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

Gene ID: 64943, updated on 10-Dec-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, Dec 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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. NT5DC2 knockdown inhibits colorectal carcinoma progression by repressing metastasis, angiogenesis and tumor-associated macrophage recruitment: A mechanism involving VEGF signaling. Zhu Z, et al. Exp Cell Res, 2020 Dec 1. PMID 32991874
  2. Gastric cancer metastasis-related NT5DC2 indicates unfavorable prognosis of patients. Sha R, et al. Medicine (Baltimore), 2023 Oct 6. PMID 37800836, Free PMC Article
  3. NT5DC2 promotes tumorigenicity of glioma stem-like cells by upregulating fyn. Guo S, et al. Cancer Lett, 2019 Jul 10. PMID 30978441
  4. NT5DC2 suppression restrains progression towards metastasis of non-small-cell lung cancer through regulation p53 signaling. Jin X, et al. Biochem Biophys Res Commun, 2020 Dec 10. PMID 32962856
  5. 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. Cui Y, et al. Mol Med Rep, 2022 Sep. PMID 35894142, Free PMC Article

See all (73) citations in PubMed

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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