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LOC108251803 SHOX downstream enhancer, proximal recombination region [ Homo sapiens (human) ]

Gene ID: 108251803, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108251803
Gene description
SHOX downstream enhancer, proximal recombination region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
misc_recomb: chromosome_breakpoint, meiotic
mobile_element
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region is known to undergo recombination with another region, the SHOX downstream enhancer, distal recombination region, found about 47 kb centromere-distal to this region. This recombination region is found within the pseudoautosomal region 1 (PAR1), so the DNA sequence is present on both the X chromosome and Y chromosome at Xp22 and Yp11, respectively. Recombination between this region and the SHOX downstream enhancer, distal recombination region can result in a 47.5 kb deletion, removing the intervening sequence, including enhancer regions of the short stature homeobox (SHOX) gene. The recurrent 47.5 kb deletion is a cause of Leri-Weill dyschondrosteosis (LWD), a bone growth disorder that results in short stature as a result of shortening of the long bones in the arms and legs, and a characteristic abnormality of the forearms known as Madelung deformity. This region contains a meiotic recombination hotspot. [provided by RefSeq, Jun 2016]
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Genomic context

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Location:
Xp22.33 and Yp11.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (866905..867930)
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (866905..867930)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (701875..702901)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (721973..722999)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (827640..828665)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (777640..778665)

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 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 CNE4 enhancer downstream of SHOX Neighboring gene SHOX downstream enhancer, distal recombination region Neighboring gene CNE5 enhancer downstream of SHOX 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. Diagnostic screening identifies a wide range of mutations involving the SHOX gene, including a common 47.5 kb deletion 160 kb downstream with a variable phenotypic effect. Bunyan DJ, et al. Am J Med Genet A, 2013 Jun. PMID 23636926
  2. Identification of the first recurrent PAR1 deletion in Léri-Weill dyschondrosteosis and idiopathic short stature reveals the presence of a novel SHOX enhancer. Benito-Sanz S, et al. J Med Genet, 2012 Jul. PMID 22791839
  3. Enhancer deletions of the SHOX gene as a frequent cause of short stature: the essential role of a 250 kb downstream regulatory domain. Chen J, et al. J Med Genet, 2009 Dec. PMID 19578035, Free PMC Article
  4. A novel class of Pseudoautosomal region 1 deletions downstream of SHOX is associated with Leri-Weill dyschondrosteosis. Benito-Sanz S, et al. Am J Hum Genet, 2005 Oct. PMID 16175500, Free PMC Article
  5. Identification of the first PAR1 deletion encompassing upstream SHOX enhancers in a family with idiopathic short stature. Benito-Sanz S, et al. Eur J Hum Genet, 2012 Jan. PMID 22071895, Free PMC Article

See all (7) 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)

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_051006.1 

    Range
    101..1126
    Download
    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
    866905..867930
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    866905..867930
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    701875..702901
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    721973..722999
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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