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BARHL1 Gene

protein-coding   GIFtS: 48
GCID: GC09P135457

BarH-Like Homeobox 1

(Previous name: BarH (Drosophila)-like 1)
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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
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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for BARHL1 Gene:
BARHL1 (BarH-like homeobox 1) is a protein-coding gene. GO annotations related to this gene include sequence-specific DNA binding and RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription. An important paralog of this gene is DLX2.


(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_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   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 Chromatin IP Primers for BARHL1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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, 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: BARH1_HUMAN, Q9BZE3 (See protein sequence)
Recommended Name: BarH-like 1 homeobox protein  
Size: 327 amino acids; 35074 Da
Secondary accessions: Q5T6V2 Q9NY88

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

Explore proteomics data for BARHL1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See BARHL1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_064448.1  
    ENSEMBL proteins: 
     ENSP00000263610   ENSP00000444704  

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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:
    NKL: Homeoboxes / ANTP class : NKL subclass

    4 InterPro protein domains:
     IPR020479 Homeobox_metazoa
     IPR017970 Homeobox_CS
     IPR001356 Homeobox_dom
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry Q9BZE3

    ProtoNet protein and cluster: Q9BZE3

    1 Blocks protein domain: 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


    Find genes that share domains with BARHL1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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): 4 molecular function terms:    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:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity ----
    GO:0043565sequence-specific DNA binding IEA--
         
    Find genes that share ontologies with BARHL1           About GenesLikeMe


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

    Find genes that share phenotypes with BARHL1           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for BARHL1
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    miRNA
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    Selected qRT-PCR 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
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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
    BARH1_HUMAN, Q9BZE3: Nucleus (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4
    cytosol1
    golgi apparatus1
    plasma membrane1

    Gene Ontology (GO): 1 cellular component term:    About this table

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

    Find genes that share ontologies with BARHL1           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 BARHL1
    Interactions:

        Search GeneGlobe Interaction Network for BARHL1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 19)

    Selected Interacting proteins for BARHL1 (Q9BZE33 ENSP000002636104) via UniProtKB, MINT, STRING, and/or I2D (see all 20)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MED7O435133, ENSP000002863174I2D: score=2 STRING: ENSP00000286317
    MED31Q9Y3C73, ENSP000002257284I2D: score=1 STRING: ENSP00000225728
    TLE1Q047243, ENSP000003656824I2D: score=1 STRING: ENSP00000365682
    TLE2Q047253, ENSP000002629534I2D: score=1 STRING: ENSP00000262953
    GTF2A1P526553I2D: score=1 
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    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001764neuron migration IEA--
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0007605sensory perception of sound IEA--
    GO:0030901midbrain development IEA--
    GO:0043524negative regulation of neuron apoptotic process IEA--

    Find genes that share ontologies with BARHL1           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 BARHL1 (BARH1)



    (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 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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    Selected qRT-PCR 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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    Predesigned siRNA for gene silencing in human, mouse, rat BARHL1
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      QuantiTect SYBR Green Assays in human, mouse, rat BARHL1
      QuantiFast Probe-based Assays in human, mouse, rat BARHL1

    Additional mRNA sequence: 

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

    1 DOTS entry:

    DT.75136584 

    6 AceView cDNA sequences:

    AK054797 NM_020064 AI367090 AF321618 BX281517 AF325688 

    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™, 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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    BARHL1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGCCCGTGAC
    BARHL1 Expression
    About this image


    BARHL1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Brain (Nervous System)    fully expand to see all 17 entries
             Thalamus
             N2/LSB induced-cells
             Septum   
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Metencephalon
             Floor plate-like cells
             brain/midbrain/lateral wall   
     
     Neural Ectoderm (Nervous System)
             Neural ectoderm cells
    BARHL1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    BARHL1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.283809
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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)
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    This gene was present in the common ancestor of animals.

    Orthologs for BARHL1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Barhl11 , 5 BarH-like 1 (Drosophila)1, 5 93.17(n)1
    97.86(a)1
      2 (19.38 cM)5
    544221  NM_019446.41  NP_062319.11 
     289076795 
    chicken
    (Gallus gallus)
    Aves BARHL11 BarH-like homeobox 1 79.63(n)
    84.13(a)
      429598  XM_427153.3  XP_427153.3 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    71(a)
    1 → many
    AAWZ02039460(2318-8384)
    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 73.23(n)
    82.5(a)
      553186  NM_001018132.1  NP_001018142.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta B-H13 specific RNA polymerase II
    transcription factor
    68(a)
    (best of 2)
      16A5   --
    worm
    (Caenorhabditis elegans)
    Secernentea ceh-306
    ceh-316
    Protein CEH-31 (ceh-31) mRNA, complete cds
    35(a)
    30(a)
    many ↔ many
    many ↔ many
    X(3063585-3065551) WBGene00000451
    X(3068648-3070396) WBGene00000452


    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)
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    Paralogs for BARHL1 gene
    DLX22  BARX12  GBX12  NKX1-12  VENTX2  GBX22  BARHL22  MNX12  
    BARX22  DLX12  DLX32  LBX22  NKX1-22  BSX2  DLX52  DLX62  
    DLX42  LBX12  MSX22  MSX12  
    7 SIMAP similar genes for BARHL1 using alignment to 2 protein entries:     BARH1_HUMAN (see all proteins):
    HMX2    NKX2-5    HLX    BARHL2    HOXA4    HOXB1
    RAX2

    Find genes that share paralogs with BARHL1           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 BARHL1 (see all 196)    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
    F--135456603(+) GGGGGG/ATGGGC 1 -- us2k12Minor allele frequency- A:0.09NA 122
    rs121158011,2
    C,F--135456605(+) GGGGTG/AGGCGG 1 -- us2k13Minor allele frequency- A:0.19CSA WA 121
    rs1454726151,2
    --135456733(+) CCATCC/GGTCTC 1 -- us2k10--------
    rs1396430011,2
    C--135456915(+) CTCGA-/CGCGCG
            
    CGCGC
    1 -- cds10--------
    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
         Database of Genomic Variants (DGV) 1 variation for BARHL1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv894023CNV Gain21882294

    Site Specific Mutation Identification with 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.)
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    OMIM gene information: 605211    OMIM disorders: --


    Find genes that share disorders with BARHL1           About GenesLikeMe


    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)
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    PubMed articles for BARHL1 gene, integrated from 10 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. (Nat. Genet. 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. (Hum. Mol. Genet. 2000)
    3. Expression of BARHL1 in medulloblastoma is associated with prolonged survival in mice and humans. (PubMed id 21602885)1 PAPschl J....SchA1ller U. (Oncogene 2011)
    4. An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142)1 Ravasi T....Hayashizaki Y. (Cell 2010)
    5. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    6. Large-scale mapping of human protein-protein interactions by mass spectrometry. (PubMed id 17353931)1 Ewing R.M....Figeys D. (Mol. Syst. Biol. 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. (Am. J. Med. Genet. 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. (Genome Res. 2004)
    9. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
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      Query String
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      (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: 56751 HGNC: 953 AceView: BARHL1 Ensembl:ENSG00000125492 euGenes: HUgn56751
    ECgene: BARHL1 H-InvDB: BARHL1

    (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 BARHL1 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 BARHL1 gene:
    Search GeneIP for patents involving BARHL1

    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, LSBio, eBioscience, 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
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