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LOC109461476 GDF5 promoter region [ Homo sapiens (human) ]

Gene ID: 109461476, updated on 10-Oct-2023

Summary

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Gene symbol
LOC109461476
Gene description
GDF5 promoter region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: promoter
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region represents the proximal promoter of the growth differentiation factor 5 gene. Several naturally-occurring polymorphic sites have been characterized in this region, including rs143383, which was found to affect promoter activity and contribute to osteoarthritis risk. The rs143383 site is located within a binding region for Sp1/Sp3 and Deaf1 transcription factors, which may function as repressors of this promoter. SRY-box 11 and YY1 transcription factor also bind to and regulate activity of this sequence. This promoter is subject to epigenetic silencing by DNA methylation. [provided by RefSeq, Dec 2016]
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Genomic context

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See LOC109461476 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (35437929..35438683)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (37158774..37159536)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (34025709..34026475)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:33892105-33892925 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:33893217-33894416 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:33899341-33900264 Neighboring gene Sharpr-MPRA regulatory region 6334 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 1 Neighboring gene Sharpr-MPRA regulatory region 14546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17779 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:33999108-33999931 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:33999932-34000754 Neighboring gene MPRA-validated peak4201 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12857 Neighboring gene GDF5 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17783 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12858 Neighboring gene growth differentiation factor 5 Neighboring gene microRNA 1289-1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12859 Neighboring gene centrosomal protein 250 Neighboring gene CEP250 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17785

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. CpG methylation regulates allelic expression of GDF5 by modulating binding of SP1 and SP3 repressor proteins to the osteoarthritis susceptibility SNP rs143383. Reynard LN, et al. Hum Genet, 2014 Aug. PMID 24861163, Free PMC Article
  2. Positive selection on the osteoarthritis-risk and decreased-height associated variants at the GDF5 gene in East Asians. Wu DD, et al. PLoS One, 2012. PMID 22905146, Free PMC Article
  3. Expression of the osteoarthritis-associated gene GDF5 is modulated epigenetically by DNA methylation. Reynard LN, et al. Hum Mol Genet, 2011 Sep 1. PMID 21642387
  4. Evidence of association between GDF5 polymorphisms and congenital dislocation of the hip in a Caucasian population. Rouault K, et al. Osteoarthritis Cartilage, 2010 Sep. PMID 20633687
  5. A meta-analysis of European and Asian cohorts reveals a global role of a functional SNP in the 5' UTR of GDF5 with osteoarthritis susceptibility. Chapman K, et al. Hum Mol Genet, 2008 May 15. PMID 18299287

See all (13) 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_052612.1 

    Range
    101..855
    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
    35437929..35438683
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    37158774..37159536
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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