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    NT5DC3 5'-nucleotidase domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 51559, updated on 10-Dec-2024

    Summary

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    Official Symbol
    NT5DC3provided by HGNC
    Official Full Name
    5'-nucleotidase domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:30826
    See related
    Ensembl:ENSG00000111696 MIM:611076; AllianceGenome:HGNC:30826
    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
    Also known as
    TU12B1TY; TU12B1-TY
    Summary
    Predicted to enable 5'-nucleotidase activity. Located in mitochondrion. Part of receptor complex. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in bone marrow (RPKM 4.0), brain (RPKM 3.1) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NT5DC3 in Genome Data Viewer
    Location:
    12q23.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (103746315..103841234, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (103707632..103803005, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (104166088..104235012, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene stabilin 2 Neighboring gene uncharacterized LOC105369946 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:104151936-104152436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:104163275-104163784 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23254 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23277 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:104192073-104193272 Neighboring gene uncharacterized LOC124903000 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23314 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23365 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23460 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4782 Neighboring gene uncharacterized LOC107984433 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:104252387-104253586 Neighboring gene tetratricopeptide repeat domain 41, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6896 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:104295143-104295644 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6898 Neighboring gene uncharacterized LOC124903001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6900

    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. TU12B1-TY, a novel gene in the region at 12q22-q23.1 frequently deleted in pancreatic cancer, shows reduced expression in pancreatic cancer cells. Yatsuoka T, et al. Oncol Rep, 2004 Dec. PMID 15547748
    2. A genome-wide association study identifies a region at chromosome 12 as a potential susceptibility locus for restenosis after percutaneous coronary intervention. Sampietro ML, et al. Hum Mol Genet, 2011 Dec 1. PMID 21878436, Free PMC Article
    3. The common viral insertion site Evi12 is located in the 5'-noncoding region of Gnn, a novel gene with enhanced expression in two subclasses of human acute myeloid leukemia. van den Akker E, et al. J Virol, 2005 May. PMID 15827139, Free PMC Article
    4. Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. Lesch KP, et al. J Neural Transm (Vienna), 2008 Nov. PMID 18839057
    5. Structural basis for endosomal trafficking of diverse transmembrane cargos by PX-FERM proteins. Ghai R, et al. Proc Natl Acad Sci U S A, 2013 Feb 19. PMID 23382219, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TU12B1-TY may contribute to the development and/or progression of human pancreatic cancer
      Title: TU12B1-TY, a novel gene in the region at 12q22-q23.1 frequently deleted in pancreatic cancer, shows reduced expression in pancreatic cancer cells.
    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
    A genome-wide association study identifies a region at chromosome 12 as a potential susceptibility locus for restenosis after percutaneous coronary intervention.
    EBI GWAS Catalog
    Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies.
    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

    • FLJ11266

    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
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion HTP PubMed 
    part_of receptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    5'-nucleotidase domain-containing protein 3
    NP_001026871.1
    XP_011536778.1
    XP_016874943.1
    XP_047284932.1
    XP_047284933.1
    XP_054228216.1
    XP_054228217.1
    XP_054228218.1

    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_001031701.3 → NP_001026871.1  5'-nucleotidase domain-containing protein 3

      See identical proteins and their annotated locations for NP_001026871.1

      Status: VALIDATED

      Source sequence(s)
      AC012555, AC025265, BC052293
      Consensus CDS
      CCDS41824.1
      UniProtKB/Swiss-Prot
      Q86UY8, Q9NUM7, Q9P2T2, Q9P2T3
      Related
      ENSP00000376615.3, ENST00000392876.8
      Conserved Domains (1) summary
      pfam05761
      Location:93 → 526
      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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      103746315..103841234 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011538476.3 → XP_011536778.1  5'-nucleotidase domain-containing protein 3 isoform X2

      Conserved Domains (1) summary
      pfam05761
      Location:24 → 379
      5_nucleotid; 5' nucleotidase family

    2. XM_047428976.1 → XP_047284932.1  5'-nucleotidase domain-containing protein 3 isoform X1

    3. XM_017019454.2 → XP_016874943.1  5'-nucleotidase domain-containing protein 3 isoform X3

    4. XM_047428977.1 → XP_047284933.1  5'-nucleotidase domain-containing protein 3 isoform X4

    RNA

    1. XR_001748758.2 RNA Sequence

    2. XR_007063093.1 RNA Sequence

    3. XR_007063092.1 RNA Sequence

    4. XR_007063091.1 RNA Sequence

    5. XR_007063090.1 RNA Sequence

    6. XR_007063089.1 RNA Sequence

    7. XR_944581.3 RNA Sequence

    8. XR_944580.3 RNA Sequence

    9. XR_944582.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      103707632..103803005 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372241.1 → XP_054228216.1  5'-nucleotidase domain-containing protein 3 isoform X2

    2. XM_054372242.1 → XP_054228217.1  5'-nucleotidase domain-containing protein 3 isoform X3

    3. XM_054372243.1 → XP_054228218.1  5'-nucleotidase domain-containing protein 3 isoform X4

    RNA

    1. XR_008488614.1 RNA Sequence

    2. XR_008488612.1 RNA Sequence

    3. XR_008488613.1 RNA Sequence

    4. XR_008488615.1 RNA Sequence

    5. XR_008488618.1 RNA Sequence

    6. XR_008488616.1 RNA Sequence

    7. XR_008488617.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_016575.1: Suppressed sequence

      Description
      NM_016575.1: This RefSeq was permanently suppressed because the CDS was partial; the full-length CDS is already represented by NM_001031701.1.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86UY8.1 GenPept UniProtKB/Swiss-Prot:Q86UY8

    Gene LinkOut

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

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