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LOC107436002 meiotic recombination hotspot F [ Homo sapiens (human) ]

Gene ID: 107436002, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107436002
Gene description
meiotic recombination hotspot F
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 anoctamin 2 (ANO2) 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. Individuals with a PRDM9 A/A genotype tend to have higher recombination frequencies at this meiotic recombination hotspot than that observed in individuals with other genotypes, and little to no meiotic recombination hotspot activity is observed in some individuals with other PRDM9 alleles. 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 linkage disequilibrium 'CCNCCNTNNCCNC' motif is found in this region. [provided by RefSeq, Apr 2016]
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Genomic context

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Location:
12p13.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (5638845..5641797)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (5646373..5649325)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (5748011..5750963)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902865 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:5618629-5619828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:5626075-5626631 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:5629720-5630919 Neighboring gene OCT4 hESC enhancer GRCh37_chr12:5681388-5681889 Neighboring gene dynein light chain roadblock-type 1 pseudogene Neighboring gene anoctamin 2 Neighboring gene MPRA-validated peak1541 silencer Neighboring gene meiotic recombination hotspot 12D Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:5916007-5917206 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:5921895-5922394 Neighboring gene NANOG hESC enhancer GRCh37_chr12:5927975-5928488 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:5936424-5937202 Neighboring gene uncharacterized LOC105369621 Neighboring gene MPRA-validated peak1543 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6017201-6017701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6030281-6030782 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:6040249-6041448 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:6075167-6075353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6076959-6077460 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6078733-6079346 Neighboring gene Sharpr-MPRA regulatory region 15487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6127715-6128214 Neighboring gene von Willebrand factor Neighboring gene small nucleolar RNA, H/ACA box 120

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. PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans. Berg IL, et al. Nat Genet, 2010 Oct. PMID 20818382, Free PMC Article
  2. Sperm cross-over activity in regions of the human genome showing extreme breakdown of marker association. Webb AJ, et al. Proc Natl Acad Sci U S A, 2008 Jul 29. PMID 18650392, Free PMC Article
  3. A common sequence motif associated with recombination hot spots and genome instability in humans. Myers S, et al. Nat Genet, 2008 Sep. PMID 19165926
  4. Fine-scale recombination rate differences between sexes, populations and individuals. Kong A, et al. Nature, 2010 Oct 28. PMID 20981099
  5. 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_046825.1 

    Range
    101..3053
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    5638845..5641797
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    5646373..5649325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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