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FLASH GENE
Symbol LHX3 contributors: mct - updated : 31-05-2014
HGNC name LIM homeobox 3
HGNC id 6595
Corresponding disease
CPHD3 combined pituitary hormone deficiency 3
Location 9q34.3      Physical location : 139.088.097 - 139.096.955
Synonym name
  • LIM homeobox protein 3
  • LIM/homeobox protein Lhx3
  • Synonym symbol(s) DKFZp762A2013, LIM3, M2-LHX3, CPHD3
    DNA
    TYPE functioning gene
    STRUCTURE 6.91 kb     6 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    motif
    text structure
  • two alternative exon 1a, 1b
  • two conserved, TATA-less, GC-rich promoters that are used to transcribe the mRNAs precede exons 1a and 1b of LHX3
  • MAPPING cloned Y linked N status confirmed
    Physical map
    GLTDC1 9q34.3 galactosyltransferase family 6 domain containing 1 LOC392399 9 similar to Putative MUP-like lipocalin precursor LOC286220 9q34.3 hypothetical protein LOC286220 KCNT1 9q34.3 potassium channel, subfamily T, member 1 CAMSAP1 9q34.3 calmodulin regulated spectrin-associated protein 1 LOC389805 9 similar to 9530003A05 protein GBDR1 9q34.1-q34.3 similar to 9530003A05 protein BTBD14A 9q34.3 BTB (POZ) domain containing 14A LOC392400 9 similar to F4N2.10 LOC389806 9 hypothetical gene supported by BC009060 LOC389807 9 LOC389807 LOC389808 9 LOC389808 LOC389809 9 LOC389809 LHX3 9q34.3 LIM homeobox protein 3 QSCN6L1 9q34.3 quiescin Q6-like 1 AGS3 9q34.3 activator of G-protein signaling 3 LOC389810 9 LOC389810 CARD9 9q34.3 caspase recruitment domain family, member 9 SNAPC4 9q34.2-q34.3 small nuclear RNA activating complex, polypeptide 4, 190kDa SDCCAG3 9q34.3 serologically defined colon cancer antigen 3 PMPCA 9q34.3 peptidase (mitochondrial processing) alpha INPP5E 9q34.3 inositol polyphosphate-5-phosphatase, 72kDa KIAA0310 9q34.1 inositol polyphosphate-5-phosphatase, 72kDa FLJ36779 9q34.3 hypothetical protein FLJ36779 NOTCH1 9q34.3 Notch homolog 1, translocation-associated (Drosophila) LOC389811 9 similar to HSPC324 EGFL7 9q34.3 EGF-like-domain, multiple 7 AGPAT2 9q34.3 1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta) MGC20262 9q34.3 hypothetical protein MGC20262 MGC16037 9q34.3 hypothetical protein MGC16037 LCN6 9q34.3 lipocalin 6 LOC138307 LOC389812 LOC392401 9 similar to vacuolar H(+)-ATPase subunit; V-ATPase subunit; M16 MGC14141 9q34.3 hypothetical protein MGC14141
    RNA
    TRANSCRIPTS type messenger
    text dual promoters allow regulated production of two LHX3 mRNAs
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    6 initiation site 2376 43.4 397 restricted to glycoprotein subunit-expressing thyrotropes and gonadotropes 2006 16179410
  • two proteins, isoform a and M2-LHX3 generated by an internal translation initiation codon
  • differ in their amino-terminal sequences
  • 6 splicing initiation site 2413 44 402 . nucleus . corticotrop cells 2001 11470784
  • differ in their amino-terminal sequences
  • inhibiting DNA binding and gene activation functions of LHX3
  • a distal element within intron 1a that is recognized by nuclear factor I is critical for LHX3b promoter function
  • - - - - - present in pituitary cells 2007 17616267
  • also called M2-LHX3
  • lacking the LIM domain
  • three homeodomains and carboxyl activation domain
  • generated by an internal translation initiation codon
  • inhibited by the LHX3b-specific domain coding sequence
  • displaying an increased binding to the DNA sites
  • can synergize with POU1F1 to induce transcription of the PRL and TSH promoters
  • EXPRESSION
    Type
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Hearing/EquilibriumearinnercochleaCorti 
    Nervousbrain    
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Epithelialsensorystato-auditory  
    Nervouscentral   
    cells
    SystemCellPubmedSpeciesStageRna symbol
    Hearing / Equilibriumhair cell receptor
    Nervousneuron
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    physiological period embryo, fetal
    Text in the rostrocaudal region of the spinal cord (ventral part) and hindbrain, Rathke pouch at stages of development
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • two amino terminal tandemly repeated LIM motifs
  • three homeodomains
  • a C terminus helix-turn-helix (homeodomain) binding protein, carboxyl activation domain
  • mono polymer tetramer
    HOMOLOGY
    interspecies ortholog to murine Lhx3
    Homologene
    FAMILY
    CATEGORY transcription factor
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,nucleus,chromatin/chromosome
    basic FUNCTION
  • LIM homeodomain class transcription factors with important roles in pituitary and nervous system development
  • play essential roles in pituitary gland and nervous system development
  • transactivator of pituitary genes
  • required for the function of both motoneuron and interneuron complex in presence of ISL1 and LDB1
  • involved in activation of the FSH beta-subunit gene in the pituitary gonadotrope cell, via its LIM homeodomain
  • required for cochlea hair cell differentiation and is regulated in part either directly or indirectly by POU4F3 specifically in the cochlea sensory epithelium
  • essential for pituitary gland and nervous system development
  • LHX3/VSX2 medullary reticular formation neurons are likely involved in locomotion
  • CELLULAR PROCESS nucleotide, transcription
    PHYSIOLOGICAL PROCESS development
    text pituitary development
    PATHWAY
    metabolism
    signaling
    a component
  • tetramer with LDB1-ISL1
  • LIM complex composed of ISL1 and LHX3 directs the specification of spinal motor neurons (MNs) in embryos
  • crucial regulatory axis for the ventral axonal trajectory of developing spinal MNs, consisting of the ISL1-LHX3 complex, STAM1 and CXCR4
  • INTERACTION
    DNA
    RNA
    small molecule
    protein
  • isoform a coinducing TSGB with POU1F1
  • isoform b transactivating the alpha-glyco protein subunit (CGA) promoter
  • LDB1-ISL1 (by the LIM domain)
  • SLB
  • possible interaction between LHX3 and SOX2 likely to be important for development of both the inner ear and the anterior pituitary in embryonic development (SOX2 is able to activate transcription of the LHX3 promoter)
  • ISL1 is a novel transcriptional regulator of LHX3
  • cell & other
    REGULATION
    Other expression of LHX3 is regulated differently in auditory and vestibular hair cells
    ASSOCIATED DISORDERS
    corresponding disease(s) CPHD3
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS
    cooperating with Lhx4 in pituitary development in mice