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LOC109621227 nuclear receptor coactivator 3 repeat instability region [ Homo sapiens (human) ]

Gene ID: 109621227, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109621227
Gene description
nuclear receptor coactivator 3 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 the coding region of the nuclear receptor coactivator 3 (NCOA3) gene on the q arm of chromosome 20, and contains a polyglutamine-coding repeat region. This region is highly polymorphic, containing multiple alleles with different CAG and CAA repeat configurations. The repeat represented in the reference genome is (CAG)6CAA(CAG)9(CAACAG)4(CAGCAA)(CAG)2CAA. Somatic instability of this repeat has been observed in some cells. Some studies suggest that alleles with longer polyglutamine-coding tracts may be at increased risk for some tumors. [provided by RefSeq, Feb 2017]
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Genomic context

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Location:
20q13.12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (47651071..47651158)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (49389482..49389560)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (46279815..46279902)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr20.2047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12980 Neighboring gene RNA, U6 small nuclear 563, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46152763-46153530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46158187-46158687 Neighboring gene nuclear receptor coactivator 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:46190110-46190292 Neighboring gene MPRA-validated peak4234 silencer Neighboring gene ribosomal protein S3A pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:46277615-46278332 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:46276897-46277614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46293563-46294548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46294549-46295532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46303203-46304168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46307531-46308031 Neighboring gene sulfatase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46316712-46317262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46317263-46317814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:46326206-46326710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46339340-46339840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46339841-46340341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46381589-46382088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46381087-46381588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46386138-46386895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46386896-46387654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:46387655-46388411 Neighboring gene NANOG hESC enhancer GRCh37_chr20:46390145-46390683 Neighboring gene Sharpr-MPRA regulatory region 8498 Neighboring gene uncharacterized LOC124904922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18007 Neighboring gene uncharacterized LOC124904920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18008

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. Rapid detection of CAA/CAG repeat polymorphism in the AIB1 gene using DHPLC. Kleibl Z, et al. J Biochem Biophys Methods, 2007 Apr 10. PMID 17234271
  2. Polymorphisms of short tandem repeat of genes and breast cancer susceptibility. Zhang W, et al. Eur J Surg Oncol, 2007 Jun. PMID 17215102
  3. Modification of BRCA1- and BRCA2-associated breast cancer risk by AIB1 genotype and reproductive history. Rebbeck TR, et al. Cancer Res, 2001 Jul 15. PMID 11454686
  4. Frequent amplification of chromosomal region 20q12-q13 in ovarian cancer. Tanner MM, et al. Clin Cancer Res, 2000 May. PMID 10815905
  5. AIB1 gene amplification and the instability of polyQ encoding sequence in breast cancer cell lines. Wong LJ, et al. BMC Cancer, 2006 May 2. PMID 16670003, Free PMC Article

See all (12) 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

  • AIB1 repeat instability region
  • NCOA3 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_052821.1 

    Range
    101..188
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    47651071..47651158
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    49389482..49389560
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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