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

NDNF Gene

protein-coding   GIFtS: 40
GCID: GC04M121957

neuron-derived neurotrophic factor

(Previous name: chromosome 4 open reading frame 31 )
(Previous symbol: C4orf31)
 Explore 3 diseases affiliated with
NDNF via our new
 Human Malady Compendium 
Biological research products
for NDNF
    

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

Aliases
Neuron-Derived Neurotrophic Factor1 2 3
C4orf311 2 3
FLJ231911
Chromosome 4 Open Reading Frame 311
Fibronectin Type-III Domain-Containing Protein C4orf312
Protein NDNF2

External Ids:    HGNC: 262561   Entrez Gene: 796252   Ensembl: ENSG000001733767   UniProtKB: Q8TB733   

Export aliases for NDNF gene to outside databases


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

UniProtKB/Swiss-Prot: NDNF_HUMAN, Q8TB73
Function: Promotes matrix assembly and cell adhesiveness (By similarity). Promotes neuron migration, growth and
survival as well as neurite outgrowth




(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_000004.11  NC_018915.1  NT_016354.19  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for NDNF
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for NDNF

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


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

Entrez Gene cytogenetic band: 4q27   Ensembl cytogenetic band:  4q27   HGNC cytogenetic band: 4q27

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

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M121957:  view genomic region     (about GC identifiers)

Start:
121,956,768 bp from pter      End:
121,994,176 bp from pter
Size:
37,409 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: NDNF_HUMAN, Q8TB73 (See protein sequence)
Recommended Name: Protein NDNF precursor  
Size: 568 amino acids; 64673 Da
Subunit: Binds heparin and chondroitin sulfate (By similarity)
Subcellular location: Secreted
Sequence caution: Sequence=BAB15573.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAB15573.1; Type=Frameshift; Positions=364, 435;
Secondary accessions: A8K0Q0 Q6UWE5 Q9H5P7

Explore the universe of human proteins at neXtProt for NDNF: NX_Q8TB73

Post-translational modifications:

  • O-glycosylated; contains heparan sulfate and chondroitin sulfate (By similarity)1
  • N-glycosylated (By similarity)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8TB73

  • NDNF Protein expression data from MOPED and PaxDb:    About this image 
    NDNF Protein Expression
    REFSEQ proteins: NP_078850.3  
    ENSEMBL proteins: 
     ENSP00000369014   ENSP00000423352   ENSP00000426723  

    Human Recombinant Protein Products for NDNF: 
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    Uscn Proteins for NDNF

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IDA--
    GO:0031012extracellular matrix ISS--

    NDNF for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for NDNF


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

    NDNF for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR003961 Fibronectin_type3
     IPR013783 Ig-like_fold
     IPR019326 DUF2369

    Graphical View of Domain Structure for InterPro Entry Q8TB73

    ProtoNet protein and cluster: Q8TB73

    UniProtKB/Swiss-Prot: NDNF_HUMAN, Q8TB73
    Similarity: Contains 2 fibronectin type-III domains


    (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: NDNF_HUMAN, Q8TB73
    Function: Promotes matrix assembly and cell adhesiveness (By similarity). Promotes neuron migration, growth and
    survival as well as neurite outgrowth

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005539glycosaminoglycan binding ISS--
    GO:0008201heparin binding ISS--
         
    NDNF for ontologies           About GeneDecksing


    Phenotypes:
         1 MGI phenotypic allele for Ndnf (no phenotypes)

    NDNF for phenotypes           About GeneDecksing

    Animal Models:
         Mouse knock-out Ndnftm1Lex for NDNF
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for NDNF 

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    hsa-miR-3163 hsa-miR-338-5p hsa-miR-1206 hsa-miR-493* hsa-miR-330-3p hsa-miR-32* hsa-miR-590-3p hsa-miR-340
    SwitchGear 3'UTR luciferase reporter plasmidNDNF 3' UTR sequence
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    In Situ Assay
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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 NDNF

    Gene Ontology (GO): 5/7 biological process terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001764neuron migration IDA--
    GO:0010811positive regulation of cell-substrate adhesion ISS--
    GO:0010976positive regulation of neuron projection development IDA--
    GO:0016049cell growth IDA--
    GO:0019800peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan ISS--

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

    (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, Sirion Biotech, 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 NDNF gene: 
    NM_024574.3  

    Unigene Cluster for NDNF:

    Neuron-derived neurotrophic factor
    Hs.709520  [show with all ESTs]
    Unigene Representative Sequence: NM_024574
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000379692(uc003idq.1) ENST00000506900 ENST00000515757 ENST00000511408


    miRNA
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    8 QIAGEN miScript miRNA Assays for microRNAs that regulate NDNF:
    hsa-miR-3163 hsa-miR-338-5p hsa-miR-1206 hsa-miR-493* hsa-miR-330-3p hsa-miR-32* hsa-miR-590-3p hsa-miR-340
    SwitchGear 3'UTR luciferase reporter plasmidNDNF 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AK026844.1 AK289615.1 AY358821.1 BC019351.1 

    3 DOTS entries:

    DT.111340  DT.95338983  DT.100694572 

    24/63 AceView cDNA sequences (see all 63):

    BM714644 CA397262 BM725519 AA453143 CR593973 AI245420 AI492491 BP369424 
    BU739276 AA010797 BQ774423 BP344718 BM554196 AW662834 BI491602 BX370023 
    BQ894004 W20402 NM_024574 BX370024 AA953484 BU741776 BE503717 BQ015985 

    GeneLoc Exon Structure

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

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


    ECgene alternative splicing isoforms for NDNF

    (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

    NDNF expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TACATAAAAT
    NDNF Expression
    About this image

    NDNF expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    10/16 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 16
    Tissue Anatomical Compartment CellCategory (developmental path)
    BoneSacral VertebraeOsteochondro Mesenchymal CellsBone, Cartilage
    BrainBlood Brain BarrierAdult Endothelial CellsBlood Brain Barrier, Endothelium
    CartilageCervical Intervertebral DiscIntervertebral Disc Annulus Fibrosus CellsCartilage
    CartilageCervical Intervertebral DiscIntervertebral Disc Nucleus Pulposus CellsCartilage
    BoneMandibular ProcessBone
    BoneMaxillary ProcessBone
    BrainHypothalamusBrain
    BrainMedulla OblongataBrain
    CartilageCervical Intervertebral DiscCartilage
    CartilageLumbar Intervertebral DiscCartilage
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    PureStem™ mesenchymal progenitor MEL2 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage

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

    SOURCE GeneReport for Unigene cluster: Hs.709520
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    In Situ
    Assay Products:
     

     
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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 animals.

    Orthologs for NDNF gene from 7/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ndnf1 , 5 RIKEN cDNA A930038C07 gene5
    neuron-derived neurotrophic factor1
    85.56(n)1
    87.5(a)1
      6 (30.29 cM)5
    681691  NM_172399.31  NP_765987.21 
     656715905 
    chicken
    (Gallus gallus)
    Aves NDNF1 neuron-derived neurotrophic factor 80.48(n)
    90.65(a)
      422672  XM_420627.3  XP_420627.2 
    lizard
    (Anolis carolinensis)
    Reptilia NDNF6
    --
    89(a)
    1 ↔ 1
    5(139444834-139449654)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.241582 Xenopus laevis transcribed sequences 82.17(n)    BJ090801.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wu:fb16h091 wu:fb16h09 69.99(n)
    79.18(a)
      561437  XM_684842.5  XP_689934.5 
    fruit fly
    (Drosophila melanogaster)
    Insecta nord6
    nord
    16(a)
    1 ↔ 1
    2R(20130786-20142617)
    worm
    (Caenorhabditis elegans)
    Secernentea ndnf-16
    Protein NDNF-1
    21(a)
    1 ↔ 1
    IV(3023393-3028940)


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

    10/648 NCBI SNPs in NDNF are shown (see all 648    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1455110021,2
    --121956342(+) CTTACC/TAATAA 1 -- int10--------
    rs117243441,2
    C,F,H--121956350(+) TAAAAG/ATCCTG 1 -- int17Minor allele frequency- A:0.03EA NS NA 404
    rs556620201,2
    C--121956367(+) GTTTGT/CTAAGT 1 -- int12Minor allele frequency- C:0.10WA 120
    rs284380031,2
    F--121956428(+) ACAGAT/CGGAAA 1 -- int11Minor allele frequency- C:0.02WA 118
    rs104612041,2
    C,F,H--121956610(+) TCAACG/ATCAAA 1 -- int120Minor allele frequency- A:0.36NS EA NA WA 2346
    rs726840251,2
    C--121956632(+) TAATAA/TCTATT 1 -- int14Minor allele frequency- T:0.17WA NA EA 360
    rs1494487471,2
    --121956845(+) TTGTAC/TATGAG 1 -- ut310--------
    rs10450801,2
    C,F,A,H--121957051(-) TCTCTA/GTAGAT 1 -- ut31 ese319Minor allele frequency- G:0.40MN NS EA NA WA 2318
    rs729116701,2
    C,F--121957201(+) CCAACC/TGGCAT 1 -- ut313Minor allele frequency- T:0.11WA CSA 122
    rs755969221,2
    F--121957202(+) CAACCG/AGCATC 1 -- ut311Minor allele frequency- A:0.10EA 120

    HapMap Linkage Disequilibrium report for NDNF (121956768 - 121994176 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for NDNF: --

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

    (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

    NDNF for disorders           About GeneDecksing

    3 diseases for NDNF:    About MalaCards
    neuronitis    alcohol dependence    alcoholism


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

    1. Spatio-temporal expression of a novel neuron-derived neurotrophic factor (NDNF) in mouse brains during development. (PubMed id 20969804)1, 2, 3 Kuang X.L....Sun G.T. (2010)
    2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2, 3 Clark H.F.... Gray A.M. (2003)
    3. A systematic gene-based screen of chr4q22-q32 identif ies association of a novel susceptibility gene, DKK2, with the quantitative tra it of alcohol dependence symptom counts. (PubMed id 20332099)1 Kalsi G....Riley B.P. (2010)
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    5. Mosaicism for terminal deletion of 4q. (PubMed id 16970039)1 Utine G.E. and Aktas D. (2006)
    6. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    7. 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)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 79625 HGNC: 26256 AceView: FLJ23191 Ensembl:ENSG00000173376 euGenes: HUgn79625
    ECgene: NDNF H-InvDB: NDNF

    (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 NDNF 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 NDNF gene:
    Search GeneIP for patents involving NDNF

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

     
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