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FOXR1 Gene

protein-coding   GIFtS: 44
GCID: GC11P118843

Forkhead Box R1

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(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
Forkhead Box R11 2
Forkhead Box Protein N52 3
FOXN52 3
Forkhead Box Protein R12
Forkhead Box R1 Variant 12

External Ids:    HGNC: 299801   Entrez Gene: 2831502   Ensembl: ENSG000001763027   UniProtKB: Q6PIV23   

Export aliases for FOXR1 gene to outside databases

Previous GC identifers: GC11P118379 GC11P118347 GC11P114782


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for FOXR1 Gene:
This gene encodes a member of the forkhead box (FOX) family of transcription factors. FOX family members are
monomeric, helix-turn-helix proteins with a core DNA-binding domain of approximately 110 aa. Many FOX
transcription factors play roles in determining cell fates during early development. This forkhead box protein
lacks the C-terminal basic region found in many other FOX family members. It is located within the 11q23.3 region
which is commonly deleted in neuroblastomas. (provided by RefSeq, Jul 2008)

GeneCards Summary for FOXR1 Gene:
FOXR1 (forkhead box R1) is a protein-coding gene. GO annotations related to this gene include double-stranded DNA binding and sequence-specific DNA binding. An important paralog of this gene is FOXF1.




(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 at NCBI GenBank:
NC_000011.9  NT_033899.9  NC_018922.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the FOXR1 gene promoter:
         Spz1   RP58   AML1a   MAZR   p53   Roaz   S8   deltaCREB   SEF-1 (1)   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFOXR1 promoter sequence
   Search Chromatin IP Primers for FOXR1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FOXR1


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

Entrez Gene cytogenetic band: 11q23.3   Ensembl cytogenetic band:  11q23.3   HGNC cytogenetic band: 11q23.3

FOXR1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FOXR1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P118843:  view genomic region     (about GC identifiers)

Start:
118,842,417 bp from pter      End:
118,852,001 bp from pter
Size:
9,585 bases      Orientation:
plus 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: FOXR1_HUMAN, Q6PIV2 (See protein sequence)
Recommended Name: Forkhead box protein R1  
Size: 292 amino acids; 33310 Da
Secondary accessions: B0YJ15 Q86UT9 Q8IXX2

Explore the universe of human proteins at neXtProt for FOXR1: NX_Q6PIV2

Explore proteomics data for FOXR1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See FOXR1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_859072.1  
    ENSEMBL proteins: 
     ENSP00000314806   ENSP00000433394   ENSP00000432358  

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    antibodies-online proteins for FOXR1 (3 products) 

     
    antibodies-online peptides for FOXR1

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    Cloud-Clone Corp. ELISAs for FOXR1
    Cloud-Clone Corp. CLIAs for FOXR1
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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:
    FOX: Forkhead boxes

    2 InterPro protein domains:
     IPR011991 WHTH_DNA-bd_dom
     IPR001766 TF_fork_head

    Graphical View of Domain Structure for InterPro Entry Q6PIV2

    ProtoNet protein and cluster: Q6PIV2

    UniProtKB/Swiss-Prot: FOXR1_HUMAN, Q6PIV2
    Similarity: Contains 1 fork-head DNA-binding domain


    Find genes that share domains with FOXR1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003690double-stranded DNA binding IBA--
    GO:0003700sequence-specific DNA binding transcription factor activity ----
    GO:0003705RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity IBA--
    GO:0008134transcription factor binding IBA--
    GO:0008301DNA binding, bending IBA--
         
    Find genes that share ontologies with FOXR1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for FOXR1:
     Synthetic lethal with Ras 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for FOXR1

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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
    FOXR1_HUMAN, Q6PIV2: Nucleus (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4
    cytosol2
    extracellular1
    plasma membrane1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005667transcription factor complex IBA--

    Find genes that share ontologies with FOXR1           About GenesLikeMe


    (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 FOXR1
    Interactions:

        Search GeneGlobe Interaction Network for FOXR1

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IBA--
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0006366transcription from RNA polymerase II promoter IBA--
    GO:0007389pattern specification process IBA--
    GO:0009790embryo development IBA--

    Find genes that share ontologies with FOXR1           About GenesLikeMe



    (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 FOXR1



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for FOXR1 gene: 
    NM_181721.2  

    Unigene Cluster for FOXR1:

    Forkhead box R1
    Hs.116679  [show with all ESTs]
    Unigene Representative Sequence: BC028191
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000317011(uc001pui.3 uc001puk.3) ENST00000531539(uc001puj.3)
    ENST00000533282
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat FOXR1
      QuantiFast Probe-based Assays in human, mouse, rat FOXR1

    Additional mRNA sequence: 

    AB094092.1 BC028191.1 BC038969.1 BC125040.1 

    1 DOTS entry:

    DT.100697249 

    13 AceView cDNA sequences:

    BI825543 BC028191 BC038969 AI638832 AB094092 NM_181721 BI830675 AI968909 
    AW589848 AI992357 BX089058 AA669512 BC064340 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for FOXR1    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6
    SP1:                                    
    SP2:                    -               


    ECgene alternative splicing isoforms for FOXR1

    (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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    FOXR1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGCCAGCCAG
    FOXR1 Expression
    About this image


    FOXR1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Ovary (Reproductive System)
             Secondary Oocyte Antral Follicle
     
     Gonad
             Secondary Oocyte Antral Follicle
    FOXR1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FOXR1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.116679
        Custom PCR Arrays for FOXR1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FOXR1

    (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 FOXR1 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Foxr11 , 5 forkhead box R11, 5 73.48(n)1
    65.75(a)1
      9 (24.84 cM)5
    3820741  NM_001033469.21  NP_001028641.11 
     444342345 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia AL853396.12   -- 77.56(n)    AL853396.1 
    zebrafish
    (Danio rerio)
    Actinopterygii FOXR16
    forkhead box R1
    30(a)
    1 → many
    5(60147744-60153128) ENSDARG00000004864
    fruit fly
    (Drosophila melanogaster)
    Insecta CHES-1-like6
    Checkpoint suppressor homologue
    5(a)
    1 → many
    X(7576371-7603418)


    ENSEMBL Gene Tree for FOXR1 (if available)
    TreeFam Gene Tree for FOXR1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FOXR1 gene
    FOXF12  FOXQ12  FOXN32  FOXJ12  FOXF22  FOXK12  FOXN42  FOXH12  
    FOXK22  FOXN12  FOXJ32  FOXG12  FOXJ22  FOXN22  FOXR22  
    1 SIMAP similar gene for FOXR1 using alignment to 4 protein entries:     FOXR1_HUMAN (see all proteins):
    FOXR2

    Find genes that share paralogs with FOXR1           About GenesLikeMe



    (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 FOXR1 (see all 303)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1153809781,2
    C,F--118840454(+) GAACCG/TGGATG 1 -- us2k11Minor allele frequency- T:0.09WA 118
    rs2007829301,2
    C--118840481(+) TCCTTA/GGCAAA 1 -- us2k10--------
    rs557365211,2
    C--118840506(+) GAAAAT/CCAAAT 1 -- us2k12Minor allele frequency- C:0.25NA CSA 4
    rs1509249211,2
    --118840524(+) GTTCTC/TACTTG 1 -- us2k10--------
    rs795982381,2
    C,F--118840534(+) ACAAGC/TGGGAG 1 -- us2k13Minor allele frequency- T:0.33NA 6
    rs1168361341,2
    C,F--118840617(+) TGGGAA/GGAGGG 1 -- us2k11Minor allele frequency- G:0.09WA 118
    rs455346321,2
    C,F--118840705(+) GTGACA/GTGAGT 1 -- us2k19Minor allele frequency- G:0.22NS NA WA CSA EA 406
    rs1407468021,2
    --118840733(+) CACATA/GTACAC 1 -- us2k10--------
    rs590895651,2
    C,F--118840747(+) AACCTG/AAAAGT 1 -- us2k11Minor allele frequency- A:0.50WA 2
    rs1386993691,2
    --118840816(+) AAGAGA/GAAACA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for FOXR1 (118842417 - 118852001 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for FOXR1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv819166CNV Loss19587683

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing FOXR1
    DNA2.0 Custom Variant and Variant Library Synthesis for FOXR1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    Find genes that share disorders with FOXR1           About GenesLikeMe

    2 Novoseek inferred disease relationships for FOXR1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hematologic malignancies 49.9 2 15289880 (1)
    tumors 0 1 15067358 (1)


    Export disorders for FOXR1 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 FOXR1 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with FOXR1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of human FOXN5 and rat Foxn5 genes in silico. (PubMed id 15067358)1, 3, 9 Katoh M. and Katoh M. (Int. J. Oncol. 2004)
    2. 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. (Genome Res. 2004)
    3. Human FOX gene family (Review). (PubMed id 15492844)1, 9 Katoh M. and Katoh M. (Int. J. Oncol. 2004)
    4. Oncogenic activation of FOXR1 by 11q23 intrachromosomal deletion-fusions in neuroblastoma. (PubMed id 21860421)1 Santo E.E....Molenaar J.J. (Oncogene 2012)
    5. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    6. (PubMed id )2 
    7. Germ-line mutation of Foxn5 gene in mouse lineage. (PubMed id 15289901)9 Katoh M. and Katoh M. (Int. J. Mol. Med. 2004)
    8. Identification and characterization of human FOXK1 gene in silico. (PubMed id 15202027)9 Katoh M. and Katoh M. (Int. J. Mol. Med. 2004)
    9. Characterization of human FOXN4 gene in silico. (PubMed id 15492871)9 Katoh M. and Katoh M. (Int. J. Mol. Med. 2004)
    10. Identification and characterization of TMEM24 family genes in silico. (PubMed id 15289880)9 Katoh M. and Katoh M. (Int. J. Oncol. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 283150 HGNC: 29980 AceView: FOXR1 Ensembl:ENSG00000176302 euGenes: HUgn283150
    ECgene: FOXR1 H-InvDB: FOXR1

    (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 FOXR1 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 FOXR1 gene:
    Search GeneIP for patents involving FOXR1

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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