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LOC109504727 NOP56 ribonucleoprotein repeat instability region [ Homo sapiens (human) ]

Gene ID: 109504727, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109504727
Gene description
NOP56 ribonucleoprotein 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 biological region is found within an intron of the NOP56 ribonucleoprotein gene, and is just upstream of microRNA 1292, on the p arm of chromosome 20. This region contains a GGCCTG hexanucleotide repeat, and expansions of this repeat are associated with spinocerebellar ataxia type 36 (SCA36), an autosomal dominant disorder. This is a highly polymorphic region, with about 3-14 repeats observed in unaffected individuals, while expansions of up to 2500 repeats have been found in affected individuals. Expansion of the GGCCTG repeat causes RNA focus formation, sequestration of the serine and arginine rich splicing factor 2 gene product, and reduced expression of mature and precursor microRNA 1292. These have been suggested as possible contributors to development of the disorder. [provided by RefSeq, Jan 2017]
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Genomic context

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See LOC109504727 in Genome Data Viewer
Location:
20p13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (2652733..2652775)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (2683200..2683242)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (2633379..2633421)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372504 Neighboring gene transmembrane channel like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2538685-2539395 Neighboring gene uncharacterized LOC105372505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17470 Neighboring gene small nucleolar RNA, C/D box 110 Neighboring gene microRNA 1292 Neighboring gene NOP56 ribonucleoprotein

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. Spinocerebellar ataxia 36 accompanied by cervical dystonia. Nakazato Y, et al. J Neurol Sci, 2015 Oct 15. PMID 26189053
  2. Spinocerebellar ataxia type 36 exists in diverse populations and can be caused by a short hexanucleotide GGCCTG repeat expansion. Obayashi M, et al. J Neurol Neurosurg Psychiatry, 2015 Sep. PMID 25476002
  3. Characteristic RNA foci of the abnormal hexanucleotide GGCCUG repeat expansion in spinocerebellar ataxia type 36 (Asidan). Liu W, et al. Eur J Neurol, 2014 Nov. PMID 24985895
  4. GGCCTG repeats put a hex on Purkinje cells and motor neurons in SCA36. Ashizawa T, et al. Neurology, 2012 Jul 24. PMID 22744663
  5. Spinocerebellar Ataxia Type 36 – RETIRED CHAPTER, FOR HISTORICAL REFERENCE ONLY. Adam MP, et al. , 1993. PMID 25101480

See all (8) 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

  • NOP56 repeat instability region
  • SCA36 repeat instability region
  • spinocerebellar ataxia type 36 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_052631.1 

    Range
    101..143
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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
    2652733..2652775
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    2683200..2683242
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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