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Aliases for LHX1 Gene

Aliases for LHX1 Gene

  • LIM Homeobox 1 2 3
  • LIM1 3 4 6
  • Homeobox Protein Lim-1 3 4
  • LIM Homeobox Protein 1 3 4
  • LIM-1 3 4
  • LIM/Homeobox Protein Lhx1 3
  • HLim-1 4

External Ids for LHX1 Gene

Summaries for LHX1 Gene

Entrez Gene Summary for LHX1 Gene

  • This gene encodes a member of a large protein family which contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor important for the development of the renal and urogenital systems. This gene is a candidate for Mayer-Rokitansky-Kuster-Hauser syndrome, a disorder characterized by anomalies in the female genital tract. [provided by RefSeq, Dec 2010]

GeneCards Summary for LHX1 Gene

LHX1 (LIM Homeobox 1) is a Protein Coding gene. Diseases associated with LHX1 include 17q12 microdeletion syndrome and mayer-rokitansky-kuster-hauser syndrome. Among its related pathways are Neural Crest Differentiation. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and transcription corepressor activity.

UniProtKB/Swiss-Prot for LHX1 Gene

  • Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.

Gene Wiki entry for LHX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX1 Gene

Genomics for LHX1 Gene

Genomic Location for LHX1 Gene

36,936,785 bp from pter
36,944,615 bp from pter
7,831 bases
Plus strand

Genomic View for LHX1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LHX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX1 Gene

Regulatory Elements for LHX1 Gene

Proteins for LHX1 Gene

  • Protein details for LHX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    LIM/homeobox protein Lhx1
    Protein Accession:
    Secondary Accessions:
    • Q3MIW0

    Protein attributes for LHX1 Gene

    406 amino acids
    Molecular mass:
    44808 Da
    Quaternary structure:
    • Interacts with LDB1 via the tandem LIM domains.

neXtProt entry for LHX1 Gene

Proteomics data for LHX1 Gene at MOPED

Post-translational modifications for LHX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LHX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LHX1 Gene

Domains for LHX1 Gene

Gene Families for LHX1 Gene

  • LIM :Homeoboxes / LIM class

Suggested Antigen Peptide Sequences for LHX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The LIM domains exert a negative regulatory function and disruption of the LIM domains produces an activated form. In addition, two activation domains and a negative regulatory domain exist C-terminally to the homeobox (By similarity).:
    • P48742
  • Contains 1 homeobox DNA-binding domain.:
    • P48742
  • Contains 2 LIM zinc-binding domains.:
    • P48742
genes like me logo Genes that share domains with LHX1: view

Function for LHX1 Gene

Molecular function for LHX1 Gene

GENATLAS Biochemistry: LIM motif containing protein kinase,putative transcription factor,expressed in brain,thymus and tonsillar tissue,involved in transcriptional regulation of neural and lymphoid cell
UniProtKB/Swiss-Prot Function: Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.

Gene Ontology (GO) - Molecular Function for LHX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0003700 sequence-specific DNA binding transcription factor activity ISS --
GO:0003714 transcription corepressor activity ISS --
GO:0005515 protein binding --
GO:0008270 zinc ion binding IEA --
genes like me logo Genes that share ontologies with LHX1: view
genes like me logo Genes that share phenotypes with LHX1: view

Animal Models for LHX1 Gene

MGI Knock Outs for LHX1:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for LHX1 Gene

Localization for LHX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX1 Gene

Subcellular locations from

Jensen Localization Image for LHX1 Gene COMPARTMENTS Subcellular localization image for LHX1 gene
Compartment Confidence
nucleus 4
cytosol 1

Gene Ontology (GO) - Cellular Components for LHX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular --
GO:0005634 nucleus ISS --
GO:0043234 protein complex ISS --
genes like me logo Genes that share ontologies with LHX1: view

Pathways for LHX1 Gene

SuperPathways for LHX1 Gene

genes like me logo Genes that share pathways with LHX1: view

Pathways by source for LHX1 Gene

1 BioSystems pathway for LHX1 Gene

Interacting Proteins for LHX1 Gene

Selected Interacting proteins: P48742-LHX1_HUMAN for LHX1 Gene via I2D

Gene Ontology (GO) - Biological Process for LHX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001655 urogenital system development ISS --
GO:0001656 metanephros development --
GO:0001657 ureteric bud development ISS --
GO:0001658 branching involved in ureteric bud morphogenesis IEA --
GO:0001702 gastrulation with mouth forming second ISS --
genes like me logo Genes that share ontologies with LHX1: view

Transcripts for LHX1 Gene

Unigene Clusters for LHX1 Gene

LIM homeobox 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LHX1 Gene

No ASD Table

Relevant External Links for LHX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LHX1 Gene

mRNA expression in normal human tissues for LHX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LHX1 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (21.0), Brain - Cerebellum (20.7), and Kidney - Cortex (6.1).

Integrated Proteomics: protein expression from ProteomicsDB and MOPED for LHX1 Gene

SOURCE GeneReport for Unigene cluster for LHX1 Gene Hs.443727

mRNA Expression by UniProt/SwissProt for LHX1 Gene

Tissue specificity: Expressed in the brain, thymus, and tonsils. Expressed in samples from patients with chronic myeloid leukemia (CML) and in 58% of acute myeloid leukemia (AML) cell lines.
genes like me logo Genes that share expressions with LHX1: view

Orthologs for LHX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LHX1 35
  • 99.67 (n)
  • 99.75 (a)
(Bos Taurus)
Mammalia LHX1 35
  • 94.01 (n)
  • 99.51 (a)
(Canis familiaris)
Mammalia LHX1 35
  • 93.02 (n)
  • 99.75 (a)
(Mus musculus)
Mammalia Lhx1 35
  • 88.67 (n)
  • 99.51 (a)
Lhx1 16
(Rattus norvegicus)
Mammalia Lhx1 35
  • 89 (n)
  • 99.51 (a)
(Gallus gallus)
Aves LHX1 35
  • 85.88 (n)
  • 94.33 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.1226 35
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx1 35
  • 79.34 (n)
  • 92.84 (a)
Str.12750 35
(Danio rerio)
Actinopterygii lhx1a 35
  • 76.73 (n)
  • 88.37 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011134 35
  • 62.62 (n)
  • 59.74 (a)
fruit fly
(Drosophila melanogaster)
Insecta Lim1 35
  • 60.24 (n)
  • 58.84 (a)
Lim1 37
  • 49 (a)
(Caenorhabditis elegans)
Secernentea mec-3 37
  • 38 (a)
lin-11 37
  • 52 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9454 35
Species with no ortholog for LHX1:
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • 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)
  • wheat (Triticum aestivum)

Evolution for LHX1 Gene

Gene Tree for LHX1 (if available)
Gene Tree for LHX1 (if available)

Paralogs for LHX1 Gene

Selected SIMAP similar genes for LHX1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with LHX1: view

No data available for Paralogs for LHX1 Gene

Variants for LHX1 Gene

Sequence variations from dbSNP and Humsavar for LHX1 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type MAF
rs3785949 -- 36,939,209(-) GTGTA(C/G)GATAA intron-variant
rs3826452 -- 36,939,062(-) GCGGA(C/G)CCCGT intron-variant
rs7216867 -- 36,938,929(+) GACAT(A/G)CCTCC intron-variant
rs8071723 -- 36,945,031(+) TTTCA(A/T)TTCAT downstream-variant-500B
rs8075069 -- 36,939,901(+) CTAAT(A/C)GGAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LHX1 Gene

Variant ID Type Subtype PubMed ID
nsv833430 CNV Gain+Loss 17160897

Relevant External Links for LHX1 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX1 Gene

Disorders for LHX1 Gene

(1) University of Copenhagen DISEASES for LHX1 Gene

genes like me logo Genes that share disorders with LHX1: view

No data available for UniProtKB/Swiss-Prot for LHX1 Gene

Publications for LHX1 Gene

  1. Cloning, expression, and chromosomal localization to 11p12-13 of a human LIM/homeobox gene, hLim-1. (PMID: 9212161) Dong W.F. … Minden M.D. (DNA Cell Biol. 1997) 2 3 4
  2. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PMID: 16625196) Zody M.C. … Nusbaum C. (Nature 2006) 3 4
  3. 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
  4. LIM-homeodomain genes in mammalian development and human disease. (PMID: 16022279) Hunter C.S. … Rhodes S.J. (Mol. Biol. Rep. 2005) 3
  5. Cell and molecular biology of kidney development. (PMID: 19615554) Reidy K.J. … Rosenblum N.D. (Semin. Nephrol. 2009) 3

Products for LHX1 Gene

Sources for LHX1 Gene

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