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BHLHA9 Gene

protein-coding   GIFtS: 32
GCID: GC17P001175

Basic Helix-Loop-Helix Family, Member A9

  See related diseases
at  

(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
Basic Helix-Loop-Helix Family, Member A91 2     Class II Basic Helix-Loop-Helix Protein2
BHLHF422 3 5     bHLHa93
Class F Basic Helix-Loop-Helix Factor 422 3     bHLHf423
Class A Basic Helix-Loop-Helix Protein 92     

External Ids:    HGNC: 351261   Entrez Gene: 7278572   Ensembl: ENSG000002058997   OMIM: 6154165   UniProtKB: Q7RTU43   

Export aliases for BHLHA9 gene to outside databases

Previous GC identifers: GC17P001121 GC17P001174 GC17P001076


(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 BHLHA9 Gene:
BHLHA9 (basic helix-loop-helix family, member a9) is a protein-coding gene. Diseases associated with BHLHA9 include ectrodactyly with tibial hemimelia, and tibial aplasia - ectrodactyly. GO annotations related to this gene include protein dimerization activity.

UniProtKB/Swiss-Prot: BHA09_HUMAN, Q7RTU4
Function: Putative transcription factor, which may play a role in limb development




(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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Regulatory elements:
   Regulatory transcription factor binding sites in the BHLHA9 gene promoter:
         AhR   RFX1   CUTL1   GATA-1   C/EBPalpha   PPAR-alpha   CREB   PPAR-gamma1   deltaCREB   PPAR-gamma2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for BHLHA9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BHLHA9


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

Entrez Gene cytogenetic band: 17p13.3   Ensembl cytogenetic band:  17p13.3   HGNC cytogenetic band: 17p13.3

BHLHA9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BHLHA9 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P001175:  view genomic region     (about GC identifiers)

Start:
1,173,853 bp from pter      End:
1,174,754 bp from pter
Size:
902 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., 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: BHA09_HUMAN, Q7RTU4 (See protein sequence)
Recommended Name: Class A basic helix-loop-helix protein 9  
Size: 235 amino acids; 24132 Da
Sequence caution: Sequence=DAA00302.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: A8MSH6

Explore the universe of human proteins at neXtProt for BHLHA9: NX_Q7RTU4

Explore proteomics data for BHLHA9 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See BHLHA9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001157877.1  
    ENSEMBL proteins: 
     ENSP00000375248  

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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:
    bHLH: Basic helix-loop-helix proteins

    1 InterPro protein domain:
     IPR011598 bHLH_dom

    Graphical View of Domain Structure for InterPro Entry Q7RTU4

    ProtoNet protein and cluster: Q7RTU4

    1 Blocks protein domain: IPB001092 Basic helix-loop-helix dimerization domain bHLH

    UniProtKB/Swiss-Prot: BHA09_HUMAN, Q7RTU4
    Similarity: Contains 1 bHLH (basic helix-loop-helix) domain


    BHLHA9 for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: BHA09_HUMAN, Q7RTU4
    Function: Putative transcription factor, which may play a role in limb development

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0046983protein dimerization activity IEA--
         
    BHLHA9 for ontologies           About GeneDecksing


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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
    BHA09_HUMAN, Q7RTU4: Nucleus (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    extracellular1

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

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

    BHLHA9 for ontologies           About GeneDecksing


    (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 BHLHA9
    Interactions:

        Search GeneGlobe Interaction Network for BHLHA9

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0007275multicellular organismal development IEA--

    BHLHA9 for ontologies           About GeneDecksing



    (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 BHLHA9 (BHA09)



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for BHLHA9 gene: 
    NM_001164405.1  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000391429(uc021tnd.1)
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    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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    BHLHA9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    BHLHA9 Expression
    About this image

    BHLHA9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    BHLHA9 Protein Expression
        Custom PCR Arrays for BHLHA9
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    In Situ
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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 human and mouse.

    Orthologs for BHLHA9 gene from Selected species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Bhlha91 , 5 basic helix-loop-helix family, member a91, 5 76.11(n)1
    68.58(a)1
      11 (45.97 cM)5
    3205221  NM_177182.41  NP_796156.31 
     766724705 


    ENSEMBL Gene Tree for BHLHA9 (if available)
    TreeFam Gene Tree for BHLHA9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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      --

    (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 BHLHA9 (see all 52)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2009527061,2
    C--1171974(+) TGACC-/TTTTTTT 1 -- us2k10--------
    rs1821099621,2
    C--1172043(+) TGGAGC/TGCAGT 1 -- us2k10--------
    rs1866624181,2
    --1172051(+) AGTGGC/TGGGAT 1 -- us2k10--------
    rs287545581,2
    C--1172237(+) CGCCCA/GCCTCG 1 -- us2k10--------
    rs1915110621,2
    --1172304(+) TTTATA/TATTCG 1 -- us2k10--------
    rs1479322581,2
    C--1172337(+) ACATAG/TAACCT 1 -- us2k10--------
    rs728162571,2
    C--1172399(+) AATCAC/GAGAAG 1 -- us2k10--------
    rs1129937231,2
    F--1172404(+) CAGAAG/CTAAAT 1 -- us2k11Minor allele frequency- C:0.50CSA 2
    rs287590821,2
    C,F--1172662(+) ACATCA/TTCTTT 1 -- us2k14Minor allele frequency- T:0.21WA CSA 124
    rs284530491,2
    C,F--1172669(+) CTTTTT/ATCTGA 1 -- us2k1 trp34Minor allele frequency- A:0.21WA CSA 124

    HapMap Linkage Disequilibrium report for BHLHA9 (1173853 - 1174754 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for BHLHA9:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509645CNV Insertion20534489
    nsv907496CNV Loss21882294
    nsv907493CNV Loss21882294
    nsv907497CNV Loss21882294

    Human Gene Mutation Database (HGMD): BHLHA9
    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: 615416    OMIM disorders: --

    UniProtKB/Swiss-Prot: BHA09_HUMAN, Q7RTU4
  • Split-hand/foot malformation with long bone deficiency 3 (SHFLD3) [MIM:612576]: A disease characterized
    by the association of split-hand/foot malformation with long bone deficiency involving the tibia and fibula.
    Split-hand/foot malformation is a limb malformation involving the central rays of the autopod. Phenotypic
    expression is extremely variable between and within families, and even between limbs of a single patient, ranging
    from syndactyly and oligodactyly to the most severe monodactyly with only a single phalanx. Limb features include
    median clefts of the hands and feet, and aplasia and/or hypoplasia of the phalanges, metacarpals, and
    metatarsals. Note=Disease susceptibility may be associated with variations affecting the gene represented in this
    entry. A copy number variation (CNV) resulting in BHLHA9 duplications is a necessary but not sufficient
    susceptibility factor for Split-hand/foot malformation with long bone deficiency, a highly variable phenotype
    with reduced penetrance, particularly in females (PubMed:22147889)

  • 2 diseases for BHLHA9:    
    About MalaCards
    ectrodactyly with tibial hemimelia    tibial aplasia - ectrodactyly


    BHLHA9 for disorders           About GeneDecksing


    Export disorders for BHLHA9 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 BHLHA9 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with BHLHA9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Exhaustive identification of human class II basic helix-loop-helix proteins by virtual library screening. (PubMed id 14516699)1, 2, 3 McLellan A.S.... Kealey T. (Mech. Dev. 2002)
    2. Duplications of BHLHA9 are associated with ectrodactyly and tibia hemimelia inherited in non-Mendelian fashion. (PubMed id 22147889)1, 2 Klopocki E....Mundlos S. (J. Med. Genet. 2012)
    3. Phylogenetic and expression analysis of the basic helix-loop-helix transcription factor gene family: genomic approach to cellular differentiation. (PubMed id 18557763)1, 3 Stevens J.D....Skinner M.K. ( research in biological diversity 2008)
    4. Identification of a rare 17p13.3 duplication including the BHLHA9 and YWHAE genes in a family with developmental delay and behavioural problems. (PubMed id 23035971)1 Capra V....Gimelli G. (BMC Med. Genet. 2012)
    5. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)2 Zody M.C.... Nusbaum C. (Nature 2006)
    6. Exhaustive identification of human class II basic helix-loop-helix proteins by virtual library screening. (PubMed id 12617822)1 McLellan A.S.... Kealey T. (Gene Expr. Patterns 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 727857 HGNC: 35126 Ensembl:ENSG00000205899 euGenes: HUgn727857 ECgene: BHLHA9
    H-InvDB: BHLHA9

    (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 BHLHA9 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 BHLHA9 gene:
    Search GeneIP for patents involving BHLHA9

    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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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