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    NT5DC2 5'-nucleotidase domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 64943, updated on 14-Nov-2024

    Summary

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    Official Symbol
    NT5DC2provided by HGNC
    Official Full Name
    5'-nucleotidase domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:25717
    See related
    Ensembl:ENSG00000168268 AllianceGenome:HGNC:25717
    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
    Predicted to enable 5'-nucleotidase activity. Located in mitochondrion. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in adrenal (RPKM 25.8), ovary (RPKM 16.7) and 23 other tissues See more
    Orthologs
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    Genomic context

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    See NT5DC2 in Genome Data Viewer
    Location:
    3p21.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52524387..52535027, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52557295..52567927, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52558403..52569043, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52486099-52486919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52490599-52491274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52505250-52505750 Neighboring gene troponin C1, slow skeletal and cardiac type Neighboring gene nischarin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52538009-52538514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52538515-52539020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52540387-52540986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52540987-52541588 Neighboring gene stabilin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52553072-52553680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52553681-52554287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19943 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14447 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14448 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52570940-52571473 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 5 Neighboring gene RNA, U6 small nuclear 856, pseudogene Neighboring gene polybromo 1

    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 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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NT5DC2 knockdown suppresses progression, glycolysis, and neuropathic pain in triple-negative breast cancer by blocking the EGFR pathway.
      Title: NT5DC2 knockdown suppresses progression, glycolysis, and neuropathic pain in triple-negative breast cancer by blocking the EGFR pathway.
    2. Gastric cancer metastasis-related NT5DC2 indicates unfavorable prognosis of patients.
      Title: Gastric cancer metastasis-related NT5DC2 indicates unfavorable prognosis of patients.
    3. Decreased RNAbinding protein IGF2BP2 downregulates NT5DC2, which suppresses cell proliferation, and induces cell cycle arrest and apoptosis in diffuse large Bcell lymphoma cells by regulating the p53 signaling pathway.
      Title: Decreased RNA‑binding protein IGF2BP2 downregulates NT5DC2, which suppresses cell proliferation, and induces cell cycle arrest and apoptosis in diffuse large B‑cell lymphoma cells by regulating the p53 signaling pathway.
    4. NT5DC2 knockdown inhibits colorectal carcinoma progression by repressing metastasis, angiogenesis and tumor-associated macrophage recruitment: A mechanism involving VEGF signaling.
      Title: NT5DC2 knockdown inhibits colorectal carcinoma progression by repressing metastasis, angiogenesis and tumor-associated macrophage recruitment: A mechanism involving VEGF signaling.
    5. NT5DC2 suppression restrains progression towards metastasis of non-small-cell lung cancer through regulation p53 signaling.
      Title: NT5DC2 suppression restrains progression towards metastasis of non-small-cell lung cancer through regulation p53 signaling.
    6. NT5DC2 promotes tumor cell proliferation by stabilizing EGFR in hepatocellular carcinoma.
      Title: NT5DC2 promotes tumor cell proliferation by stabilizing EGFR in hepatocellular carcinoma.
    7. Disruption of NT5DC2 in GSCs markedly reduces the expression of Fyn, a Src family proto-oncogene that has been implicated in the regulation of GBM progression. The expression of NT5DC2 strongly correlated with increased aggression of human gliomas, but not that of other brain tumors.
      Title: NT5DC2 promotes tumorigenicity of glioma stem-like cells by upregulating fyn.
    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

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12442

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-nucleotidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of catecholamine metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of dopamine biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of oxidoreductase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of peptidyl-serine phosphorylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in mitochondrion HTP PubMed 

    General protein information

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    Preferred Names
    5'-nucleotidase domain-containing protein 2
    NP_001127703.1
    NP_075059.1
    XP_006713366.1
    XP_047304716.1
    XP_054203581.1
    XP_054203582.1

    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_001134231.2 → NP_001127703.1  5'-nucleotidase domain-containing protein 2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer protein (isoform 1).
      Source sequence(s)
      AC112215, AK022504, AK023995, AW510639, DR003312
      Consensus CDS
      CCDS46843.1
      UniProtKB/Swiss-Prot
      Q9H857
      Related
      ENSP00000406933.2, ENST00000422318.7
      Conserved Domains (1) summary
      pfam05761
      Location:101 → 533
      5_nucleotid; 5' nucleotidase family

    2. NM_022908.3 → NP_075059.1  5'-nucleotidase domain-containing protein 2 isoform 2

      See identical proteins and their annotated locations for NP_075059.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains a different segment for its 5' UTR and coding region, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct N-terminus when it is compared to isoform 1.
      Source sequence(s)
      AK023995, DA013090
      Consensus CDS
      CCDS2858.1
      UniProtKB/Swiss-Prot
      C9JTZ6, E9PAL9, O95888, Q96C80, Q9H857, Q9H9Z8
      Related
      ENSP00000302468.4, ENST00000307076.8
      Conserved Domains (1) summary
      pfam05761
      Location:64 → 496
      5_nucleotid; 5' nucleotidase family

    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
      52524387..52535027 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448760.1 → XP_047304716.1  5'-nucleotidase domain-containing protein 2 isoform X2

    2. XM_006713303.4 → XP_006713366.1  5'-nucleotidase domain-containing protein 2 isoform X1

      Conserved Domains (1) summary
      pfam05761
      Location:101 → 493
      5_nucleotid; 5' nucleotidase family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      52557295..52567927 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347607.1 → XP_054203582.1  5'-nucleotidase domain-containing protein 2 isoform X2

    2. XM_054347606.1 → XP_054203581.1  5'-nucleotidase domain-containing protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H857.1 GenPept UniProtKB/Swiss-Prot:Q9H857

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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