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LOC110594337 B6.7 minisatellite repeat instability region [ Homo sapiens (human) ]

Gene ID: 110594337, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110594337
Gene description
B6.7 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 on the q arm of chromosome 20. This unstable variable number tandem repeat (VNTR) has a repeat unit length of 34 nucleotides, with a tandem array of similar, but non-identical repeats. The consensus repeat motif is TCTCTAYAGGMCAYGAGRGTKGACAGTGAGGGGG,relative to the minus strand of the reference genome, with Y, R, M, and K being pyrimidine, purine, amino and keto, according to the IUPAC nucleotide code. Sequences within the consensus repeat sequence shares similarity to the PRDM9 A binding motif (LD hotspot motif), differing by just a single nucleotide from the 13-mer consensus motif, CCNCCNTNNCCNC, compared to the plus strand of the reference genome. There is a meiotic recombination hotspot that overlaps the repeat region. This region shows very high heterozygosity, and has alleles ranging from six repeat units to greater than 500 repeat units. Differences in allele structures are seen amongst different populations. Instability at this locus is observed in germline cells, with a much lower incidence of instability in somatic cells. Repeat instability is seen in both maternal and paternal germlines, with higher instability seen in alleles with larger repeat arrays. The very high heterozygosity of this region and its high mutation rate makes it useful for forensic analyses and monitoring of mutation rates. [provided by RefSeq, Jul 2017]
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Genomic context

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Location:
20q13.33
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (64129292..64136769)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65950776..65956229)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62760645..62768122)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13209 Neighboring gene MPRA-validated peak4324 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62723260-62723993 Neighboring gene LKAAEAR motif containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62723994-62724726 Neighboring gene opioid related nociceptin receptor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62732783-62733284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62738466-62738966 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62740950-62741133 Neighboring gene neuropeptides B and W receptor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62751601-62752100 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:62754467-62755666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62768655-62769156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62769157-62769656 Neighboring gene uncharacterized LOC105372727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62771493-62772406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62782269-62782948 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:62782949-62784148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62790052-62790772 Neighboring gene VISTA enhancer hs2609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62809687-62810387 Neighboring gene myelin transcription factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62819145-62820082 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62820083-62821020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62842693-62843192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62854891-62855746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62857693-62858192

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. Allelic structures at hypervariable minisatellite B6.7 in Japanese show population specificity. Mizukoshi T, et al. J Hum Genet, 2002. PMID 12032590
  2. Extremely complex repeat shuffling during germline mutation at human minisatellite B6.7. Tamaki K, et al. Hum Mol Genet, 1999 May. PMID 10196378
  3. Paternal lifestyle as a potential source of germline mutations transmitted to offspring. Linschooten JO, et al. FASEB J, 2013 Jul. PMID 23538710, Free PMC Article
  4. Minisatellite mutation frequency in human sperm following radiotherapy. May CA, et al. Mutat Res, 2000 Sep 20. PMID 11006413
  5. Human VNTR mutation and sex. Olaisen B, et al. EXS, 1993. PMID 8400715

See all (16) 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_055426.1 

    Range
    101..7578
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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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    64129292..64136769
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65950776..65956229
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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