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LOC107648859 meiotic recombination hotspot DMB2 [ Homo sapiens (human) ]

Gene ID: 107648859, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107648859
Gene description
meiotic recombination hotspot DMB2
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 upstream of the major histocompatibility complex, class II, DM beta (HLA-DMB) gene on the p arm of chromosome 6 relative to the reference genome. 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. HapMap data shows an increased recombination rate in the region. Another meiotic recombination hotspot has been identified close to this region and is located within the HLA-DMB gene. 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. A linkage disequilibrium 'CCNCCNTNNCCNC' motif is found in this region. [provided by RefSeq, Oct 2016]
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Genomic context

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Location:
6p21.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32931739..32933172)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32753089..32754521)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32899516..32900949)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 2 pseudogene 1 Neighboring gene uncharacterized LOC100294145 Neighboring gene major histocompatibility complex, class I, Z (pseudogene) Neighboring gene meiotic recombination hotspot DMB1 Neighboring gene major histocompatibility complex, class II, DM beta Neighboring gene major histocompatibility complex, class II, DM alpha

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. Meiotic recombination hot spots and human DNA diversity. Jeffreys AJ, et al. Philos Trans R Soc Lond B Biol Sci, 2004 Jan 29. PMID 15065666, Free PMC Article
  2. 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
  3. 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
  4. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Jeffreys AJ, et al. Nat Genet, 2001 Oct. PMID 11586303
  5. Characterization of recombination in the HLA class II region. Cullen M, et al. Am J Hum Genet, 1997 Feb. PMID 9012413, Free PMC Article

See all (15) 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_046883.1 

    Range
    101..1534
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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
    32931739..32933172
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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
    4175268..4176701
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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
    4351105..4352540
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    4230780..4232215
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    4330968..4332405
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    32753089..32754521
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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