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Aliases for LHX3 Gene

Aliases for LHX3 Gene

  • LIM Homeobox 3 2 3
  • LIM Homeobox Protein 3 3 4
  • CPHD3 3 6
  • LIM/Homeodomain Protein LHX3 3
  • LIM/Homeobox Protein Lhx3 3
  • M2-LHX3 3
  • LIM3 3

External Ids for LHX3 Gene

Summaries for LHX3 Gene

Entrez Gene Summary for LHX3 Gene

  • This gene encodes a member a large protein family 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. [provided by RefSeq, Dec 2010]

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 Ca-dependent events. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and RNA polymerase II transcription factor binding transcription factor activity. 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

Genomic Location for LHX3 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LHX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX3 Gene

Regulatory Elements for LHX3 Gene

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

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:
    • 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.

    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

No data available for DME Specific Peptides for LHX3 Gene

Domains for LHX3 Gene

Gene Families for LHX3 Gene

HGNC:
  • LIM :Homeoboxes / LIM class

Protein Domains for LHX3 Gene

UniProtKB/Swiss-Prot:

LHX3_HUMAN
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.:
    • Q9UBR4
  • Contains 1 homeobox DNA-binding domain.:
    • Q9UBR4
  • Contains 2 LIM zinc-binding domains.:
    • Q9UBR4
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.

Gene Ontology (GO) - Molecular Function for LHX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001076 RNA polymerase II transcription factor binding transcription factor activity IEA --
GO:0003677 DNA binding --
GO:0005515 protein binding --
GO:0008270 zinc ion binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with LHX3: view
genes like me logo Genes that share phenotypes with LHX3: view

Animal Models for LHX3 Gene

MGI Knock Outs for LHX3:
Targeting motifs for LHX3 Gene
HOMER Transcription Factor Regulatory Elements motif LHX3
  • Consensus sequence: ADBTAATTAR Submotif: canonical Cell Type: Neuron GeoId: GSE31456

No data available for Enzyme Numbers (IUBMB) , miRNA and Transcription Factor Targeting 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 4
cytosol 2

Gene Ontology (GO) - Cellular Components for LHX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular --
GO:0005634 nucleus IEA --
GO:0005667 transcription factor complex IEA --
genes like me logo Genes that share ontologies with LHX3: view

Pathways for LHX3 Gene

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

Pathways by source for LHX3 Gene

1 GeneGo (Thomson Reuters Life Sciences Research) 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:0006366 transcription from RNA polymerase II promoter IEA --
GO:0008045 motor neuron axon guidance IEA --
GO:0009887 organ morphogenesis TAS 10598593
GO:0009953 dorsal/ventral pattern formation --
genes like me logo Genes that share ontologies with LHX3: view

Compounds for LHX3 Gene

(3) Novoseek inferred chemical compound relationships for LHX3 Gene

Compound -log(P) Hits PubMed IDs
gnrh 35.3 2
tyrosine 0 3
cysteine 0 2
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 expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Pituitary (52.1).

Integrated Proteomics: protein expression 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 expressions with LHX3: view

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
  • 99.5 (n)
  • 99.25 (a)
LHX3 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LHX3 36
  • 91.54 (n)
  • 94.78 (a)
LHX3 37
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LHX3 36
  • 90.3 (n)
  • 94.03 (a)
LHX3 37
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lhx3 36
  • 88.06 (n)
  • 94.03 (a)
Lhx3 16
Lhx3 37
  • 94 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LHX3 37
  • 78 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lhx3 36
  • 88.47 (n)
  • 94.53 (a)
chicken
(Gallus gallus)
Aves LHX3 36
  • 80.14 (n)
  • 82.75 (a)
LHX3 37
  • 79 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LHX3 37
  • 81 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xlim-3 36
zebrafish
(Danio rerio)
Actinopterygii -- 36
CABZ01029738.1 37
  • 63 (a)
OneToOne
lhx3 36
  • 73.85 (n)
  • 77.09 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009088 36
  • 62.72 (n)
  • 61.7 (a)
fruit fly
(Drosophila melanogaster)
Insecta Lim3 36
  • 61.64 (n)
  • 56.21 (a)
Lim3 37
  • 39 (a)
OneToMany
Lim3 38
  • 66 (a)
worm
(Caenorhabditis elegans)
Secernentea ceh-14 37
  • 44 (a)
OneToMany
ceh-14 38
  • 57 (a)
lim-4 38
  • 38 (a)
lim-6 38
  • 38 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13878 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2190 37
  • 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 MAF
rs1886296 -- 136,200,434(+) AGGCC(A/G)CAGGG intron-variant
rs1924521 -- 136,199,951(+) GAGAG(A/C)GGCAA intron-variant
rs2274114 -- 136,199,614(+) CCCTG(A/G)GCGTG intron-variant
rs2274115 -- 136,202,927(+) CAGCC(A/G)CTCGG intron-variant, upstream-variant-2KB
rs2274116 -- 136,202,959(+) AGGTC(C/T)GCCCT synonymous-codon, reference, intron-variant, upstream-variant-2KB

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

Relevant External Links for LHX3 Gene

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

Disorders for LHX3 Gene

(1) OMIM Diseases for LHX3 Gene (600577)

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.

(4) University of Copenhagen DISEASES for LHX3 Gene

(10) Novoseek inferred disease relationships for LHX3 Gene

Disease -log(P) Hits PubMed IDs
panhypopituitarism 93.3 15
septo-optic dysplasia 91.4 1
hormone deficiency 87.7 3
hypopituitarism 84.7 5
deficiency diseases 78.9 2

Relevant External Links for LHX3

Genetic Association Database (GAD)
LHX3
Human Genome Epidemiology (HuGE) Navigator
LHX3
genes like me logo Genes that share disorders with LHX3: view

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
  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. Mutations in LHX3 result in a new syndrome revealed by combined pituitary hormone deficiency. (PMID: 10835633) Netchine I. … Amselem S. (Nat. Genet. 2000) 3 4 23
  4. Serine/threonine/tyrosine phosphorylation of the LHX3 LIM-homeodomain transcription factor. (PMID: 15517599) Parker G.E. … Rhodes S.J. (J. Cell. Biochem. 2005) 3 4 23
  5. Four novel mutations of the LHX3 gene cause combined pituitary hormone deficiencies with or without limited neck rotation. (PMID: 17327381) Pfaeffle R.W. … Rhodes S.J. (J. Clin. Endocrinol. Metab. 2007) 3 4 23

Products for LHX3 Gene

Sources for LHX3 Gene

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