EMX1 Gene (Protein Coding)

Empty Spiracles Homeobox 1

GC02P072916
GIFtS:
35

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

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 and Epileptic Encephalopathy, Early Infantile, 6. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is EMX2.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for EMX1 Gene

Genomics for EMX1 Gene

GeneHancer (GH) Regulatory Elements for EMX1 Gene

Promoters and enhancers for EMX1 Gene
- 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:
  • Elk-1
  • Lhx3a
  • LHX3b
  • NF-kappaB
  • NF-kappaB1
  • Nkx6-1
  • Pax-4a
  • POU3F1
  • S8
  • STAT3

Genomic Locations for EMX1 Gene

Genomic Locations for EMX1 Gene
chr2:72,911,148-72,936,071
(GRCh38/hg38)
Size:
24,924 bases
Orientation:
Plus strand
chr2:73,143,389-73,162,020
(GRCh37/hg19)
Size:
18,632 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for EMX1 Gene

Proteins for EMX1 Gene

Products:

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

    Protein Symbol:
    Q04741-EMX1_HUMAN
    Recommended name:
    Homeobox protein EMX1
    Protein Accession:
    Q04741
    Secondary Accessions:
    • Q0D2P0
    • Q53T30
    • Q86XB0

    Protein attributes for EMX1 Gene

    Size:
    257 amino acids
    Molecular mass:
    28039 Da
    Quaternary structure:
    • Interacts with WRD11 (via the N-terminal and the central portion of the protein); the interaction associates EMX1 with GLI3.
    SequenceCaution:
    • Sequence=AAH45762.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for EMX1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EMX1 Gene

Post-translational modifications for EMX1 Gene

No Post-translational modifications

Other Protein References for EMX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for EMX1 Gene

Domains & Families for EMX1 Gene

Gene Families for EMX1 Gene

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

Protein Domains for EMX1 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for EMX1 Gene

GenScript: Design optimal peptide antigens:
  • Empty spiracles-like protein 1 (EMX1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q04741

UniProtKB/Swiss-Prot:

EMX1_HUMAN :
  • Belongs to the EMX homeobox family.
Family:
  • Belongs to the EMX homeobox family.
genes like me logo Genes that share domains with EMX1: view

Function for EMX1 Gene

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

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:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001162 RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding IBA 21873635
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IBA 21873635
GO:0003677 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<tm1Jlr>
  • Emx1 Emx1<tm1Sia>

Animal Model Products

CRISPR 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

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 EMX1 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EMX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 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

PathCards logo

SuperPathways 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:0007417 central nervous system development IBA 21873635
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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for EMX1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for EMX1 Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(28) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

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
EMX1
ECgene alternative splicing isoforms for
EMX1

Expression for EMX1 Gene

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  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for EMX1 Gene
mRNA expression by GTEx for EMX1 GenemRNA expression by BioGPS 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:

EMX1

SOURCE GeneReport for Unigene cluster for EMX1 Gene:

Hs.516090

mRNA Expression by UniProt/SwissProt for EMX1 Gene:

Q04741-EMX1_HUMAN
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
dog
(Canis familiaris)
 Mammalia EMX1 33
  • 100 (a)
 OneToOne
LOC483117 32
  • 95.97 (n)
chimpanzee
(Pan troglodytes)
 Mammalia EMX1 33 32
  • 99.66 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia EMX1 33 32
  • 94.1 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Emx1 17 33 32
  • 91.18 (n)
rat
(Rattus norvegicus)
 Mammalia Emx1 32
  • 89.31 (n)
oppossum
(Monodelphis domestica)
 Mammalia -- 33
  • 56 (a)
 ManyToMany
chicken
(Gallus gallus)
 Aves EMX1 33 32
  • 80.43 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia EMX1 33
  • 94 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia emx1.2 32
  • 76.25 (n)
Str.5241 32
zebrafish
(Danio rerio)
 Actinopterygii emx1 33 32
  • 71.01 (n)
 OneToOne
-- 32
fruit fly
(Drosophila melanogaster)
 Insecta ems 33
  • 23 (a)
 ManyToMany
E5 33
  • 22 (a)
 ManyToMany
worm
(Caenorhabditis elegans)
 Secernentea ceh-2 33
  • 37 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 33
  • 37 (a)
 OneToMany
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

ENSEMBL:
Gene Tree for EMX1 (if available)
TreeFam:
Gene Tree for EMX1 (if available)
Aminode:
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:

  • EMX1_HUMAN
  • F8VXD0_HUMAN
  • F8W1B5_HUMAN
genes like me logo Genes that share paralogs with EMX1: view

Variants for EMX1 Gene

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  1. SNP Genotyping and Copy Number Assay

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
EMX1

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

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

Disorder Aliases PubMed IDs
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
epileptic encephalopathy, early infantile, 6
  • ds
- 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

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 23 56
  2. WDR11-mediated Hedgehog signalling defects underlie a new ciliopathy related to Kallmann syndrome. (PMID: 29263200) Kim YJ … Kim SH (EMBO reports 2018) 3 4 56
  3. 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 56
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 56
  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 56

ExternalLinks

View latest publications for EMX1 gene in Mastermind

Products for EMX1 Gene

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