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LOC108021844 SOX9 enhancer E1 [ Homo sapiens (human) ]

Gene ID: 108021844, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108021844
Gene description
SOX9 enhancer E1
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 28 kb downstream. This sequence drives expression of a transgene in the developing notochord, gut, bronchial epithelium, and pancreas. [provided by RefSeq, Jun 2016]
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Genomic context

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See LOC108021844 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (72092646..72093159)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (72965843..72966356)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (70088787..70089300)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes 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 Neighboring gene long intergenic non-protein coding RNA 2097 Neighboring gene SOX9 antisense RNA 1 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 SOX9 enhancer E7 Neighboring gene uncharacterized LOC124900392

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_050874.1 

    Range
    101..614
    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
    72092646..72093159
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    72965843..72966356
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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