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LOC108281116 SOX18 promoter region [ Homo sapiens (human) ]

Gene ID: 108281116, updated on 17-Sep-2024

Summary

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Gene symbol
LOC108281116
Gene description
SOX18 promoter region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: enhancer, 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 promoter of the SRY-box 18 (SOX18) gene. This promoter is stimulated by hedgehog signaling and binding by nuclear transcription factor Y and early growth response 1, and is downregulated by tumor necrosis factor and zinc finger protein 148. A subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC108281116 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (64049510..64050624)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (65869535..65870649)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (62680863..62681977)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13198 Neighboring gene pre-mRNA processing factor 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62631004-62631506 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:62636447-62636619 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:62642795-62643994 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:62648052-62649251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62667815-62668408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62668409-62669002 Neighboring gene chromosome 20 open reading frame 204 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62676871-62677791 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62684293-62684982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62686363-62687052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:62687053-62687742 Neighboring gene SRY-box transcription factor 18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62688433-62689122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:62689123-62689810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18263 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13205 Neighboring gene transcription elongation factor A2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13206 Neighboring gene regulator of G protein signaling 19 Neighboring gene microRNA 6813

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. Early growth response protein 1 acts as an activator of SOX18 promoter. Petrovic I, et al. Exp Mol Med, 2010 Feb 28. PMID 20054233, Free PMC Article
  2. Comparison of promoter regions of SOX3, SOX14 and SOX18 orthologs in mammals. Kovacevic-Grujicic N, et al. DNA Seq, 2008 Jun. PMID 17852354
  3. SOX18 Is a Novel Target Gene of Hedgehog Signaling in Cervical Carcinoma Cell Lines. Petrovic I, et al. PLoS One, 2015. PMID 26588701, Free PMC Article
  4. TNFα-induced down-regulation of Sox18 in endothelial cells is dependent on NF-κB. Basílio J, et al. Biochem Biophys Res Commun, 2013 Dec 13. PMID 24269235
  5. Heterogeneity and degree of TIMP4, GATA4, SOX18, and EGFL7 gene promoter methylation in non-small cell lung cancer and surrounding tissues. Azhikina T, et al. Cancer Genet, 2011 Sep. PMID 22018271

See all (7) 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

  • H3K4me1 hESC enhancer GRCh37_chr20:62680863-62681544

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_051060.2 

    Range
    101..1215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    64049510..64050624
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    65869535..65870649
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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