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LOC107648866 meiotic recombination hotspot DNA3 [ Homo sapiens (human) ]

Gene ID: 107648866, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107648866
Gene description
meiotic recombination hotspot DNA3
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 found within the intergenic region between the bromodomain containing 2 (BRD2) gene and the major histocompatibility complex, class II, DO alpha (HLA-DOA) gene on the p arm of chromosome 6. This region 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. Two meiotic recombination hotspots have been identified near this region, the DNA2 and DNA1 meiotic recombination hotspots, located downstream of this region relative to the reference genome. Differences in recombination rates in this region have been reported for some individuals with Acute Lymphoblastic Leukemia (ALL). Higher recombination frequencies in females relative to males has been reported in the MHC class II region. 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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See LOC107648866 in Genome Data Viewer
Location:
6p21.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32995239..32998860)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32816590..32820210)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32963016..32966637)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901302 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:32935448-32935987 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:32937286-32938485 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32939954-32940562 Neighboring gene bromodomain containing 2 Neighboring gene meiotic recombination hotspot DNA2 Neighboring gene meiotic recombination hotspot DNA1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32977249-32977764 Neighboring gene major histocompatibility complex, class II, DO alpha Neighboring gene meiotic recombination hotspot DPA1 Neighboring gene major histocompatibility complex, class II, DP alpha 1 Neighboring gene major histocompatibility complex, class II, DP beta 1 Neighboring gene ribosomal protein L32 pseudogene 1

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. Differences in meiotic recombination rates in childhood acute lymphoblastic leukemia at an MHC class II hotspot close to disease associated haplotypes. Thompson P, et al. PLoS One, 2014. PMID 24959916, Free PMC Article
  2. Meiotic recombinations within major histocompatibility complex of human embryos. Taylan F, et al. Immunogenetics, 2012 Nov. PMID 22893033
  3. Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region. Kauppi L, et al. Hum Mol Genet, 2003 Jan 1. PMID 12490530
  4. High-resolution patterns of meiotic recombination across the human major histocompatibility complex. Cullen M, et al. Am J Hum Genet, 2002 Oct. PMID 12297984, Free PMC Article
  5. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Jeffreys AJ, et al. Nat Genet, 2001 Oct. PMID 11586303

See all (16) 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_046889.1 

    Range
    101..3722
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    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    32995239..32998860
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    4407435..4411056
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    4238777..4242398
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    4414591..4418215
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    4189550..4193170
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    32816590..32820210
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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