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CNE4 CNE4 enhancer downstream of SHOX [ Homo sapiens (human) ]

Gene ID: 108383234, updated on 10-Oct-2023

Summary

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Gene symbol
CNE4
Gene description
CNE4 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
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 94 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. Mutations that include this 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, Jul 2016]
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Genomic context

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See CNE4 in Genome Data Viewer
Location:
Xp22.33; Yp11.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (753349..754018)
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (753349..754018)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (592543..593213)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (608768..609436)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (714084..714753)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (664084..664753)

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 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 CNE9 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 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 CNE9 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. Unexpected phenotype in a boy with trisomy of the SHOX gene. Iughetti L, et al. J Pediatr Endocrinol Metab, 2010 Jan-Feb. PMID 20432819
  2. Microdeletion in the SHOX 3' region associated with skeletal phenotypes of Langer mesomelic dysplasia in a 45,X/46,X,r(X) infant and Leri-Weill dyschondrosteosis in her 46,XX mother: implication for the SHOX enhancer. Fukami M, et al. Am J Med Genet A, 2005 Aug 15. PMID 16007631
  3. Copy number variants in short children born small for gestational age. Wit JM, et al. Horm Res Paediatr, 2014. PMID 25300501, Free PMC Article
  4. 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
  5. Genotypes and phenotypes of children with SHOX deficiency in France. Rosilio M, et al. J Clin Endocrinol Metab, 2012 Jul. PMID 22518848

See all (32) 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 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_051277.1 

    Range
    101..770
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    753349..754018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    753349..754018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    592543..593213
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    608768..609436
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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