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LOC108021843 SOX9 enhancer E3 [ Homo sapiens (human) ]

Gene ID: 108021843, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108021843
Gene description
SOX9 enhancer E3
Gene type
biological region
Feature type(s)
misc_feature: conserved_region
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 contains a conserved sequence that is thought to function as an enhancer of the SRY-box 9 (SOX9) gene, located 245 kb downstream. This sequence drives expression of a transgene in the developing neural crest and inner ear. [provided by RefSeq, Jun 2016]
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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 (71870457..71870989)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (72743545..72744077)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (69866598..69867130)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:69314163-69314663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:69353619-69354118 Neighboring gene SOX9 enhancer enh3 Neighboring gene eSR-A sex determination enhancer Neighboring gene SOX9 testis enhancer F8 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:69518499-69519033 Neighboring gene reversal of sex (RevSex) determining region Neighboring gene MYL6 pseudogene 5 Neighboring gene SOX9 enhancer enh4 Neighboring gene SOX9 enhancer enh5 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:69824267-69824886 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:69841665-69842864 Neighboring gene SOX9 enhancer enh6 Neighboring gene SOX9 enhancer enh7 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:69867322-69868521 Neighboring gene uncharacterized LOC107985015 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:69896473-69897672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12667 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:70025920-70026690 Neighboring gene uncharacterized LOC102723517 Neighboring gene long intergenic non-protein coding RNA 1152 Neighboring gene regulator of chondrogenesis 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. 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

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_050873.1 

    Range
    101..633
    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
    71870457..71870989
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    72743545..72744077
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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