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EMX2 empty spiracles homeobox 2 [ Homo sapiens (human) ]

Gene ID: 2018, updated on 27-Nov-2024

Summary

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Official Symbol
EMX2provided by HGNC
Official Full Name
empty spiracles homeobox 2provided by HGNC
Primary source
HGNC:HGNC:3341
See related
Ensembl:ENSG00000170370 MIM:600035; AllianceGenome:HGNC:3341
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Biased expression in endometrium (RPKM 36.5), kidney (RPKM 19.4) and 4 other tissues See more
Orthologs
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Genomic context

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See EMX2 in Genome Data Viewer
Location:
10q26.11
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (117542746..117549546)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (118437136..118443925)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (119302257..119309057)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene solute carrier family 18 member A2 Neighboring gene PDZ domain containing 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4099 Neighboring gene CRISPRi-validated cis-regulatory element chr10.4281 Neighboring gene CRISPRi-validated cis-regulatory element chr10.4282 Neighboring gene uncharacterized LOC105378502 Neighboring gene Sharpr-MPRA regulatory region 14976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2861 Neighboring gene EMX2 opposite strand/antisense RNA Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:119294387-119295350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:119303472-119304094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:119304095-119304717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:119305963-119306585 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4100 Neighboring gene Sharpr-MPRA regulatory region 1864 Neighboring gene VISTA enhancers hs935 and hs1032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:119321491-119321992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:119321993-119322492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2862 Neighboring gene uncharacterized LOC124902555 Neighboring gene uncharacterized LOC107984274 Neighboring gene uncharacterized LOC124902556 Neighboring gene Sharpr-MPRA regulatory region 1206

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. EMX2 is epigenetically silenced and suppresses growth in human lung cancer. Okamoto J, et al. Oncogene, 2010 Nov 4. PMID 20697358, Free PMC Article
  2. Rare somatic mutation and loss of expression of EMX2 gene in common solid cancers. Kim MS, et al. APMIS, 2011 Oct. PMID 21917011
  3. Germline mutations in the homeobox gene EMX2 in patients with severe schizencephaly. Brunelli S, et al. Nat Genet, 1996 Jan. PMID 8528262
  4. A number of schizencephaly patients including 2 brothers are heterozygous for germline mutations in the homeobox gene EMX2. Faiella A, et al. Eur J Hum Genet, 1997 Jul-Aug. PMID 9359037
  5. No major role for the EMX2 gene in schizencephaly. Merello E, et al. Am J Med Genet A, 2008 May 1. PMID 18409201

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. EMX2 inhibits clear cell renal cell carcinoma progress via modulating Akt/FOXO3a pathway.
    Title: EMX2 inhibits clear cell renal cell carcinoma progress via modulating Akt/FOXO3a pathway.
  2. Spatial control of astrogenesis progression by cortical arealization genes.
    Title: Spatial control of astrogenesis progression by cortical arealization genes.
  3. Empty spiracles homeobox genes EMX1 and EMX2 regulate WNT pathway activation in sarcomagenesis.
    Title: Empty spiracles homeobox genes EMX1 and EMX2 regulate WNT pathway activation in sarcomagenesis.
  4. Regulation of sarcomagenesis by the empty spiracles homeobox genes EMX1 and EMX2.
    Title: Regulation of sarcomagenesis by the empty spiracles homeobox genes EMX1 and EMX2.
  5. Low EMX2 expression is associated with multiple myeloma.
    Title: Wnt and BMP signaling pathways co-operatively induce the differentiation of multiple myeloma mesenchymal stem cells into osteoblasts by upregulating EMX2.
  6. Results identify the EMX2 mRNA as a major miss-spliced down stream target of SNRPE with heterozygous missense mutation causing microcephaly.
    Title: A missense mutation in SNRPE linked to non-syndromal microcephaly interferes with U snRNP assembly and pre-mRNA splicing.
  7. In the three variants of papillary thyroid cancer (PTC), EMX2 was significantly downregulated in classical PTC, while EMX2OS was significantly downregulated in follicular and classical PTC, compared with adjacent normal tissues. Kaplan-Meier survival curves showed that EMX2 and EMX2OS expression was not related to relapse-free survival in follicular PTC.
    Title: The downregulation of lncRNA EMX2OS might independently predict shorter recurrence-free survival of classical papillary thyroid cancer.
  8. EMX2 is frequently down-regulated in human colorectal cancer, and down-regulation of EMX2 is a prognostic marker for disease-free and overall survival.
    Title: EMX2 gene expression predicts liver metastasis and survival in colorectal cancer.
  9. Emx2 is a novel promising tool for therapy of glioblastoma and prevention of its recurrences.
    Title: Emx2 as a novel tool to suppress glioblastoma.
  10. EMX2 inhibits proliferation and tumorigenesis through inactivation of the Wnt/beta-catenin pathway in CRC cells.
    Title: Empty Spiracles Homeobox 2 (EMX2) Inhibits the Invasion and Tumorigenesis in Colorectal Cancer Cells.
Submit: New GeneRIF Correction See all GeneRIFs (30)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Schizencephaly
MedGen: C0266484 OMIM: 269160 GeneReviews: Not available
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Copy number response

Description
Copy number response
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2021-11-09)

ClinGen Genome Curation PagePubMed
Triplosensitivity

No evidence available (Last evaluated 2021-11-09)

ClinGen Genome Curation Page

EBI GWAS Catalog

Description
A meta-analysis of genome-wide association studies of the electrocardiographic early repolarization pattern.
EBI GWAS Catalog
A possible mechanism behind autoimmune disorders discovered by genome-wide linkage and association analysis in celiac disease.
EBI GWAS Catalog
Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.
EBI GWAS Catalog
Genome-wide association study identifies TH1 pathway genes associated with lung function in asthmatic patients.
EBI GWAS Catalog
Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in anterior/posterior pattern specification IEA
Inferred from Electronic Annotation
more info
  
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell proliferation in forebrain IEA
Inferred from Electronic Annotation
more info
  
involved_in central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cerebral cortex regionalization IEA
Inferred from Electronic Annotation
more info
  
involved_in dentate gyrus development IEA
Inferred from Electronic Annotation
more info
  
involved_in forebrain cell migration IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron migration IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to xenobiotic stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in stereocilium bundle organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in ureter morphogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in axon IEA
Inferred from Electronic Annotation
more info
  
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
homeobox protein EMX2
Names
empty spiracles homolog 2
empty spiracles-like protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_013009.1 RefSeqGene

    Range
    5302..12102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001165924.2 → NP_001159396.1  homeobox protein EMX2 isoform 2

    See identical proteins and their annotated locations for NP_001159396.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, compared to variant 1, which results in a frameshift and a protein (isoform 2) with a shorter and distinct C-terminus, compared to isoform 1. Isoform 2 lacks the C-terminal homeodomain of isoform 1
    Source sequence(s)
    AC005871, AF301598, AI701984
    Consensus CDS
    CCDS53583.1
    UniProtKB/Swiss-Prot
    Q04743
    Related
    ENSP00000474874.1, ENST00000442245.5

  2. NM_004098.4 → NP_004089.1  homeobox protein EMX2 isoform 1

    See identical proteins and their annotated locations for NP_004089.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AF301598, AI701984
    Consensus CDS
    CCDS7601.1
    UniProtKB/Swiss-Prot
    G3V305, Q04743, Q96NN8, Q9BQF4
    Related
    ENSP00000450962.3, ENST00000553456.5
    Conserved Domains (1) summary
    pfam00046
    Location:158 → 211
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    117542746..117549546
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    118437136..118443925
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q04743.2 GenPept UniProtKB/Swiss-Prot:Q04743

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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