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    NT5C 5', 3'-nucleotidase, cytosolic [ Homo sapiens (human) ]

    Gene ID: 30833, updated on 5-Mar-2024

    Summary

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    Official Symbol
    NT5Cprovided by HGNC
    Official Full Name
    5', 3'-nucleotidase, cytosolicprovided by HGNC
    Primary source
    HGNC:HGNC:17144
    See related
    Ensembl:ENSG00000125458 MIM:191720; AllianceGenome:HGNC:17144
    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
    DNT; cdN; DNT1; P5N2; PN-I; HEL74; PN-II; UMPH2; dNT-1
    Summary
    This gene encodes a nucleotidase that catalyzes the dephosphorylation of the 5' deoxyribonucleotides (dNTP) and 2'(3')-dNTP and ribonucleotides, but not 5' ribonucleotides. Of the different forms of nucleotidases characterized, this enzyme is unique in its preference for 5'-dNTP. It may be one of the enzymes involved in regulating the size of dNTP pools in cells. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2011]
    Expression
    Ubiquitous expression in colon (RPKM 12.8), spleen (RPKM 11.1) and 25 other tissues See more
    Orthologs
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    Genomic context

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    Location:
    17q25.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (75130228..75131742, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (76021691..76023204, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73126323..73127837, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73074528-73075727 Neighboring gene tripartite motif containing 80, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73089299-73089872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73089873-73090445 Neighboring gene solute carrier family 16 member 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73100784-73101284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73101285-73101785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8955 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73110035-73110574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12735 Neighboring gene armadillo repeat containing 7 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:73120068-73121267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12736 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:73126856-73127060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8956 Neighboring gene uncharacterized LOC107985034 Neighboring gene Jupiter microtubule associated homolog 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73143638-73144837 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8957 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73151095-73151690 Neighboring gene small ubiquitin like modifier 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73178362-73179012

    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. 5'-(3')-nucleotidase mRNA levels in blast cells are a prognostic factor in acute myeloid leukemia patients treated with cytarabine. Galmarini CM, et al. Haematologica, 2004 May. PMID 15136231
    2. Assignment of the human gene for uridine 5'-monophosphate phosphohydrolase (UMPH2) to the long arm of chromosome 17. Wilson DE, et al. Ann Hum Genet, 1986 Jul. PMID 2833155
    3. Molecular characterization of Turkish patients with pyrimidine 5' nucleotidase-I deficiency. Balta G, et al. Blood, 2003 Sep 1. PMID 12714505
    4. Kinetic evidence for covalent phosphoryl-enzyme intermediate in phosphotransferase activity of human red cell pyrimidine nucleotidases. Amici A, et al. Methods Enzymol, 2002. PMID 12418222
    5. Construction of a genetic map of human chromosome 17 by use of chromosome-mediated gene transfer. Xu WM, et al. Proc Natl Acad Sci U S A, 1988 Nov. PMID 3186746, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    2. Data show that PN-I shows a higher affinity for oxynucleosides rather than deoxynucleosides, while the opposite is true for PN-II.
      Title: Kinetic evidence for covalent phosphoryl-enzyme intermediate in phosphotransferase activity of human red cell pyrimidine nucleotidases.
    3. Mutation analysis in the P5N-I gene led to the identification of 3 novel mutations
      Title: Molecular characterization of Turkish patients with pyrimidine 5' nucleotidase-I deficiency.
    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 variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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
    enables 5'-nucleotidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables IMP 5'-nucleotidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables pyrimidine nucleotide binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in IMP catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in UMP catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in allantoin metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in amide catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dCMP catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dGMP catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dTMP catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dUMP catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in pyrimidine deoxyribonucleotide catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in pyrimidine deoxyribonucleotide 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 cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    5'(3')-deoxyribonucleotidase, cytosolic type
    Names
    5' nucleotidase, deoxy (pyrimidine), cytosolic type C
    cytosolic 5',3'-pyrimidine nucleotidase
    deoxy-5'-nucleotidase 1
    epididymis luminal protein 74
    epididymis secretory sperm binding protein
    uridine 5'-monophosphate phosphohydrolase 2
    uridine 5-prime monophosphate hydrolase 2
    NP_001239306.1
    NP_055410.1
    XP_011523002.3
    XP_054171866.1

    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.

    mRNA and Protein(s)

    1. NM_001252377.2 → NP_001239306.1  5'(3')-deoxyribonucleotidase, cytosolic type isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame coding exon, and uses an alternate in-frame acceptor splice site at the 3' terminal exon compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.
      Source sequence(s)
      AF154829, BG034032, BQ431723
      UniProtKB/TrEMBL
      J3KSX6
      Related
      ENSP00000462697.1, ENST00000578407.5
      Conserved Domains (1) summary
      cl21460
      Location:7 → 132
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    2. NM_014595.3 → NP_055410.1  5'(3')-deoxyribonucleotidase, cytosolic type isoform 1

      See identical proteins and their annotated locations for NP_055410.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript, and encodes the longer isoform (1).
      Source sequence(s)
      AF154829
      Consensus CDS
      CCDS11715.1
      UniProtKB/Swiss-Prot
      Q8TCD5, Q96HS6, Q9NP82
      UniProtKB/TrEMBL
      A0A384NYP3, V9HWF3
      Related
      ENSP00000245552.2, ENST00000245552.7
      Conserved Domains (1) summary
      cd02587
      Location:5 → 168
      HAD_5-3dNT; 5'(3')-deoxyribonucleotidase

    RNA

    1. NR_045513.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses alternate acceptor and donor splice sites at an internal exon compared to variant 1. It is represented as non-coding because the use of the 5'-most supported translational start codon as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF154829, BC008183, BQ431723
      Related
      ENST00000580758.5

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      75130228..75131742 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011524700.3 → XP_011523002.3  5'(3')-deoxyribonucleotidase, cytosolic type isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      76021691..76023204 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315891.1 → XP_054171866.1  5'(3')-deoxyribonucleotidase, cytosolic type isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TCD5.2 GenPept UniProtKB/Swiss-Prot:Q8TCD5

    Gene LinkOut

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