexopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphodiesterase decapping endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables phosphodiesterase decapping endonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables snoRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables snoRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in NAD-cap decapping IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in dITP catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in mRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in mRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of rRNA processing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell cycle process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sno(s)RNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sno(s)RNA catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus HDA PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    U8 snoRNA-decapping enzyme
    Names
    IDP phosphatase
    IDPase
    U8 snoRNA-binding protein H29K
    inosine diphosphate phosphatase
    m7GpppN-mRNA hydrolase
    nucleoside diphosphate-linked moiety X motif 16
    nudix (nucleoside diphosphate linked moiety X)-type motif 16
    nudix motif 16
    testicular tissue protein Li 129
    NP_001165376.1
    NP_001165377.1
    NP_689608.2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001171905.2 → NP_001165376.1  U8 snoRNA-decapping enzyme isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC010210, BP199028
      Consensus CDS
      CCDS54641.1
      UniProtKB/TrEMBL
      B4DIZ6
      Related
      ENSP00000440230.1, ENST00000537561.5
      Conserved Domains (1) summary
      cl00447
      Location:7 → 36
      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_001171906.2 → NP_001165377.1  U8 snoRNA-decapping enzyme isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC010210, AK304650, BP219080
      Consensus CDS
      CCDS54640.1
      UniProtKB/Swiss-Prot
      Q96DE0
      Related
      ENSP00000422375.1, ENST00000502852.1
      Conserved Domains (1) summary
      cl00447
      Location:53 → 82
      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_152395.3 → NP_689608.2  U8 snoRNA-decapping enzyme isoform 2

      See identical proteins and their annotated locations for NP_689608.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and 3' coding region, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC010210, CB121755
      Consensus CDS
      CCDS3070.2
      UniProtKB/Swiss-Prot
      B4E3B4, E9PED4, F5GYJ1, Q96DE0, Q96N82
      UniProtKB/TrEMBL
      A0A140VJQ3
      Related
      ENSP00000429274.2, ENST00000521288.2
      Conserved Domains (2) summary
      PRK05379
      Location:53 → 131
      PRK05379; bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase
      cl00447
      Location:53 → 82
      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+ ...

    RNA

    1. NR_033268.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has multiple differences, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC010210, AK295852, DC343245

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      131381671..131388830
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      134125463..134132622
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)