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LOC114841038 5K-Del enhancer in SHFM1 region [ Homo sapiens (human) ]

Gene ID: 114841038, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114841038
Gene description
5K-Del enhancer in SHFM1 region
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 genomic sequence, which is located in the split-hand/split-foot malformation 1 (SHFM1) region on chromosome 7, represents an enhancer element. It can activate a minimal beta-globin promoter in the inner ear and developing bones of E12.5 transgenic mouse embryos. This enhancer is removed in some deletions associated with limb malformations, hearing loss and craniofacial defects, including a 5,115 bp deletion, and it is thought to regulate the expression of the nearby DLX5 and DLX6 genes. [provided by RefSeq, May 2019]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (96934654..96940737)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (98164331..98170415)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (96563966..96570049)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375414 Neighboring gene Sharpr-MPRA regulatory region 10792 Neighboring gene eDlx#8 enhancer in SHFM1 region Neighboring gene MARK2 pseudogene 10 Neighboring gene uncharacterized LOC124901703 Neighboring gene RNA, 7SL, cytoplasmic 252, pseudogene Neighboring gene DLX6 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:96621779-96622304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:96622305-96622831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:96627585-96628528 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:96630843-96631552 Neighboring gene VISTA enhancer hs298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18385 Neighboring gene distal-less homeobox 6

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. Deletion of an enhancer near DLX5 and DLX6 in a family with hearing loss, craniofacial defects, and an inv(7)(q21.3q35). Brown KK, et al. Hum Genet, 2010 Jan. PMID 19707792, Free PMC Article
  2. Split hand/foot malformation due to chromosome 7q aberrations(SHFM1): additional support for functional haploinsufficiency as the causative mechanism. van Silfhout AT, et al. Eur J Hum Genet, 2009 Nov. PMID 19401716, Free PMC Article
  3. Deletions of exons with regulatory activity at the DYNC1I1 locus are associated with split-hand/split-foot malformation: array CGH screening of 134 unrelated families. Tayebi N, et al. Orphanet J Rare Dis, 2014 Jul 29. PMID 25231166, Free PMC Article
  4. Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus. Kouwenhoven EN, et al. PLoS Genet, 2010 Aug 19. PMID 20808887, Free PMC Article
  5. Next generation sequencing of chromosomal rearrangements in patients with split-hand/split-foot malformation provides evidence for DYNC1I1 exonic enhancers of DLX5/6 expression in humans. Lango Allen H, et al. J Med Genet, 2014 Apr. PMID 24459211, Free PMC Article

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)

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_065169.1 

    Range
    101..6184
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    96934654..96940737
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    98164331..98170415
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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