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LOC114803469 SORL1 eExon liver enhancer [ Homo sapiens (human) ]

Gene ID: 114803469, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114803469
Gene description
SORL1 eExon liver enhancer
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 region, which overlaps a protein-coding exon of the SORL1 (sortilin related receptor 1) gene, was predicted to be an exonic enhancer (eExon) based on an enhancer-associated chromatin signature (H3K4me1, H3K27ac and p300) in liver. It was validated as a functional enhancer by reporter assays in HepG2 cells, HeLa cells and mouse liver. It also functioned as an enhancer when co-transfected with the HNF4A and AP-1 transcription factors in HEK293T cells (additive effect), and mutations in the predicted binding sites resulted in decreased enhancer activity. This eExon was found to be associated with the FOXA1, FOXA2, HNF4A and HNF4G transcription factors by ChIP assays in human liver cells. [provided by RefSeq, Apr 2019]
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Genomic context

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Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (121553768..121554365)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (121580126..121580723)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (121424477..121425074)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4005 Neighboring gene SORL1 antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:121336477-121337676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5657 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5658 Neighboring gene uncharacterized LOC105369535 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5659 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121368848-121369348 Neighboring gene sortilin related receptor 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:121421721-121422920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5660 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121441955-121442454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5661 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121441453-121441954 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5662 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:121465964-121467163 Neighboring gene Sharpr-MPRA regulatory region 6864 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:121507637-121508302 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:121508303-121508966 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:121514837-121515520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:121543162-121543662 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:121559556-121560755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5664 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121673071-121673918 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:121694789-121695360 Neighboring gene uncharacterized LOC107984402 Neighboring gene VISTA enhancer hs872 Neighboring gene RNA, U6 small nuclear 256, pseudogene

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. Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. Birnbaum RY, et al. PLoS Genet, 2014 Oct. PMID 25340400, Free PMC Article
  2. Exonic enhancers: proceed with caution in exome and genome sequencing studies. Ahituv N. Genome Med, 2016 Feb 8. PMID 26856702, Free PMC Article

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

  • enhancer exon of SORL1

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_064645.1 

    Range
    101..698
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    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    121553768..121554365
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    121580126..121580723
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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