Aliases for NT5DC3 Gene

Aliases for NT5DC3 Gene

  • 5'-Nucleotidase Domain Containing 3 2 3 5
  • 5'-Nucleotidase Domain-Containing Protein 3 3 4
  • TU12B1-TY 3 4
  • GRP94-Neighboring Nucleotidase 4
  • EC 3.1.3.- 4
  • TU12B1TY 3
  • GNN 4

External Ids for NT5DC3 Gene

Previous GeneCards Identifiers for NT5DC3 Gene

  • GC12M102669
  • GC12M104164
  • GC12M101226

Summaries for NT5DC3 Gene

GeneCards Summary for NT5DC3 Gene

NT5DC3 (5'-Nucleotidase Domain Containing 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include hydrolase activity and 5'-nucleotidase activity. An important paralog of this gene is NT5DC2.

Additional gene information for NT5DC3 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NT5DC3 Gene

Genomics for NT5DC3 Gene

GeneHancer (GH) Regulatory Elements for NT5DC3 Gene

Promoters and enhancers for NT5DC3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J103839 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 759.9 +0.3 309 3.5 SP1 ZBTB6 LCORL MLX POLR2A ZNF217 MYC NFYC ZNF701 RBM39 NT5DC3 ENSG00000257327 TDG RPL18AP3 C12orf73 TTC41P ENSG00000257754
GH12J103797 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 35.1 +39.2 39192 9.2 FOXA1 SMARCE1 TCF7L2 L3MBTL2 MAX DACH1 ZNF121 MNT TEAD4 NFIB HSALNG0093618 lnc-C12orf73-3 NT5DC3 ENSG00000257681 TDG lnc-C12orf73-4
GH12J103827 Enhancer 1 FANTOM5 Ensembl ENCODE 36.1 +9.7 9745 8.2 CTCF ZNF133 IKZF1 ZIC2 PKNOX1 SP1 DPF2 OSR2 FOXA2 NR2C2 NT5DC3 ENSG00000257681 TDG ENSG00000257754
GH12J103808 Enhancer 0.9 Ensembl ENCODE 35.4 +31.8 31791 1.3 SMARCE1 TEAD4 CBFA2T2 SMARCA4 DPF2 ZIC2 PKNOX1 HDAC1 LEF1 EP300 NT5DC3 ENSG00000257681 HSALNG0093618 ENSG00000257754
GH12J103821 Enhancer 0.5 Ensembl 36.5 +17.8 17844 4 ZIC2 POLR2A ZBTB20 SCRT2 JUND GLIS1 NT5DC3 ENSG00000257681 TDG ENSG00000257754
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NT5DC3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NT5DC3 gene promoter:
  • Arnt
  • GATA-1
  • HEN1
  • ISGF-3
  • POU2F1
  • POU2F1a
  • RORalpha2

Genomic Locations for NT5DC3 Gene

Genomic Locations for NT5DC3 Gene
chr12:103,763,312-103,841,245
(GRCh38/hg38)
Size:
77,934 bases
Orientation:
Minus strand
chr12:104,164,231-104,234,975
(GRCh37/hg19)
Size:
70,745 bases
Orientation:
Minus strand

Genomic View for NT5DC3 Gene

Genes around NT5DC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NT5DC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NT5DC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NT5DC3 Gene

Proteins for NT5DC3 Gene

  • Protein details for NT5DC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86UY8-NT5D3_HUMAN
    Recommended name:
    5'-nucleotidase domain-containing protein 3
    Protein Accession:
    Q86UY8
    Secondary Accessions:
    • Q9NUM7
    • Q9P2T2
    • Q9P2T3

    Protein attributes for NT5DC3 Gene

    Size:
    548 amino acids
    Molecular mass:
    63420 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA92095.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA93053.1; Type=Frameshift; Positions=62; Evidence={ECO:0000305};

    Alternative splice isoforms for NT5DC3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NT5DC3 Gene

Post-translational modifications for NT5DC3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NT5DC3 Gene

No data available for DME Specific Peptides for NT5DC3 Gene

Domains & Families for NT5DC3 Gene

Gene Families for NT5DC3 Gene

Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for NT5DC3 Gene

Suggested Antigen Peptide Sequences for NT5DC3 Gene

GenScript: Design optimal peptide antigens:
  • GRP94-neighboring nucleotidase (NT5D3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q86UY8

UniProtKB/Swiss-Prot:

NT5D3_HUMAN :
  • Belongs to the 5'(3')-deoxyribonucleotidase family.
Family:
  • Belongs to the 5'(3')-deoxyribonucleotidase family.
genes like me logo Genes that share domains with NT5DC3: view

Function for NT5DC3 Gene

Enzyme Numbers (IUBMB) for NT5DC3 Gene

Phenotypes From GWAS Catalog for NT5DC3 Gene

Gene Ontology (GO) - Molecular Function for NT5DC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008253 5'-nucleotidase activity IBA 21873635
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with NT5DC3: view
genes like me logo Genes that share phenotypes with NT5DC3: view

Animal Model Products

CRISPR Products

miRNA for NT5DC3 Gene

miRTarBase miRNAs that target NT5DC3

Clone Products

No data available for Molecular function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NT5DC3 Gene

Localization for NT5DC3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NT5DC3 gene
Compartment Confidence
mitochondrion 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NT5DC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043235 receptor complex IDA 23382219
genes like me logo Genes that share ontologies with NT5DC3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for NT5DC3 Gene

Pathways & Interactions for NT5DC3 Gene

PathCards logo

SuperPathways for NT5DC3 Gene

No Data Available

Interacting Proteins for NT5DC3 Gene

Gene Ontology (GO) - Biological Process for NT5DC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016311 dephosphorylation IEA --
genes like me logo Genes that share ontologies with NT5DC3: view

No data available for Pathways by source and SIGNOR curated interactions for NT5DC3 Gene

Drugs & Compounds for NT5DC3 Gene

(1) Drugs for NT5DC3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved, Experimental, Investigational Pharma 0
genes like me logo Genes that share compounds with NT5DC3: view

Transcripts for NT5DC3 Gene

mRNA/cDNA for NT5DC3 Gene

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NT5DC3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18 ^ 19
SP1: - - -
SP2:
SP3: -
SP4:
SP5:

Relevant External Links for NT5DC3 Gene

GeneLoc Exon Structure for
NT5DC3
ECgene alternative splicing isoforms for
NT5DC3

Expression for NT5DC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NT5DC3 Gene

mRNA differential expression in normal tissues according to GTEx for NT5DC3 Gene

This gene is overexpressed in Colon - Sigmoid (x11.3) and Esophagus - Muscularis (x4.7).

Protein differential expression in normal tissues from HIPED for NT5DC3 Gene

This gene is overexpressed in Frontal cortex (14.9), Colon (9.1), Rectum (7.7), Uterus (6.8), and Urinary Bladder (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NT5DC3 Gene



NURSA nuclear receptor signaling pathways regulating expression of NT5DC3 Gene:

NT5DC3

SOURCE GeneReport for Unigene cluster for NT5DC3 Gene:

Hs.48428

mRNA Expression by UniProt/SwissProt for NT5DC3 Gene:

Q86UY8-NT5D3_HUMAN
Tissue specificity: Expressed in brain, placenta, skeletal muscle, pancreas, testis, uterus, and small intestine. Reduced expression in pancreatic cancer cells.

Evidence on tissue expression from TISSUES for NT5DC3 Gene

  • Skin(4.3)
  • Nervous system(2.5)
genes like me logo Genes that share expression patterns with NT5DC3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NT5DC3 Gene

Orthologs for NT5DC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NT5DC3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NT5DC3 33 32
  • 99.64 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NT5DC3 33
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NT5DC3 33 32
  • 89.82 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NT5DC3 33 32
  • 89.48 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NT5DC3 33
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nt5dc3 32
  • 86.76 (n)
mouse
(Mus musculus)
Mammalia Nt5dc3 17 33 32
  • 86.69 (n)
chicken
(Gallus gallus)
Aves NT5DC3 33 32
  • 80.81 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NT5DC3 33
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nt5dc3 32
  • 73.43 (n)
zebrafish
(Danio rerio)
Actinopterygii nt5dc3 33 32
  • 71.91 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG1814 33 32
  • 53.29 (n)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 41 (a)
OneToMany
Species where no ortholog for NT5DC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NT5DC3 Gene

ENSEMBL:
Gene Tree for NT5DC3 (if available)
TreeFam:
Gene Tree for NT5DC3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NT5DC3: view image

Paralogs for NT5DC3 Gene

Paralogs for NT5DC3 Gene

(2) SIMAP similar genes for NT5DC3 Gene using alignment to 3 proteins:

  • NT5D3_HUMAN
  • H7C193_HUMAN
  • H7C3S8_HUMAN
genes like me logo Genes that share paralogs with NT5DC3: view

Variants for NT5DC3 Gene

Sequence variations from dbSNP and Humsavar for NT5DC3 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000003215 -- 103,813,814(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000057624 -- 103,811,959(-) T/A genic_upstream_transcript_variant, intron_variant
rs1000073332 -- 103,812,226(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000103413 -- 103,807,574(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000106539 -- 103,812,135(-) T/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NT5DC3 Gene

Variant ID Type Subtype PubMed ID
esv34031 CNV loss 18971310
esv3892262 CNV gain 25118596
nsv1126318 CNV deletion 24896259
nsv52873 CNV deletion 16902084
nsv560039 CNV gain 21841781

Variation tolerance for NT5DC3 Gene

Residual Variation Intolerance Score: 20.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.56; 30.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NT5DC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NT5DC3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NT5DC3 Gene

Disorders for NT5DC3 Gene

Additional Disease Information for NT5DC3

No disorders were found for NT5DC3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NT5DC3 Gene

Publications for NT5DC3 Gene

  1. Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. (PMID: 18839057) Lesch KP … Jacob C (Journal of neural transmission (Vienna, Austria : 1996) 2008) 3 43 56
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  3. TU12B1-TY, a novel gene in the region at 12q22-q23.1 frequently deleted in pancreatic cancer, shows reduced expression in pancreatic cancer cells. (PMID: 15547748) Yatsuoka T … Horii A (Oncology reports 2004) 3 4 56
  4. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. (PMID: 29568061) Liu X … Varjosalo M (Nature communications 2018) 3 56
  5. Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS. (PMID: 29478914) Yamauchi T … Maeda T (Cancer cell 2018) 3 56

Products for NT5DC3 Gene

Sources for NT5DC3 Gene