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Aliases for LHX1 Gene

Aliases for LHX1 Gene

  • LIM Homeobox 1 2 3 5
  • Homeobox Protein Lim-1 3 4
  • LIM Homeobox Protein 1 3 4
  • LIM-1 3 4
  • LIM1 3 4
  • LIM/Homeobox Protein Lhx1 3
  • HLim-1 4

External Ids for LHX1 Gene

Previous GeneCards Identifiers for LHX1 Gene

  • GC17P034678
  • GC17P037247
  • GC17P035025
  • GC17P035490
  • GC17P032368
  • GC17P035294
  • GC17P031230

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 Chromosome 17Q12 Deletion Syndrome and Mayer-Rokitansky-Kuster-Hauser Syndrome. Among its related pathways are Ectoderm Differentiation and Neural Crest Differentiation. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and transcription corepressor activity. An important paralog of this gene is LHX5.

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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX1 Gene

Genomics for LHX1 Gene

Regulatory Elements for LHX1 Gene

Enhancers for LHX1 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
GH17G037088 2 VISTA FANTOM5 Ensembl ENCODE dbSUPER 10.5 +155.0 155032 6.7 HDGF ZNF207 FOS TBX21 ZNF518A CBX8 SMARCA4 GLIS1 MYNN NBN LHX1 C17orf78 GC17M037087 GC17M037085
GH17G036978 2 VISTA ENCODE 9.7 +43.0 43044 2.1 PKNOX1 FEZF1 GATA2 ZNF366 FOS KLF8 ZNF680 ZNF362 CEBPB OVOL3 AATF LHX1 ENSG00000277911 GC17M036967
GH17G036934 1.4 FANTOM5 ENCODE 7 -0.7 -738 3.1 ATF1 SIN3A GLI4 ZNF2 ZNF48 GLIS2 ZNF416 KLF7 ZNF263 SP3 ENSG00000274756 ENSG00000277501 LHX1 AATF ACACA LOC102723471 GC17P036813
GH17G037082 0.9 ENCODE dbSUPER 10.6 +148.1 148052 4.7 PAF1 SCRT1 FOXA3 HLF MNT ATF2 POLR2A ATF3 SCRT2 NFE2 LHX1 GC17M037085 GC17P037067
GH17G036870 0.8 ENCODE 11.5 -66.4 -66419 0.2 BCOR CTCF ATF1 ZMYM3 NFXL1 CEBPG FOSL1 ZNF316 FOS NFE2 LHX1 GC17P036813 LOC102723471
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LHX1 on UCSC Golden Path with GeneCards custom track

Genomic Location for LHX1 Gene

Chromosome:
17
Start:
36,936,785 bp from pter
End:
36,944,615 bp from pter
Size:
7,831 bases
Orientation:
Plus strand

Genomic View for LHX1 Gene

Genes around LHX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX1 Gene

Proteins for LHX1 Gene

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

    Protein Symbol:
    P48742-LHX1_HUMAN
    Recommended name:
    LIM/homeobox protein Lhx1
    Protein Accession:
    P48742
    Secondary Accessions:
    • Q3MIW0

    Protein attributes for LHX1 Gene

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

neXtProt entry for LHX1 Gene

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 & Families for LHX1 Gene

Gene Families for LHX1 Gene

Suggested Antigen Peptide Sequences for LHX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P48742

UniProtKB/Swiss-Prot:

LHX1_HUMAN :
  • 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).
Domain:
  • 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).
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 IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding NAS,ISS --
GO:0003714 transcription corepressor activity ISS --
GO:0008270 zinc ion binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with LHX1: view
genes like me logo Genes that share phenotypes with LHX1: view

Human Phenotype Ontology for LHX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for LHX1 Gene

MGI Knock Outs for LHX1:

Animal Model Products

CRISPR Products

miRNA for LHX1 Gene

Targeted motifs for LHX1 Gene
HOMER Transcription Factor Regulatory Elements motif LHX1
  • Consensus sequence: NNYTAATTAR Submotif: canonical Cell Type: EmbryoCarcinoma GEO ID: GSE70957

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LHX1

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for LHX1 Gene

Localization for LHX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX1 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 LHX1 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for LHX1 Gene

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

Pathways & Interactions for LHX1 Gene

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

Pathways by source for LHX1 Gene

Interacting Proteins for LHX1 Gene

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 IEA --
GO:0001657 ureteric bud development IEA,ISS --
GO:0001658 branching involved in ureteric bud morphogenesis IEA --
GO:0001702 gastrulation with mouth forming second IEA,ISS --
genes like me logo Genes that share ontologies with LHX1: view

No data available for SIGNOR curated interactions for LHX1 Gene

Drugs & Compounds for LHX1 Gene

No Compound Related Data Available

Transcripts for LHX1 Gene

Unigene Clusters for LHX1 Gene

LIM homeobox 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LHX1

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

No ASD Table

Relevant External Links for LHX1 Gene

GeneLoc Exon Structure for
LHX1
ECgene alternative splicing isoforms for
LHX1

Expression for LHX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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 (x21.0), Brain - Cerebellum (x20.7), and Kidney - Cortex (x6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LHX1 Gene



NURSA nuclear receptor signaling pathways regulating expression of LHX1 Gene:

LHX1

SOURCE GeneReport for Unigene cluster for LHX1 Gene:

Hs.443727

mRNA Expression by UniProt/SwissProt for LHX1 Gene:

P48742-LHX1_HUMAN
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.

Evidence on tissue expression from TISSUES for LHX1 Gene

  • Nervous system(4.5)
  • Kidney(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LHX1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • chin
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • skull
Thorax:
  • heart
Abdomen:
  • kidney
  • pancreas
Pelvis:
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with LHX1: view

Primer Products

No data available for Protein differential expression in normal tissues and Protein tissue co-expression partners for LHX1 Gene

Orthologs for LHX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LHX1 34
  • 99.67 (n)
cow
(Bos Taurus)
Mammalia LHX1 34
  • 94.01 (n)
dog
(Canis familiaris)
Mammalia LHX1 34
  • 93.02 (n)
rat
(Rattus norvegicus)
Mammalia Lhx1 34
  • 89 (n)
mouse
(Mus musculus)
Mammalia Lhx1 34 16
  • 88.67 (n)
chicken
(Gallus gallus)
Aves LHX1 34
  • 85.88 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx1 34
  • 79.34 (n)
Str.12750 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.1226 34
zebrafish
(Danio rerio)
Actinopterygii lhx1a 34
  • 76.73 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011134 34
  • 62.62 (n)
fruit fly
(Drosophila melanogaster)
Insecta Lim1 36 34
  • 60.24 (n)
worm
(Caenorhabditis elegans)
Secernentea lin-11 36
  • 52 (a)
mec-3 36
  • 38 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9454 34
Species where no ortholog for LHX1 was found in the sources mined by GeneCards:
  • 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

ENSEMBL:
Gene Tree for LHX1 (if available)
TreeFam:
Gene Tree for LHX1 (if available)

Paralogs for LHX1 Gene

Paralogs for LHX1 Gene

(18) SIMAP similar genes for LHX1 Gene using alignment to 2 proteins:

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

Variants for LHX1 Gene

Sequence variations from dbSNP and Humsavar for LHX1 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1000296484 -- 36,941,031(+) GCCTG(A/C)GGGAC intron-variant
rs1000875830 -- 36,938,834(+) TGCGT(-/AG)AGTGT intron-variant
rs1001296353 -- 36,939,606(+) TACCC(C/G)CTGCC intron-variant
rs1001349723 -- 36,939,353(+) GAGTT(C/T)GTGGT intron-variant
rs1001727182 -- 36,943,378(+) GGAAA(C/T)GCAGA utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
esv3640480 CNV gain 21293372
nsv833430 CNV gain+loss 17160897

Variation tolerance for LHX1 Gene

Residual Variation Intolerance Score: 45.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.02; 50.07% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LHX1 Gene

Human Gene Mutation Database (HGMD)
LHX1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LHX1

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

Disorders for LHX1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for LHX1 Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
chromosome 17q12 deletion syndrome
  • 17q12 microdeletion syndrome
mayer-rokitansky-kuster-hauser syndrome
  • cauv
ureterocele
17q12 deletion syndrome
  • 17q12 recurrent deletion syndrome
- elite association - COSMIC cancer census association via MalaCards
Search LHX1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LHX1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LHX1
genes like me logo Genes that share disorders with LHX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas 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 64
  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 64
  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 64
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64
  5. TBX6, LHX1 and copy number variations in the complex genetics of MA1llerian aplasia. (PMID: 23954021) Sandbacka M. … AittomAoki K. (Orphanet J Rare Dis 2013) 3 64

Products for LHX1 Gene

Sources for LHX1 Gene

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