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LOC107522028 meiotic recombination hotspot T [ Homo sapiens (human) ]

Gene ID: 107522028, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107522028
Gene description
meiotic recombination hotspot T
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 contactin 4 (CNTN4) gene located on the p arm of chromosome 3, 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 meiotic recombination hotspot tends to have a higher recombination frequency in individuals with the PRDM9 A/A genotype than 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. [provided by RefSeq, Apr 2016]
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Genomic context

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Location:
3p26.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (2380639..2386455)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (2374523..2380339)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (2422323..2428139)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene CNTN4 antisense RNA 2 Neighboring gene contactin 4 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_68491 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_68954 Neighboring gene histidine triad nucleotide binding protein 2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19336 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:2806697-2807249 Neighboring gene NANOG hESC enhancer GRCh37_chr3:2812162-2812685 Neighboring gene uncharacterized LOC105376926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19340 Neighboring gene MPRA-validated peak4526 silencer Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 pseudogene 4

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. A common sequence motif associated with recombination hot spots and genome instability in humans. Myers S, et al. Nat Genet, 2008 Sep. PMID 19165926
  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_046851.1 

    Range
    101..5917
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    2380639..2386455
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    2374523..2380339
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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