U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC107832852 meiotic recombination hotspot 12B [ Homo sapiens (human) ]

Gene ID: 107832852, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC107832852
Gene description
meiotic recombination hotspot 12B
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 on the p arm of chromosome 12, and has been identified as a meiotic recombination hotspot by sperm typing assays and linkage disequilibrium studies. This recombination hotspot is specific to individuals with the L6 and L8 alleles of the PR domain 9 (PRDM9) gene, more prevalent in African populations. Little to no meiotic recombination hotspot activity is observed in some individuals with other PRDM9 alleles. While this region does not contain an exact match to the PRDM9 C-type consensus motif, CCNCNNTNNNCNTNNC, there is a sequence near the center of the hotspot region that shares similarity to the consensus motif. 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, May 2016]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
12p13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (4044062..4047461)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (4050743..4054142)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (4153228..4156627)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369608 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:4053989-4054502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:4099402-4099924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:4099925-4100447 Neighboring gene uncharacterized LOC105369611 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4127463-4128060 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4128061-4128656 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4132239-4132836 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4132837-4133432 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4134031-4134626 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4134627-4135224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:4136249-4136754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:4136755-4137259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4144 Neighboring gene uncharacterized LOC124900317 Neighboring gene Sharpr-MPRA regulatory region 7545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5818 Neighboring gene heat shock protein family A (Hsp70) member 8 pseudogene 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:4226148-4227142 Neighboring gene ribosomal protein L18 pseudogene 9

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Variants of the protein PRDM9 differentially regulate a set of human meiotic recombination hotspots highly active in African populations. Berg IL, et al. Proc Natl Acad Sci U S A, 2011 Jul 26. PMID 21750151, Free PMC Article
  2. Fine-scale recombination rate differences between sexes, populations and individuals. Kong A, et al. Nature, 2010 Oct 28. PMID 20981099

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_047023.1 

    Range
    101..3500
    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
    4044062..4047461
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    4050743..4054142
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases