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Aliases for LHX5 Gene

Aliases for LHX5 Gene

  • LIM Homeobox 5 2 3
  • 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 Neural Crest Differentiation and Transcriptional Regulatory Network in Embryonic Stem Cell. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and 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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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:

No data available for DME Specific Peptides for LHX5 Gene

Domains for LHX5 Gene

Gene Families for LHX5 Gene

  • LIM :Homeoboxes / LIM class

Suggested Antigen Peptide Sequences for LHX5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Q9H2C1
  • 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

Gene Ontology (GO) - Molecular Function for LHX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0008270 zinc ion binding IEA --
GO:0043565 sequence-specific DNA 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

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

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

Pathways 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 --
GO:0021527 spinal cord association neuron differentiation IEA --
GO:0021549 cerebellum development --
GO:0021702 cerebellar Purkinje cell differentiation IEA --
genes like me logo Genes that share ontologies with LHX5: view

Transcripts for LHX5 Gene

mRNA/cDNA for LHX5 Gene

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

Unigene Clusters for LHX5 Gene

LIM homeobox 5:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LHX5

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for LHX5

Flow Cytometry 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 for LHX5 Gene

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

This gene is overexpressed in Brain - Hypothalamus (16.3), Brain - Cerebellum (11.6), Brain - Cerebellar Hemisphere (7.3), Stomach (6.7), Brain - Substantia nigra (4.5), and Brain - Spinal cord (cervical c-1) (4.1).

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 expressions with LHX5: view

In Situ Assay Products

No data available for Protein expression 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 35
  • 99.42 (n)
  • 100 (a)
LHX5 36
  • 100 (a)
(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)
(Monodelphis domestica)
Mammalia LHX5 36
  • 92 (a)
(Ornithorhynchus anatinus)
Mammalia LHX5 36
  • 93 (a)
(Rattus norvegicus)
Mammalia Lhx5 35
  • 90.88 (n)
  • 98.76 (a)
(Gallus gallus)
Aves LHX5 35
  • 82.59 (n)
  • 90.8 (a)
LHX5 36
  • 91 (a)
(Anolis carolinensis)
Reptilia LHX5 36
  • 91 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1047 35
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx5 35
  • 73.48 (n)
  • 86.28 (a)
(Danio rerio)
Actinopterygii lhx5 35
  • 73.99 (n)
  • 80.3 (a)
lhx5 36
  • 79 (a)
fruit fly
(Drosophila melanogaster)
Insecta Lim1 36
  • 39 (a)
Lim1 37
  • 46 (a)
(Caenorhabditis elegans)
Secernentea lin-11 36
  • 36 (a)
mec-3 37
  • 39 (a)
lin-11 37
  • 52 (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

Selected 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 MAF
rs736122 -- 113,468,821(-) TGTCA(C/T)TTGAG intron-variant
rs1319875 -- 113,469,754(-) AGGCA(A/G)AGCCA intron-variant
rs1573956 -- 113,470,200(+) AGGCT(C/T)AGGTT intron-variant
rs1991309 -- 113,465,968(+) AGCAC(A/T)GCCTG intron-variant
rs3803074 -- 113,471,252(+) GGGGT(A/C)TCCCC intron-variant

Relevant External Links for LHX5 Gene

HapMap Linkage Disequilibrium report

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

Disorders for LHX5 Gene

(1) University of Copenhagen DISEASES for LHX5 Gene

Relevant External Links for LHX5

Genetic Association Database (GAD)
genes like me logo Genes that share disorders with LHX5: view

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

Publications for LHX5 Gene

  1. Genomic structure, chromosomal localization and expression of the human LIM-homeobox gene LHX5. (PMID: 11137295) Zhao Y. … Westphal H. (Gene 2000) 3 4
  2. 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
  3. Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. (PMID: 17903301) Vasan R.S. … Benjamin E.J. (BMC Med. Genet. 2007) 48
  4. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. (PMID: 19197348) Lowe J.K. … Friedman J.M. (PLoS Genet. 2009) 48
  5. Control of hippocampal morphogenesis and neuronal differentiation by the LIM homeobox gene Lhx5. (PMID: 10325223) Zhao Y. … Westphal H. (Science 1999) 3

Products for LHX5 Gene

Sources for LHX5 Gene

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