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

    Gene ID: 2016, updated on 10-Dec-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, Dec 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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

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

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