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Aliases for EMX2 Gene

Aliases for EMX2 Gene

  • Empty Spiracles Homeobox 2 2 3 5
  • Empty Spiracles-Like Protein 2 3 4
  • Empty Spiracles Homolog 2 3 4
  • Empty Spiracles Homolog 2 (Drosophila) 2
  • Homeobox Protein EMX2 3

External Ids for EMX2 Gene

Previous GeneCards Identifiers for EMX2 Gene

  • GC10P118220
  • GC10P118545
  • GC10P119433
  • GC10P118966
  • GC10P119291
  • GC10P112930

Summaries for EMX2 Gene

Entrez Gene Summary for EMX2 Gene

  • This gene encodes a homeobox-containing transcription factor that is the homolog to the 'empty spiracles' gene in Drosophila. Research on this gene in humans has focused on its expression in three tissues: dorsal telencephalon, olfactory neuroepithelium, and urogenetial system. It is expressed in the dorsal telencephalon during development in a low rostral-lateral to high caudal-medial gradient and is proposed to pattern the neocortex into defined functional areas. It is also expressed in embryonic and adult olfactory neuroepithelia where it complexes with eukaryotic translation initiation factor 4E (eIF4E) and possibly regulates mRNA transport or translation. In the developing urogenital system, it is expressed in epithelial tissues and is negatively regulated by HOXA10. Alternative splicing results in multiple transcript variants encoding distinct proteins.[provided by RefSeq, Sep 2009]

GeneCards Summary for EMX2 Gene

EMX2 (Empty Spiracles Homeobox 2) is a Protein Coding gene. Diseases associated with EMX2 include Schizencephaly and Acquired Schizencephaly. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is EMX1.

UniProtKB/Swiss-Prot for EMX2 Gene

  • Transcription factor, which in cooperation with EMX2, acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.

Gene Wiki entry for EMX2 Gene

Additional gene information for EMX2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EMX2 Gene

Genomics for EMX2 Gene

GeneHancer (GH) Regulatory Elements for EMX2 Gene

Promoters and enhancers for EMX2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J117541 Promoter/Enhancer 1.9 EPDnew FANTOM5 ENCODE dbSUPER 663.7 +1.4 1426 5.6 FEZF1 GLI4 ZNF2 YY1 ZNF121 GLIS2 ZNF213 KLF7 KLF13 SP3 EMX2 EMX2OS ENSG00000231104 VAX1
GH10J117551 Enhancer 0.9 FANTOM5 ENCODE dbSUPER 27.4 +10.4 10363 1.6 CTCF POLR2A SUZ12 EZH2 EMX2 RAB11FIP2 EMX2OS ENSG00000235198
GH10J117535 Enhancer 0.7 FANTOM5 dbSUPER 12.2 -7.1 -7054 0.2 SUZ12 NRF1 EZH2 EMX2 EMX2OS GC10P117520
GH10J117496 Enhancer 1.1 FANTOM5 ENCODE 1.9 -45.7 -45689 0.2 PKNOX1 FOXA2 RB1 RAD21 ETS1 TCF12 ZNF213 ZNF143 BCLAF1 CREM KCNK18 EMX2 SHTN1 GC10P117520 EMX2OS LOC105378502
GH10J117537 Enhancer 0.8 ENCODE dbSUPER 0.7 -4.7 -4679 0.2 CTCF L3MBTL2 SUZ12 BACH1 REST ZBTB8A RAD21 ZFHX2 ZNF143 ZBTB26 EMX2 EMX2OS GC10P117520
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EMX2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EMX2 gene promoter:
  • SRY
  • E2F
  • E2F-1
  • E2F-3a
  • E2F-4
  • E2F-5
  • C/EBPalpha
  • CHOP-10
  • AP-2alphaA
  • AP-2alpha isoform 4

Genomic Locations for EMX2 Gene

Genomic Locations for EMX2 Gene
7,103 bases
Plus strand
7,103 bases
Plus strand

Genomic View for EMX2 Gene

Genes around EMX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EMX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EMX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EMX2 Gene

Proteins for EMX2 Gene

  • Protein details for EMX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein EMX2
    Protein Accession:
    Secondary Accessions:
    • G3V305
    • Q96NN8
    • Q9BQF4

    Protein attributes for EMX2 Gene

    252 amino acids
    Molecular mass:
    28303 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for EMX2 Gene


neXtProt entry for EMX2 Gene

Post-translational modifications for EMX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for EMX2 Gene

No data available for DME Specific Peptides for EMX2 Gene

Domains & Families for EMX2 Gene

Gene Families for EMX2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for EMX2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the EMX homeobox family.
  • Belongs to the EMX homeobox family.
genes like me logo Genes that share domains with EMX2: view

Function for EMX2 Gene

Molecular function for EMX2 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor, which in cooperation with EMX2, acts to generate the boundary between the roof and archipallium in the developing brain. May function in combinations with OTX1/2 to specify cell fates in the developing central nervous system.
GENATLAS Biochemistry:
Drosophila empty spiracles (ems) homolog 2,homeo domain encoding gene involved in brain development

Phenotypes From GWAS Catalog for EMX2 Gene

Gene Ontology (GO) - Molecular Function for EMX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 15247416
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with EMX2: view
genes like me logo Genes that share phenotypes with EMX2: view

Human Phenotype Ontology for EMX2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for EMX2 Gene

MGI Knock Outs for EMX2:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for EMX2 Gene

Localization for EMX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EMX2 Gene

Subcellular locations from

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 EMX2 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for EMX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with EMX2: view

Pathways & Interactions for EMX2 Gene

No Data Available

Interacting Proteins for EMX2 Gene

Gene Ontology (GO) - Biological Process for EMX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IEA --
GO:0007420 brain development IEA --
GO:0009952 anterior/posterior pattern specification IEA --
genes like me logo Genes that share ontologies with EMX2: view

No data available for Pathways by source and SIGNOR curated interactions for EMX2 Gene

Drugs & Compounds for EMX2 Gene

No Compound Related Data Available

Transcripts for EMX2 Gene

mRNA/cDNA for EMX2 Gene

Unigene Clusters for EMX2 Gene

Empty spiracles homeobox 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for EMX2 Gene

ExUns: 1a · 1b ^ 2 ^ 3
SP2: -

Relevant External Links for EMX2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for EMX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EMX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for EMX2 Gene

This gene is overexpressed in Uterus (x8.8), Fallopian Tube (x5.7), Cervix - Endocervix (x5.4), and Kidney - Cortex (x4.6).

Protein differential expression in normal tissues from HIPED for EMX2 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for EMX2 Gene

Protein tissue co-expression partners for EMX2 Gene

NURSA nuclear receptor signaling pathways regulating expression of EMX2 Gene:


SOURCE GeneReport for Unigene cluster for EMX2 Gene:


mRNA Expression by UniProt/SwissProt for EMX2 Gene:

Tissue specificity: Cerebral cortex.

Evidence on tissue expression from TISSUES for EMX2 Gene

  • Nervous system(4.6)
  • Kidney(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for EMX2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with EMX2: view

Orthologs for EMX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for EMX2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia EMX2 34 33
  • 100 (n)
(Monodelphis domestica)
Mammalia EMX2 34
  • 99 (a)
(Ornithorhynchus anatinus)
Mammalia EMX2 34
  • 97 (a)
(Canis familiaris)
Mammalia EMX2 34 33
  • 96.43 (n)
(Bos Taurus)
Mammalia EMX2 34 33
  • 95.24 (n)
(Rattus norvegicus)
Mammalia Emx2 33
  • 94.44 (n)
(Mus musculus)
Mammalia Emx2 16 34 33
  • 94.18 (n)
(Gallus gallus)
Aves EMX2 34 33
  • 85.16 (n)
(Anolis carolinensis)
Reptilia EMX2 34
  • 87 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia emx2 33
  • 80.97 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.8697 33
(Danio rerio)
Actinopterygii emx2 34 33 33
  • 75.71 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7487 33
fruit fly
(Drosophila melanogaster)
Insecta E5 34
  • 21 (a)
ems 34
  • 21 (a)
(Caenorhabditis elegans)
Secernentea ceh-2 34
  • 33 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 38 (a)
Species where no ortholog for EMX2 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 EMX2 Gene

Gene Tree for EMX2 (if available)
Gene Tree for EMX2 (if available)
Evolutionary constrained regions (ECRs) for EMX2: view image

Paralogs for EMX2 Gene

Paralogs for EMX2 Gene

(2) SIMAP similar genes for EMX2 Gene using alignment to 2 proteins:

  • L8E7K8_HUMAN
genes like me logo Genes that share paralogs with EMX2: view

Variants for EMX2 Gene

Sequence variations from dbSNP and Humsavar for EMX2 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs756693906 conflicting-interpretations-of-pathogenicity, uncertain-significance, not specified 117,543,427(+) GCCGCCGCCGCCGCCGCCG/GCCGCCGCCGCCG/GCCGCCGCCGCCGCCG/GCCGCCGCCGCCGCCGCCGCCG/GCCGCCGCCGCCGCCGCCGCCGCCG coding_sequence_variant, inframe_deletion, inframe_insertion
rs373030604 likely-benign, not specified 117,543,372(+) A/T coding_sequence_variant, synonymous_variant
rs773003342 uncertain-significance, not specified 117,545,800(+) G/C coding_sequence_variant, intron_variant, missense_variant
rs1000103340 -- 117,547,008(+) GGGGGG/GGGGG intron_variant
rs1000183187 -- 117,541,880(+) C/G/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for EMX2 Gene

Variant ID Type Subtype PubMed ID
nsv1045212 CNV gain 25217958
nsv1069966 CNV deletion 25765185
nsv520464 CNV loss 19592680
nsv825579 CNV gain 20364138
nsv832003 CNV loss 17160897
nsv951857 CNV deletion 24416366

Variation tolerance for EMX2 Gene

Residual Variation Intolerance Score: 38.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.53; 11.46% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EMX2 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EMX2 Gene

Disorders for EMX2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for EMX2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
  • familial schizencephaly
acquired schizencephaly
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
periventricular nodular heterotopia
  • periventricular heterotopia
- elite association - COSMIC cancer census association via MalaCards
Search EMX2 in MalaCards View complete list of genes associated with diseases


  • Schizencephaly (SCHZC) [MIM:269160]: Extremely rare human congenital disorder characterized by a full-thickness cleft within the cerebral hemispheres. These clefts are lined with gray matter and most commonly involve the parasylvian regions. Large portions of the cerebral hemispheres may be absent and replaced by cerebro-spinal fluid. {ECO:0000269 PubMed:8528262}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for EMX2 Gene


Additional Disease Information for EMX2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with EMX2: view

Publications for EMX2 Gene

  1. Comprehensive EMX2 genotyping of a large schizencephaly case series. (PMID: 17506092) Tietjen I … Walsh CA (American journal of medical genetics. Part A 2007) 3 22 44 58
  2. Variants in EMX2 and PTEN do not contribute to risk of endometriosis. (PMID: 17563403) Treloar SA … Montgomery GW (Molecular human reproduction 2007) 3 22 44 58
  3. Chromosome locations of human EMX and OTX genes. (PMID: 7959790) Kastury K … Boncinelli E (Genomics 1994) 2 3 22 58
  4. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 44 58
  5. Pathway-based approaches to imaging genetics association studies: Wnt signaling, GSK3beta substrates and major depression. (PMID: 20219685) Inkster B … Matthews PM (NeuroImage 2010) 3 44 58

Products for EMX2 Gene

Sources for EMX2 Gene

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