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NTN5 Gene

protein-coding   GIFtS: 41
GCID: GC19M049164

Netrin 5

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Netrin 51 2
Netrin-1-Like Protein2 3
Netrin-51
netrin-52
CNB25

External Ids:    HGNC: 252081   Entrez Gene: 1261472   Ensembl: ENSG000001422337   OMIM: 6072195   UniProtKB: Q8WTR83   

Export aliases for NTN5 gene to outside databases

Previous GC identifers: GC19M053857 GC19M045544


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for NTN5 Gene:
NTN5 (netrin 5) is a protein-coding gene. Diseases associated with NTN5 include bipolar disorder. An important paralog of this gene is NTN1.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000019.10  NT_011109.17  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the NTN5 gene promoter:
         Bach1   AhR   Elk-1   Spz1   Tal-1   p53   HTF   E47   Max   SRY   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for NTN5

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NTN5


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

Entrez Gene cytogenetic band: 19q13.33   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.33

NTN5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NTN5 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M049164:  view genomic region     (about GC identifiers)

Start:
49,164,664 bp from pter      End:
49,176,338 bp from pter
Size:
11,675 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: NET5_HUMAN, Q8WTR8 (See protein sequence)
Recommended Name: Netrin-5 precursor  
Size: 489 amino acids; 53174 Da
Secondary accessions: Q8N4X9 Q8WU63
Alternative splicing: 2 isoforms:  Q8WTR8-1   Q8WTR8-2   

Explore the universe of human proteins at neXtProt for NTN5: NX_Q8WTR8

Explore proteomics data for NTN5 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn62

  • See NTN5 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_665806.1  
    ENSEMBL proteins: 
     ENSP00000270235   ENSP00000469490  

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

    4 InterPro protein domains:
     IPR008993 TIMP-like_OB-fold
     IPR001134 Netrin_domain
     IPR002049 EGF_laminin
     IPR018933 Netrin_module_non-TIMP

    Graphical View of Domain Structure for InterPro Entry Q8WTR8

    ProtoNet protein and cluster: Q8WTR8

    1 Blocks protein domain: IPB002049 Laminin-type EGF-like domain

    UniProtKB/Swiss-Prot: NET5_HUMAN, Q8WTR8
    Similarity: Contains 3 laminin EGF-like domains
    Similarity: Contains 1 NTR domain


    NTN5 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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    NTN5 for ontologies           About GeneDecksing


    Animal Models:
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    NET5_HUMAN, Q8WTR8: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    NTN5 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NTN5
    Interactions:

        Search GeneGlobe Interaction Network for NTN5

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for NTN5 (NET5)



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for NTN5 gene: 
    NM_145807.1  

    Unigene Cluster for NTN5:

    Netrin 5
    Hs.326217  [show with all ESTs]
    Unigene Representative Sequence: BC021210
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000270235(uc002pkb.3 uc002pkc.3) ENST00000596844 ENST00000600468

    miRNA
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    hsa-miR-3920 hsa-miR-29a* hsa-miR-3672 hsa-miR-509-3p
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat NTN5
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    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat NTN5
      QuantiTect SYBR Green Assays in human, mouse, rat NTN5
      QuantiFast Probe-based Assays in human, mouse, rat NTN5

    Additional mRNA sequence: 

    BC018654.2 BC018697.2 BC021210.2 BC033207.1 

    3 DOTS entries:

    DT.86857092  DT.97833296  DT.100021778 

    Selected AceView cDNA sequences (see all 27):

    AW410201 BC021210 BX283519 BG826960 BC033207 NM_145807 AW411433 BF309789 
    BC018697 AW409817 BE270309 BE270224 BG825494 BC018654 BF307277 BE298601 
    BG826066 AW409705 BF307017 AW410548 BF205793 BG827394 AW410200 BI004259 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for NTN5    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b
    SP1:                                                  -     -               
    SP2:                    -                             -     -               
    SP3:                                                                        
    SP4:                                                                        


    ECgene alternative splicing isoforms for NTN5

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    NTN5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGGCCGCGC
    NTN5 Expression
    About this image

    NTN5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    NTN5 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.326217
        Custom PCR Arrays for NTN5
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NTN5

    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for NTN5 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ntn51 , 5 netrin 51, 5 79.47(n)1
    77.8(a)1
      7 (29.43 cM)5
    2439671  NM_001033356.21  NP_001028528.21 
     456840225 
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    8(a)
    many ↔ many
    3(19699492-19792198)
    lizard
    (Anolis carolinensis)
    Reptilia NTN56
    netrin 5
    37(a)
    1 ↔ 1
    GL343279.1(1053114-1093318)
    zebrafish
    (Danio rerio)
    Actinopterygii NTN56
    netrin 5
    22(a)
    1 ↔ 1
    7(21590796-21603978) ENSDARG00000036422
    fruit fly
    (Drosophila melanogaster)
    Insecta NetA6
    NetB6
    Netrin-B
    25(a)
    22(a)
    many ↔ many
    many ↔ many
    X(14498045-14547864)
    X(14580071-14643409)
    worm
    (Caenorhabditis elegans)
    Secernentea unc-66
    Protein UNC-6 (unc-6) mRNA, complete cds
    29(a)
    1 → many
    X(6889689-6897140) WBGene00006746


    ENSEMBL Gene Tree for NTN5 (if available)
    TreeFam Gene Tree for NTN5 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for NTN5 gene
    NTN12  NTNG12  NTN32  LAMB32  NTN42  NTNG22  
    1 SIMAP similar gene for NTN5 using alignment to 2 protein entries:     NET5_HUMAN (see all proteins):
    NTN1

    NTN5 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for NTN5 (see all 265)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs766741841,2
    C--49172206(+) CCACCG/ATCATC 1 -- int11Minor allele frequency- A:0.50WA 2
    rs783621221,2
    F--49340677(+) CTGGCG/TTGCAG 1 -- int11Minor allele frequency- T:0.02WA 118
    rs81064301,2
    C--49340679(+) GGCGTG/ACAGGC 1 -- int14Minor allele frequency- A:0.16WA NA EA 360
    rs1475810261,2
    --49340694(+) TGTTGA/TGTGGG 1 -- int10--------
    rs1177025931,2
    C,F--49340793(+) CTCAAT/CTCCTT 1 -- int11Minor allele frequency- C:0.01NA 120
    rs1490532581,2
    --49340835(+) CCAACA/GGTTCC 1 -- int10--------
    rs1430964181,2
    C--49340899(+) TTCCCA/GCCTTT 1 -- int10--------
    rs2813911,2
    C,F,A,H--49341200(+) AAATGC/TTGGGA 1 -- ut31 ese325Minor allele frequency- T:0.39NS EA NA WA CSA 2351
    rs1159193471,2
    C,F--49341404(+) GCTCCG/AGCCTG 2 /P /L mis11Minor allele frequency- A:0.03WA 118
    rs1998483941,2
    --49341413(+) TGGGAC/TTGGGT 2 N S mis10--------

    HapMap Linkage Disequilibrium report for NTN5 (49164664 - 49176338 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for NTN5:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2718680CNV Deletion23290073
    esv2718679CNV Deletion23290073
    esv2718681CNV Deletion23290073
    nsv912235CNV Loss21882294
    dgv3967n71CNV Loss21882294
    dgv3966n71CNV Loss21882294
    nsv912236CNV Gain21882294
    nsv9739CNV Gain+Loss18304495

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607219    OMIM disorders: --

    1 disease for NTN5:    
    About MalaCards
    bipolar disorder


    NTN5 for disorders           About GeneDecksing


    Export disorders for NTN5 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)
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    PubMed articles for NTN5 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with NTN5)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    2. Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. (PubMed id 21926972)1 (Nat. Genet. 2011)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. (PubMed id )2 

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 126147 HGNC: 25208 AceView: LOC126147 Ensembl:ENSG00000142233 euGenes: HUgn126147
    ECgene: NTN5 H-InvDB: NTN5

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for NTN5 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for NTN5 gene:
    Search GeneIP for patents involving NTN5

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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