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

Gene ID: 51559, updated on 27-Nov-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, Nov 2024]
Expression
Broad expression in bone marrow (RPKM 4.0), brain (RPKM 3.1) and 24 other tissues See more
Orthologs
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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: 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. 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

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