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LOC108021842 SOX9 enhancer E7 [ Homo sapiens (human) ]

Gene ID: 108021842, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108021842
Gene description
SOX9 enhancer E7
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer that is thought to regulate expression of the SRY-box 9 (SOX9) gene, located approximately 100 kb upstream. A subregion can drive expression of a transgene in the developing brain. Another subregion was also validated as an enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed 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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Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (72218991..72220434)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (73092209..73093650)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (70215437..70216575)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2097 Neighboring gene SOX9 antisense RNA 1 Neighboring gene SOX9 enhancer E1 Neighboring gene SOX9 enhancer eALDI Neighboring gene TES enhancer upstream of SOX9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70113837-70114458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70115824-70116324 Neighboring gene SOX9 promoter region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70119336-70119859 Neighboring gene SRY-box transcription factor 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70181507-70182008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70201265-70201766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70201767-70202266 Neighboring gene uncharacterized LOC124900392 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12668 Neighboring gene long intergenic non-protein coding RNA 2003

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. Campomelic dysplasia translocation breakpoints are scattered over 1 Mb proximal to SOX9: evidence for an extended control region. Pfeifer D, et al. Am J Hum Genet, 1999 Jul. PMID 10364523, Free PMC Article
  2. Long-range upstream and downstream enhancers control distinct subsets of the complex spatiotemporal Sox9 expression pattern. Bagheri-Fam S, et al. Dev Biol, 2006 Mar 15. PMID 16458883
  3. Deletion of long-range regulatory elements upstream of SOX9 causes campomelic dysplasia. Wunderle VM, et al. Proc Natl Acad Sci U S A, 1998 Sep 1. PMID 9724758, Free PMC Article
  4. Long-range regulation at the SOX9 locus in development and disease. Gordon CT, et al. J Med Genet, 2009 Oct. PMID 19473998
  5. Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions. Bagheri-Fam S, et al. Genomics, 2001 Nov. PMID 11707075

See all (6) 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_chr17:70215132-70216040

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_050872.2 

    Range
    101..1544
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    72218991..72220434
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    73092209..73093650
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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