Aliases for NTN3 Gene

Aliases for NTN3 Gene

  • Netrin 3 2 3 5
  • Netrin-3 2 3 4
  • Netrin-2-Like Protein 3 4
  • NTN2L 3 4
  • Netrin-2, Chicken, Homolog Of, Like 3
  • Netrin 2 (Chicken)-Like 2
  • Netrin 2-Like (Chicken) 2
  • NTN3 5

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 Deafness, Autosomal Recessive 74 and Deafness, Autosomal Recessive 86. Among its related pathways are Myogenesis and Developmental Biology. Gene Ontology (GO) annotations related to this gene include signaling receptor binding. An important paralog of this gene is NTN1.

UniProtKB/Swiss-Prot Summary for NTN3 Gene

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

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NTN3 Gene

Genomics for NTN3 Gene

GeneHancer (GH) Regulatory Elements Pubs

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
GH16J002467 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 259 -1.1 -1097 6.4 SP1 ZNF207 ZNF600 IKZF1 ZNF580 ATF2 ZNF10 NFIC POLR2A ZIC2 NTN3 HSALNG0109011 ZNF75A ZNF213-AS1 CRAMP1 ZNF263 TELO2 TSC2 E4F1 MIR3677HG
GH16J002364 Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas 11.5 -105.5 -105471 3.5 NCOR1 IKZF1 NFIC BCL11A ZNF341 EBF1 SKIL TAL1 PRDM10 BHLHE40 HSALNG0109003 ABCA17P ABCA3 CCNF NTN3 TBC1D24 SRRM2-AS1 HSALNG0109001 lnc-CCNF-4 MK280269-018
GH16J002423 Enhancer 0.9 Ensembl ENCODE 12 -48.3 -48296 1.2 MYC CTCF REST TRIM22 BHLHE40 SIN3A RAD21 SMC3 EBF1 SMARCA5 lnc-CCNF-3 piR-57133-212 NTN3 ABCA17P ABCA3 TBC1D24 CCNF HSALNG0109005
GH16J002439 Enhancer 0.6 Ensembl ENCODE 12.3 -31.1 -31096 1.6 ELF1 STAT1 ZNF217 POLR2A NTN3 TBC1D24 ABCA3 ABCA17P RNPS1 ECI1 MIR940 PKD1 LOC652276 ENSG00000285970
GH16J002369 Enhancer 0.3 Ensembl 11.6 -99.9 -99896 1.6 FOS ESRRA ABCA17P ABCA3 CCNF NTN3 TBC1D24 SRRM2-AS1 HSALNG0109003 RF00017-1715 MK280269-018
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NTN3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NTN3

Top Transcription factor binding sites by QIAGEN in the NTN3 gene promoter:
  • AP-4
  • AREB6
  • CREB
  • Elk-1
  • HSF2
  • ITF-2
  • Nkx2-5
  • Pax-2a
  • Pax-5
  • Tal-1beta

Genomic Locations for NTN3 Gene

Latest Assembly
2,849 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
2,849 bases
Plus strand

(GRCh37/hg19 by Ensembl)
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 Asn387
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

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

Protein Domains for NTN3 Gene

  • Laminin-type EGF-like domain
  • Netrin, C-terminal
  • Laminin, N-terminal 2

Suggested Antigen Peptide Sequences for NTN3 Gene

GenScript: Design optimal peptide antigens:
  • Netrin-2-like protein (NET3_HUMAN)
genes like me logo Genes that share domains with NTN3: view

No data available for Graphical View of Domain Structure and 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 signaling receptor binding IEA,IBA 21873635
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 Models for research

  • Taconic Biosciences Mouse Models for NTN3

miRNA for NTN3 Gene

miRTarBase miRNAs that target NTN3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NTN3

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
cytoskeleton 1
nucleus 1
mitochondrion 0
peroxisome 0
cytosol 0

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:0005604 basement membrane IBA 21873635
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

PathCards logo

SuperPathways 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
GO:0008045 motor neuron axon guidance IBA 21873635
GO:0009887 animal organ morphogenesis IBA 21873635
GO:0009888 tissue development IBA 21873635
GO:0016358 dendrite development IBA 21873635
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 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NTN3

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

No ASD Table

Relevant External Links for NTN3 Gene

GeneLoc Exon Structure for

Expression for NTN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NTN3

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 for research

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 29 30
  • 98.01 (n)
(Bos Taurus)
Mammalia NTN3 29 30
  • 88.55 (n)
(Canis familiaris)
Mammalia NTN3 29 30
  • 87.48 (n)
(Rattus norvegicus)
Mammalia Ntn3 29
  • 83.75 (n)
(Mus musculus)
Mammalia Ntn3 29 16 30
  • 83.45 (n)
(Ornithorhynchus anatinus)
Mammalia NTN3 30
  • 70 (a)
(Monodelphis domestica)
Mammalia NTN3 30
  • 70 (a)
(Gallus gallus)
Aves NTN3 30
  • 55 (a)
(Anolis carolinensis)
Reptilia NTN3 30
  • 50 (a)
(Danio rerio)
Actinopterygii ntn2 30
  • 53 (a)
Fruit Fly
(Drosophila melanogaster)
Insecta NetA 30
  • 36 (a)
NetB 30
  • 32 (a)
(Caenorhabditis elegans)
Secernentea unc-6 30
  • 42 (a)
Species where no ortholog for NTN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Evolutionary constrained regions (ECRs) for NTN3: view image
Alliance of Genome Resources:
Additional Orthologs for NTN3

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NTN3 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs34818219 -- p.Pro425Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NTN3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

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

Disorders for NTN3 Gene

MalaCards: The human disease database

(5) MalaCards diseases for NTN3 Gene - From: COP and GCD

- 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
  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
  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
  4. The midbody interactome reveals unexpected roles for PP1 phosphatases in cytokinesis. (PMID: 31586073) Capalbo L … D'Avino PP (Nature communications 2019) 3
  5. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3

Products for NTN3 Gene

Sources for NTN3 Gene