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CNE9 CNE9 enhancer downstream of SHOX [ Homo sapiens (human) ]

Gene ID: 108410392, updated on 17-Sep-2024

Summary

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Gene symbol
CNE9
Gene description
CNE9 enhancer downstream of SHOX
Gene type
biological region
Feature type(s)
misc_feature: conserved_region
regulatory: enhancer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ECS4; ECS4/CNE9
Summary
This genomic element is found within the pseudoautosomal region 1 (PAR1) of chromosomes X and Y, where each chromosome contains the same DNA region. It is located approximately 215 kb downstream of the SHOX (short stature homeobox) gene, and is one of several conserved elements that surround that gene. It can function as an enhancer of SHOX gene expression. Chromosome conformation capture (3C) assays show that the orthologous chicken region can form looping interactions with a region upstream of the SHOX gene in chicken limb. Mutations that include this human element, including deletions and microduplications, are associated with Leri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS), and they have also been implicated in autism spectrum disorders (ASDs) and related neurodevelopmental conditions. [provided by RefSeq, Aug 2016]
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Genomic context

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See CNE9 in Genome Data Viewer
Location:
Xp22.33; Yp11.3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (856168..874963)
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (856168..874963)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (711219..730031)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (816903..835698)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (766903..785698)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene keratin 18 pseudogene 53 Neighboring gene CNE-2 enhancer upstream of SHOX Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrY:534047-534914 Neighboring gene meiotic recombination hotspot SHOX Neighboring gene SHOX homeobox Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:639405-639905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:644837-645338 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:727399-727565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:753798-754298 Neighboring gene CNE4 enhancer downstream of SHOX Neighboring gene SHOX downstream enhancer, distal recombination region Neighboring gene CNE5 enhancer downstream of SHOX Neighboring gene SHOX downstream enhancer, proximal recombination region Neighboring gene CNE6 enhancer downstream of SHOX Neighboring gene CNE7 enhancer downstream of SHOX Neighboring gene CNE8 enhancer downstream of SHOX Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:941763-942262 Neighboring gene H3K27ac hESC enhancers GRCh37_chrX:958477-959001 and GRCh37_chrY:908292-908926 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:959002-959525 Neighboring gene ribosomal protein L14 pseudogene 5 Neighboring gene NANOG hESC enhancer GRCh37_chrX:1104952-1105491 Neighboring gene repetin pseudogene

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene keratin 18 pseudogene 53 Neighboring gene CNE-2 enhancer upstream of SHOX Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrY:534047-534914 Neighboring gene meiotic recombination hotspot SHOX Neighboring gene SHOX homeobox Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:639405-639905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrY:644837-645338 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:727399-727565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:753798-754298 Neighboring gene CNE4 enhancer downstream of SHOX Neighboring gene SHOX downstream enhancer, distal recombination region Neighboring gene CNE5 enhancer downstream of SHOX Neighboring gene SHOX downstream enhancer, proximal recombination region Neighboring gene CNE6 enhancer downstream of SHOX Neighboring gene CNE7 enhancer downstream of SHOX Neighboring gene CNE8 enhancer downstream of SHOX Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:941763-942262 Neighboring gene H3K27ac hESC enhancers GRCh37_chrX:958477-959001 and GRCh37_chrY:908292-908926 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:959002-959525 Neighboring gene ribosomal protein L14 pseudogene 5 Neighboring gene NANOG hESC enhancer GRCh37_chrX:1104952-1105491 Neighboring gene repetin pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Transactivation function of an approximately 800-bp evolutionarily conserved sequence at the SHOX 3' region: implication for the downstream enhancer. Fukami M, et al. Am J Hum Genet, 2006 Jan. PMID 16385461, Free PMC Article
  2. Copy number variants in short children born small for gestational age. Wit JM, et al. Horm Res Paediatr, 2014. PMID 25300501, Free PMC Article
  3. Homozygosity for a novel deletion downstream of the SHOX gene provides evidence for an additional long range regulatory region with a mild phenotypic effect. Bunyan DJ, et al. Am J Med Genet A, 2014 Nov. PMID 25125269
  4. The homozygous deletion of the 3' enhancer of the SHOX gene causes Langer mesomelic dysplasia. Bertorelli R, et al. Clin Genet, 2007 Nov. PMID 17935511
  5. Spectrum of phenotypic anomalies in four families with deletion of the SHOX enhancer region. Gatta V, et al. BMC Med Genet, 2014 Jul 23. PMID 25056248, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • conserved non-coding element 9
  • evolutionarily conserved sequence 4

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_051296.1 

    Range
    101..18896
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    856168..874963
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    856168..874963
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    711219..730031
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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