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LOC111589210 FOXA motif-containing MPRA enhancer 238 [ Homo sapiens (human) ]

Gene ID: 111589210, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111589210
Gene description
FOXA motif-containing MPRA enhancer 238
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
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 was predicted to be a cell type-specific enhancer based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by high-throughput massively parallel reporter assays (MPRAs) in liver carcinoma HepG2 cells. This enhancer contains a motif for the FOXA activator. Mutation of this motif results in reduced enhancer activity. [provided by RefSeq, Dec 2017]
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Genomic context

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See LOC111589210 in Genome Data Viewer
Location:
4q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (69103076..69103220)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (72543593..72543738)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (69968794..69968938)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene UDP glucuronosyltransferase family 2 member B26, pseudogene Neighboring gene uncharacterized LOC105377265 Neighboring gene MPRA-validated peak5046 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15466 Neighboring gene UDP glucuronosyltransferase family 2 member B7 Neighboring gene UGT2B7 (B) eExon liver enhancer Neighboring gene SPOPL pseudogene 1 Neighboring gene UDP-glucuronosyltransferase 2A1-like

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 regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Kheradpour P, et al. Genome Res, 2013 May. PMID 23512712, Free PMC Article
  2. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, et al. Nature, 2011 May 5. PMID 21441907, 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

  • FOXA activator MPRA enhancer 238
  • massively parallel reporter assay enhancer 238

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_056081.1 

    Range
    101..245
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    69103076..69103220
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    72543593..72543738
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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