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LOC107652445 meiotic recombination hotspot SHOX [ Homo sapiens (human) ]

Gene ID: 107652445, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107652445
Gene description
meiotic recombination hotspot SHOX
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif
misc_recomb: meiotic
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 located within the short stature homeobox (SHOX) gene, and has been identified as a meiotic recombination hotspot by sperm typing assays, molecular assays in male germ cells to identify meiotic double strand breaks, and linkage disequilibrium studies. This recombination hotspot 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. This region is highly recombinogenic in males, and studies have shown that there is an obligatory crossover in the PAR1 region per male meiosis, while the recombination rate in the region in females is similar to the genome-wide recombination average. Reduced recombination in this region can lead to aneuploidy sperm, and can be a cause of Turner syndrome (XO) or Kleinfelter syndrome (XXY) in the offspring. Studies in mice indicate that recombination in the PAR region occurs at later times than that observed on autosomes. Meiotic hotspot activity can vary widely amongst individuals and can be influenced by both the nucleotide sequence at the meiotic recombination hotspot and the specific alleles present at the PR domain 9 (PRDM9) locus. A consensus PRDM9 C binding motif 'CCNCNNTNNNCNTNNC' is found in this region. [provided by RefSeq, Apr 2016]
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Genomic context

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See LOC107652445 in Genome Data Viewer
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 (633053..636275)
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (633053..636275)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (473224..476450)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (486355..489575)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (593788..597010)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (543788..547010)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene fatty acid binding protein 5 pseudogene 13 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 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 CNE4 enhancer downstream of SHOX 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 fatty acid binding protein 5 pseudogene 13 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 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 CNE4 enhancer downstream of SHOX 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. Recombination in the human Pseudoautosomal region PAR1. Hinch AG, et al. PLoS Genet, 2014 Jul. PMID 25033397, Free PMC Article
  2. The Human Pseudoautosomal Region (PAR): Origin, Function and Future. Helena Mangs A, et al. Curr Genomics, 2007 Apr. PMID 18660847, Free PMC Article
  3. The human pseudoautosomal regions: a review for genetic epidemiologists. Flaquer A, et al. Eur J Hum Genet, 2008 Jul. PMID 18398439
  4. The pseudoautosomal regions, SHOX and disease. Blaschke RJ, et al. Curr Opin Genet Dev, 2006 Jun. PMID 16650979
  5. Single sperm typing demonstrates that reduced recombination is associated with the production of aneuploid 24,XY human sperm. Shi Q, et al. Am J Med Genet, 2001 Feb 15. PMID 11170091

See all (19) 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

  • meiotic recombination hotspot PAR1

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_046891.1 

    Range
    101..3323
    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
    633053..636275
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    633053..636275
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    473224..476450
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    486355..489575
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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