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CNE-3 CNE-3 enhancer upstream of SHOX [ Homo sapiens (human) ]

Gene ID: 108353831, updated on 10-Oct-2023

Summary

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Gene symbol
CNE-3
Gene description
CNE-3 enhancer upstream of SHOX
Gene type
biological region
Feature type(s)
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 region 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 124 kb upstream of the SHOX (short stature homeobox) gene, and is one of several conserved elements that surround that gene. A subregion can function as an enhancer of SHOX gene expression in human U2OS osteosarcoma cells, and forms looping interactions with the SHOX promoter in 4C-seq assays. An overlapping subregion was also validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. Mutations that include this genomic region, 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, Oct 2022]
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Genomic context

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See CNE-3 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 (499544..500343)
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (499544..500343)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (332262..333059)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (348882..349677)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (460279..460664)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (410279..410664)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 2 regulatory subunit B''beta Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chrX:323668-324173 and GRCh37_chrY:273658-274173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrY:274174-274688 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:333708-333890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:335885-336775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:357819-358704 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:389565-389736 Neighboring gene uncharacterized LOC102724521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:396687-397186 Neighboring gene OCT4-NANOG hESC enhancers GRCh37_chrX:406609-407442 and GRCh37_chrY:356916-357447 Neighboring gene CNE-5 enhancer upstream of SHOX Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:461079-461645 Neighboring gene fatty acid binding protein 5 pseudogene 13 Neighboring gene keratin 18 pseudogene 53

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene protein phosphatase 2 regulatory subunit B''beta Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chrX:323668-324173 and GRCh37_chrY:273658-274173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrY:274174-274688 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:333708-333890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:335885-336775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:357819-358704 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:389565-389736 Neighboring gene uncharacterized LOC102724521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:396687-397186 Neighboring gene OCT4-NANOG hESC enhancers GRCh37_chrX:406609-407442 and GRCh37_chrY:356916-357447 Neighboring gene CNE-5 enhancer upstream of SHOX Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:461079-461645 Neighboring gene fatty acid binding protein 5 pseudogene 13 Neighboring gene keratin 18 pseudogene 53

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. Enhancer elements upstream of the SHOX gene are active in the developing limb. Durand C, et al. Eur J Hum Genet, 2010 May. PMID 19997128, Free PMC Article
  2. Different approaches in the molecular analysis of the SHOX gene dysfunctions. Stuppia L, et al. J Endocrinol Invest, 2010 Jun. PMID 21057183
  3. The SHOX gene: a new indication for GH treatment. Cicognani A, et al. J Endocrinol Invest, 2010 Jun. PMID 21057180
  4. Duplications upstream and downstream of SHOX identified as novel causes of Leri-Weill dyschondrosteosis or idiopathic short stature. Bunyan DJ, et al. Am J Med Genet A, 2016 Apr. PMID 26698168
  5. Profiling of conserved non-coding elements upstream of SHOX and functional characterisation of the SHOX cis-regulatory landscape. Verdin H, et al. Sci Rep, 2015 Dec 3. PMID 26631348, Free PMC Article

See all (18) 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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:460511-461078
  • conserved non-coding element -3

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_051264.2 

    Range
    101..900
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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
    499544..500343
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    499544..500343
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187634.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    182897..183696
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187667.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    172037..172836
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    332262..333059
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    348882..349677
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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