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LOC107648851 meiotic recombination hotspot TAP2 [ Homo sapiens (human) ]

Gene ID: 107648851, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107648851
Gene description
meiotic recombination hotspot TAP2
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 transporter 2, ATP-binding cassette, sub-family B (MDR/TAP) (TAP2) gene within the class II region of the major histocompatibility complex (MHC) on the p arm of chromosome 6. This region has been identified as a meiotic recombination hotspot by sperm typing assays and linkage disequilibrium studies. 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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Location:
6p21.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32835539..32837694)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32656915..32659070)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32803316..32805471)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene major histocompatibility complex, class II, DQ beta 2 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32746394 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 6:32747727 and 6:32747786 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32748021 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32748137 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32749836 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32750346 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32751751 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32752130 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 6:32752436, 6:32752477 and 6:32752546 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32752973 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32753654 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32754294 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32754458 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32754921 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32755087 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32756916 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 6:32762528 Neighboring gene major histocompatibility complex, class II, DO beta Neighboring gene transporter 2, ATP binding cassette subfamily B member Neighboring gene PSMB8 antisense RNA 1 (head to head) Neighboring gene proteasome 20S subunit beta 8 Neighboring gene transporter 1, ATP binding cassette subfamily B member

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. Haplotypic variation of the transporter associated with antigen processing (TAP) genes and their extension of HLA class II region haplotypes. Carrington M, et al. Immunogenetics, 1993. PMID 8267790
  2. TAP2 gene polymorphism segregates with DR-DQ in DR/DP recombinant siblings. Eiermann TH, et al. Hum Immunol, 1993 Nov. PMID 8106280
  3. Molecular mapping of a recombination hotspot located in the second intron of the human TAP2 locus. Cullen M, et al. Am J Hum Genet, 1995 Jun. PMID 7762558, Free PMC Article
  4. Alleles and haplotypes of the MHC-encoded ABC transporters TAP1 and TAP2. Powis SH, et al. Immunogenetics, 1993. PMID 8428770
  5. High resolution analysis of haplotype diversity and meiotic crossover in the human TAP2 recombination hotspot. Jeffreys AJ, et al. Hum Mol Genet, 2000 Mar 22. PMID 10749979

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_046880.1 

    Range
    101..2256
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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
    32835539..32837694
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    4140405..4142560
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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
    4247739..4249893
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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
    4254891..4257046
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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
    4029826..4031981
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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
    4234793..4236948
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    32656915..32659070
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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