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LOC110594336 MS1 minisatellite repeat instability region [ Homo sapiens (human) ]

Gene ID: 110594336, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110594336
Gene description
MS1 minisatellite repeat instability region
Gene type
biological region
Feature type(s)
misc_feature: nucleotide_motif, repeat_instability_region
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 is a highly variable minisatellite region that overlaps the serine incorporator 2 (SERINC2) gene on the p arm of chromosome 1. The MS1 (D1S7) minisatellite is a highly unstable GC-rich variable number tandem repeat (VNTR) with a repeat unit length of nine nucleotides, with a consensus motif of CCACCCTATC. The repeat is an imperfect repeat, with a tandem array of similar, but non-identical repeats. When appended together, the consensus motif forms the PRDM9 A binding motif (LD hotspot motif), CCNCCNTNNCCNC. This region contains a meiotic recombination hotspot that overlaps the tandem repeat. This region shows very high heterozygosity, and has alleles ranging from 60 repeat units to greater than 1000 repeat units. The very high heterozygosity of this region makes it useful for forensic analyses. Instability at this locus is observed in both germline and somatic cells, with similar germline mutation rates observed in both males and females. Greater instability is seen in alleles with long arrays of homogeneous repeats, with deletions of the repeat observed. Repeat instability is also observed in colorectal carcinomas. [provided by RefSeq, Jul 2017]
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Genomic context

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Location:
1p35.2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (31428806..31434663)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31281142..31291881)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (31901653..31907510)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903892 Neighboring gene Sharpr-MPRA regulatory region 3310 Neighboring gene uncharacterized LOC105378623 Neighboring gene Sharpr-MPRA regulatory region 2178 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:31885808-31886308 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31887579-31888127 Neighboring gene serine incorporator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 569 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31897069-31897630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:31897631-31898192 Neighboring gene uncharacterized LOC124903900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:31907359-31908163 Neighboring gene uncharacterized LOC105378625 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:31926120-31927319 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:31943609-31944808 Neighboring gene uncharacterized LOC105379772

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. Genetic structure and affinity among eight ethnic populations of Eastern India: based on 22 polymorphic DNA loci. Kashyap VK, et al. Am J Hum Biol, 2004 May-Jun. PMID 15101056
  2. Two modes of germline instability at human minisatellite MS1 (locus D1S7): complex rearrangements and paradoxical hyperdeletion. Berg I, et al. Am J Hum Genet, 2003 Jun. PMID 12748906, Free PMC Article
  3. Geographic contiguity and genetic affinity among five ethnic populations of Manipur, India: further molecular studies based on VNTR and STR loci. Ranjan D, et al. Ann Hum Biol, 2003 Mar-Apr. PMID 12637188
  4. Genetic variation at minisatellite loci D1S7, D4S139, D5S110 and D17S79 among three population groups of eastern India. Dutta R, et al. J Genet, 2001 Apr. PMID 11910121
  5. Genetic analysis of the Utah population: a comparison of STR and VNTR loci. Jorde LB, et al. Hum Biol, 2000 Dec. PMID 11236864

See all (46) 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

  • D1S7 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_055425.1 

    Range
    101..5958
    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
    31428806..31434663
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    31281142..31291881
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
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