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Aliases for LHX6 Gene

Aliases for LHX6 Gene

  • LIM Homeobox 6 2 3 5
  • LIM/Homeobox Protein Lhx6.1 3 4
  • LHX6.1 3 4
  • LIM Homeodomain Protein 6.1 3
  • LIM/Homeobox Protein Lhx6 3
  • LIM Homeobox Protein 6 4

External Ids for LHX6 Gene

Previous GeneCards Identifiers for LHX6 Gene

  • GC09M116069
  • GC09M116611
  • GC09M118418
  • GC09M120340
  • GC09M122044
  • GC09M124004
  • GC09M124964
  • GC09M094579

Summaries for LHX6 Gene

Entrez Gene Summary for LHX6 Gene

  • This gene encodes a member of a large protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017]

GeneCards Summary for LHX6 Gene

LHX6 (LIM Homeobox 6) is a Protein Coding gene. Diseases associated with LHX6 include Intrauterine Growth Retardation, Metaphyseal Dysplasia, Adrenal Hypoplasia Congenita, And Genital Anomalies. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is LHX8.

UniProtKB/Swiss-Prot for LHX6 Gene

  • Probable transcription factor required for the expression of a subset of genes involved in interneurons migration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex (By similarity).

Gene Wiki entry for LHX6 Gene

Additional gene information for LHX6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX6 Gene

Genomics for LHX6 Gene

GeneHancer (GH) Regulatory Elements for LHX6 Gene

Promoters and enhancers for LHX6 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
GH09I122225 Promoter/Enhancer 1.3 EPDnew Ensembl 550.8 +2.2 2231 4.1 ZSCAN4 SIN3A NFXL1 ZNF335 GLIS2 EGR1 FOS EGR2 ZNF263 SP3 LHX6 RBM18 MRRF GC09P122163
GH09I122263 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.3 -35.1 -35136 3.4 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 RBM18 MRRF LHX6 ZBTB26
GH09I122178 Enhancer 0.8 ENCODE 11.8 +49.9 49902 2.2 FOXA2 RARA TCF12 CEBPB USF2 REST RAD51 GLIS1 IKZF1 GTF2F1 LHX6 TTLL11 GC09P122163 MORN5
GH09I122180 Enhancer 0.7 ENCODE 11.8 +48.7 48729 0.2 GTF2F1 ZNF449 TEAD4 JUN MAX FOSL1 TCF12 CTBP1 FOXK2 CBFA2T2 LHX6 TTLL11 GC09P122163 MORN5
GH09I122325 Enhancer 0.6 ENCODE 10.7 -95.7 -95731 0.2 FOXA2 SAP130 HLF MAX CEBPB CEBPG RARA YY1 NFIL3 JUND GC09P122327 GC09P122328 PIR42770 PIR62540 MRRF RBM18 LHX6 TTLL11 OR1K1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LHX6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LHX6 gene promoter:

Genomic Locations for LHX6 Gene

Genomic Locations for LHX6 Gene
chr9:122,185,652-122,229,626
(GRCh38/hg38)
Size:
43,975 bases
Orientation:
Minus strand
chr9:124,964,856-124,991,905
(GRCh37/hg19)

Genomic View for LHX6 Gene

Genes around LHX6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX6 Gene

Proteins for LHX6 Gene

  • Protein details for LHX6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPM6-LHX6_HUMAN
    Recommended name:
    LIM/homeobox protein Lhx6
    Protein Accession:
    Q9UPM6
    Secondary Accessions:
    • A6PVQ1
    • A6PVQ2
    • A8K1B2
    • B7Z4D0
    • H0YN76
    • Q5T7S7
    • Q5T7S8
    • Q9NTK3
    • Q9UPM5

    Protein attributes for LHX6 Gene

    Size:
    363 amino acids
    Molecular mass:
    40045 Da
    Quaternary structure:
    • Interacts with LDB1 (via the LIM zinc-binding domains).
    SequenceCaution:
    • Sequence=AAI03937.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI03938.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAB66505.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for LHX6 Gene

neXtProt entry for LHX6 Gene

Post-translational modifications for LHX6 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LHX6 Gene

Domains & Families for LHX6 Gene

Gene Families for LHX6 Gene

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

Protein Domains for LHX6 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LHX6: view

No data available for UniProtKB/Swiss-Prot for LHX6 Gene

Function for LHX6 Gene

Molecular function for LHX6 Gene

UniProtKB/Swiss-Prot Function:
Probable transcription factor required for the expression of a subset of genes involved in interneurons migration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex (By similarity).

Phenotypes From GWAS Catalog for LHX6 Gene

Gene Ontology (GO) - Molecular Function for LHX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 DNA binding transcription factor activity NAS 10393337
GO:0005515 protein binding IPI 25416956
GO:0043565 sequence-specific DNA binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with LHX6: view
genes like me logo Genes that share phenotypes with LHX6: view

Animal Models for LHX6 Gene

MGI Knock Outs for LHX6:

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LHX6 Gene

Localization for LHX6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX6 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 LHX6 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (1)
  • Plasma membrane (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LHX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
genes like me logo Genes that share ontologies with LHX6: view

Pathways & Interactions for LHX6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LHX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0021799 cerebral cortex radially oriented cell migration ISS --
genes like me logo Genes that share ontologies with LHX6: view

No data available for Pathways by source and SIGNOR curated interactions for LHX6 Gene

Drugs & Compounds for LHX6 Gene

No Compound Related Data Available

Transcripts for LHX6 Gene

Unigene Clusters for LHX6 Gene

LIM homeobox 6:
Representative Sequences:

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LHX6 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b · 12c ^ 13 ^ 14a · 14b · 14c · 14d
SP1: - - - - - - -
SP2: - - - - - - - -
SP3: - - - -
SP4:
SP5:
SP6:
SP7: - - -
SP8: -
SP9: - -

Relevant External Links for LHX6 Gene

GeneLoc Exon Structure for
LHX6
ECgene alternative splicing isoforms for
LHX6

Expression for LHX6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LHX6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LHX6 Gene

This gene is overexpressed in Heart (64.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LHX6 Gene



Protein tissue co-expression partners for LHX6 Gene

NURSA nuclear receptor signaling pathways regulating expression of LHX6 Gene:

LHX6

SOURCE GeneReport for Unigene cluster for LHX6 Gene:

Hs.103137

Evidence on tissue expression from TISSUES for LHX6 Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with LHX6: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LHX6 Gene

Orthologs for LHX6 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LHX6 33 34
  • 99.83 (n)
cow
(Bos Taurus)
Mammalia LHX6 33 34
  • 93.88 (n)
dog
(Canis familiaris)
Mammalia LHX6 33 34
  • 93.54 (n)
oppossum
(Monodelphis domestica)
Mammalia LHX6 34
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lhx6 33
  • 92.96 (n)
mouse
(Mus musculus)
Mammalia Lhx6 33 16 34
  • 92.35 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LHX6 34
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves LHX6 33 34
  • 73.67 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx6 33
  • 71.89 (n)
zebrafish
(Danio rerio)
Actinopterygii lhx6 33 34
  • 72.84 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12957 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006537 33
  • 59.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta Awh 35 34
  • 48 (a)
worm
(Caenorhabditis elegans)
Secernentea lim-4 35 34
  • 44 (a)
Species where no ortholog for LHX6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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 LHX6 Gene

ENSEMBL:
Gene Tree for LHX6 (if available)
TreeFam:
Gene Tree for LHX6 (if available)

Paralogs for LHX6 Gene

Paralogs for LHX6 Gene

(14) SIMAP similar genes for LHX6 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with LHX6: view

Variants for LHX6 Gene

Sequence variations from dbSNP and Humsavar for LHX6 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000037055 -- 122,203,968(-) A/T 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1000068487 -- 122,219,726(-) G/A intron_variant
rs1000084821 -- 122,203,984(-) A/G 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1000110021 -- 122,210,075(-) C/T genic_downstream_transcript_variant, intron_variant
rs1000114675 -- 122,216,960(-) C/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LHX6 Gene

Variant ID Type Subtype PubMed ID
nsv831715 CNV gain 17160897
nsv1145261 CNV deletion 24896259

Variation tolerance for LHX6 Gene

Residual Variation Intolerance Score: 30.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.41; 27.71% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LHX6 Gene

Human Gene Mutation Database (HGMD)
LHX6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LHX6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX6 Gene

Disorders for LHX6 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LHX6 Gene - From: HGMD and DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search LHX6 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LHX6

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LHX6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LHX6 Gene

Publications for LHX6 Gene

  1. A brain region-specific gene product Lhx6.1 interacts with Ldb1 through tandem LIM-domains. (PMID: 10393337) Kimura N … Taga T (Journal of biochemistry 1999) 2 3 4 22 58
  2. Human variation in alcohol response is influenced by variation in neuronal signaling genes. (PMID: 20201926) Joslyn G … White RL (Alcoholism, clinical and experimental research 2010) 3 44 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4 58

Products for LHX6 Gene

Sources for LHX6 Gene

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