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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. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding 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

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

Genomics for LHX6 Gene

Regulatory Elements for LHX6 Gene

Enhancers for LHX6 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
GH09G122263 1.4 ENCODE dbSUPER 11.3 -35.1 -35137 3.4 HDGF PKNOX1 FOXA2 CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 LHX6 RBM18 MRRF
GH09G122178 1.1 ENCODE 11.8 +49.9 49902 2.2 HNRNPUL1 HDGF FOXA2 ARNT CREB3L1 ARID4B SIN3A DMAP1 FEZF1 ZNF2 LHX6 TTLL11 GC09P122163
GH09G122180 0.8 ENCODE 11.8 +48.7 48730 0.2 GTF2F1 TAL1 JUN MAX FOSL1 TCF12 FOXK2 FOSL2 NFE2 FOS LHX6 TTLL11 GC09P122163
GH09G122202 0.8 ENCODE 11.7 +27.3 27310 0.2 ARNT CREB3L1 GTF2E2 DDX20 TAL1 ZNF175 RBBP5 ZNF644 TCF12 ZNF766 LHX6 MRRF RBM18 TTLL11 GC09P122163
GH09G122203 0.8 ENCODE 11.6 +25.3 25299 1.0 LEF1 DDX20 ZNF175 BACH1 CEBPG ZNF507 IRF9 SCRT2 ZNF584 TRIM24 LHX6 TTLL11-IT1 GC09P122163
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LHX6 on UCSC Golden Path with GeneCards custom track

Genomic Location for LHX6 Gene

Chromosome:
9
Start:
122,185,652 bp from pter
End:
122,229,626 bp from pter
Size:
43,975 bases
Orientation:
Minus strand

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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LHX6 Gene

Domains & Families for LHX6 Gene

Gene Families for LHX6 Gene

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).

Gene Ontology (GO) - Molecular Function for LHX6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 transcription factor activity, sequence-specific DNA binding NAS 10393337
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 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

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

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

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 34 35
  • 99.83 (n)
cow
(Bos Taurus)
Mammalia LHX6 34 35
  • 93.88 (n)
dog
(Canis familiaris)
Mammalia LHX6 34 35
  • 93.54 (n)
oppossum
(Monodelphis domestica)
Mammalia LHX6 35
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lhx6 34
  • 92.96 (n)
mouse
(Mus musculus)
Mammalia Lhx6 34 16 35
  • 92.35 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LHX6 35
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves LHX6 34 35
  • 73.67 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx6 34
  • 71.89 (n)
zebrafish
(Danio rerio)
Actinopterygii lhx6 34 35
  • 72.84 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12957 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006537 34
  • 59.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta Awh 36 35
  • 48 (a)
worm
(Caenorhabditis elegans)
Secernentea lim-4 36 35
  • 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 Sequence Context AA Info Type
rs1000037055 -- 122,203,968(+) GCTGG(A/T)TAATT intron-variant, utr-variant-3-prime
rs1000068487 -- 122,219,726(+) AGCCG(A/G)CGAGT intron-variant
rs1000084821 -- 122,203,984(+) GGGGT(A/G)GGGTC intron-variant, utr-variant-3-prime
rs1000110021 -- 122,210,075(+) TTCAC(C/T)GTGTT intron-variant
rs1000114675 -- 122,216,960(+) TATAC(C/G)GGGAG intron-variant

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

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

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)

Relevant External Links 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

Relevant External Links for LHX6

Genetic Association Database (GAD)
LHX6
Human Genome Epidemiology (HuGE) Navigator
LHX6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LHX6

No disorders were found for LHX6 Gene.

No data available for MalaCards , 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. (J. Biochem. 1999) 2 3 4 22 64
  2. Human variation in alcohol response is influenced by variation in neuronal signaling genes. (PMID: 20201926) Joslyn G. … White R.L. (Alcohol. Clin. Exp. Res. 2010) 3 46 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray S.J. … Dunham I. (Nature 2004) 3 4 64

Products for LHX6 Gene

Sources for LHX6 Gene

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