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 proliferatio... See more...

Aliases for LHX5 Gene

Aliases for LHX5 Gene

  • LIM Homeobox 5 2 3 5
  • LIM/Homeobox Protein Lhx5 3 4
  • LIM Homeobox Protein 5 3 4
  • LHX5 5

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. Diseases associated with LHX5 include Scapuloperoneal Spinal Muscular Atrophy and Scapuloperoneal Myopathy. Among its related pathways are Neural Crest Differentiation and Signaling pathways regulating pluripotency of stem cells. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is LHX1.

UniProtKB/Swiss-Prot Summary 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 CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LHX5 Gene

Genomics for LHX5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LHX5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J113471 Promoter/Enhancer 0.8 EPDnew ENCODE 600.7 +0.3 347 0.2 RFX1 POLR2A EZH2 ATF1 LHX5 LHX5-AS1 lnc-LHX5-1 SDS
GH12J113472 Enhancer 0.6 FANTOM5 ENCODE 602.1 -0.7 -690 0.3 EZH2 SP1 EGR1 LHX5 LHX5-AS1 lnc-LHX5-1 SDSL piR-47675-026 RBM19
GH12J113474 Enhancer 0.3 ENCODE 600.7 -0.5 -497 0 EZH2 EGR1 LHX5 LHX5-AS1 lnc-LHX5-1 piR-47675-026 RBM19
GH12J113473 Enhancer 0.3 ENCODE 600.7 -1.7 -1741 0.2 TBP EZH2 LHX5 lnc-LHX5-1 LHX5-AS1 piR-47675-026 RBM19
GH12J113475 Enhancer 0.3 ENCODE 600.7 -0.1 -141 0.2 EZH2 LHX5 LHX5-AS1 lnc-LHX5-1 SDSL piR-47675-026 RBM19
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LHX5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LHX5

Top Transcription factor binding sites by QIAGEN in the LHX5 gene promoter:
  • AREB6
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • NRSF form 1
  • NRSF form 2

Genomic Locations for LHX5 Gene

Genomic Locations for LHX5 Gene
chr12:113,462,033-113,472,280
(GRCh38/hg38)
Size:
10,248 bases
Orientation:
Minus strand
chr12:113,899,839-113,910,085
(GRCh37/hg19)
Size:
10,247 bases
Orientation:
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:
    Q9H2C1-LHX5_HUMAN
    Recommended name:
    LIM/homeobox protein Lhx5
    Protein Accession:
    Q9H2C1
    Secondary Accessions:
    • Q32MA4

    Protein attributes for LHX5 Gene

    Size:
    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

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

Protein Domains for LHX5 Gene

InterPro:
Blocks:
  • Lambda and other repressor helix-turn-helix signature
  • Zn-binding protein, LIM
ProtoNet:

Suggested Antigen Peptide Sequences for LHX5 Gene

GenScript: Design optimal peptide antigens:
  • LIM/homeobox protein Lhx5 (LHX5_HUMAN)
genes like me logo Genes that share domains with LHX5: view

No data available for Graphical View of Domain Structure and 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.

Phenotypes From GWAS Catalog for LHX5 Gene

Gene Ontology (GO) - Molecular Function for LHX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0003677 DNA binding IEA --
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:
  • Lhx5 Lhx5<tm1Lmgd>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LHX5

No data available for Enzyme Numbers (IUBMB) , 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

COMPARTMENTS
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 4
plasma membrane 1
extracellular 1
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for LHX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA 21873635
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
1 Qiagen pathway for LHX5 Gene
  • Transcriptional Regulatory Network in Embryonic Stem Cell

Gene Ontology (GO) - Biological Process for LHX5 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 --
GO:0021702 cerebellar Purkinje cell differentiation 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 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LHX5

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

No ASD Table

Relevant External Links for LHX5 Gene

GeneLoc Exon Structure for
LHX5

Expression for LHX5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LHX5

SOURCE GeneReport for Unigene cluster for LHX5 Gene:

Hs.302029

mRNA Expression by UniProt/SwissProt for LHX5 Gene:

Q9H2C1-LHX5_HUMAN
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.

Evidence on tissue expression from TISSUES for LHX5 Gene

  • Nervous system(2.4)
genes like me logo Genes that share expression patterns with LHX5: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners 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
Chimpanzee
(Pan troglodytes)
Mammalia LHX5 30 31
  • 99.42 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LHX5 30 31
  • 93.62 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LHX5 30 31
  • 93.28 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LHX5 31
  • 93 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LHX5 31
  • 92 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lhx5 30
  • 90.88 (n)
Mouse
(Mus musculus)
Mammalia Lhx5 30 17 31
  • 90.71 (n)
OneToOne
Chicken
(Gallus gallus)
Aves LHX5 30 31
  • 82.59 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LHX5 31
  • 91 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lhx5 30
  • 73.48 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1047 30
Zebrafish
(Danio rerio)
Actinopterygii lhx5 30 31
  • 73.99 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Lim1 31 32
  • 39 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea mec-3 32
  • 39 (a)
lin-11 31 32
  • 36 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 35 (a)
ManyToMany
Species where no ortholog for LHX5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for LHX5 (if available)
TreeFam:
Gene Tree for LHX5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LHX5: view image

Paralogs for LHX5 Gene

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

  • LHX5_HUMAN
genes like me logo Genes that share paralogs with LHX5: view

Variants for LHX5 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LHX5 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs1555212451 Likely Benign: not specified 113,468,123(-) G/T INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for LHX5 Gene

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

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

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)

Additional Variant Information for LHX5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LHX5

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX5 Gene

Disorders for LHX5 Gene

MalaCards: The human disease database

(2) MalaCards diseases for LHX5 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search LHX5 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LHX5

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

No data available for 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
  2. Genomic structure, chromosomal localization and expression of the human LIM-homeobox gene LHX5. (PMID: 11137295) Zhao Y … Westphal H (Gene 2000) 3 4
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3
  4. Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. (PMID: 19197348) Lowe JK … Friedman JM (PLoS genetics 2009) 41
  5. A census of human transcription factors: function, expression and evolution. (PMID: 19274049) Vaquerizas JM … Luscombe NM (Nature reviews. Genetics 2009) 3

Products for LHX5 Gene

Sources for LHX5 Gene