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LOC107838685 meiotic recombination hotspot PAR2A [ Homo sapiens (human) ]

Gene ID: 107838685, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107838685
Gene description
meiotic recombination hotspot PAR2A
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 an intron of the sprouty RTK signaling antagonist 3 (SPRY3) 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, so the DNA sequence is present on both the X chromosome and Y chromosome at Xq28 and Yq12, respectively. This meiotic recombination hotspot tends to have a higher recombination frequency in individuals with a PR domain 9 (PRDM9) C-type allele, with little to no meiotic recombination activity observed in some individuals with some other PRDM9 alleles. This region contains a PRDM9 C-type consensus motif, CCNCNNTNNNCNTNNC, and there is also a sequence near the center of the hotspot region that shares similarity to the consensus motif. 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. [provided by RefSeq, May 2016]
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Genomic context

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See LOC107838685 in Genome Data Viewer
Location:
Xq28 and Yq12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (155747397..155751379)
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (56933917..56937899)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (153972604..153976586)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (62169605..62173587)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (154977059..154981041)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (59080065..59084047)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene int22h-3 recombination region Neighboring gene TMLHE antisense RNA 1 Neighboring gene H2A.B variant histone 3 Neighboring gene trimethyllysine hydroxylase, epsilon Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30078 Neighboring gene sprouty RTK signaling antagonist 3 Neighboring gene meiotic recombination hotspot PAR2 Neighboring gene adenosylmethionine decarboxylase 1 pseudogene 2 Neighboring gene diphthamide biosynthesis 3 pseudogene 2

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:28797811-28798580 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:28798753-28799442 Neighboring gene poly(ADP-ribose) polymerase family member 4 pseudogene 1 Neighboring gene CCNQ pseudogene 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrY:58981135-58981878 Neighboring gene meiotic recombination hotspot PAR2 Neighboring gene H3K27ac hESC enhancer GRCh37_chrY:58996593-58997092 Neighboring gene OCT4 hESC enhancer GRCh37_chrY:58993067-58993568 Neighboring gene OCT4 hESC enhancer GRCh37_chrY:58991323-58991865 Neighboring gene OCT4 hESC enhancer GRCh37_chrY:58988210-58988711 Neighboring gene OCT4 hESC enhancer GRCh37_chrY:58987057-58987801 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:58985458-58986055 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:58982623-58983366 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:58981879-58982622 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrY:58979645-58980388 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrY:58978901-58979644 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrY:58978157-58978900 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrY:58977411-58978156 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:58976667-58977410 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:58975923-58976666 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrY:58975179-58975922 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:58971453-58972198 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:58861881-58862424 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:58862425-58862968 Neighboring gene CTBP2 pseudogene 1 Neighboring gene adenosylmethionine decarboxylase 1 pseudogene 2 Neighboring gene diphthamide biosynthesis 3 pseudogene 2 Neighboring gene sprouty RTK signaling antagonist 3

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. Differentially regulated and evolved genes in the fully sequenced Xq/Yq pseudoautosomal region. Ciccodicola A, et al. Hum Mol Genet, 2000 Feb 12. PMID 10655549
  2. Variants of the protein PRDM9 differentially regulate a set of human meiotic recombination hotspots highly active in African populations. Berg IL, et al. Proc Natl Acad Sci U S A, 2011 Jul 26. PMID 21750151, Free PMC Article
  3. Fine-scale recombination rate differences between sexes, populations and individuals. Kong A, et al. Nature, 2010 Oct 28. PMID 20981099
  4. DNA recombination. Recombination initiation maps of individual human genomes. Pratto F, et al. Science, 2014 Nov 14. PMID 25395542, Free PMC Article

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_047039.1 

    Range
    101..4083
    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
    155747397..155751379
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    56933917..56937899
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    153972604..153976586
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    62169605..62173587
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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