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LOC109611589 runt related transcription factor 2 polyalanine expansion region [ Homo sapiens (human) ]

Gene ID: 109611589, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109611589
Gene description
runt related transcription factor 2 polyalanine expansion 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 runt related transcription factor 2 (RUNX2) gene on the p arm of chromosome 6. This region contains both a polyglutamine and polyalanine stretch that are susceptible to expansions and deletions, resulting in cleidocranial dysplasia (CCD). Polyalanine expanded gene products can mislocalize from the nucleus to the cytoplasm, and form protein aggregates. Changes in the polyglutamine-coding stretch can disrupt the encoded protein. [provided by RefSeq, Jan 2017]
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Genomic context

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Location:
6p21.1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (45422679..45422801)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (45257496..45257618)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (45390416..45390538)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene SPT3 homolog, SAGA and STAGA complex component Neighboring gene MPRA-validated peak5821 silencer Neighboring gene microRNA 586 Neighboring gene MPRA-validated peak5822 silencer Neighboring gene RUNX2 P1 promoter region Neighboring gene MPRA-validated peak5825 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:45345603-45346146 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17265 Neighboring gene RUNX family transcription factor 2 Neighboring gene uncharacterized LOC124901324 Neighboring gene NANOG hESC enhancer GRCh37_chr6:45413685-45414186 Neighboring gene Sharpr-MPRA regulatory region 695 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:45487956-45488510 Neighboring gene Sharpr-MPRA regulatory region 12811 Neighboring gene RUNX2 antisense RNA 1 Neighboring gene U6 spliceosomal RNA

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. Characterisation of novel RUNX2 mutation with alanine tract expansion from Japanese cleidocranial dysplasia patient. Shibata A, et al. Mutagenesis, 2016 Jan. PMID 26220009
  2. Association of polyalanine and polyglutamine coiled coils mediates expansion disease-related protein aggregation and dysfunction. Pelassa I, et al. Hum Mol Genet, 2014 Jul 1. PMID 24497578, Free PMC Article
  3. Length-dependent aggregation of uninterrupted polyalanine peptides. Bernacki JP, et al. Biochemistry, 2011 Nov 1. PMID 21932820
  4. Alanine tracts: the expanding story of human illness and trinucleotide repeats. Brown LY, et al. Trends Genet, 2004 Jan. PMID 14698619
  5. Polyalanine repeat polymorphism in RUNX2 is associated with site-specific fracture in post-menopausal females. Morrison NA, et al. PLoS One, 2013. PMID 24086263, Free PMC Article

See all (11) 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

  • RUNX2 polyalanine expansion 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_052657.1 

    Range
    101..223
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    45422679..45422801
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    45257496..45257618
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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