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EMX1 empty spiracles homeobox 1 [ Homo sapiens (human) ]

Gene ID: 2016, updated on 2-Nov-2024

Summary

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Official Symbol
EMX1provided by HGNC
Official Full Name
empty spiracles homeobox 1provided by HGNC
Primary source
HGNC:HGNC:3340
See related
Ensembl:ENSG00000135638 MIM:600034; AllianceGenome:HGNC:3340
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in brain development; neuron differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including nervous system development; neuroepithelial cell differentiation; and regulation of oligodendrocyte progenitor proliferation. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in kidney (RPKM 6.4), brain (RPKM 1.7) and 1 other tissue See more
Orthologs
mouse all
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Genomic context

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See EMX1 in Genome Data Viewer
Location:
2p13.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (72916189..72934891)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (72924096..72947833)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (73144648..73162020)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11626 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:73115417-73115591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73119309-73119810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16022 Neighboring gene VISTA enhancer hs1025 Neighboring gene CRISPRi-validated cis-regulatory element chr2.2721 Neighboring gene zinc finger MYM-type containing 1 pseudogene Neighboring gene sepiapterin reductase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73143395-73144012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73144013-73144629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73164255-73164932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73165285-73165786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73168998-73169986 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73177215-73177716 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73177717-73178218 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73178721-73179222 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73179223-73179724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73186243-73186743 Neighboring gene sideroflexin 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73191385-73192078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73192079-73192770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73209618-73210118 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:73216229-73216428 Neighboring gene Sharpr-MPRA regulatory region 2442 Neighboring gene uncharacterized LOC107985897 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73263753-73264638 Neighboring gene Sharpr-MPRA regulatory region 10332 Neighboring gene uncharacterized LOC105374800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73282484-73282984

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 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. EMX1 functions as a tumor inhibitor in spinal cord glioma through transcriptional suppression of WASF2 and inactivation of the Wnt/β-catenin axis. Han Z, et al. Brain Behav, 2022 Aug. PMID 35849030, Free PMC Article
  2. Detection and partial purification of a cruciform-resolving activity (X-solvase) from nuclear extracts of mouse B-cells. Solaro P, et al. Eur J Biochem, 1995 Jun 15. PMID 7601155
  3. Bacteriophage lambda display of complex cDNA libraries: a new approach to functional genomics. Santi E, et al. J Mol Biol, 2000 Feb 18. PMID 10669604
  4. Empty spiracles homeobox genes EMX1 and EMX2 regulate WNT pathway activation in sarcomagenesis. Jimenez-García MP, et al. J Exp Clin Cancer Res, 2021 Aug 7. PMID 34364391, Free PMC Article
  5. Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1. Ang CE, et al. Proc Natl Acad Sci U S A, 2024 Mar 12. PMID 38446849, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1.
    Title: Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1.
  2. EMX1 functions as a tumor inhibitor in spinal cord glioma through transcriptional suppression of WASF2 and inactivation of the Wnt/beta-catenin axis.
    Title: EMX1 functions as a tumor inhibitor in spinal cord glioma through transcriptional suppression of WASF2 and inactivation of the Wnt/β-catenin axis.
  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. An intersectional fate-mapping analysis reveals that transgenic Emx1-lineage cells coexpressing Dlx exclusively generate medium spiny neurons but do not contribute to the excitatory neurons in the amygdala.
    Title: Emx1-lineage progenitors differentially contribute to neural diversity in the striatum and amygdala.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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 brain development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in brain morphogenesis 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 neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in cerebral cortex regionalization IEA
Inferred from Electronic Annotation
more info
  
involved_in homeostasis of number of cells IEA
Inferred from Electronic Annotation
more info
  
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in neuroepithelial cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron projection extension IEA
Inferred from Electronic Annotation
more info
  
involved_in post-embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in radial glial cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of oligodendrocyte progenitor proliferation 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
  
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in chromosome IDA
Inferred from Direct Assay
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
homeobox protein EMX1
Names
empty spiracles homolog 1
empty spiracles-like protein 1

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.

mRNA and Protein(s)

  1. NM_004097.3 → NP_004088.2  homeobox protein EMX1

    See identical proteins and their annotated locations for NP_004088.2

    Status: VALIDATED

    Source sequence(s)
    AC012366, BC045762
    Consensus CDS
    CCDS1921.2
    UniProtKB/Swiss-Prot
    Q04741, Q0D2P0, Q53T30, Q86XB0
    Related
    ENSP00000258106.6, ENST00000258106.11
    Conserved Domains (2) summary
    COG5576
    Location:140 → 251
    COG5576; Homeodomain-containing transcription factor [Transcription]
    pfam00046
    Location:196 → 249
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    72916189..72934891
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532697.4 → XP_011530999.1  homeobox protein EMX1 isoform X1

    See identical proteins and their annotated locations for XP_011530999.1

    UniProtKB/Swiss-Prot
    Q04741
    Conserved Domains (1) summary
    pfam00046
    Location:25 → 77
    Homeobox; Homeobox domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    72924096..72947833
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341014.1 → XP_054196989.1  homeobox protein EMX1 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001040404.1: Suppressed sequence

    Description
    NM_001040404.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q04741.3 GenPept UniProtKB/Swiss-Prot:Q04741

Gene LinkOut

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