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Aliases for LHX5 Gene

Aliases for LHX5 Gene

  • LIM Homeobox 5 2 3 5
  • LIM Homeobox Protein 5 4

External Ids for LHX5 Gene

Previous GeneCards Identifiers for LHX5 Gene

  • GC12M112809
  • GC12M113683
  • GC12M112312
  • GC12M112363
  • GC12M113900
  • GC12M110911

Summaries for LHX5 Gene

Entrez Gene Summary for LHX5 Gene

  • This gene encodes a protein belonging to a large protein family, members of which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein may function as a transcriptional regulator and be involved in the control of differentiation and development of the forebrain. In mice, this protein is essential for the regulation of precursor cell proliferation and the control of neuronal differentiation and migration during hippocampal development. This protein is involved in learning and motor functions in adult mice. [provided by RefSeq, Jul 2008]

GeneCards Summary for LHX5 Gene

LHX5 (LIM Homeobox 5) is a Protein Coding gene. Among its related pathways are Transcriptional Regulatory Network in Embryonic Stem Cell and Signaling pathways regulating pluripotency of stem cells. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is LHX4.

UniProtKB/Swiss-Prot for LHX5 Gene

  • Plays an essential role in the regulation of neuronal differentiation and migration during development of the central nervous system.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX5 Gene

Genomics for LHX5 Gene

Regulatory Elements for LHX5 Gene

Enhancers for LHX5 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around LHX5 on UCSC Golden Path with GeneCards custom track

Genomic Location for LHX5 Gene

113,462,034 bp from pter
113,472,280 bp from pter
10,247 bases
Minus strand

Genomic View for LHX5 Gene

Genes around LHX5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX5 Gene

Proteins for LHX5 Gene

  • Protein details for LHX5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    LIM/homeobox protein Lhx5
    Protein Accession:
    Secondary Accessions:
    • Q32MA4

    Protein attributes for LHX5 Gene

    402 amino acids
    Molecular mass:
    44406 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LHX5 Gene

Proteomics data for LHX5 Gene at MOPED

Post-translational modifications for LHX5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LHX5 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for LHX5 Gene

Domains & Families for LHX5 Gene

Gene Families for LHX5 Gene

Suggested Antigen Peptide Sequences for LHX5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 homeobox DNA-binding domain.
  • Contains 1 homeobox DNA-binding domain.
  • Contains 2 LIM zinc-binding domains.
genes like me logo Genes that share domains with LHX5: view

Function for LHX5 Gene

Molecular function for LHX5 Gene

UniProtKB/Swiss-Prot Function:
Plays an essential role in the regulation of neuronal differentiation and migration during development of the central nervous system.
genes like me logo Genes that share phenotypes with LHX5: view

Animal Models for LHX5 Gene

MGI Knock Outs for LHX5:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LHX5 Gene

Localization for LHX5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX5 Gene

Subcellular locations from

Jensen Localization Image for LHX5 Gene COMPARTMENTS Subcellular localization image for LHX5 gene
Compartment Confidence
nucleus 5

No data available for Gene Ontology (GO) - Cellular Components for LHX5 Gene

Pathways & Interactions for LHX5 Gene

genes like me logo Genes that share pathways with LHX5: view

Pathways by source for LHX5 Gene

1 BioSystems pathway for LHX5 Gene

Gene Ontology (GO) - Biological Process for LHX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0007267 cell-cell signaling IEA --
GO:0021527 spinal cord association neuron differentiation IEA --
GO:0021549 cerebellum development IEA --
GO:0021766 hippocampus development IEA --
genes like me logo Genes that share ontologies with LHX5: view

No data available for SIGNOR curated interactions for LHX5 Gene

Drugs & Compounds for LHX5 Gene

No Compound Related Data Available

Transcripts for LHX5 Gene

mRNA/cDNA for LHX5 Gene

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

Unigene Clusters for LHX5 Gene

LIM homeobox 5:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LHX5 Gene

No ASD Table

Relevant External Links for LHX5 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LHX5 Gene

mRNA expression in normal human tissues for LHX5 Gene

mRNA differential expression in normal tissues according to GTEx for LHX5 Gene

This gene is overexpressed in Brain - Hypothalamus (x16.3), Brain - Cerebellum (x11.6), Brain - Cerebellar Hemisphere (x7.3), Stomach (x6.7), Brain - Substantia nigra (x4.5), and Brain - Spinal cord (cervical c-1) (x4.1).

SOURCE GeneReport for Unigene cluster for LHX5 Gene Hs.302029

mRNA Expression by UniProt/SwissProt for LHX5 Gene

Tissue specificity: Expressed in fetal brain and in various regions of the adult central nervous system including the spinal cord, the thalamus, and the cerebellum.
genes like me logo Genes that share expression patterns with LHX5: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for LHX5 Gene

Orthologs for LHX5 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX5 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia LHX5 35
  • 93.62 (n)
  • 99 (a)
LHX5 36
  • 99 (a)
(Canis familiaris)
Mammalia LHX5 35
  • 93.28 (n)
  • 98.01 (a)
LHX5 36
  • 98 (a)
(Mus musculus)
Mammalia Lhx5 35
  • 90.71 (n)
  • 98.76 (a)
Lhx5 16
Lhx5 36
  • 99 (a)
(Pan troglodytes)
Mammalia LHX5 35
  • 99.42 (n)
  • 100 (a)
LHX5 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Lhx5 35
  • 90.88 (n)
  • 98.76 (a)
(Monodelphis domestica)
Mammalia LHX5 36
  • 92 (a)
(Ornithorhynchus anatinus)
Mammalia LHX5 36
  • 93 (a)
(Gallus gallus)
Aves LHX5 35
  • 82.59 (n)
  • 90.8 (a)
LHX5 36
  • 91 (a)
(Anolis carolinensis)
Reptilia LHX5 36
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx5 35
  • 73.48 (n)
  • 86.28 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1047 35
(Danio rerio)
Actinopterygii lhx5 35
  • 73.99 (n)
  • 80.3 (a)
lhx5 36
  • 79 (a)
fruit fly
(Drosophila melanogaster)
Insecta Lim1 37
  • 46 (a)
Lim1 36
  • 39 (a)
(Caenorhabditis elegans)
Secernentea lin-11 37
  • 52 (a)
mec-3 37
  • 39 (a)
lin-11 36
  • 36 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 35 (a)
Species with no ortholog for LHX5:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for LHX5 Gene

Gene Tree for LHX5 (if available)
Gene Tree for LHX5 (if available)

Paralogs for LHX5 Gene

Paralogs for LHX5 Gene

(11) SIMAP similar genes for LHX5 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with LHX5: view

Variants for LHX5 Gene

Sequence variations from dbSNP and Humsavar for LHX5 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1991309 -- 113,465,968(+) AGCAC(A/T)GCCTG intron-variant
rs12813507 -- 113,467,364(+) GGCGC(A/C)TAGGG reference, missense
rs13378000 -- 113,466,571(+) GGTCT(C/T)GGGGC intron-variant
rs736122 -- 113,468,821(-) TGTCA(C/T)TTGAG intron-variant
rs34046886 -- 113,469,034(+) GACAG(-/CA)CACCG intron-variant

Variation tolerance for LHX5 Gene

Residual Variation Intolerance Score: 34.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.77; 16.29% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Structural Variations from Database of Genomic Variants (DGV) and Relevant External Links for LHX5 Gene

Disorders for LHX5 Gene

Relevant External Links for LHX5

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for LHX5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LHX5 Gene

Publications for LHX5 Gene

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 67
  2. Mutational analysis of two positional candidate susceptibility genes for bipolar disorder on chromosome 12q23-q24: phenylalanine hydroxylase and human LIM-homeobox LHX5. (PMID: 12782966) Green E.K. … Craddock N. (Psychiatr. Genet. 2003) 3
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3
  4. Learning impairments and motor dysfunctions in adult Lhx5-deficient mice displaying hippocampal disorganization. (PMID: 11566211) Paylor R. … Crawley J.N. (Physiol. Behav. 2001) 3
  5. Genomic structure, chromosomal localization and expression of the human LIM-homeobox gene LHX5. (PMID: 11137295) Zhao Y. … Westphal H. (Gene 2000) 3

Products for LHX5 Gene

Sources for LHX5 Gene