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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 Signaling pathways regulating pluripotency of stem cells and Neural Crest Differentiation. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is LHX1.

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.

Additional gene information for LHX5 Gene

No data available for CIViC summary , 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12H113403 1 Ensembl ENCODE 10 +68.2 68180 1 HDAC1 TAF1 YY1 ZNF316 NFE2 SMARCE1 L3MBTL2 BHLHE40 MAFG DPF2 SDSL PLBD2 LHX5 LOC105369989
GH12H113912 0.7 ENCODE 10.5 -440.6 -440611 0.2 SMARCA5 CTCF ZNF654 RB1 TRIM22 REST RAD21 KLF16 ID3 ZNF143 LHX5 SDSL GC12P113919 GC12P113854
GH12H113407 0.7 Ensembl 10.4 +64.1 64118 0.5 SMARCE1 MAFG ZBTB40 ZNF592 FOSL1 MEF2D JUND ZNF316 SMARCA4 NFE2 PLBD2 LHX5 SDSL LOC105369989
GH12H113896 0.4 ENCODE 10.4 -424.1 -424091 0.2 SREBF1 USF2 LHX5 GC12P113919 GC12P113854
GH12H113591 1.2 FANTOM5 ENCODE 1.3 -119.3 -119279 0.2 HDAC1 RB1 GLIS2 ELK1 ATF7 CREM SMAD5 ZEB2 ELF1 ZFP69B LHX5 GC12M113580 GC12M113572
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LHX5 on UCSC Golden Path with GeneCards custom track

Genomic Locations for LHX5 Gene

Genomic Locations for LHX5 Gene
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

Post-translational modifications for LHX5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LHX5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LHX5 Gene

Domains & Families for LHX5 Gene

Gene Families for LHX5 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for LHX5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for LHX5 Gene

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.

Gene Ontology (GO) - Molecular Function for LHX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043565 sequence-specific DNA binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LHX5: view
genes like me logo Genes that share phenotypes with LHX5: view

Animal Models for LHX5 Gene

MGI Knock Outs for LHX5:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LHX5 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for LHX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with LHX5: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) 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:0006355 regulation of transcription, DNA-templated IEA --
GO:0007267 cell-cell signaling IEA --
GO:0021527 spinal cord association neuron differentiation IEA --
GO:0021549 cerebellum 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:

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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).

NURSA nuclear receptor signaling pathways regulating expression of LHX5 Gene:


SOURCE GeneReport for Unigene cluster for LHX5 Gene:


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 , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Pan troglodytes)
Mammalia LHX5 33 34
  • 99.42 (n)
(Bos Taurus)
Mammalia LHX5 33 34
  • 93.62 (n)
(Canis familiaris)
Mammalia LHX5 33 34
  • 93.28 (n)
(Ornithorhynchus anatinus)
Mammalia LHX5 34
  • 93 (a)
(Monodelphis domestica)
Mammalia LHX5 34
  • 92 (a)
(Rattus norvegicus)
Mammalia Lhx5 33
  • 90.88 (n)
(Mus musculus)
Mammalia Lhx5 33 16 34
  • 90.71 (n)
(Gallus gallus)
Aves LHX5 33 34
  • 82.59 (n)
(Anolis carolinensis)
Reptilia LHX5 34
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx5 33
  • 73.48 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1047 33
(Danio rerio)
Actinopterygii lhx5 33 34
  • 73.99 (n)
fruit fly
(Drosophila melanogaster)
Insecta Lim1 35 34
  • 46 (a)
(Caenorhabditis elegans)
Secernentea lin-11 35 34
  • 52 (a)
mec-3 35
  • 39 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
Species where no ortholog for LHX5 was found in the sources mined by GeneCards:
  • 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
rs1000011920 -- 113,471,931(+) GTAGG(A/G)GGCCC upstream-variant-2KB, utr-variant-5-prime
rs1000164313 -- 113,468,584(+) CCACT(C/G)TCTCC intron-variant
rs1000322803 -- 113,469,028(+) AGCAC(A/G)GACAG intron-variant
rs1000346175 -- 113,462,872(+) GGGGG(C/T)CCGGG downstream-variant-500B
rs1000863871 -- 113,463,063(+) GTGCG(C/G)ACCCG utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for LHX5 Gene

Variant ID Type Subtype PubMed ID
nsv952482 CNV deletion 24416366
nsv1071055 CNV deletion 25765185
esv3892265 CNV gain 25118596
esv3630792 CNV gain 21293372

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)

Relevant External Links for LHX5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot 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 DS … MGC Project Team (Genome research 2004) 3 4 60
  2. Genomic structure, chromosomal localization and expression of the human LIM-homeobox gene LHX5. (PMID: 11137295) Zhao Y … Westphal H (Gene 2000) 3 4 60
  3. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. (PMID: 19197348) Lowe JK … Friedman JM (PLoS genetics 2009) 45 60
  4. Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. (PMID: 17903301) Vasan RS … Benjamin EJ (BMC medical genetics 2007) 45 60
  5. 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 EK … Craddock N (Psychiatric genetics 2003) 3 60

Products for LHX5 Gene

Sources for LHX5 Gene

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