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LOC110599568 MS43a minisatellite repeat instability region [ Homo sapiens (human) ]

Gene ID: 110599568, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110599568
Gene description
MS43a minisatellite repeat instability region
Gene type
biological region
Feature type(s)
misc_feature: repeat_instability_region
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 found within an intron of the polypeptide N-acetylgalactosaminyltransferase 9 (GALNT9) gene, on the q arm of chromosome 12. This minisatellite is an unstable GC-rich variable number tandem repeat (VNTR) with a 45 nucleotide consensus motif of tgtgtgtaatgggtatagggagggccccgggaagggggtgtggyg, relative to the minus strand of the reference genome. The repeat is an imperfect repeat, with a tandem array of similar, but non-identical repeats. Repeat instability has been observed in germline cells. [provided by RefSeq, Jul 2017]
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Genomic context

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Location:
12q24.33
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (132240334..132243802)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (132289894..132296418)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 (PATCHES) NW_003315937.1 (14373..17841)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5115 Neighboring gene long intergenic non-protein coding RNA 2361 Neighboring gene uncharacterized LOC105370091 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132703817-132704677 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:132831859-132832379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132832380-132832899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132849568-132850462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132850463-132851355 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132852165-132852941 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132854851-132855501 Neighboring gene GALNT9 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132860363-132861016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132861671-132862324 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:132863043-132864242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132899827-132900476 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:132903614-132904813 Neighboring gene uncharacterized LOC101928416

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. A validation study of four single locus probes (MS1, MS31, MS43 and g3) in a Korean population--further evaluation for paternity testing. Lee KO, et al. J Korean Med Sci, 1995 Aug. PMID 8593203, Free PMC Article
  2. Study of three hypervariable DNA loci (D1S7; D7S22 and D12S11) in three European populations. Papiha SS, et al. Ann Hum Biol, 1998 Jan-Feb. PMID 9483206
  3. Frequent rearrangements at minisatellite loci D1S7 (1p33-35), D7S22 (7q36-ter) and D12S11 (12q24.3-ter) in hepatitis B virus-positive hepatocellular carcinomas from Thai patients. Kaplanski C, et al. Int J Cancer, 1997 Jul 17. PMID 9219828
  4. Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA. Jeffreys AJ, et al. Nature, 1988 Mar 17. PMID 3347271
  5. Human VNTR mutation and sex. Olaisen B, et al. EXS, 1993. PMID 8400715

See all (10) 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

  • D12S11 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_055434.1 

    Range
    101..3569
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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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    132240334..132243802
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160007.1 Reference GRCh38.p14 PATCHES

    Range
    146694..150162
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    132289894..132296418
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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