Free for academic non-profit institutions. Other users need a Commercial license

Aliases for EMX1 Gene

Aliases for EMX1 Gene

  • Empty Spiracles Homeobox 1 2 3 5
  • Empty Spiracles-Like Protein 1 3 4
  • Empty Spiracles Homolog 1 3 4
  • Empty Spiracles Homolog 1 (Drosophila) 2
  • Homeobox Protein EMX1 3

External Ids for EMX1 Gene

Previous GeneCards Identifiers for EMX1 Gene

  • GC02P073154
  • GC02P073356
  • GC02P073119
  • GC02P073056
  • GC02P072880
  • GC02P073144
  • GC02P073148

Summaries for EMX1 Gene

GeneCards Summary for EMX1 Gene

EMX1 (Empty Spiracles Homeobox 1) is a Protein Coding gene. Diseases associated with EMX1 include Kallmann Syndrome. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is EMX2.

UniProtKB/Swiss-Prot for EMX1 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 EMX1 Gene

Additional gene information for EMX1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EMX1 Gene

Genomics for EMX1 Gene

GeneHancer (GH) Regulatory Elements for EMX1 Gene

Promoters and enhancers for EMX1 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
GH02J072915 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE 650.4 +6.3 6255 4.2 PKNOX1 ARID4B ZNF48 GLIS2 ZNF207 RUNX3 SP3 SP5 NFYC REST EMX1 SPR SFXN5 ENSG00000278060
GH02J073109 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.3 +200.7 200747 5.2 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 FOS SP3 SP5 NFYC RAB11FIP5 ENSG00000272702 ENSG00000273245 DUSP11 SFXN5 ALMS1 EMX1 SPR SMYD5 GC02M073122
GH02J073175 Enhancer 1.6 FANTOM5 Ensembl ENCODE 10.5 +265.5 265506 3.2 HDGF ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B SLC30A9 ZNF213 E2F8 ALMS1 ENSG00000273245 SMYD5 DUSP11 SFXN5 PRADC1 NOTO SPR EMX1 CCT7
GH02J073062 Enhancer 1.1 Ensembl ENCODE 10.1 +152.7 152733 3.3 HDAC1 PKNOX1 ZNF335 ZNF121 GLIS2 ARID2 ZNF366 FOS ATF7 SMARCC1 EMX1 RAB11FIP5 LOC105374800 SFXN5 PIR43769 GC02M073124
GH02J073020 Enhancer 0.9 ENCODE 10.6 +110.0 110049 1.7 CLOCK FOXA2 MLX ARID4B ZNF48 SLC30A9 ATF7 FOS NFKBIZ RXRA RAB11FIP5 SFXN5 EMX1 SPR GC02P072995 LOC105374800
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EMX1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EMX1 gene promoter:
  • STAT3
  • Pax-4a
  • NF-kappaB1
  • NF-kappaB
  • Elk-1
  • Nkx6-1
  • S8
  • Lhx3a
  • POU3F1
  • LHX3b

Genomic Locations for EMX1 Gene

Genomic Locations for EMX1 Gene
24,924 bases
Plus strand
18,632 bases
Plus strand

Genomic View for EMX1 Gene

Genes around EMX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EMX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EMX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EMX1 Gene

Proteins for EMX1 Gene

  • Protein details for EMX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein EMX1
    Protein Accession:
    Secondary Accessions:
    • Q0D2P0
    • Q53T30
    • Q86XB0

    Protein attributes for EMX1 Gene

    257 amino acids
    Molecular mass:
    28039 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH45762.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for EMX1 Gene


neXtProt entry for EMX1 Gene

Post-translational modifications for EMX1 Gene

No Post-translational modifications

Other Protein References for EMX1 Gene

No data available for DME Specific Peptides for EMX1 Gene

Domains & Families for EMX1 Gene

Gene Families for EMX1 Gene

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

Suggested Antigen Peptide Sequences for EMX1 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 EMX1: view

Function for EMX1 Gene

Molecular function for EMX1 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 1,Dres93,mouse homolog expressed in optic cup in early embryo (E9,5),homeo domain encoding gene involved in brain development

Phenotypes From GWAS Catalog for EMX1 Gene

Gene Ontology (GO) - Molecular Function for EMX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM 19274049
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 20887964
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with EMX1: view
genes like me logo Genes that share phenotypes with EMX1: view

Animal Models for EMX1 Gene

MGI Knock Outs for EMX1:
  • Emx1 Emx1<tm1.1(KOMP)Vlcg>
  • Emx1 Emx1<tm1Sia>
  • Emx1 Emx1<tm1Jlr>

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for EMX1 Gene

Localization for EMX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EMX1 Gene

Nucleus. Cytoplasm. Note=Might be shuttling between the nucleus and the cytoplasm.

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 EMX1 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for EMX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 20887964
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with EMX1: view

Pathways & Interactions for EMX1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for EMX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
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 --
genes like me logo Genes that share ontologies with EMX1: view

No data available for Pathways by source and SIGNOR curated interactions for EMX1 Gene

Drugs & Compounds for EMX1 Gene

No Compound Related Data Available

Transcripts for EMX1 Gene

mRNA/cDNA for EMX1 Gene

Unigene Clusters for EMX1 Gene

Empty spiracles homeobox 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for EMX1 Gene

No ASD Table

Relevant External Links for EMX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for EMX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EMX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for EMX1 Gene

This gene is overexpressed in Kidney - Cortex (x18.2), Brain - Frontal Cortex (BA9) (x8.4), Brain - Cortex (x8.3), and Brain - Anterior cingulate cortex (BA24) (x5.5).

NURSA nuclear receptor signaling pathways regulating expression of EMX1 Gene:


SOURCE GeneReport for Unigene cluster for EMX1 Gene:


mRNA Expression by UniProt/SwissProt for EMX1 Gene:

Tissue specificity: Cerebral cortex.

Evidence on tissue expression from TISSUES for EMX1 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with EMX1: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for EMX1 Gene

Orthologs for EMX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for EMX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia EMX1 34
  • 100 (a)
LOC483117 33
  • 95.97 (n)
(Pan troglodytes)
Mammalia EMX1 34 33
  • 99.66 (n)
(Bos Taurus)
Mammalia EMX1 34 33
  • 94.1 (n)
(Mus musculus)
Mammalia Emx1 16 34 33
  • 91.18 (n)
(Rattus norvegicus)
Mammalia Emx1 33
  • 89.31 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 56 (a)
(Gallus gallus)
Aves EMX1 34 33
  • 80.43 (n)
(Anolis carolinensis)
Reptilia EMX1 34
  • 94 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia emx1.2 33
  • 76.25 (n)
Str.5241 33
(Danio rerio)
Actinopterygii emx1 34 33
  • 71.01 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta ems 34
  • 23 (a)
E5 34
  • 22 (a)
(Caenorhabditis elegans)
Secernentea ceh-2 34
  • 37 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 37 (a)
Species where no ortholog for EMX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 EMX1 Gene

Gene Tree for EMX1 (if available)
Gene Tree for EMX1 (if available)
Evolutionary constrained regions (ECRs) for EMX1: view image

Paralogs for EMX1 Gene

Paralogs for EMX1 Gene

(4) SIMAP similar genes for EMX1 Gene using alignment to 3 proteins:

  • F8W1B5_HUMAN
genes like me logo Genes that share paralogs with EMX1: view

Variants for EMX1 Gene

Sequence variations from dbSNP and Humsavar for EMX1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000261240 -- 72,935,722(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000459269 -- 72,917,019(+) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1000488950 -- 72,917,279(+) C/G/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000585357 -- 72,936,362(+) C/G 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000605674 -- 72,922,795(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for EMX1 Gene

Variant ID Type Subtype PubMed ID
esv2677197 CNV deletion 23128226
nsv1143941 CNV deletion 24896259

Variation tolerance for EMX1 Gene

Gene Damage Index Score: 0.20; 4.53% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EMX1 Gene

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 EMX1 Gene

Disorders for EMX1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for EMX1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
- elite association - COSMIC cancer census association via MalaCards
Search EMX1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for EMX1

genes like me logo Genes that share disorders with EMX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EMX1 Gene

Publications for EMX1 Gene

  1. Chromosome locations of human EMX and OTX genes. (PMID: 7959790) Kastury K … Boncinelli E (Genomics 1994) 2 3 22 58
  2. WDR11, a WD protein that interacts with transcription factor EMX1, is mutated in idiopathic hypogonadotropic hypogonadism and Kallmann syndrome. (PMID: 20887964) Kim HG … Layman LC (American journal of human genetics 2010) 3 4 58
  3. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 58
  4. 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
  5. Two vertebrate homeobox genes related to the Drosophila empty spiracles gene are expressed in the embryonic cerebral cortex. (PMID: 1352754) Simeone A … Boncinelli E (The EMBO journal 1992) 3 4 58

Products for EMX1 Gene

Sources for EMX1 Gene

Loading form....