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LOC107546745 meiotic recombination hotspot NID1 [ Homo sapiens (human) ]

Gene ID: 107546745, updated on 4-Mar-2025

Summary

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Gene symbol
LOC107546745
Gene description
meiotic recombination hotspot NID1
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif, sequence_alteration
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 nidogen 1 (NID1) gene, 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 region is one of several regions near the NID1 gene that has been identified as a meiotic recombination hotspot. There are repetitive elements within this region, including AT-rich repeats and a palindromic region. Recombination exchange points within this region are skewed, with an excess of exchanges in non-repeat regions. In addition, higher recombination frequencies have been observed amongst individuals with the 'C' allele at the single nucleotide polymorphism (SNP) rs1570113 site within this region, relative to those with the 'T' allele at this site. 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 LOC107546745 in Genome Data Viewer
Location:
1q43
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (236036058..236040337)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (235432369..235436650)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (236199358..236203637)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene lysosomal trafficking regulator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1991 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1993 Neighboring gene uncharacterized LOC105373215 Neighboring gene RNA, U5E small nuclear 2, pseudogene Neighboring gene MPRA-validated peak780 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:236073306-236074505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236081529-236082028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2808 Neighboring gene long intergenic non-protein coding RNA 2768 Neighboring gene RNA, U6 small nuclear 968, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1994 Neighboring gene MPRA-validated peak781 silencer Neighboring gene meiotic recombination hotspot NID3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2809 Neighboring gene MPRA-validated peak782 silencer Neighboring gene meiotic recombination hotspot NID2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:236162526-236163725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:236164752-236165460 Neighboring gene nidogen 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:236221449-236221986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236244555-236245056 Neighboring gene MS32 minisatellite repeat instability region Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:236259904-236261103 Neighboring gene meiotic recombination hotspot MSTM1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2813 Neighboring gene meiotic recombination hotspot MSTM2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1997 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236306063-236306566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236313713-236314481 Neighboring gene ACO2 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2817 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2818 Neighboring gene G protein-coupled receptor 137B

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. Factors influencing recombination frequency and distribution in a human meiotic crossover hotspot. Jeffreys AJ, et al. Hum Mol Genet, 2005 Aug 1. PMID 15987698
  2. Polymorphism in the activity of human crossover hotspots independent of local DNA sequence variation. Neumann R, et al. Hum Mol Genet, 2006 May 1. PMID 16543360
  3. Human recombination hot spots hidden in regions of strong marker association. Jeffreys AJ, et al. Nat Genet, 2005 Jun. PMID 15880103
  4. Fine-scale recombination rate differences between sexes, populations and individuals. Kong A, et al. Nature, 2010 Oct 28. PMID 20981099
  5. 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_046861.1 

    Range
    101..4380
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    236036058..236040337
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    235432369..235436650
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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