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Aliases for LHX2 Gene

Aliases for LHX2 Gene

  • LIM Homeobox 2 2 3 5
  • LIM Homeobox Protein 2 3 4
  • Homeobox Protein LH-2 3 4
  • LH2 3 4
  • LIM/Homeobox Protein Lhx2 3
  • LIM HOX Gene 2 3
  • HLhx2 3

External Ids for LHX2 Gene

Previous GeneCards Identifiers for LHX2 Gene

  • GC09P117888
  • GC09P118420
  • GC09P120227
  • GC09P122149
  • GC09P123853
  • GC09P125813
  • GC09P126773
  • GC09P096387
  • GC09P126763

Summaries for LHX2 Gene

Entrez Gene Summary for LHX2 Gene

  • This gene encodes a protein belonging to a large protein family, members of which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein may function as a transcriptional regulator. The protein can recapitulate or rescue phenotypes in Drosophila caused by a related protein, suggesting conservation of function during evolution. [provided by RefSeq, Jul 2008]

GeneCards Summary for LHX2 Gene

LHX2 (LIM Homeobox 2) is a Protein Coding gene. Diseases associated with LHX2 include Schizencephaly. Among its related pathways are Neural Crest Differentiation. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and transcription factor activity, RNA polymerase II transcription factor binding. An important paralog of this gene is LHX9.

UniProtKB/Swiss-Prot for LHX2 Gene

  • Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types (By similarity).

Gene Wiki entry for LHX2 Gene

Additional gene information for LHX2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LHX2 Gene

Genomics for LHX2 Gene

GeneHancer (GH) Regulatory Elements for LHX2 Gene

Promoters and enhancers for LHX2 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
GH09J124011 Promoter/Enhancer 1.4 EPDnew ENCODE 650.4 +9.9 9863 1.3 PKNOX1 RB1 INSM2 NFXL1 BRCA1 ZNF335 EGR1 ZNF366 ZNF143 RCOR1 ENSG00000231227 LHX2 GOLGA1 LOC105376268
GH09J123998 Promoter/Enhancer 1.3 EPDnew Ensembl 650.7 -2.0 -2015 1.7 HDGF SMAD1 SUZ12 ZMYM3 BMI1 ZNF2 ZNF335 GLIS2 ZNF366 PATZ1 LHX2 LOC105376267 LOC105376268
GH09J124390 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 9.7 +391.7 391658 6 HDGF PKNOX1 FOXA2 ARNT SIN3A GATA2 FOS RUNX3 REST TSHZ1 NEK6 PSMB7 NR5A1 ENSG00000231149 LHX2 ENSG00000231227 LOC100505588 DENND1A GC09P124378
GH09J124054 Enhancer 1.1 Ensembl ENCODE 10.9 +53.2 53226 0.6 ARNT FEZF1 IRF4 NCOA2 TCF12 GATA2 ZFP91 FOS ATF7 RUNX3 GOLGA1 LOC105376268 ENSG00000231227 LOC100505588 LHX2 GC09M124203
GH09J124077 Enhancer 1 Ensembl ENCODE 11.3 +77.0 76997 2.8 ELF3 FOXA2 SIN3A RCOR1 ATF7 FOS RXRA CEBPB PPARG MTA1 LOC100505588 ENSG00000231227 LHX2 LOC105376268 GC09M124203
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LHX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LHX2 gene promoter:
  • E2F-1
  • E2F
  • Max
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • S8
  • Pbx1a
  • C/EBPalpha

Genomic Locations for LHX2 Gene

Genomic Locations for LHX2 Gene
chr9:124,001,670-124,033,301
(GRCh38/hg38)
Size:
31,632 bases
Orientation:
Plus strand
chr9:126,763,949-126,795,580
(GRCh37/hg19)
Size:
31,632 bases
Orientation:
Plus strand

Genomic View for LHX2 Gene

Genes around LHX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LHX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LHX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LHX2 Gene

Proteins for LHX2 Gene

  • Protein details for LHX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P50458-LHX2_HUMAN
    Recommended name:
    LIM/homeobox protein Lhx2
    Protein Accession:
    P50458
    Secondary Accessions:
    • O95860
    • Q52M57
    • Q8N1Z3

    Protein attributes for LHX2 Gene

    Size:
    406 amino acids
    Molecular mass:
    44373 Da
    Quaternary structure:
    • Interacts (via LIM domains) with CITED2. Interacts with POU4F2.
    SequenceCaution:
    • Sequence=BAC04371.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for LHX2 Gene

Post-translational modifications for LHX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LHX2 Gene

No data available for DME Specific Peptides for LHX2 Gene

Domains & Families for LHX2 Gene

Gene Families for LHX2 Gene

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

Protein Domains for LHX2 Gene

Suggested Antigen Peptide Sequences for LHX2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P50458

UniProtKB/Swiss-Prot:

LHX2_HUMAN :
  • LIM domains are necessary for transcription activation.
Domain:
  • LIM domains are necessary for transcription activation.
genes like me logo Genes that share domains with LHX2: view

Function for LHX2 Gene

Molecular function for LHX2 Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types (By similarity).
GENATLAS Biochemistry:
putative transcription factor with two LIM and one Hox domain,expressed in chronic myelogenous leukemia,may be inactivated by the BCR-ABL translocation

Phenotypes From GWAS Catalog for LHX2 Gene

Gene Ontology (GO) - Molecular Function for LHX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001076 transcription factor activity, RNA polymerase II transcription factor binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with LHX2: view
genes like me logo Genes that share phenotypes with LHX2: view

Animal Models for LHX2 Gene

MGI Knock Outs for LHX2:
  • Lhx2 Lhx2<tm1Dra>
  • Lhx2 Lhx2<tm1.1Monu>
  • Lhx2 Lhx2<tm1.2Ddmo>

Animal Model Products

miRNA for LHX2 Gene

miRTarBase miRNAs that target LHX2
Targeted motifs for LHX2 Gene
HOMER Transcription Factor Regulatory Elements motif LHX2
  • Consensus sequence: TAATTAGN Submotif: canonical Cell Type: HFSC GEO ID: GSE48068

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for LHX2 Gene

Localization for LHX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LHX2 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 LHX2 gene
Compartment Confidence
nucleus 5
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LHX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with LHX2: view

Pathways & Interactions for LHX2 Gene

SuperPathway Contained pathways
1 Neural Crest Differentiation
genes like me logo Genes that share pathways with LHX2: view

Pathways by source for LHX2 Gene

1 BioSystems pathway for LHX2 Gene

Gene Ontology (GO) - Biological Process for LHX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001843 neural tube closure IEA --
GO:0001942 hair follicle development IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
genes like me logo Genes that share ontologies with LHX2: view

No data available for SIGNOR curated interactions for LHX2 Gene

Drugs & Compounds for LHX2 Gene

No Compound Related Data Available

Transcripts for LHX2 Gene

mRNA/cDNA for LHX2 Gene

Unigene Clusters for LHX2 Gene

LIM homeobox 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LHX2 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7
SP1: - -
SP2: -
SP3: -
SP4:

Relevant External Links for LHX2 Gene

GeneLoc Exon Structure for
LHX2
ECgene alternative splicing isoforms for
LHX2

Expression for LHX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LHX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LHX2 Gene

This gene is overexpressed in Brain - Amygdala (x7.4), Brain - Cortex (x7.0), Brain - Anterior cingulate cortex (BA24) (x6.6), Brain - Frontal Cortex (BA9) (x6.5), Brain - Hippocampus (x6.3), Brain - Caudate (basal ganglia) (x4.9), Brain - Putamen (basal ganglia) (x4.8), and Brain - Nucleus accumbens (basal ganglia) (x4.4).

NURSA nuclear receptor signaling pathways regulating expression of LHX2 Gene:

LHX2

SOURCE GeneReport for Unigene cluster for LHX2 Gene:

Hs.696425

Evidence on tissue expression from TISSUES for LHX2 Gene

  • Nervous system(4.9)
  • Eye(3.4)
  • Skin(3.1)
genes like me logo Genes that share expression patterns with LHX2: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LHX2 Gene

Orthologs for LHX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for LHX2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LHX2 34 33
  • 99.82 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LHX2 34 33
  • 95.81 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LHX2 34 33
  • 93.99 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lhx2 16 34 33
  • 91.79 (n)
rat
(Rattus norvegicus)
Mammalia Lhx2 33
  • 91.3 (n)
oppossum
(Monodelphis domestica)
Mammalia LHX2 34
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LHX2 34
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves LHX2 34 33
  • 77.78 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LHX2 34
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lhx2 33
  • 74.62 (n)
zebrafish
(Danio rerio)
Actinopterygii lhx2b 34 33
  • 74.6 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta ap 34 35 33
  • 57.79 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008980 33
  • 57.58 (n)
worm
(Caenorhabditis elegans)
Secernentea ttx-3 34
  • 33 (a)
OneToMany
Species where no ortholog for LHX2 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)
  • 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 LHX2 Gene

ENSEMBL:
Gene Tree for LHX2 (if available)
TreeFam:
Gene Tree for LHX2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LHX2: view image

Paralogs for LHX2 Gene

Paralogs for LHX2 Gene

(19) SIMAP similar genes for LHX2 Gene using alignment to 4 proteins:

  • LHX2_HUMAN
  • H0YM35_HUMAN
  • H7C0H1_HUMAN
  • U3KQT5_HUMAN
genes like me logo Genes that share paralogs with LHX2: view

Variants for LHX2 Gene

Sequence variations from dbSNP and Humsavar for LHX2 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000136269 -- 124,030,623(+) TTTTCTTTTTTTT/TTTT intron_variant
rs1000414233 -- 124,018,974(+) A/G intron_variant
rs1000507258 -- 124,026,197(+) G/A intron_variant
rs1000570000 -- 124,009,609(+) G/C
rs1000617319 -- 124,030,830(+) A/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LHX2 Gene

Variant ID Type Subtype PubMed ID
nsv1119607 CNV deletion 24896259
nsv47 OTHER inversion 15895083
nsv615287 CNV loss 21841781
nsv7435 OTHER inversion 18451855
nsv825072 CNV gain 20364138
nsv825073 CNV gain 20364138

Variation tolerance for LHX2 Gene

Residual Variation Intolerance Score: 24.7% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LHX2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LHX2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LHX2 Gene

Disorders for LHX2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LHX2 Gene - From: GeneCards

Disorder Aliases PubMed IDs
schizencephaly
  • familial schizencephaly
- elite association - COSMIC cancer census association via MalaCards
Search LHX2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LHX2

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 LHX2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LHX2 Gene

Publications for LHX2 Gene

  1. Identification of a human LIM-Hox gene, hLH-2, aberrantly expressed in chronic myelogenous leukaemia and located on 9q33-34.1. (PMID: 8649822) Wu HK … Minden MD (Oncogene 1996) 2 3 4 22 58
  2. Conservation of the expression and function of apterous orthologs in Drosophila and mammals. (PMID: 10051612) Rincón-Limas DE … Botas J (Proceedings of the National Academy of Sciences of the United States of America 1999) 2 3 4 58
  3. Mutations in the LHX2 gene are not a frequent cause of micro/anophthalmia. (PMID: 21203406) Desmaison A … Chassaing N (Molecular vision 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. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for LHX2 Gene

Sources for LHX2 Gene

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