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LHX6 Gene(Protein Coding)

LIM Homeobox 6

GCID:
GC09M122202
GIFtS:
54
Genes Participants
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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 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 may function as a transcriptional regulator and may be involved in the control of differentiation and development of neural and lymphoid cells. Two alternatively spliced transcript variants encoding distinct isoforms have been described for this gene. Alternatively spliced transcript variants have been identified, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for LHX6 Gene

LHX6 (LIM Homeobox 6) is a Protein Coding gene. Diseases associated with LHX6 include Image Syndrome. 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 LHX4.

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 Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX6 Gene

Genomics for LHX6 Gene

Products:

  1. Regulatory Element

Regulatory Elements for LHX6 Gene

Enhancers for LHX6 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around LHX6 on UCSC Golden Path with GeneCards custom track

Promoters for LHX6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around LHX6 on UCSC Golden Path with GeneCards custom track

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

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 Structure • Gene Density

RefSeq DNA sequence for LHX6 Gene

Proteins for LHX6 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for LHX6 Gene

Proteomics data for LHX6 Gene at MOPED

Protein Expression for LHX6 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for LHX6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LHX6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LHX6 Gene

Domains & Families for LHX6 Gene

Gene Families for LHX6 Gene

HGNC:

Protein Domains for LHX6 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for LHX6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UPM6

UniProtKB/Swiss-Prot:

LHX6_HUMAN :
  • Contains 1 homeobox DNA-binding domain.
Domain:
  • Contains 1 homeobox DNA-binding domain.
  • Contains 2 LIM zinc-binding domains.
genes like me logo Genes that share domains with LHX6: view

Function for LHX6 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

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:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with LHX6: view

Phenotypes for LHX6 Gene

MGI mutant phenotypes for LHX6:
inferred from 4 alleles
GenomeRNAi human phenotypes for LHX6:
genes like me logo Genes that share phenotypes with LHX6: view

Animal Models for LHX6 Gene

MGI Knock Outs for LHX6:

miRNA for LHX6 Gene

miRTarBase miRNAs that target LHX6

Flow Cytometry 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

Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LHX6 Gene COMPARTMENTS Subcellular localization image for LHX6 gene
Compartment Confidence
nucleus 5

No data available for Gene Ontology (GO) - Cellular Components for LHX6 Gene

Pathways & Interactions for LHX6 Gene

SuperPathways for LHX6 Gene

PathCards logoMore details on SuperPathways for LHX6
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:0021800 cerebral cortex tangential migration ISS --
GO:0048469 cell maturation 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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for LHX6 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for LHX6 Gene

(9) REFSEQ mRNAs :
(11) Additional mRNA sequences :
(50) Selected AceView cDNA sequences:
(12) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LHX6 Gene

LIM homeobox 6:
Representative Sequences:

Flow Cytometry 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

Products:

  1. Primer

mRNA expression in normal human tissues for LHX6 Gene

mRNA expression in normal human tissues for LHX6 Gene
mRNA expression by BioGPS for LHX6 GenemRNA expression by GTEx 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



SOURCE GeneReport for Unigene cluster for LHX6 Gene Hs.103137

genes like me logo Genes that share expression patterns with LHX6: view

Protein tissue co-expression partners for LHX6 Gene

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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
cow
(Bos Taurus)
 Mammalia LHX6 35
  • 93.88 (n)
  • 98.98 (a)
LHX6 36
  • 99 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia LHX6 35
  • 93.54 (n)
  • 98.21 (a)
LHX6 36
  • 98 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Lhx6 35
  • 92.35 (n)
  • 97.96 (a)
Lhx6 16
Lhx6 36
  • 98 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia LHX6 35
  • 99.83 (n)
  • 99.74 (a)
LHX6 36
  • 100 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Lhx6 35
  • 92.96 (n)
  • 98.2 (a)
oppossum
(Monodelphis domestica)
 Mammalia LHX6 36
  • 93 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia LHX6 36
  • 75 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves LHX6 35
  • 73.67 (n)
  • 77.36 (a)
LHX6 36
  • 74 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia lhx6 35
  • 71.89 (n)
  • 82.52 (a)
zebrafish
(Danio rerio)
 Actinopterygii lhx6 35
  • 72.84 (n)
  • 79.37 (a)
lhx6 36
  • 75 (a)
 OneToOne
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.12957 35
fruit fly
(Drosophila melanogaster)
 Insecta Awh 37
  • 48 (a)
Awh 36
  • 41 (a)
 OneToMany
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP006537 35
  • 59.67 (n)
  • 52.5 (a)
worm
(Caenorhabditis elegans)
 Secernentea lim-4 37
  • 44 (a)
lim-4 36
  • 32 (a)
 OneToMany
Species with no ortholog for LHX6:
  • 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
rs913934 -- 122,221,505(-) CTTCA(G/T)GCAAG intron-variant, utr-variant-5-prime
rs932922 -- 122,218,269(-) GGTGA(C/G)TCATC intron-variant
rs932923 -- 122,218,254(-) TTAAA(A/G)AACAC intron-variant
rs989798 -- 122,209,763(-) ATCCT(A/G)TGTGC intron-variant
rs1004308 -- 122,214,995(+) TTAAC(C/T)GGCGT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv831715 CNV Gain 17160897
dgv8280n71 CNV Loss 21882294

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

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: DISEASES

Disorder Aliases PubMed IDs
image syndrome
  • intrauterine growth restriction, metaphyseal dysplasia, adrenal hypoplasia congenita, genital abnormalities
- elite association - COSMIC cancer census association via MalaCards
Search LHX6 in MalaCards View complete list of genes associated with diseases

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
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. (J. Biochem. 1999) 2 3 4 23 67
  2. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  3. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3
  4. The LIM homeodomain transcription factor LHX6: a transcriptional repressor that interacts with pituitary homeobox 2 (PITX2) to regulate odontogenesis. (PMID: 23229549) Zhang Z. … Amendt B.A. (J. Biol. Chem. 2013) 3
  5. LHX6 acts as a novel potential tumour suppressor with epigenetic inactivation in lung cancer. (PMID: 24157876) Liu W.B. … Liu J.Y. (Cell Death Dis 2013) 3

Products for LHX6 Gene

Sources for LHX6 Gene

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