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Aliases for LHX3 Gene

Aliases for LHX3 Gene

  • LIM Homeobox 3 2 3 5
  • LIM Homeobox Protein 3 3 4
  • LIM/Homeodomain Protein LHX3 3
  • M2-LHX3 3
  • CPHD3 3
  • LIM3 3

External Ids for LHX3 Gene

Previous GeneCards Identifiers for LHX3 Gene

  • GC09M130237
  • GC09M130859
  • GC09M132611
  • GC09M134527
  • GC09M136314
  • GC09M138227
  • GC09M139088
  • GC09M108552

Summaries for LHX3 Gene

Entrez Gene Summary for LHX3 Gene

  • This gene encodes a member of a large family of proteins which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor that is required for pituitary development and motor neuron specification. Mutations in this gene cause combined pituitary hormone deficiency 3. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

GeneCards Summary for LHX3 Gene

LHX3 (LIM Homeobox 3) is a Protein Coding gene. Diseases associated with LHX3 include pituitary hormone deficiency, combined, 3 and non-acquired combined pituitary hormone deficiency with spine abnormalities. Among its related pathways are DAG and IP3 signaling. GO annotations related to this gene include sequence-specific DNA binding and transcription factor activity, RNA polymerase II transcription factor binding. An important paralog of this gene is LHX4.

UniProtKB/Swiss-Prot for LHX3 Gene

  • Acts as a transcriptional activator. Binds to and activates the promoter of the alpha-glycoprotein gene, and synergistically enhances transcription from the prolactin promoter in cooperation with POU1F1/Pit-1 (By similarity). Required for the establishment of the specialized cells of the pituitary gland and the nervous system. Involved in the development of interneurons and motor neurons in cooperation with LDB1 and ISL1.

Gene Wiki entry for LHX3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX3 Gene

Genomics for LHX3 Gene

Regulatory Elements for LHX3 Gene

Transcription factor binding sites by QIAGEN in the LHX3 gene promoter:

Genomic Location for LHX3 Gene

Chromosome:
9
Start:
136,196,250 bp from pter
End:
136,205,109 bp from pter
Size:
8,860 bases
Orientation:
Minus strand

Genomic View for LHX3 Gene

Genes around LHX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX3 Gene

Proteins for LHX3 Gene

  • Protein details for LHX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBR4-LHX3_HUMAN
    Recommended name:
    LIM/homeobox protein Lhx3
    Protein Accession:
    Q9UBR4
    Secondary Accessions:
    • Q5TB39
    • Q5TB40
    • Q9NZB5
    • Q9P0I8
    • Q9P0I9

    Protein attributes for LHX3 Gene

    Size:
    397 amino acids
    Molecular mass:
    43358 Da
    Quaternary structure:
    • Interacts with POU1F1 (PubMed:26612202). At neuronal promoters, interacts with LDB1, in motor neurons LDB1 is displaced by ISL1 and a ternary complex is formed in which ISL1 contacts both LHX3 and LDB1 (By similarity).

    Alternative splice isoforms for LHX3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LHX3 Gene

Proteomics data for LHX3 Gene at MOPED

Post-translational modifications for LHX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LHX3 Gene

Antibody Products

No data available for DME Specific Peptides for LHX3 Gene

Domains & Families for LHX3 Gene

Gene Families for LHX3 Gene

Protein Domains for LHX3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9UBR4

UniProtKB/Swiss-Prot:

LHX3_HUMAN :
  • The LIM domain specifically interacts with the Pit-1 POU domain and is required for synergistic interactions with Pit-1, but not for basal transcriptional activation events.
Domain:
  • The LIM domain specifically interacts with the Pit-1 POU domain and is required for synergistic interactions with Pit-1, but not for basal transcriptional activation events.
  • Contains 1 homeobox DNA-binding domain.
  • Contains 2 LIM zinc-binding domains.
genes like me logo Genes that share domains with LHX3: view

Function for LHX3 Gene

Molecular function for LHX3 Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional activator. Binds to and activates the promoter of the alpha-glycoprotein gene, and synergistically enhances transcription from the prolactin promoter in cooperation with POU1F1/Pit-1 (By similarity). Required for the establishment of the specialized cells of the pituitary gland and the nervous system. Involved in the development of interneurons and motor neurons in cooperation with LDB1 and ISL1.
genes like me logo Genes that share phenotypes with LHX3: view

Human Phenotype Ontology for LHX3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LHX3 Gene

MGI Knock Outs for LHX3:

Animal Model Products

Targeted motifs for LHX3 Gene
HOMER Transcription Factor Regulatory Elements motif LHX3
  • Consensus sequence: ADBTAATTAR Submotif: canonical Cell Type: Neuron GEO ID: GSE31456

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , miRNA and Transcription Factor Targets for LHX3 Gene

Localization for LHX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX3 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LHX3 Gene COMPARTMENTS Subcellular localization image for LHX3 gene
Compartment Confidence
nucleus 5
cytosol 2

No data available for Gene Ontology (GO) - Cellular Components for LHX3 Gene

Pathways & Interactions for LHX3 Gene

genes like me logo Genes that share pathways with LHX3: view

Pathways by source for LHX3 Gene

1 GeneGo (Thomson Reuters) pathway for LHX3 Gene

Gene Ontology (GO) - Biological Process for LHX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001890 placenta development IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0008045 motor neuron axon guidance IEA --
GO:0009887 organ morphogenesis TAS 10598593
GO:0021520 spinal cord motor neuron cell fate specification IEA --
genes like me logo Genes that share ontologies with LHX3: view

No data available for SIGNOR curated interactions for LHX3 Gene

Drugs & Compounds for LHX3 Gene

(2) Drugs for LHX3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for LHX3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with LHX3: view

Transcripts for LHX3 Gene

mRNA/cDNA for LHX3 Gene

(3) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(16) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LHX3 Gene

LIM homeobox 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LHX3 Gene

No ASD Table

Relevant External Links for LHX3 Gene

GeneLoc Exon Structure for
LHX3
ECgene alternative splicing isoforms for
LHX3

Expression for LHX3 Gene

mRNA expression in normal human tissues for LHX3 Gene

mRNA differential expression in normal tissues according to GTEx for LHX3 Gene

This gene is overexpressed in Pituitary (x52.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LHX3 Gene



SOURCE GeneReport for Unigene cluster for LHX3 Gene Hs.148427

genes like me logo Genes that share expression patterns with LHX3: view

Primer Products

In Situ Assay Products

No data available for Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for LHX3 Gene

Orthologs for LHX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LHX3 36
  • 99 (a)
OneToOne
LHX3 35
  • 99.5 (n)
  • 99.25 (a)
cow
(Bos Taurus)
Mammalia LHX3 35
  • 91.54 (n)
  • 94.78 (a)
LHX3 36
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LHX3 36
  • 88 (a)
OneToOne
LHX3 35
  • 90.3 (n)
  • 94.03 (a)
mouse
(Mus musculus)
Mammalia Lhx3 16
Lhx3 36
  • 94 (a)
OneToOne
Lhx3 35
  • 88.06 (n)
  • 94.03 (a)
oppossum
(Monodelphis domestica)
Mammalia LHX3 36
  • 78 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lhx3 35
  • 88.47 (n)
  • 94.53 (a)
chicken
(Gallus gallus)
Aves LHX3 35
  • 80.14 (n)
  • 82.75 (a)
LHX3 36
  • 79 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LHX3 36
  • 81 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xlim-3 35
zebrafish
(Danio rerio)
Actinopterygii CABZ01029738.1 36
  • 63 (a)
OneToOne
-- 35
lhx3 35
  • 73.85 (n)
  • 77.09 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009088 35
  • 62.72 (n)
  • 61.7 (a)
fruit fly
(Drosophila melanogaster)
Insecta Lim3 37
  • 66 (a)
Lim3 35
  • 61.64 (n)
  • 56.21 (a)
Lim3 36
  • 39 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ceh-14 36
  • 44 (a)
OneToMany
ceh-14 37
  • 57 (a)
lim-4 37
  • 38 (a)
lim-6 37
  • 38 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13878 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2190 36
  • 36 (a)
OneToMany
Species with no ortholog for LHX3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for LHX3 Gene

ENSEMBL:
Gene Tree for LHX3 (if available)
TreeFam:
Gene Tree for LHX3 (if available)

Paralogs for LHX3 Gene

Paralogs for LHX3 Gene

genes like me logo Genes that share paralogs with LHX3: view

Variants for LHX3 Gene

Sequence variations from dbSNP and Humsavar for LHX3 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
VAR_010713 Pituitary hormone deficiency, combined, 3 (CPHD3)
VAR_063240 Pituitary hormone deficiency, combined, 3 (CPHD3)
rs2274115 -- 136,202,927(+) CAGCC(A/G)CTCGG intron-variant, upstream-variant-2KB
rs2274116 -- 136,202,959(+) AGGTC(C/T)GCCCT intron-variant, upstream-variant-2KB, reference, synonymous-codon
rs1924521 -- 136,199,951(+) GAGAG(A/C/T)GGCAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LHX3 Gene

Variant ID Type Subtype PubMed ID
nsv825173 CNV Gain 20364138
nsv894294 CNV Loss 21882294
dgv8382n71 CNV Loss 21882294
dgv8383n71 CNV Loss 21882294
dgv8384n71 CNV Loss 21882294
dgv8385n71 CNV Loss 21882294
nsv894319 CNV Gain 21882294
nsv894322 CNV Loss 21882294
nsv469917 CNV Loss 18288195
nsv894324 CNV Loss 21882294
dgv8386n71 CNV Loss 21882294
dgv8387n71 CNV Loss 21882294
dgv8388n71 CNV Loss 21882294

Variation tolerance for LHX3 Gene

Residual Variation Intolerance Score: 37.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.90; 18.66% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LHX3 Gene

HapMap Linkage Disequilibrium report
LHX3
Human Gene Mutation Database (HGMD)
LHX3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX3 Gene

Disorders for LHX3 Gene

MalaCards: The human disease database

(16) MalaCards diseases for LHX3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

UniProtKB/Swiss-Prot

LHX3_HUMAN
  • Pituitary hormone deficiency, combined, 3 (CPHD3) [MIM:221750]: Combined pituitary hormone deficiency is defined as the impaired production of growth hormone and one or more of the other five anterior pituitary hormones. CPHD3 is characterized by a complete deficit in all but one (adrenocorticotropin) anterior pituitary hormone and a rigid cervical spine leading to limited head rotation. {ECO:0000269 PubMed:10835633, ECO:0000269 PubMed:17327381}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for LHX3

Genetic Association Database (GAD)
LHX3
Human Genome Epidemiology (HuGE) Navigator
LHX3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LHX3
genes like me logo Genes that share disorders with LHX3: view

No data available for Genatlas for LHX3 Gene

Publications for LHX3 Gene

  1. Differential activation of pituitary hormone genes by human Lhx3 isoforms with distinct DNA binding properties. (PMID: 10598593) Sloop K.W. … Rhodes S.J. (Mol. Endocrinol. 1999) 2 3 4 23 67
  2. Analysis of the human LHX3 neuroendocrine transcription factor gene and mapping to the subtelomeric region of chromosome 9. (PMID: 10717474) Sloop K.W. … Rhodes S.J. (Gene 2000) 2 3 23
  3. A novel mutation in the LIM homeobox 3 gene is responsible for combined pituitary hormone deficiency, hearing impairment, and vertebral malformations. (PMID: 19126629) KristrAPm B. … Escher S.A. (J. Clin. Endocrinol. Metab. 2009) 3 23
  4. Novel mutations in LHX3 are associated with hypopituitarism and sensorineural hearing loss. (PMID: 18407919) Rajab A. … Dattani M.T. (Hum. Mol. Genet. 2008) 3 23
  5. Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes. (PMID: 18583962) Bhati M. … Matthews J.M. (EMBO J. 2008) 3 23

Products for LHX3 Gene

Sources for LHX3 Gene

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