Free for academic non-profit institutions. Other users need a Commercial license

Aliases for LHX9 Gene

Aliases for LHX9 Gene

  • LIM Homeobox 9 2 3 5
  • LIM Homeobox Protein 9 4

External Ids for LHX9 Gene

Previous GeneCards Identifiers for LHX9 Gene

  • GC01P195608
  • GC01P193340
  • GC01P194348
  • GC01P195169
  • GC01P194613
  • GC01P196148
  • GC01P169037

Summaries for LHX9 Gene

Entrez Gene Summary for LHX9 Gene

  • This gene encodes a member of the LIM homeobox gene family of developmentally expressed transcription factors. The encoded protein contains a homeodomain and two cysteine-rich zinc-binding LIM domains involved in protein-protein interactions. The protein is highly similar to a mouse protein that causes gonadal agenesis when inactivated, suggesting a role in gonadal development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

GeneCards Summary for LHX9 Gene

LHX9 (LIM Homeobox 9) is a Protein Coding gene. GO annotations related to this gene include sequence-specific DNA binding and transcription corepressor activity. An important paralog of this gene is LHX2.

UniProtKB/Swiss-Prot for LHX9 Gene

  • Involved in gonadal development.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX9 Gene

Genomics for LHX9 Gene

Regulatory Elements for LHX9 Gene

Enhancers for LHX9 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
GH01F198461 1.3 FANTOM5 Ensembl ENCODE 10.7 +550.7 550701 1.3 MAFF JUND STAT1 JUN NR3C1 MAFK ATP6V1G3 LHX9 C1orf53 LOC105371677 GC01P198285
GH01F198465 1.2 Ensembl ENCODE 10.7 +553.6 553553 0.7 CTCF ZNF654 CEBPB REST EP300 BRCA1 RAD21 RFX5 GATA3 SMC3 ATP6V1G3 LHX9 C1orf53 LOC105371677 GC01P198285
GH01F197814 0.5 ENCODE 10.4 -97.4 -97440 0.6 JUND BCL11A POLR2A POU5F1 ZBTB40 PRDM1 C1orf53 LHX9 DENND1B
GH01F197659 0.2 Ensembl 10.3 -252.3 -252302 0.4 LHX9 C1orf53 GC01P197674 ENSG00000230260
GH01F197781 1.2 Ensembl ENCODE 10.1 -128.7 -128748 2.7 BCOR HDAC1 ZNF146 PKNOX1 CBX3 TAL1 ZMYM3 NFXL1 ZBTB40 CHAMP1 C1orf53 LHX9 DENND1B
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around LHX9 on UCSC Golden Path with GeneCards custom track

Genomic Location for LHX9 Gene

197,911,902 bp from pter
197,935,478 bp from pter
23,577 bases
Plus strand

Genomic View for LHX9 Gene

Genes around LHX9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX9 Gene

Proteins for LHX9 Gene

  • Protein details for LHX9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    LIM/homeobox protein Lhx9
    Protein Accession:
    Secondary Accessions:
    • Q5VUE2
    • Q5VUE3
    • Q5VUE6
    • Q86UH2
    • Q9BYU6
    • Q9NQ70

    Protein attributes for LHX9 Gene

    397 amino acids
    Molecular mass:
    43976 Da
    Quaternary structure:
    • Interacts with LDB1 and LDB2.

    Three dimensional structures from OCA and Proteopedia for LHX9 Gene

    Alternative splice isoforms for LHX9 Gene


neXtProt entry for LHX9 Gene

Post-translational modifications for LHX9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LHX9 Gene

Domains & Families for LHX9 Gene

Gene Families for LHX9 Gene

Protein Domains for LHX9 Gene

Suggested Antigen Peptide Sequences for LHX9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 homeobox DNA-binding domain.
  • Contains 1 homeobox DNA-binding domain.
  • Contains 2 LIM zinc-binding domains.
genes like me logo Genes that share domains with LHX9: view

Function for LHX9 Gene

Molecular function for LHX9 Gene

UniProtKB/Swiss-Prot Function:
Involved in gonadal development.

Gene Ontology (GO) - Molecular Function for LHX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003714 transcription corepressor activity ISS --
GO:0005515 protein binding IPI 25416956
GO:0008270 zinc ion binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LHX9: view
genes like me logo Genes that share phenotypes with LHX9: view

Animal Models for LHX9 Gene

MGI Knock Outs for LHX9:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LHX9 Gene

Localization for LHX9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX9 Gene

Subcellular locations from

Jensen Localization Image for LHX9 Gene COMPARTMENTS Subcellular localization image for LHX9 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for LHX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with LHX9: view

Pathways & Interactions for LHX9 Gene

SuperPathways for LHX9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LHX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0008045 motor neuron axon guidance ISS --
GO:0008283 cell proliferation IEA --
GO:0008584 male gonad development IEA --
GO:0008585 female gonad development IEA --
genes like me logo Genes that share ontologies with LHX9: view

No data available for Pathways by source and SIGNOR curated interactions for LHX9 Gene

Transcripts for LHX9 Gene

Unigene Clusters for LHX9 Gene

LIM homeobox 9:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LHX9 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12
SP1: -
SP2: - - -
SP3: - - -
SP4: -

Relevant External Links for LHX9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LHX9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LHX9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LHX9 Gene

This gene is overexpressed in Ovary (x20.8) and Testis (x4.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LHX9 Gene

Protein tissue co-expression partners for LHX9 Gene

NURSA nuclear receptor signaling pathways regulating expression of LHX9 Gene:


SOURCE GeneReport for Unigene cluster for LHX9 Gene:

genes like me logo Genes that share expression patterns with LHX9: view

Primer Products

No data available for Protein differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for LHX9 Gene

Orthologs for LHX9 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LHX9 34 35
  • 99.83 (n)
(Canis familiaris)
Mammalia LHX9 34 35
  • 96.14 (n)
(Mus musculus)
Mammalia Lhx9 34 16 35
  • 94.71 (n)
(Bos Taurus)
Mammalia LHX9 34 35
  • 94.44 (n)
(Rattus norvegicus)
Mammalia Lhx9 34
  • 94.37 (n)
(Monodelphis domestica)
Mammalia LHX9 35
  • 91 (a)
(Ornithorhynchus anatinus)
Mammalia LHX9 35
  • 67 (a)
(Gallus gallus)
Aves LHX9 34 35
  • 88.27 (n)
(Anolis carolinensis)
Reptilia LHX9 35
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx9 34
  • 77.89 (n)
African clawed frog
(Xenopus laevis)
Amphibia lhx9-A 34
(Danio rerio)
Actinopterygii lhx9 34 35
  • 80.68 (n)
fruit fly
(Drosophila melanogaster)
Insecta ap 35
  • 35 (a)
(Caenorhabditis elegans)
Secernentea ttx-3 35
  • 31 (a)
Species where no ortholog for LHX9 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 LHX9 Gene

Gene Tree for LHX9 (if available)
Gene Tree for LHX9 (if available)

Paralogs for LHX9 Gene

Paralogs for LHX9 Gene

(14) SIMAP similar genes for LHX9 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with LHX9: view

Variants for LHX9 Gene

Sequence variations from dbSNP and Humsavar for LHX9 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs10494762 -- 197,918,708(+) CCACT(C/G)TTTCT intron-variant
rs10566483 -- 197,913,241(+) AGAGG(-/TT)TTTTT intron-variant
rs10664707 -- 197,928,900(+) TATCA(-/A/AA)AAAAA intron-variant
rs10801633 -- 197,928,366(+) CATCA(C/T)GGCAA intron-variant
rs10801634 -- 197,931,459(+) ATAAA(A/C)CATTT intron-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for LHX9 Gene

Variant ID Type Subtype PubMed ID
dgv44e201 CNV deletion 23290073
dgv558n100 CNV gain 25217958
esv1002483 CNV deletion 20482838
esv2143475 CNV deletion 18987734
esv2520814 CNV deletion 19546169
esv2660965 CNV deletion 23128226
esv2721095 CNV deletion 23290073
esv2721117 CNV deletion 23290073
esv2762214 CNV gain 21179565
esv3513 CNV loss 18987735
esv3544755 CNV deletion 23714750
esv3588508 CNV loss 21293372
esv8658 CNV loss 19470904
nsv1071825 CNV deletion 25765185
nsv1110664 CNV insertion 24896259
nsv1122440 CNV deletion 24896259
nsv506971 OTHER sequence alteration 20534489
nsv958115 CNV deletion 24416366

Variation tolerance for LHX9 Gene

Residual Variation Intolerance Score: 29.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.34; 26.61% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LHX9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX9 Gene

Disorders for LHX9 Gene

Relevant External Links for LHX9

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for LHX9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LHX9 Gene

Publications for LHX9 Gene

  1. Transcriptional control of axonal guidance and sorting in dorsal interneurons by the Lim-HD proteins Lhx9 and Lhx1. (PMID: 19545367) Avraham O. … Klar A. (Neural Dev 2009) 3 22 64
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  3. Absence of mutations involving the LIM homeobox domain gene LHX9 in 46,XY gonadal agenesis and dysgenesis. (PMID: 11397841) Ottolenghi C. … McElreavey K. (J. Clin. Endocrinol. Metab. 2001) 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. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3 64

Products for LHX9 Gene

Sources for LHX9 Gene

Loading form....