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

NKD1 Gene

protein-coding   GIFtS: 49
GCID: GC16P050582

naked cuticle homolog 1 (Drosophila)

 Explore 5 diseases affiliated with
NKD1 via our new
 Human Malady Compendium 
Biological research products
for NKD1
    

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

Aliases
Naked Cuticle Homolog 1 (Drosophila)1 2     Protein Naked Cuticle Homolog 12
Naked12     NKD3
Dvl-Binding Protein2     Naked-13
Naked Cuticle-12     HNkd1
Naked-13     HNkd11

External Ids:    HGNC: 170451   Entrez Gene: 854072   Ensembl: ENSG000001408077   OMIM: 6078515   UniProtKB: Q969G93   

Export aliases for NKD1 gene to outside databases

Previous GC identifers: GC16P040995 GC16P050629 GC16P050319 GC16P050360 GC16P049139 GC16P036470


(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 NKD1:
In the mouse, Nkd is a Dishevelled (see DVL1; MIM 601365)-binding protein that functions as a negative regulator of the
Wnt (see WNT1; MIM 164820)-beta-catenin (see MIM 116806)-Tcf (see MIM 602272) signaling pathway.(supplied by OMIM, Jun
2003)

UniProtKB/Swiss-Prot: NKD1_HUMAN, Q969G9
Function: Cell autonomous antagonist of the canonical Wnt signaling pathway. May activate a second Wnt signaling
pathway that controls planar cell polarity




(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_000016.9  NC_018927.1  NT_010498.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the NKD1 gene promoter:
         PPAR-gamma1   AP-4   PPAR-gamma2   LCR-F1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNKD1 promoter sequence
   Search SABiosciences Chromatin IP Primers for NKD1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NKD1


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

Entrez Gene cytogenetic band: 16q12.1   Ensembl cytogenetic band:  16q12.1   HGNC cytogenetic band: 16q12.1

NKD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NKD1 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P050582:  view genomic region     (about GC identifiers)

Start:
50,582,241 bp from pter      End:
50,670,647 bp from pter
Size:
88,407 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: NKD1_HUMAN, Q969G9 (See protein sequence)
Recommended Name: Protein naked cuticle homolog 1  
Size: 470 amino acids; 52285 Da
Subunit: Interacts with DVL1, DVL2, DVL3 and PPP2R3A
Subcellular location: Cell membrane (By similarity). Cytoplasm (By similarity)
Developmental stage: Expressed in fetal brain, kidney, liver and lung
Secondary accessions: B2RC39 Q8WZ08

Explore the universe of human proteins at neXtProt for NKD1: NX_Q969G9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q969G9

  • NKD1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_149110.1  
    ENSEMBL proteins: 
     ENSP00000268459  

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    Uscn Proteins for NKD1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000159colocalizes with protein phosphatase type 2A complex IDA15687260
    GO:0005737cytoplasm IEA--
    GO:0005886plasma membrane IEA--


    NKD1 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

    NKD1 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR018247 EF_Hand_1_Ca_BS
     IPR011992 EF-hand-like_dom
     IPR002048 EF_hand_Ca-bd

    Graphical View of Domain Structure for InterPro Entry Q969G9

    ProtoNet protein and cluster: Q969G9

    UniProtKB/Swiss-Prot: NKD1_HUMAN, Q969G9
    Similarity: Belongs to the NKD family
    Similarity: Contains 1 EF-hand domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: NKD1_HUMAN, Q969G9
    Function: Cell autonomous antagonist of the canonical Wnt signaling pathway. May activate a second Wnt signaling
    pathway that controls planar cell polarity
    Induction: Expression is induced by activation of the Wnt signaling pathway

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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat NKD1
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    hsa-miR-100* hsa-miR-642a hsa-miR-607 hsa-miR-188-5p hsa-miR-15a hsa-miR-605 hsa-miR-3122 hsa-miR-376c
    SwitchGear 3'UTR luciferase reporter plasmidNKD1 3' UTR sequence
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NKD1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
    GO:0005515protein binding IPI16567647
    GO:0030165PDZ domain binding IEA--


    NKD1 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Nkd1tm1Tko for NKD1
         7 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Nkd1):
     behavior/neurological  craniofacial  digestive/alimentary  endocrine/exocrine gland  growth/size 
     reproductive system  skeleton 

    NKD1 for phenotypes           About GeneDecksing


    (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

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Wnt Signaling Pathway
    Wnt Signaling Pathway and Pluripotency0.55
    Wnt Signaling Pathway NetPath0.22
    Wnt signaling pathway0.30
    2Wnt / Hedgehog / Notch
    Wnt / Hedgehog / Notch1.00
    3Presenilin action in Notch and Wnt signaling
    Presenilin action in Notch and Wnt signaling1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for NKD1
        Wnt / Hedgehog / Notch

    3 BioSystems Pathways for NKD1 
        Wnt Signaling Pathway and Pluripotency
    Wnt Signaling Pathway NetPath
    Presenilin action in Notch and Wnt signaling


    1         Kegg Pathway  (Kegg details for NKD1):
        Wnt signaling pathway


    NKD1 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NKD1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    5/97 Interacting proteins for NKD1 (Q969G91, 3 ENSP000002684594) via UniProtKB, MINT, STRING, and/or I2D (see all 97)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPP2R1AP301533, ENSP000003248044I2D: score=1 STRING: ENSP00000324804
    PPP2CAP677753, ENSP000004184474I2D: score=2 STRING: ENSP00000418447
    DVL3Q929973, ENSP000003160544I2D: score=3 STRING: ENSP00000316054
    DVL2O146413, ENSP000000053404I2D: score=2 STRING: ENSP00000005340
    DVL1O146403, ENSP000003681694I2D: score=2 STRING: ENSP00000368169
    About this table

    Gene Ontology (GO): 5/9 biological process terms (GO ID links to tree view) (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001754eye photoreceptor cell differentiation ISS15687260
    GO:0007525somatic muscle development ISS15687260
    GO:0016055Wnt receptor signaling pathway IEA--
    GO:0045732positive regulation of protein catabolic process IMP15687260
    GO:0090090negative regulation of canonical Wnt receptor signaling pathway ISS--


    NKD1 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 NKD1
    Search CenterWatch for drugs/clinical trials and news about NKD1 

    (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,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for NKD1 gene: 
    NM_033119.4  

    Unigene Cluster for NKD1:

    Naked cuticle homolog 1 (Drosophila)
    Hs.187578  [show with all ESTs]
    Unigene Representative Sequence: NM_033119
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000268459(uc002egg.2) ENST00000564336 ENST00000566396

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    hsa-miR-100* hsa-miR-642a hsa-miR-607 hsa-miR-188-5p hsa-miR-15a hsa-miR-605 hsa-miR-3122 hsa-miR-376c
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    Inhib. RNA
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    Clone
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat NKD1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat NKD1

    Additional cDNA sequence: 

    AB062886.1 AF289584.1 AF358135.1 AK000276.1 AK021701.1 AK023784.1 AK314930.1 AY061883.1 
    BC051288.1 

    5 DOTS entries:

    DT.92046947  DT.92015373  DT.203755  DT.453967  DT.91673444 

    24/56 AceView cDNA sequences (see all 56):

    AW268418 BU846054 BG820139 CD675898 BQ645656 AB062886 NM_033119 AI884849 
    BQ644360 D11959 BQ644956 AK000276 BQ653673 CB215756 BC051288 BQ064678 
    AF358135 AY061883 AI333791 BM711145 BF588561 AI167910 AA262960 AA236306 

    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

    NKD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    NKD1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Paraxial MesodermParaxial MesodermParaxial Mesoderm CellsMesoderm
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See NKD1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for NKD1

    SOURCE GeneReport for Unigene cluster: Hs.187578

    UniProtKB/Swiss-Prot: NKD1_HUMAN, Q969G9
    Tissue specificity: Expressed in colon, heart, kidney, leukocyte, liver, lung, ovary, pancreas, placenta, prostate,
    skeletal muscle, small intestine and spleen

        SABiosciences Expression via Pathway-Focused PCR Array including NKD1: 
              WNT Signaling Pathway in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NKD1

    (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 NKD1 gene from 4/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves NKD11 naked cuticle homolog 1 (Drosophila) 66.52(n)
    66.67(a)
      415729  XM_414094.3  XP_414094.3 
    lizard
    (Anolis carolinensis)
    Reptilia NKD16
    --
    64(a)
    1 ↔ 1
    GL343227.1(1313029-1346850)
    zebrafish
    (Danio rerio)
    Actinopterygii nkd11 naked cuticle homolog 1 (Drosophila) 58.33(n)
    53.01(a)
      751108  NM_001043333.1  NP_001036798.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta nkd6
    naked cuticle
    9(a)
    1 → many
    3L(18996841-19038549)


    ENSEMBL Gene Tree for NKD1 (if available)
    TreeFam Gene Tree for NKD1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for NKD1 gene
    NKD22  
    1 SIMAP similar gene for NKD1 using alignment to 1 protein entry:     NKD1_HUMAN:
    NKD2

    NKD1 for paralogs           About GeneDecksing



    (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

    10/1425 NCBI SNPs in NKD1 are shown (see all 1425    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs30376651,2
    C--36562549(+) AAGTT-/AAAAAG
            
    AAAAA
    2 -- ut310--------
    rs575953401,2
    C,F,--50580271(+) CACCTC/TTCTGA 1 -- us2k13Minor allele frequency- T:0.07WA CSA 122
    rs590276581,2
    F,--50580304(+) TAGAAC/GAAGTA 1 -- us2k11Minor allele frequency- G:0.08WA 118
    rs1439437351,2
    --50580335(+) GTTGCA/GAGGGC 1 -- us2k10--------
    rs71995231,2
    C,F,A,H,--50580414(+) CAACAG/ATAATA 1 -- us2k1 tfbs37Minor allele frequency- A:0.05NS EA NA WA 540
    rs587193511,2
    C,--50580442(+) CACTCC/TTCAAA 1 -- us2k11Minor allele frequency- T:0.50WA 2
    rs1433713481,2
    --50580688(+) ATATGA/GCTAGT 1 -- us2k10--------
    rs1467262061,2
    --50580746(+) TTAGCA/GCAATA 1 -- us2k10--------
    rs735879731,2
    C,--50580833(+) GGACTG/TGTTCC 1 -- us2k12Minor allele frequency- T:0.03WA 120
    rs1844038421,2
    --50580869(+) CCAGAC/TGTCAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for NKD1 (50582241 - 50670647 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for NKD1: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing NKD1
    DNA2.0 Custom Variant and Variant Library Synthesis for NKD1

    (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

    NKD1 for disorders           About GeneDecksing

    OMIM gene information: 607851    OMIM disorders: --

    5 diseases for NKD1:    About MalaCards
    hyperopia    strabismus    colorectal cancer    lung cancer
    prostatitis


    Export disorders for NKD1 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 NKD1 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with NKD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Vertebrate proteins related to Drosophila Naked Cuticle bind Dishevelled and antagonize Wnt signaling. (PubMed id 11356022)1, 2, 3, 9 Wharton K.A. Jr.... Scott M.P. (2001)
    2. Molecular cloning, gene structure, and expression analyses of NKD1 and NKD2. (PubMed id 11604995)1, 2, 9 Katoh M. (2001)
    3. PR130 is a modulator of the Wnt-signaling cascade that counters repression of the antagonist Naked cuticle. (PubMed id 16567647)1, 2 Creyghton M.P....Bernards R. (2006)
    4. PR72, a novel regulator of Wnt signaling required for Naked cuticle function. (PubMed id 15687260)1, 2 Creyghton M.P.... Bernards R. (2005)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. Elevated expression of axin2 and hnkd mRNA provides evidence that Wnt/beta-catenin signaling is activated in human colon tumors. (PubMed id 11752446)1, 2 Yan D.... Williams L.T. (2001)
    7. A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci. (PubMed id 22412388)1 Kenny E.E....Peter I. (2012)
    8. Down-regulation of NKD1 increases the invasive potent ial of non-small-cell lung cancer and correlates with a poor prognosis. (PubMed id 21599923)1 Zhang S....Wang E.H. (2011)
    9. Mutations in the human naked cuticle homolog NKD1 fou nd in colorectal cancer alter Wnt/Dvl/beta-catenin signaling. (PubMed id 19956716)1 Guo J....Liu W. (2009)
    10. 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. (2004)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 85407 HGNC: 17045 AceView: NKD1 Ensembl:ENSG00000140807 euGenes: HUgn85407
    ECgene: NKD1 Kegg: 85407 H-InvDB: NKD1

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for NKD1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for NKD1 gene:
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