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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

NTN3 Gene

protein-coding   GIFtS: 48
GCID: GC16P002521

Netrin 3

(Previous names: netrin 2 (chicken)-like, netrin 2-like (chicken))
(Previous symbol: NTN2L)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Netrin 31 2     Netrin 2 (Chicken)-Like1
NTN2L1 2 3 5     Netrin 2-Like (Chicken)1
Netrin-2-Like Protein2 3     Netrin-2, Chicken, Homolog Of, Like2
Netrin-31     netrin-32

External Ids:    HGNC: 80301   Entrez Gene: 49172   Ensembl: ENSG000001620687   OMIM: 6023495   UniProtKB: O006343   

Export aliases for NTN3 gene to outside databases

Previous GC identifer: GC16P002462


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for NTN3 Gene: 
NTN3 (netrin 3) is a protein-coding gene. Diseases associated with NTN3 include polycystic kidney disease, type 1, and mantle cell lymphoma, and among its related super-pathways are Myogenesis and Axon guidance. GO annotations related to this gene include molecular_function and receptor binding. An important paralog of this gene is LAMC1.

UniProtKB/Swiss-Prot: NET3_HUMAN, O00634
Function: Netrins control guidance of CNS commissural axons and peripheral motor axons (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NC_018927.2  NT_010393.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NTN3 gene promoter:
         Elk-1   Pax-5   Pax-2a   AP-4   Nkx2-5   Tal-1beta   CREB   AREB6   HSF2   ITF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNTN3 promoter sequence
   Search SABiosciences Chromatin IP Primers for NTN3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NTN3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p13.3   Ensembl cytogenetic band:  16p13.3   HGNC cytogenetic band: 16p13.3

NTN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NTN3 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P002521:  view genomic region     (about GC identifiers)

Start:
2,521,500 bp from pter      End:
2,524,146 bp from pter
Size:
2,647 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: NET3_HUMAN, O00634 (See protein sequence)
Recommended Name: Netrin-3 precursor  
Size: 580 amino acids; 61466 Da
Subcellular location: Secreted, extracellular space, extracellular matrix (By similarity)

Explore the universe of human proteins at neXtProt for NTN3: NX_O00634

Explore proteomics data for NTN3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_O00634

  • NTN3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    NTN3 Protein Expression
    REFSEQ proteins: NP_006172.1  
    ENSEMBL proteins: 
     ENSP00000293973  
    Reactome Protein details: O00634
    Human Recombinant Protein Products for NTN3: 
    Browse Purified and Recombinant Proteins at EMD Millipore
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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005576extracellular region ----
    GO:0005578proteinaceous extracellular matrix IEA--
    GO:0005794Golgi apparatus IEA--

    NTN3 for ontologies           About GeneDecksing



    NTN3 Antibody Products: 
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    NTN: Netrins

    5 InterPro protein domains:
     IPR008993 TIMP-like_OB-fold
     IPR008211 Laminin_N
     IPR001134 Netrin_domain
     IPR002049 EGF_laminin
     IPR018933 Netrin_module_non-TIMP

    Graphical View of Domain Structure for InterPro Entry O00634

    ProtoNet protein and cluster: O00634

    3 Blocks protein domains:
    IPB001134 Netrin
    IPB002049 Laminin-type EGF-like domain
    IPB008212 Laminin


    UniProtKB/Swiss-Prot: NET3_HUMAN, O00634
    Similarity: Contains 3 laminin EGF-like domains
    Similarity: Contains 1 laminin N-terminal domain
    Similarity: Contains 1 NTR domain


    NTN3 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NET3_HUMAN, O00634
    Function: Netrins control guidance of CNS commissural axons and peripheral motor axons (By similarity)

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005102receptor binding IEA--
    GO:0005515protein binding ----
         
    NTN3 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for NTN3:
     Increased gamma-H2AX phosphory  Small cells 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for NTN3 
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for NTN3 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1CDO in myogenesis
    CDO in myogenesis1.00
    Myogenesis1.00
    2Axon guidance
    Developmental Biology0.69
    3Axon guidance
    Axon guidance

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    3        Reactome Pathways for NTN3
        Developmental Biology
    Myogenesis
    CDO in myogenesis


    1         Kegg Pathway  (Kegg details for NTN3):
        Axon guidance


    NTN3 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NTN3

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for NTN3 (O006343 ENSP000002939734) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NEO1Q928593, ENSP000002619084I2D: score=1 STRING: ENSP00000261908
    CDONENSP000002635774STRING: ENSP00000263577
    DCCENSP000003891404STRING: ENSP00000389140
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007411axon guidance NAS9143507
    GO:0042692muscle cell differentiation TAS--
    GO:0051149positive regulation of muscle cell differentiation TAS--

    NTN3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for NTN3 (NET3)

    Search CenterWatch for drugs/clinical trials and news about NTN3 / NET3

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for NTN3 gene: 
    NM_006181.2  

    Unigene Cluster for NTN3:

    Netrin 3
    Hs.158336  [show with all ESTs]
    Unigene Representative Sequence: NM_006181
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000293973(uc002cqj.3)
    miRNA
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    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat NTN3

    Additional mRNA sequence: U86759.1 

    1 DOTS entry:

    DT.404096 

    4 AceView cDNA sequences:

    NM_006181 BF512861 U86759 AI951694 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    NTN3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    NTN3 Expression
    About this image


    See NTN3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for NTN3

    SOURCE GeneReport for Unigene cluster: Hs.158336

    UniProtKB/Swiss-Prot: NET3_HUMAN, O00634
    Tissue specificity: Spinal cord

        SABiosciences Expression via Pathway-Focused PCR Array including NTN3: 
              Cancer Drug Targets in human mouse rat

    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NTN3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for NTN3 gene from 6/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ntn31 , 5 netrin 31, 5 83.51(n)1
    87.41(a)1
      17 (12.31 cM)5
    182091  NM_010947.31  NP_035077.11 
     242038485 
    chicken
    (Gallus gallus)
    Aves NTN16
    --
    --
    54(a)
    1(a)
    1 ↔ many
    possible ortholog
    14(14014723-14042108)
    2(102780728-102893609)
    lizard
    (Anolis carolinensis)
    Reptilia NTN36
    NTN56
    Uncharacterized protein
    50(a)
    44(a)
    1 ↔ many
    possible ortholog
    GL343621.1(158069-223926)
    GL343279.1(1053114-1093318)
    zebrafish
    (Danio rerio)
    Actinopterygii ntn26
    --
    --
    53(a)
    28(a)
    1 ↔ many
    possible ortholog
    24(40240951-40300903)
    7(21590796-21603978)
    fruit fly
    (Drosophila melanogaster)
    Insecta NetA6
    NetB6
    (see all 3)
    Netrin-B
    (see all 3)
    36(a)
    32(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    X(14498045-14547864)
    X(14580071-14643409)
    worm
    (Caenorhabditis elegans)
    Secernentea unc-66
    epi-16
    Laminin-like protein epi-1
    41(a)
    3(a)
    1 ↔ many
    possible ortholog
    X(6889689-6897140)
    IV(10666827-10679441)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for NTN3 gene
    LAMC12  LAMC22  NTN42  LAMB32  NTN52  LAMC32  NTN12  NTNG12  
    USH2A2  NTNG22  LAMB42  LAMB22  LAMB12  
    1 SIMAP similar gene for NTN3 using alignment to 1 protein entry:     NET3_HUMAN:
    NTN1

    NTN3 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/99 SNPs in NTN3 are shown (see all 99)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0500864
    ----see VAR_0500862 P S mis40--------
    rs1441262421,2
    C--2519529(+) CACCC-/TTAGGGT 1 -- us2k10--------
    rs1172103911,2
    F--2519802(+) GATGTG/ATGGCA 1 -- us2k11Minor allele frequency- A:0.04EA 120
    rs1435469951,2
    --2520098(+) CTGAAA/GCGGGG 1 -- us2k10--------
    rs1480732051,2
    --2520101(+) AAACGA/GGGCAT 1 -- us2k10--------
    rs1902788661,2
    --2520238(+) CCTCTC/TTGGTG 1 -- us2k10--------
    rs1471494321,2
    --2520239(+) CTCTTC/TGGTGG 1 -- us2k10--------
    rs1386790121,2
    C--2520329(+) CCAAAC/TGTGCT 1 -- us2k10--------
    rs1816988091,2
    --2520341(+) TGACGA/TAGGGC 1 -- us2k10--------
    rs1426841991,2
    --2520346(+) TAGGGC/TAGTGG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for NTN3 (2521500 - 2524146 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for NTN3:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2422427CNV Duplication17116639
    nsv905153CNV Loss21882294
    dgv2545n71CNV Loss21882294
    esv29545CNV Loss19812545
    nsv905152CNV Loss21882294
    dgv2569n71CNV Loss21882294
    nsv905149CNV Loss21882294
    nsv905139CNV Loss21882294
    nsv833121CNV Loss17160897
    dgv2570n71CNV Loss21882294

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 602349    OMIM disorders: --

    8 diseases for NTN3:    About MalaCards
    polycystic kidney disease, type 1    mantle cell lymphoma    tuberous sclerosis    polycystic kidney disease
    chronic lymphocytic leukemia    kidney disease    leukemia    prostatitis


    NTN3 for disorders           About GeneDecksing


    Export disorders for NTN3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for NTN3 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with NTN3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The NTN2L gene encoding a novel human netrin maps to the autosomal dominant polycystic kidney disease region on chromosome 16p13.3. (PubMed id 9143507)1, 2, 3, 9 Van Raay T.J....Burn T.C. (1997)
    2. Netrin-3, a mouse homolog of human NTN2L, is highly expressed in sensory ganglia and shows differential binding to netrin receptors. (PubMed id 10366627)1, 3, 9 Wang H....Tessier-Lavigne M. (1999)
    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. (PubMed id 8828041)1, 2 Burn T.C.... Landes G.M. (1996)
    4. Autocrine netrin function inhibits glioma cell motili ty and promotes focal adhesion formation. (PubMed id 21980448)1 Jarjour A.A....Kennedy T.E. (2011)
    5. Close encounters: regulation of vertebrate skeletal m yogenesis by cell-cell contact. (PubMed id 15923648)1 Krauss R.S....Kang J.S. (2005)
    6. Quantification of expression of netrins, slits and their receptors in human prostate tumors. (PubMed id 12471613)1 Latil A....Cussenot O. (2003)
    7. Immunoglobulin V(H) gene mutational analysis suggests that blastic variant of mantle cell lymphoma derives from different stages of B-cell maturation. (PubMed id 10634642)1 Laszlo T....Matolcsy A. (2000)
    8. Analysis of heavy and light chain pairings indicates that receptor editing shapes the human antibody repertoire. (PubMed id 9887257)1 de Wildt R.M....Winter G. (1999)
    9. Unmutated Ig V(H) genes are associated with a more aggressive form of chronic lymphocytic leukemia. (PubMed id 10477713)1 Hamblin T.J....Stevenson F.K. (1999)
    10. Expression of mRNA for axon guidance molecules, such as semaphorin-III, netrins and neurotrophins, in human osteoblasts and osteoclasts. (PubMed id 10996153)9 Togari A....Koshihara Y. (2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 4917 HGNC: 8030 AceView: NTN2L Ensembl:ENSG00000162068 euGenes: HUgn4917
    ECgene: NTN3 Kegg: 4917 H-InvDB: NTN3

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for NTN3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for NTN3 gene:
    Search GeneIP for patents involving NTN3

    GeneCards and IP:
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