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

NCDN Gene

protein-coding   GIFtS: 48
GCID: GC01P036023

neurochondrin

 Explore 3 diseases affiliated with
NCDN via our new
 Human Malady Compendium 
Biological research products
for NCDN
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Neurochondrin1
KIAA06073 5
NCDN-11
NCDN-21

External Ids:    HGNC: 175971   Entrez Gene: 231542   Ensembl: ENSG000000201297   OMIM: 6084585   UniProtKB: Q9UBB63   

Export aliases for NCDN gene to outside databases

Previous GC identifers: GC01P035844 GC01P035080 GC01P035449 GC01P035451 GC01P035692 GC01P035795 GC01P034141


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

Entrez Gene summary for NCDN:
This gene encodes a leucine-rich cytoplasmic protein, which is highly similar to a mouse protein that negatively
regulates Ca/calmodulin-dependent protein kinase II phosphorylation and may be essential for spatial learning
processes. Several alternatively spliced transcript variants of this gene have been described. (provided by RefSeq,
Jul 2008)

UniProtKB/Swiss-Prot: NCDN_HUMAN, Q9UBB6
Function: Probably involved in signal transduction, in the nervous system, via increasing cell surface localization of
GRM5 and positively regulating its signaling (By similarity). Required for the spatial learning process. Acts as a
negative regulator of Ca(2+)-calmodulin-dependent protein kinase 2 (CaMK2) phosphorylation. May play a role in
modulating melanin-concentrating hormone-mediated functions via its interaction with MCHR1 that interferes with G
protein-coupled signal transduction. May be involved in bone metabolism. May also be involved in neurite outgrowth

Gene Wiki entry for NCDN


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NCDN gene promoter:
         Brachyury   CUTL1   E4BP4   GATA-2   MZF-1   HEN1   AREB6   Ik-2   ZID   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNCDN promoter sequence
   Search SABiosciences Chromatin IP Primers for NCDN

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


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

Entrez Gene cytogenetic band: 1p34.3   Ensembl cytogenetic band:  1p34.3   HGNC cytogenetic band: 1p34.3

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

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P036023:  view genomic region     (about GC identifiers)

Start:
36,023,074 bp from pter      End:
36,032,875 bp from pter
Size:
9,802 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: NCDN_HUMAN, Q9UBB6 (See protein sequence)
Recommended Name: Neurochondrin  
Size: 729 amino acids; 78864 Da
Subunit: Interacts with SEMA4C, DIAPH1 (via FH3 domain) and GRM5 (By similarity). Interacts with MCHR1
Subcellular location: Cytoplasm, cytosol. Cell projection, dendrite. Note=Localizes to somatic regions of neurons
Sequence caution: Sequence=AAD05029.1; Type=Erroneous gene model prediction;
Secondary accessions: D3DPR9 Q9UBY2 Q9Y4A6 Q9Y4D9
Alternative splicing: 3 isoforms:  Q9UBB6-1   Q9UBB6-2   Q9UBB6-3   (Incomplete sequence. No experimental confirmation available)

Explore the universe of human proteins at neXtProt for NCDN: NX_Q9UBB6

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UBB6

  • NCDN Protein expression data from MOPED and PaxDb:    About this image 
    NCDN Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_001014839.1  NP_001014841.1  NP_055099.1  

    ENSEMBL proteins: 
     ENSP00000362350   ENSP00000348394   ENSP00000362340   ENSP00000406511   ENSP00000407339  

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    Uscn Proteins for NCDN

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634NOT nucleus ISS--
    GO:0005829cytosol ISS--
    GO:0030424NOT axon ISS--
    GO:0030425dendrite ISS--
    GO:0043005neuron projection ----

    NCDN for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    NCDN for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR008709 Neurochondrin

    Graphical View of Domain Structure for InterPro Entry Q9UBB6

    ProtoNet protein and cluster: Q9UBB6

    UniProtKB/Swiss-Prot: NCDN_HUMAN, Q9UBB6
    Similarity: Belongs to the neurochondrin family


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

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: NCDN_HUMAN, Q9UBB6
    Function: Probably involved in signal transduction, in the nervous system, via increasing cell surface localization of
    GRM5 and positively regulating its signaling (By similarity). Required for the spatial learning process. Acts as a
    negative regulator of Ca(2+)-calmodulin-dependent protein kinase 2 (CaMK2) phosphorylation. May play a role in
    modulating melanin-concentrating hormone-mediated functions via its interaction with MCHR1 that interferes with G
    protein-coupled signal transduction. May be involved in bone metabolism. May also be involved in neurite outgrowth

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

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


    Phenotypes:
         7 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Ncdn):
     behavior/neurological  embryogenesis  endocrine/exocrine gland  mortality/aging  nervous system 
     skeleton  vision/eye 

    NCDN for phenotypes           About GeneDecksing

    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidNCDN 3' UTR sequence
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

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

    STRING Interaction Network Preview (showing 5 interactants - click image to see 12)

    5/18 Interacting proteins for NCDN (Q9UBB63 ENSP000003483944) via UniProtKB, MINT, STRING, and/or I2D (see all 18)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PTP4A3O753653, ENSP000003322744I2D: score=1 STRING: ENSP00000332274
    SEMA4CQ9C0C43, ENSP000003068444I2D: score=1 STRING: ENSP00000306844
    LYSTQ996983, ENSP000003744434I2D: score=3 STRING: ENSP00000374443
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    C1GALT1Q9NS003I2D: score=2 
    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:0031175neuron projection development ISS--
    GO:0045453bone resorption IEA--
    GO:0048168regulation of neuronal synaptic plasticity IEA--

    NCDN for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 NCDN
    Search CenterWatch for drugs/clinical trials and news about NCDN 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
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    About This Section

    REFSEQ mRNAs for NCDN gene (3 alternative transcripts): 
    NM_001014839.1  NM_001014841.1  NM_014284.2  

    Unigene Cluster for NCDN:

    Neurochondrin
    Hs.121870  [show with all ESTs]
    Unigene Representative Sequence: BC024592
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000373253 ENST00000356090(uc001bza.3 uc001bzc.3) ENST00000373243(uc001bzb.3)
    ENST00000459931 ENST00000437806 ENST00000423723

    miRNA
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    8/46 QIAGEN miScript miRNA Assays for microRNAs that regulate NCDN (see all 46):
    hsa-miR-3678-3p hsa-miR-596 hsa-miR-3194-5p hsa-miR-631 hsa-miR-1914* hsa-miR-632 hsa-miR-346 hsa-miR-449a
    SwitchGear 3'UTR luciferase reporter plasmidNCDN 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AB011179.1 AB018739.2 AB018740.2 AK293658.1 AK295979.1 BC024592.1 

    15 DOTS entries:

    DT.100777596  DT.414291  DT.97809854  DT.95076495  DT.97846756  DT.40124875  DT.100009556  DT.91764860 
    DT.100777595  DT.121377828  DT.40118600  DT.40118601  DT.95223221  DT.121001424  DT.95185397 

    24/158 AceView cDNA sequences (see all 158):

    AI216097 BQ063887 AW467935 AL043798 BG056108 BQ889558 BM737848 T09146 
    BC024592 AA653569 BX113931 BM557346 BQ071735 BQ672433 BU191849 BM802213 
    BQ070487 BQ671561 BU856256 AL133988 BU157716 BQ723024 BM905810 AL135626 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for NCDN    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b
    SP1:              -           -     -                                                   
    SP2:              -     -     -     -                                                   
    SP3:                          -     -                                                   
    SP4:                                                                                    
    SP5:              -                                                                     


    ECgene alternative splicing isoforms for NCDN

    (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

    NCDN expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGGACACTCA
    NCDN Expression
    About this image
    See NCDN Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for NCDN

    SOURCE GeneReport for Unigene cluster: Hs.121870

    UniProtKB/Swiss-Prot: NCDN_HUMAN, Q9UBB6
    Tissue specificity: Abundantly expressed in whole adult brain and in all individual brain regions examined, including
    spinal cord. Weakly expressed in ovary, testis, fetal brain and small intestine

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    (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 eukaryotes.

    Orthologs for NCDN gene from 7/19 species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ncdn1 , 5 neurochondrin1, 5 90.76(n)1
    98.22(a)1
      4 (60.93 cM)5
    265621  NM_011986.41  NP_036116.31 
     1267437505 
    chicken
    (Gallus gallus)
    Aves NCDN1 neurochondrin 64.36(n)
    61.91(a)
      419633  NM_001030901.1  NP_001026072.1 
    lizard
    (Anolis carolinensis)
    Reptilia NCDN6
    --
    57(a)
    1 ↔ 1
    GL343308.1(8335-16434)
    zebrafish
    (Danio rerio)
    Actinopterygii ncdn1 neurochondrin 51.08(n)
    40.75(a)
      571005  XM_002667083.1  XP_002667129.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Neurochondrin1 CG2330-PA 46.72(n)
    31.06(a)
      40796  NM_141401.1  NP_649658.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT4G320506
    neurochondrin family protein
    19(a)
    1 ↔ 1
    4(15496537-15500847)
    rice
    (Oryza sativa)
    Liliopsida --
    neurochondrin family protein, putative, expressed
    17(a)
    1 ↔ 1
    2(33994688-34001354)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/182 NCBI SNPs in NCDN are shown (see all 182    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1437802641,2
    --36021593(+) TAATTA/GCCTAA 4 -- int1 us2k10--------
    rs1468558111,2
    --36021682(+) ATAGTC/TTGTTA 4 -- int1 us2k10--------
    rs66968361,2
    C,F,A,H--36021738(+) AATACT/CTGACA 4 -- int1 us2k121Minor allele frequency- C:0.48NS EA NA WA CSA 2333
    rs1832926561,2
    --36021788(+) AGGGCA/GTTACA 4 -- int1 us2k10--------
    rs1863451711,2
    --36021949(+) TAAGAC/TATGTT 4 -- us2k1 int10--------
    rs1397170461,2
    --36021995(+) CAGTTA/GGTATG 4 -- us2k1 int10--------
    rs1923577511,2
    --36022033(+) AAAAGC/TCTCAG 4 -- int1 us2k10--------
    rs1823835921,2
    --36022181(+) GTTAAC/TCACAG 4 -- int1 us2k10--------
    rs107969211,2
    C,F,A,H--36022383(+) AAATCC/GTGGAT 4 -- us2k1 int110Minor allele frequency- G:0.44NS EA WA CSA NA 780
    rs1500525401,2
    --36022393(+) TGAGGC/GAGGTT 4 -- int1 us2k10--------

    HapMap Linkage Disequilibrium report for NCDN (36023074 - 36032875 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for NCDN: --

    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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    NCDN for disorders           About GeneDecksing

    OMIM gene information: 608458    OMIM disorders: --

    3 diseases for NCDN:    About MalaCards
    osteochondrosis    seizures    neuronitis

    1 disease from the University of Copenhagen DISEASES database for NCDN:
    Osteochondrosis

    Export disorders for NCDN 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 NCDN gene, integrated from 9 sources (see all 26):
    (articles sorted by number of sources associating them with NCDN)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and expression of human neurochondrin-1 and -2. (PubMed id 10524216)1, 2, 9 Mochizuki R.... Fukamizu A. (1999)
    2. Corrigendum to 'Molecular cloning and expression of human neurochondrin-1 and -2'(1). (PubMed id 10684983)1, 2 Mochizuki R....Fukamizu A. (2000)
    3. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PubMed id 9628581)1, 2 Nagase T....Ohara O. (1998)
    4. Interaction of neurochondrin with the melanin-concentrating hormone receptor 1 interferes with G protein-coupled signal transduction but not agonist-mediated internalization. (PubMed id 16945926)2, 9 Francke F.... Baechner D. (2006)
    5. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (2012)
    6. Proteomic analysis identifies dysfunction in cellular transport, energy, and protein metabolism in different brain regions of atypical frontotemporal lobar degeneration. (PubMed id 22360420)1 Martins-de-Souza D....Bahn S. (2012)
    7. A high-throughput approach for measuring temporal chan ges in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (2012)
    8. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    9. Interactome mapping suggests new mechanistic details u nderlying Alzheimer's disease. (PubMed id 21163940)1 Soler-Lopez M....Aloy P. (2011)
    10. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 23154 HGNC: 17597 AceView: NCDN Ensembl:ENSG00000020129 euGenes: HUgn23154
    ECgene: NCDN H-InvDB: NCDN

    (According to HUGE)
    About This Section
    HUGE: KIAA0607

    (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 NCDN 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 NCDN gene:
    Search GeneIP for patents involving NCDN

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



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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013 , 14 May 2013

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