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Aliases for NTN3 Gene

Aliases for NTN3 Gene

  • Netrin 3 2 3 5
  • Netrin-2-Like Protein 3 4
  • Netrin-3 2 3
  • NTN2L 3 4
  • Netrin-2, Chicken, Homolog Of, Like 3
  • Netrin 2 (Chicken)-Like 2
  • Netrin 2-Like (Chicken) 2

External Ids for NTN3 Gene

Previous HGNC Symbols for NTN3 Gene

  • NTN2L

Previous GeneCards Identifiers for NTN3 Gene

  • GC16P002462
  • GC16P002521

Summaries for NTN3 Gene

GeneCards Summary for NTN3 Gene

NTN3 (Netrin 3) is a Protein Coding gene. Diseases associated with NTN3 include Autosomal Dominant Polycystic Kidney Disease. Among its related pathways are Myogenesis and Developmental Biology. Gene Ontology (GO) annotations related to this gene include receptor binding. An important paralog of this gene is NTN1.

UniProtKB/Swiss-Prot for NTN3 Gene

  • Netrins control guidance of CNS commissural axons and peripheral motor axons.

Additional gene information for NTN3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NTN3 Gene

Genomics for NTN3 Gene

GeneHancer (GH) Regulatory Elements for NTN3 Gene

Promoters and enhancers for NTN3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I002467 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 559.1 -1.8 -1804 5.4 HDGF ARID4B SIN3A FEZF1 DMAP1 YBX1 ZNF2 IRF4 YY1 ZNF207 NTN3 LOC729652 ZNF75A ZNF213-AS1 ERVK13-1 LOC106660606 NME3 MTCO1P28 ENSG00000260646 SNORD60
GH16I002364 Enhancer 0.8 ENCODE 11.5 -105.8 -105825 3.2 PKNOX1 BMI1 ZNF366 IKZF2 RUNX3 ZNF398 ZNF217 NFIC SMARCA4 IKZF1 GC16M002363 ABCA17P ABCA3 CCNF NTN3 TBC1D24 SRRM2-AS1 GC16M002369
GH16I002423 Enhancer 0.7 ENCODE 12 -48.2 -48214 0.2 CTCF RB1 SIN3A EBF1 RAD21 ZNF335 CTBP1 POLR2A EGR1 SCRT2 ABCA17P ABCA3 NTN3 TBC1D24 GC16P002427 GC16P002400
GH16I002439 Enhancer 0.5 ENCODE 12.3 -31.1 -31098 0.8 ZNF217 POLR2A ETV6 ELF1 TBC1D24 NTN3 ABCA3 ABCA17P RNPS1 ECI1 MIR940 PKD1 MIR6767 GC16P002435
GH16I002473 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 0.8 +3.8 3818 3.5 ATF1 FOXA2 ARID4B SIN3A ZNF48 POLR2B GLIS2 ZNF143 ZNF207 KLF13 TBC1D24 ENSG00000260293 GC16P002476 IFT140 ZNF75A TIGD7 NME3 ZNF213-AS1 ZSCAN32 ZNF174
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NTN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NTN3 gene promoter:

Genomic Locations for NTN3 Gene

Genomic Locations for NTN3 Gene
2,647 bases
Plus strand

Genomic View for NTN3 Gene

Genes around NTN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NTN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NTN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NTN3 Gene

Proteins for NTN3 Gene

  • Protein details for NTN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:

    Protein attributes for NTN3 Gene

    580 amino acids
    Molecular mass:
    61466 Da
    Quaternary structure:
    No Data Available

neXtProt entry for NTN3 Gene

Post-translational modifications for NTN3 Gene

  • Glycosylation at Asn104 and isoforms=387
  • Modification sites at PhosphoSitePlus

Other Protein References for NTN3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NTN3 Gene

Domains & Families for NTN3 Gene

Gene Families for NTN3 Gene

Human Protein Atlas (HPA):
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for NTN3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with NTN3: view

No data available for UniProtKB/Swiss-Prot for NTN3 Gene

Function for NTN3 Gene

Molecular function for NTN3 Gene

UniProtKB/Swiss-Prot Function:
Netrins control guidance of CNS commissural axons and peripheral motor axons.

Gene Ontology (GO) - Molecular Function for NTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005102 receptor binding IEA --
GO:0005515 protein binding IPI 26190107
genes like me logo Genes that share ontologies with NTN3: view
genes like me logo Genes that share phenotypes with NTN3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for NTN3

CRISPR Products

miRNA for NTN3 Gene

miRTarBase miRNAs that target NTN3

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NTN3 Gene

Localization for NTN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NTN3 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

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 NTN3 gene
Compartment Confidence
extracellular 4
golgi apparatus 2
plasma membrane 1
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for NTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005576 extracellular region IEA --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005794 Golgi apparatus IEA --
genes like me logo Genes that share ontologies with NTN3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NTN3 Gene

Pathways & Interactions for NTN3 Gene

genes like me logo Genes that share pathways with NTN3: view

Pathways by source for NTN3 Gene

3 Reactome pathways for NTN3 Gene
1 KEGG pathway for NTN3 Gene

Gene Ontology (GO) - Biological Process for NTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007411 axon guidance NAS 9143507
genes like me logo Genes that share ontologies with NTN3: view

No data available for SIGNOR curated interactions for NTN3 Gene

Drugs & Compounds for NTN3 Gene

No Compound Related Data Available

Transcripts for NTN3 Gene

mRNA/cDNA for NTN3 Gene

(1) REFSEQ mRNAs :
(1) Additional mRNA sequences :
(4) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for NTN3 Gene

Netrin 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NTN3 Gene

No ASD Table

Relevant External Links for NTN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NTN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NTN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NTN3 Gene

This gene is overexpressed in Testis (x4.2).

NURSA nuclear receptor signaling pathways regulating expression of NTN3 Gene:


SOURCE GeneReport for Unigene cluster for NTN3 Gene:


mRNA Expression by UniProt/SwissProt for NTN3 Gene:

Tissue specificity: Spinal cord.
genes like me logo Genes that share expression patterns with NTN3: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for NTN3 Gene

Orthologs for NTN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NTN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NTN3 33 34
  • 98.01 (n)
(Bos Taurus)
Mammalia NTN3 33 34
  • 88.55 (n)
(Canis familiaris)
Mammalia NTN3 34 33
  • 87.48 (n)
(Rattus norvegicus)
Mammalia Ntn3 33
  • 83.75 (n)
(Mus musculus)
Mammalia Ntn3 33 16 34
  • 83.45 (n)
(Monodelphis domestica)
Mammalia NTN3 34
  • 70 (a)
(Ornithorhynchus anatinus)
Mammalia NTN3 34
  • 70 (a)
(Gallus gallus)
Aves NTN3 34
  • 55 (a)
(Anolis carolinensis)
Reptilia NTN3 34
  • 50 (a)
(Danio rerio)
Actinopterygii ntn2 34
  • 53 (a)
fruit fly
(Drosophila melanogaster)
Insecta NetA 34
  • 36 (a)
NetB 34
  • 32 (a)
(Caenorhabditis elegans)
Secernentea unc-6 34
  • 42 (a)
Species where no ortholog for NTN3 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for NTN3 Gene

Gene Tree for NTN3 (if available)
Gene Tree for NTN3 (if available)

Paralogs for NTN3 Gene

Paralogs for NTN3 Gene

(1) SIMAP similar genes for NTN3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with NTN3: view

Variants for NTN3 Gene

Sequence variations from dbSNP and Humsavar for NTN3 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000849271 -- 2,469,950(+) G/A upstream_transcript_variant
rs1001149456 -- 2,473,912(+) C/A/G coding_sequence_variant, missense_variant
rs1001337579 -- 2,470,022(+) C/G upstream_transcript_variant
rs1001517211 -- 2,474,087(+) G/A coding_sequence_variant, synonymous_variant
rs1002954837 -- 2,471,439(+) C/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for NTN3 Gene

Variant ID Type Subtype PubMed ID
dgv4864n54 CNV loss 21841781
dgv4865n54 CNV gain 21841781
dgv4866n54 CNV loss 21841781
esv2422427 CNV duplication 17116639
esv29545 CNV loss 19812545
nsv1052260 CNV gain 25217958
nsv571205 CNV gain 21841781
nsv833121 CNV loss 17160897
nsv952903 CNV deletion 24416366

Variation tolerance for NTN3 Gene

Residual Variation Intolerance Score: 67.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.28; 52.98% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NTN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NTN3 Gene

Disorders for NTN3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NTN3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
autosomal dominant polycystic kidney disease
  • adpkd
- elite association - COSMIC cancer census association via MalaCards
Search NTN3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NTN3

genes like me logo Genes that share disorders with NTN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NTN3 Gene

Publications for NTN3 Gene

  1. The NTN2L gene encoding a novel human netrin maps to the autosomal dominant polycystic kidney disease region on chromosome 16p13.3. (PMID: 9143507) Van Raay TJ … Burn TC (Genomics 1997) 2 3 4 22 58
  2. Netrin-3, a mouse homolog of human NTN2L, is highly expressed in sensory ganglia and shows differential binding to netrin receptors. (PMID: 10366627) Wang H … Tessier-Lavigne M (The Journal of neuroscience : the official journal of the Society for Neuroscience 1999) 2 3 22 58
  3. Generation of a transcriptional map for a 700-kb region surrounding the polycystic kidney disease type 1 (PKD1) and tuberous sclerosis type 2 (TSC2) disease genes on human chromosome 16p3.3. (PMID: 8828041) Burn TC … Landes GM (Genome research 1996) 3 4 58
  4. A Floor-Plate Extracellular Protein-Protein Interaction Screen Identifies Draxin as a Secreted Netrin-1 Antagonist. (PMID: 26190107) Gao X … Söllner C (Cell reports 2015) 3 58
  5. Autocrine netrin function inhibits glioma cell motility and promotes focal adhesion formation. (PMID: 21980448) Jarjour AA … Kennedy TE (PloS one 2011) 3 58

Products for NTN3 Gene

Sources for NTN3 Gene

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