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LOC107548103 MS32 minisatellite repeat instability region [ Homo sapiens (human) ]

Gene ID: 107548103, updated on 10-Oct-2023

Summary

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Gene symbol
LOC107548103
Gene description
MS32 minisatellite repeat instability region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif, repeat_instability_region, sequence_alteration
misc_recomb: meiotic
repeat_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region contains a highly variable minisatellite sequence that is located centromere-proximal to the G protein-coupled receptor 137B (GPR137B) gene on the q arm of chromosome 1. The minisatellite is an unstable GC-rich variable number tandem repeat (VNTR) with repeat units of 29 nucleotides in length that are similar, but non-identical. Instability at this locus is observed in germline cells, and there is an overlapping meiotic recombination hotspot that has been identified by sperm typing assays, molecular assays in male germ cells to identify meiotic double strand breaks, and linkage disequilibrium studies. Studies have shown that a single nucleotide polymorphism (SNP), O1 C/G (rs74149540) can drastically alter instability frequencies. This polymorphism is found directly adjacent to a PRDM9 A (LD hotspot) binding motif. The O1 C allele is associated with reduced mutation rates. The O1 C allele is rare in some European and Asian populations, but is more frequently observed in some African populations. [provided by RefSeq, Jul 2017]
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Genomic context

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Location:
1q42
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (236096118..236097991)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (235492430..235500132)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (236259418..236261291)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373215 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236081529-236082028 Neighboring gene long intergenic non-protein coding RNA 2768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2808 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 meiotic recombination hotspot NID1 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 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 ACO2 pseudogene 2 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 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. Minisatellite MS32 alleles show population specificity among Thai, Chinese, and Japanese. Yuan QH, et al. J Mol Evol, 2009 Feb. PMID 19159965
  2. Rapid individual identification by minisatellite variant repeat (MVR)-PCR at D1S8 locus using "exponential law". Suenaga E, et al. Anal Sci, 2004 Dec. PMID 15636506
  3. Evaluation of the paternity probability on an application of minisatellite variant repeat mapping using polymerase chain reaction (MVR-PCR) to paternity testing. Huang XL, et al. Leg Med (Tokyo), 1999 Sep. PMID 12935513
  4. The application of minisatellite variant repeat mapping by PCR (MVR-PCR) in a paternity case showing false exclusion due to STR mutation. Yamamoto T, et al. J Forensic Sci, 2001 Mar. PMID 11305445
  5. [Study on DNA polymorphism at D1S8 locus in Hebei Han population]. Guo X, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2000 Jun. PMID 10837523

See all (44) 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)

General gene information

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Other Names

  • D1S8 minisatellite repeat instability region

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_046870.1 

    Range
    101..1974
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    236096118..236097991
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    235492430..235500132
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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