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

DND1 Gene

protein-coding   GIFtS: 46
GCID: GC05M140030

dead end homolog 1 (zebrafish)

 Explore 5 diseases affiliated with
DND1 via our new
 Human Malady Compendium 
Biological research products
for DND1
    

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

Aliases
Dead End Homolog 1 (Zebrafish)1 2
RBMS41 2 3
RNA-Binding Motif, Single-Stranded-Interacting Protein 42 3
MGC347501
Dead End Protein Homolog 12

External Ids:    HGNC: 237991   Entrez Gene: 3738632   Ensembl: ENSG000002564537   OMIM: 6093855   UniProtKB: Q8IYX43   

Export aliases for DND1 gene to outside databases

Previous GC identifers: GC05U900202 GC05M140079 GC05M135195


(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 DND1:
This gene encodes a protein that binds to microRNA-targeting sequences of mRNAs, inhibiting microRNA-mediated
repression. Reduced expression of this gene has been implicated in tongue squamous cell carcinoma. Two pseudogenes of
this gene are located on the long arm of chromosome 17. (provided by RefSeq, Dec 2010)

UniProtKB/Swiss-Prot: DND1_HUMAN, Q8IYX4
Function: RNA-binding factor that positively regulates gene expression by prohibiting miRNA-mediated gene suppression.
Relieves miRNA repression in germline cells (By similarity). Prohibits the function of several miRNAs by blocking the
accessibility of target mRNAs. Sequence-specific RNA-binding factor that binds specifically to U-rich regions (URRs)
in the 3' untranslated region (3'-UTR) of several mRNAs. Does not bind to miRNAs. May play a role during primordial
germ cell (PGC) survival (By similarity). However, does not seem to be essential for PGC migration (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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000005.9  NC_018916.1  NT_029289.11  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the DND1 gene promoter:
         AML1a   p53   Lmo2   NF-E2 p45   YY1   PPAR-alpha   AREB6   FOXJ2   NF-E2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDND1 promoter sequence
   Search SABiosciences Chromatin IP Primers for DND1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat DND1


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

Entrez Gene cytogenetic band: 5q31.3   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31.3

DND1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DND1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M140030:  view genomic region     (about GC identifiers)

Start:
140,050,379 bp from pter      End:
140,053,171 bp from pter
Size:
2,793 bases      Orientation:
minus 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: DND1_HUMAN, Q8IYX4 (See protein sequence)
Recommended Name: Dead end protein homolog 1  
Size: 353 amino acids; 38687 Da
Subunit: Interacts with APOBEC3 (By similarity)
Subcellular location: Nucleus. Cytoplasm. Note=Perinuclear germ granules, also called germ plasm or chromatoid body.
Colocalizes in perinuclear sites with APOBEC3 (By similarity)

Explore the universe of human proteins at neXtProt for DND1: NX_Q8IYX4

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8IYX4

  • DND1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_919225.1  
    ENSEMBL proteins: 
     ENSP00000445366  

    Human Recombinant Protein Products: 
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    Uscn Proteins for DND1

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA18155131
    GO:0005737cytoplasm IDA18155131


    DND1 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for DND1


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

    DND1 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR000504 RRM_dom
     IPR012677 Nucleotide-bd_a/b_plait

    Graphical View of Domain Structure for InterPro Entry Q8IYX4

    ProtoNet protein and cluster: Q8IYX4

    1 Blocks protein family: IPB000504 RNA-binding region RNP-1 (RNA recognition motif)

    UniProtKB/Swiss-Prot: DND1_HUMAN, Q8IYX4
    Similarity: Contains 2 RRM (RNA recognition motif) domains


    (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: DND1_HUMAN, Q8IYX4
    Function: RNA-binding factor that positively regulates gene expression by prohibiting miRNA-mediated gene suppression.
    Relieves miRNA repression in germline cells (By similarity). Prohibits the function of several miRNAs by blocking the
    accessibility of target mRNAs. Sequence-specific RNA-binding factor that binds specifically to U-rich regions (URRs)
    in the 3' untranslated region (3'-UTR) of several mRNAs. Does not bind to miRNAs. May play a role during primordial
    germ cell (PGC) survival (By similarity). However, does not seem to be essential for PGC migration (By similarity)

    miRNA
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    miRTarBase miRNAs that target DND1:
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    8 QIAGEN miScript miRNA Assays for microRNAs that regulate DND1:
    hsa-miR-634 hsa-miR-324-3p hsa-miR-3155 hsa-miR-484 hsa-miR-370 hsa-miR-889 hsa-miR-24 hsa-miR-3155b
    SwitchGear 3'UTR luciferase reporter plasmidDND1 3' UTR sequence
    Inhib. RNA
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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0005515protein binding ----
    GO:0017091AU-rich element binding IDA18155131
    GO:0035198NOT miRNA binding IDA18155131


    DND1 for ontologies           About GeneDecksing


    Animal Models:
         3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Dnd1):
     endocrine/exocrine gland  reproductive system  tumorigenesis 

    DND1 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



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for DND1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--
    GO:0007281germ cell development IEA--
    GO:0060965negative regulation of gene silencing by miRNA IDA18155131


    DND1 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 DND1
    Search CenterWatch for drugs/clinical trials and news about DND1 

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    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 DND1 gene: 
    NM_194249.2  

    Unigene Cluster for DND1:

    Dead end homolog 1 (zebrafish)
    Hs.591262  [show with all ESTs]
    Unigene Representative Sequence: NM_194249
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000542735(uc003lgt.3)

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    hsa-miR-634 hsa-miR-324-3p hsa-miR-3155 hsa-miR-484 hsa-miR-370 hsa-miR-889 hsa-miR-24 hsa-miR-3155b
    SwitchGear 3'UTR luciferase reporter plasmidDND1 3' UTR sequence
    Inhib. RNA
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat DND1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat DND1

    Additional cDNA sequence: 

    AY321065.1 BC033496.1 

    7 DOTS entries:

    DT.100682955  DT.120887657  DT.456090  DT.95171401  DT.100783761  DT.91719427  DT.91725590 

    24/26 AceView cDNA sequences (see all 26):

    NM_194249 AY321065 AI699627 AA995373 BI830859 BC033496 N46447 BI825641 
    AW301097 AA689572 AI949010 AI359508 BF736582 AI207183 BQ446051 BF223894 
    BF879982 AW090043 AW615108 AA586603 BF880840 AA665559 BF849692 AA177054 

    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

    DND1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCATTCTGGT

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

    About this image

    DND1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    2 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    PlacentaAllantoisPrimordial Germ CellsGerm Cells
    Reproductive SystemEarly GonadPrimordial Germ CellsGerm Cells
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Primordial germ cell-like cells (Reconstitution of mo...)

    See DND1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for DND1

    SOURCE GeneReport for Unigene cluster: Hs.591262
        SABiosciences Custom PCR Arrays for DND1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DND1

    (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 DND1 gene from 7/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Dnd11 , 5 dead end homolog 1 (zebrafish)1, 5 84.37(n)1
    86.65(a)1
      18 (19.46 cM)5
    2132361  NM_173383.21  NP_775559.21 
     367636715 
    chicken
    (Gallus gallus)
    Aves DND11 dead end homolog 1 (zebrafish) 64.51(n)
    56.17(a)
      425270  XM_423051.3  XP_423051.3 
    lizard
    (Anolis carolinensis)
    Reptilia DND16
    --
    44(a)
    1 ↔ 1
    4(77770210-77775912)
    zebrafish
    (Danio rerio)
    Actinopterygii dnd6
    hnrpr6
    heterogeneous nuclear ribonucleoprotein R
    30(a)
    15(a)
    1 ↔ 1
    possible ortholog
    14(7366001-7377476)
    19(40444-48614)
    honey bee
    (Apis mellifera)
    Insecta --
    --
    25(a)
    1 ↔ 1
    Group14.9(338739-340838)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G447106
    AT5G283906
    (see all 4)
    RNA recognition motif-containing protein
    (see all 4)
    6(a)
    6(a)
    (see all 4)
    many ↔ many
    many ↔ many
    (see all 4)
    2(18432719-18437132)
    5(10342024-10342997)
    rice
    (Oryza sativa)
    Liliopsida --
    --
    (see all 8)
    RNA recognition motif containing protein, expresse...
    RNA recognition motif containing protein, putative...
    (see all 8)
    9(a)
    8(a)
    (see all 8)
    many ↔ many
    many ↔ many
    (see all 8)
    7(15717343-15722125)
    12(23807761-23811674)


    ENSEMBL Gene Tree for DND1 (if available)
    TreeFam Gene Tree for DND1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for DND1 gene
    RBM472  SYNCRIP2  RBM462  A1CF2  HNRNPR2  
    3 SIMAP similar genes for DND1 using alignment to 1 protein entry:     DND1_HUMAN:
    A1CF    RBM46    RBM47

    DND1 for paralogs           About GeneDecksing


    5 Pseudogenes.org Pseudogenes for DND1
    PGOHUM00000237092 PGOHUM00000237411 PGOHUM00000247395 PGOHUM00000247398 PGOHUM00000247404


    (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

    10/50 NCBI SNPs in DND1 are shown (see all 50    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2016384041,2
    F--140050894(+) CCATGG/CTACCT 2 /T /S mis11Minor allele frequency- C:0.02EU 805
    rs1486394161,2
    C,F--140050907(+) CTCAGC/TCCCAG 2 T A mis12Minor allele frequency- T:0.01NA EU 5345
    rs1453121361,2
    C,F,--140050942(+) ACTCAC/GTGAGT 2 T S mis11Minor allele frequency- G:0.00NA 4536
    rs2003895511,2
    --140050961(+) CAGCCA/GTACAG 2 R W mis10--------
    rs1462523531,2
    C,F,--140051009(+) ATCTAG/AGGTCA 2 /L syn12Minor allele frequency- A:0.01NA EU 5771
    rs2021480331,2
    --140051018(+) CAGCAC/TAACCC 2 M V mis10--------
    rs2016924471,2
    --140051115(+) CACTTC/GGTGAG 2 T syn10--------
    rs1858347061,2
    C,--140051174(+) AGCCCA/GAGCCC 2 R W mis10--------
    rs1497776191,2
    C,F--140051190(+) AACCCT/CAACTT 2 /L syn12Minor allele frequency- C:0.00NA EU 3403
    rs1456786691,2
    C,F--140051239(+) GGGACC/TGCAAG 2 Q R mis11Minor allele frequency- T:0.00NA 3376

    HapMap Linkage Disequilibrium report for DND1 (140050379 - 140053171 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for DND1: --
    Human Gene Mutation Database (HGMD): DND1

    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing DND1
    DNA2.0 Custom Variant and Variant Library Synthesis for DND1

    (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

    DND1 for disorders           About GeneDecksing

    OMIM gene information: 609385    OMIM disorders: --

    5 diseases for DND1:    About MalaCards
    squamous cell carcinoma    testicular germ cell tumor    carcinoma    germ cell tumor
    teratoma

    2 diseases from the University of Copenhagen DISEASES database for DND1:
    Teratoma     Testicular cancer
    Human Genome Epidemiology (HuGE) Navigator: DND1 (2 documents)

    Export disorders for DND1 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 DND1 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with DND1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Dead end, a novel vertebrate germ plasm component, is required for zebrafish primordial germ cell migration and survival. (PubMed id 12932328)1, 2, 3 Weidinger G.... Raz E. (2003)
    2. RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. (PubMed id 18155131)1, 2 Kedde M.... Agami R. (2007)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    4. Transcripts that associate with the RNA binding protei n, DEAD-END (DND1), in embryonic stem (ES) cells. (PubMed id 21851623)1 Zhu R....Matin A. (2011)
    5. MicroRNA-24 targeting RNA-binding protein DND1 in ton gue squamous cell carcinoma. (PubMed id 20816961)1 Liu X....Zhou X. (2010)
    6. Screening for germline DND1 mutations in testicular c ancer patients. (PubMed id 20411342)1 Sijmons R.H....Hoekstra H.J. (2010)
    7. Analysis of the DND1 gene in men with sporadic and familial testicular germ cell tumors. (PubMed id 18069663)1 Linger R....Rapley E.A. (2008)
    8. Interplay between microRNAs and RNA-binding proteins determines developmental processes. (PubMed id 18414021)1 Kedde M. and Agami R. (2008)
    9. A dead end for microRNAs. (PubMed id 18160032)1 Ketting R.F. (2007)
    10. What leads from dead-end? (PubMed id 17464447)1 Matin A. (2007)

    (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: 373863 HGNC: 23799 AceView: DND1 Ensembl:ENSG00000256453 euGenes: HUgn373863
    ECgene: DND1 H-InvDB: DND1

    (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 DND1 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 DND1 gene:
    Search GeneIP for patents involving DND1

    GeneCards and IP:
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