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

BARHL1 Gene

protein-coding   GIFtS: 48
GCID: GC09P135457

BarH-like homeobox 1

(Previous name: BarH (Drosophila)-like 1 )
 Explore 3 diseases affiliated with
BARHL1 via our new
 Human Malady Compendium 
Biological research products
for BARHL1
    

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

Aliases
BarH-Like Homeobox 11 2
BarH (Drosophila)-Like 11
BarH-Like 1 Homeobox Protein2

External Ids:    HGNC: 9531   Entrez Gene: 567512   Ensembl: ENSG000001254927   OMIM: 6052115   UniProtKB: Q9BZE33   

Export aliases for BARHL1 gene to outside databases

Previous GC identifers: GC09P126482 GC09P127014 GC09P128811 GC09P130734 GC09P132487 GC09P134447 GC09P104951


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

  --

(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_000009.11  NC_018920.1  NT_035014.4  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the BARHL1 gene promoter:
         C/EBPbeta   Spz1   NRSF form 1   CUTL1   E4BP4   NRSF form 2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidBARHL1 promoter sequence
   Search SABiosciences Chromatin IP Primers for BARHL1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat BARHL1


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

Entrez Gene cytogenetic band: 9q34   Ensembl cytogenetic band:  9q34.13   HGNC cytogenetic band: 9q34.13

BARHL1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BARHL1 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P135457:  view genomic region     (about GC identifiers)

Start:
135,457,572 bp from pter      End:
135,465,653 bp from pter
Size:
8,082 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: BARH1_HUMAN, Q9BZE3 (See protein sequence)
Recommended Name: BarH-like 1 homeobox protein  
Size: 327 amino acids; 35074 Da
Subcellular location: Nucleus (Probable)
Secondary accessions: Q5T6V2 Q9NY88

Explore the universe of human proteins at neXtProt for BARHL1: NX_Q9BZE3

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9BZE3

  • BARHL1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_064448.1  
    ENSEMBL proteins: 
     ENSP00000263610   ENSP00000444704  

    Human Recombinant Protein Products: 
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    Novus Biologicals BARHL1 Proteins
    Novus Biologicals BARHL1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins
    Uscn Proteins for BARHL1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--


    BARHL1 for ontologies           About GeneDecksing



    BARHL1 Antibody Products: 
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    Uscn Antibodies for BARHL1
    Search ThermoFisher Antibodies for BARHL1

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    Uscn ELISAs and CLIAs for BARHL1


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

    BARHL1 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR017970 Homeobox_CS
     IPR001356 Homeodomain
     IPR020479 Homeobox_metazoa
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry Q9BZE3

    ProtoNet protein and cluster: Q9BZE3

    1 Blocks protein family: IPB000047 Lambda and other repressor helix-turn-helix signature

    UniProtKB/Swiss-Prot: BARH1_HUMAN, Q9BZE3
    Similarity: Belongs to the BAR homeobox family
    Similarity: Contains 1 homeobox DNA-binding 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

    miRNA
    Products:
        
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat BARHL1
    8/10 QIAGEN miScript miRNA Assays for microRNAs that regulate BARHL1 (see all 10):
    hsa-miR-579 hsa-miR-328 hsa-miR-185* hsa-let-7a-2* hsa-miR-3653 hsa-miR-507 hsa-miR-1291 hsa-miR-3667-3p
    SwitchGear 3'UTR luciferase reporter plasmidBARHL1 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BARHL1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001077RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity ----
    GO:0043565sequence-specific DNA binding IEA--


    BARHL1 for ontologies           About GeneDecksing


    Animal Models:
         3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Barhl1):
     behavior/neurological  hearing/vestibular/ear  nervous system 

    BARHL1 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 BARHL1

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

    5/6 Interacting proteins for BARHL1 (Q9BZE33 ENSP000002636104) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MED7O435133, ENSP000002863174I2D: score=2 STRING: ENSP00000286317
    TLE1Q047243, ENSP000003656824I2D: score=1 STRING: ENSP00000365682
    TLE2Q047253, ENSP000002629534I2D: score=1 STRING: ENSP00000262953
    MED31Q9Y3C73, ENSP000002257284I2D: score=1 STRING: ENSP00000225728
    GTF2A1P526553I2D: score=1 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001764neuron migration IEA--
    GO:0006351transcription, DNA-dependent ----
    GO:0007605sensory perception of sound IEA--
    GO:0030901midbrain development IEA--
    GO:0043524negative regulation of neuron apoptotic process IEA--


    BARHL1 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 BARHL1
    Search CenterWatch for drugs/clinical trials and news about BARHL1 / BARH1 

    (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 BARHL1 gene: 
    NM_020064.3  

    Unigene Cluster for BARHL1:

    BarH-like homeobox 1
    Hs.283809  [show with all ESTs]
    Unigene Representative Sequence: NM_020064
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000263610(uc004cbp.1) ENST00000542090

    miRNA
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    8/10 QIAGEN miScript miRNA Assays for microRNAs that regulate BARHL1 (see all 10):
    hsa-miR-579 hsa-miR-328 hsa-miR-185* hsa-let-7a-2* hsa-miR-3653 hsa-miR-507 hsa-miR-1291 hsa-miR-3667-3p
    SwitchGear 3'UTR luciferase reporter plasmidBARHL1 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for BARHL1 (see all 7)
    OriGene shRNA RFP: BARHL1
    OriGene siRNA: BARHL1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat BARHL1
    Clone
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat BARHL1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat BARHL1

    Additional cDNA sequence: 

    AF321618.1 AF325688.1 AK054797.1 BC136956.1 BC136969.1 BC144433.1 

    1 DOTS entry:

    DT.75136584 

    6 AceView cDNA sequences:

    AF321618 NM_020064 AI367090 AK054797 AF325688 BX281517 

    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

    BARHL1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AGCCCGTGAC

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

    About this image

    BARHL1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    4 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BrainHypothalamusBrain
    BrainMedulla OblongataBrain
    Neural TubeMetencephalonNeural Tube
    Spinal CordPresumptive Spinal CordSpinal Cord
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    N2/LSB induced-cells (Generation of midbra...)

    See BARHL1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for BARHL1

    SOURCE GeneReport for Unigene cluster: Hs.283809
        SABiosciences Custom PCR Arrays for BARHL1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BARHL1

    (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 BARHL1 gene from 5/17 species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia BARHL16
    --
    67(a)
    1 ↔ 1
    AAWZ02039460(5285-8384)
    African clawed frog
    (Xenopus laevis)
    Amphibia barh2-A-prov2 Bar homeobox protein 2 75.25(n)    AF283692.1 
    zebrafish
    (Danio rerio)
    Actinopterygii barhl1b1 BarH-like 1b 72.57(n)
    82.28(a)
      553186  XM_677740.5  XP_682832.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta B-H13 specific RNA polymerase II transcription
    factor
    68(a)
    (best of 2)
      16A5   --
    worm
    (Caenorhabditis elegans)
    Secernentea ceh-316
    ceh-306
    Homeobox protein ceh-30
    26(a)
    24(a)
    many ↔ many
    many ↔ many
    X(3068638-3070386)
    X(3063575-3065541)


    ENSEMBL Gene Tree for BARHL1 (if available)
    TreeFam Gene Tree for BARHL1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for BARHL1 gene
    DLX22  BARX12  BSX2  DLX52  DLX62  BARHL22  DLX42  BARX22  
    DLX12  MSX22  MSX12  DLX32  
    9 SIMAP similar genes for BARHL1 using alignment to 2 protein entries:     BARH1_HUMAN (see all proteins):
    HMX2    NKX2-5    HLX    MEOX1    BARHL2    HOXA4
    HOXB1    RAX2    DLX3

    BARHL1 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

    10/153 NCBI SNPs in BARHL1 are shown (see all 153    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1174624731,2
    F,--135456234(+) TCTGTC/GCGCCC 1 -- us2k11Minor allele frequency- G:0.02NA 120
    rs1874744941,2
    --135456336(+) CCCAAC/TGCCGG 1 -- us2k10--------
    rs1441679001,2
    --135456508(+) GTCTAC/TACTCG 1 -- us2k10--------
    rs3684761,2
    C,F,A,H,--135456552(+) GGTACA/GACAGC 1 -- us2k122Minor allele frequency- G:0.37NS EA NA WA 2760
    rs3868881,2
    C,A,--135456594(+) GCCATC/AAGTGG 1 -- us2k112Minor allele frequency- A:0.24MN NA WA CSA EA 556
    rs745530761,2
    --135456603(+) GGGGGG/ATGGGC 1 -- us2k12Minor allele frequency- A:0.09NA 122
    rs121158011,2
    --135456605(+) GGGGTG/AGGCGG 1 -- us2k13Minor allele frequency- A:0.19CSA WA 121
    rs1454726151,2
    --135456733(+) CCATCC/GGTCTC 1 -- us2k10--------
    rs1396430011,2
    --135456915(+) CTCGA-/CGCGCG
            
    CGCGC
    1 -- us2k10--------
    rs132994041,2
    C--135456927(+) CGCGCG/ACACAC 1 -- us2k12Minor allele frequency- A:0.00NA 4

    HapMap Linkage Disequilibrium report for BARHL1 (135457572 - 135465653 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for BARHL1: --

    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

    BARHL1 for disorders           About GeneDecksing

    OMIM gene information: 605211    OMIM disorders: --

    3 diseases for BARHL1:    About MalaCards
    joubert syndrome    medulloblastoma    neuronitis


    Export disorders for BARHL1 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 BARHL1 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with BARHL1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    2. Barhl1, a gene belonging to a new subfamily of mammalian homeobox genes, is expressed in migrating neurons of the CNS. (PubMed id 10814725)1, 2 Bulfone A.... Banfi S. (2000)
    3. Expression of BARHL1 in medulloblastoma is associated with prolonged survival in mice and humans. (PubMed id 21602885)1 PAPschl J....SchA1ller U. (2011)
    4. An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142)1 Ravasi T....Hayashizaki Y. (2010)
    5. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    6. Large-scale mapping of human protein-protein interactions by mass spectrometry. (PubMed id 17353931)1 Ewing R.M.... Figeys D. (2007)
    7. Mutational analysis of BARHL1 and BARX1 in three new patients with Joubert syndrome. (PubMed id 15487006)2 Gould D.B. and Walter M.A. (2004)
    8. 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)
    9. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (2004)
    10. 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: 56751 HGNC: 953 AceView: BARHL1 Ensembl:ENSG00000125492 euGenes: HUgn56751
    ECgene: BARHL1 H-InvDB: BARHL1

    (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 BARHL1 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 BARHL1 gene:
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